Skip to main content Accessibility help
×
Home

Modeling and simulation of protein–surface interactions: achievements and challenges

  • Musa Ozboyaci (a1) (a2), Daria B. Kokh (a1), Stefano Corni (a3) and Rebecca C. Wade (a1) (a4) (a5)

Abstract

Understanding protein–inorganic surface interactions is central to the rational design of new tools in biomaterial sciences, nanobiotechnology and nanomedicine. Although a significant amount of experimental research on protein adsorption onto solid substrates has been reported, many aspects of the recognition and interaction mechanisms of biomolecules and inorganic surfaces are still unclear. Theoretical modeling and simulations provide complementary approaches for experimental studies, and they have been applied for exploring protein–surface binding mechanisms, the determinants of binding specificity towards different surfaces, as well as the thermodynamics and kinetics of adsorption. Although the general computational approaches employed to study the dynamics of proteins and materials are similar, the models and force-fields (FFs) used for describing the physical properties and interactions of material surfaces and biological molecules differ. In particular, FF and water models designed for use in biomolecular simulations are often not directly transferable to surface simulations and vice versa. The adsorption events span a wide range of time- and length-scales that vary from nanoseconds to days, and from nanometers to micrometers, respectively, rendering the use of multi-scale approaches unavoidable. Further, changes in the atomic structure of material surfaces that can lead to surface reconstruction, and in the structure of proteins that can result in complete denaturation of the adsorbed molecules, can create many intermediate structural and energetic states that complicate sampling. In this review, we address the challenges posed to theoretical and computational methods in achieving accurate descriptions of the physical, chemical and mechanical properties of protein-surface systems. In this context, we discuss the applicability of different modeling and simulation techniques ranging from quantum mechanics through all-atom molecular mechanics to coarse-grained approaches. We examine uses of different sampling methods, as well as free energy calculations. Furthermore, we review computational studies of protein–surface interactions and discuss the successes and limitations of current approaches.

  • View HTML
    • Send article to Kindle

      To send this article to your Kindle, first ensure no-reply@cambridge.org is added to your Approved Personal Document E-mail List under your Personal Document Settings on the Manage Your Content and Devices page of your Amazon account. Then enter the ‘name’ part of your Kindle email address below. Find out more about sending to your Kindle. Find out more about sending to your Kindle.

      Note you can select to send to either the @free.kindle.com or @kindle.com variations. ‘@free.kindle.com’ emails are free but can only be sent to your device when it is connected to wi-fi. ‘@kindle.com’ emails can be delivered even when you are not connected to wi-fi, but note that service fees apply.

      Find out more about the Kindle Personal Document Service.

      Modeling and simulation of protein–surface interactions: achievements and challenges
      Available formats
      ×

      Send article to Dropbox

      To send this article to your Dropbox account, please select one or more formats and confirm that you agree to abide by our usage policies. If this is the first time you use this feature, you will be asked to authorise Cambridge Core to connect with your <service> account. Find out more about sending content to Dropbox.

      Modeling and simulation of protein–surface interactions: achievements and challenges
      Available formats
      ×

      Send article to Google Drive

      To send this article to your Google Drive account, please select one or more formats and confirm that you agree to abide by our usage policies. If this is the first time you use this feature, you will be asked to authorise Cambridge Core to connect with your <service> account. Find out more about sending content to Google Drive.

      Modeling and simulation of protein–surface interactions: achievements and challenges
      Available formats
      ×

Copyright

Corresponding author

*Authors for correspondence: Musa Ozboyaci, Heidelberg Institute for Theoretical Studies (HITS), Schloss-Wolfsbrunnenweg 35, 69118 Heidelberg, Germany; Heidelberg Graduate School of Mathematical and Computational Methods for the Sciences (HGS MathComp), Heidelberg University, Im Neuenheimer Feld 368, 69120 Heidelberg, Germany & Rebecca C. Wade, Heidelberg Institute for Theoretical Studies (HITS), Schloss-Wolfsbrunnenweg 35, 69118 Heidelberg, Germany; Zentrum für Molekulare Biologie der Universität Heidelberg, DKFZ-ZMBH Allianz, Im Neuenheimer Feld 282, 69120 Heidelberg, Germany; Interdisciplinary Center for Scientific Computing (IWR), Heidelberg University, 69120 Heidelberg, Germany. Tel.:+49-6221-533-247; Emails: musa.oezboyaci@h-its.org, rebecca.wade@h-its.org

References

Hide All
Aarts, I. M. P., Pipino, A. C. R., Hoefnagels, J. P. M., Kessels, W. M. M. & van de Sanden, M. C. M. (2005) Quasi-ice monolayer on atomically smooth amorphous SiO2 at room temperature observed with a high-finesse optical resonator. Physical Review Letters 95, 166104.
Adnan, A., Lam, R., Chen, H., Lee, J., Schaffer, D. J., Barnard, A. S., Schatz, G. C., Ho, D. & Liu, W. K. (2011) Atomistic simulation and measurement of pH dependent cancer therapeutic interactions with nanodiamond carrier. Molecular Pharmaceutics 8, 368374.
Akdim, B., Pachter, R., Kim, S. S., Naik, R. R., Walsh, T. R., Trohalaki, S., Hong, G., Kuang, Z. & Farmer, B. L. (2013) Electronic properties of a graphene device with peptide adsorption: insight from simulation. ACS Applied Materials & Interfaces 5, 74707477.
Alava, T., Mann, J. A., Théodore, C., Benitez, J. J., Dichtel, W. R., Parpia, J. M. & Craighead, H. G. (2013) Control of the graphene–protein interface is required to preserve adsorbed protein function. Analytical Chemistry 85, 27542759.
Alessandrini, A., Salerno, M., Frabboni, S. & Facci, P. (2005) Single-metalloprotein wet biotransistor. Applied Physics Letters 86, 133902.
Aliaga, A. E., Ahumada, H., Sepúlveda, K., Gomez-Jeria, J. S., Garrido, C., Weiss-López, B. E. & Campos-Vallette, M. M. (2011) SERS, Molecular dynamics and molecular orbital studies of the MRKDV peptide on silver and membrane surfaces. The Journal of Physical Chemistry C 115, 39823989.
Allison, S. A., Northrup, S. H. & McCammon, J. A. (1986) Simulation of biomolecular diffusion and complex formation. Biophysical Journal 49, 167175.
Al-Mekhnaqi, A. M., Mayeed, M. S. & Newaz, G. M. (2009) Prediction of protein conformation in water and on surfaces by Monte Carlo simulations using united-atom method. Molecular Simulation 35, 292300.
Alvarez-Paggi, D., Castro, M. A., Tórtora, V., Castro, L., Radi, R. & Murgida, D. H. (2013) Electrostatically driven second-sphere ligand switch between high and low reorganization energy forms of native cytochrome c. Journal of the American Chemical Society 135, 43894397.
Alvarez-Paggi, D., Martín, D. F., DeBiase, P. M., Hildebrandt, P., Martí, M. A. & Murgida, D. H. (2010) Molecular basis of coupled protein and electron transfer dynamics of cytochrome c in biomimetic complexes. Journal of the American Chemical Society 132, 57695778.
Anand, G., Sharma, S., Kumar, S. K. & Belfort, G. (2009) Stability of tethered proteins. Langmuir 25, 49985005.
Andolfi, L., Bruce, D., Cannistraro, S., Canters, G. W., Davis, J. J., Hill, H. A. O., Crozier, J., Verbeet, M. P., Wrathmell, C. L. & Astier, Y. (2004) The electrochemical characteristics of blue copper protein monolayers on gold. Journal of Electroanalytical Chemistry 565, 2128.
Andreescu, S., Ornatska, M., Erlichman, J. S., Estevez, A. & Leiter, J. C. (2012) Biomedical applications of metal oxide nanoparticles. In Fine Particles in Medicine and Pharmacy (ed Matijević, E.), pp. 57100. Springer US, Boston, MA, USA.
Anker, J. N., Hall, W. P., Lyandres, O., Shah, N. C., Zhao, J. & Van Duyne, R. P. (2008) Biosensing with plasmonic nanosensors. Nature Materials 7, 442453.
Ansari, S. A. & Husain, Q. (2012) Potential applications of enzymes immobilized on/in nano materials: a review. Biotechnology Advances 30, 512523.
Apicella, A., Soncini, M., Deriu, M. A., Natalello, A., Bonanomi, M., Dellasega, D., Tortora, P., Regonesi, M. E. & Casari, C. S. (2013) A hydrophobic gold surface triggers misfolding and aggregation of the amyloidogenic josephin domain in monomeric form, while leaving the oligomers unaffected. PLoS ONE 8, e58794.
Arrouvel, C., Diawara, B., Costa, D. & Marcus, P. (2007) DFT periodic study of the adsorption of glycine on the anhydrous and hydroxylated (0001) surfaces of α-alumina. The Journal of Physical Chemistry C 111, 1816418173.
Austin, B. M., Zubarev, D. Y. & Lester, W. A. (2012) Quantum Monte Carlo and related approaches. Chemical Reviews 112, 263288.
Baier, J., Blumenstein, N. J., Preusker, J., Jeurgens, L. P. H., Welzel, U., Do, T. A., Pleiss, J. & Bill, J. (2014) The influence of ZnO-binding 12-mer peptides on bio-inspired ZnO formation. CrystEngComm 16, 53015307.
Balamurugan, K., Gopalakrishnan, R., Raman, S. S. & Subramanian, V. (2010) Exploring the changes in the structure of α-helical peptides adsorbed onto a single walled carbon nanotube using classical molecular dynamics simulation. The Journal of Physical Chemistry B 114, 1404814058.
Bandura, A. V. & Kubicki, J. D. (2003) Derivation of force field parameters for TiO2−H2O systems from ab initio calculations. The Journal of Physical Chemistry B 107, 1107211081.
Barabino, G., Cesare-Gavotti, & Marchesi, M. (1984) Molecular dynamics simulation of water near walls using an improved wall—water interaction potential. Chemical Physics Letters 104, 478484.
Barbey, R., Lavanant, L., Paripovic, D., Schüwer, N., Sugnaux, C., Tugulu, S. & Klok, H.-A. (2009) Polymer brushes via surface-initiated controlled radical polymerization: synthesis, characterization, properties, and applications. Chemical Reviews 109, 54375527.
Bellucci, L., Brancolini, G., Calzolari, A., Carrillo Parramon, O., Corni, S. & Di Felice, R. (2012) Proteins and peptides at gold surfaces: insights from atomistic simulations. In Proteins at Interfaces III State of the Art (eds Horbett, T., Brash, J. L. & Norde, W.), pp. 229250. American Chemical Society, Washington, DC, USA.
Bellucci, L. & Corni, S. (2014) Interaction with a gold surface reshapes the free energy landscape of alanine dipeptide. The Journal of Physical Chemistry C 118, 1135711364.
Bhirde, A. A., Hassan, S. A., Harr, E. & Chen, X. (2014) Role of albumin in the formation and stabilization of nanoparticle aggregates in serum studied by continuous photon correlation spectroscopy and multiscale computer simulations. The Journal of Physical Chemistry C 118, 1619916208.
Bhowmik, R., Katti, K. S. & Katti, D. (2007) Molecular dynamics simulation of hydroxyapatite–polyacrylic acid interfaces. Polymer 48, 664674.
Binnig, G., Quate, C. F. & Gerber, C. (1986) Atomic force microscope. Physical Review Letters 56, 930933.
Biswas, P. K., Vellore, N. A., Yancey, J. A., Kucukkal, T. G., Collier, G., Brooks, B. R., Stuart, S. J. & Latour, R. A. (2012) Simulation of multiphase systems utilizing independent force fields to control intraphase and interphase behavior. Journal of Computational Chemistry 33, 14581466.
Bizzarri, A. R. (2006) Topological and dynamical properties of Azurin anchored to a gold substrate as investigated by molecular dynamics simulation. Biophysical Chemistry 122, 206214.
Bonomi, M., Barducci, A. & Parrinello, M. (2009) Reconstructing the equilibrium Boltzmann distribution from well-tempered metadynamics. Journal of Computational Chemistry 30, 16151621.
Borodin, O., Smith, G. D., Bandyopadhyaya, R. & Byutner, O. (2003) Molecular dynamics study of the influence of solid interfaces on poly(ethylene oxide) structure and dynamics. Macromolecules 36, 78737883.
Boughton, A. P., Andricioaei, I. & Chen, Z. (2010) Surface orientation of magainin 2: molecular dynamics simulation and sum frequency generation vibrational spectroscopic studies. Langmuir 26, 1603116036.
Brancolini, G., Corazza, A., Vuano, M., Fogolari, F., Mimmi, M. C., Bellotti, V., Stoppini, M., Corni, S. & Esposito, G. (2015) Probing the influence of citrate-capped gold nanoparticles on an amyloidogenic protein. ACS Nano 9, 26002613.
Brancolini, G., Kokh, D. B., Calzolai, L., Wade, R. C. & Corni, S. (2012) Docking of ubiquitin to gold nanoparticles. ACS Nano 6, 98639878.
Brancolini, G., Toroz, D. & Corni, S. (2014) Can small hydrophobic gold nanoparticles inhibit β2-microglobulin fibrillation? Nanoscale 6, 79037911.
Braun, R., Sarikaya, M. & Schulten, K. (2002) Genetically engineered gold-binding polypeptides: structure prediction and molecular dynamics. Journal of Biomaterials Science, Polymer Edition 13, 747757.
Brooks, B. R., Bruccoleri, R. E., Olafson, B. D., States, D. J., Swaminathan, S. & Karplus, M. (1983) CHARMM: a program for macromolecular energy, minimization, and dynamics calculations. Journal of Computational Chemistry 4, 187217.
Buimaga-Iarinca, L. & Calborean, A. (2012) Electronic structure of the ll-cysteine dimers adsorbed on Au(111): a density functional theory study. Physica Scripta 86, 035707.
Bussi, G., Gervasio, F. L., Laio, A. & Parrinello, M. (2006a) Free-energy landscape for β hairpin folding from combined parallel tempering and metadynamics. Journal of the American Chemical Society 128, 1343513441.
Bussi, G., Laio, A. & Parrinello, M. (2006b) Equilibrium free energies from nonequilibrium metadynamics. Physical Review Letters 96, 090601.
Butenuth, A., Moras, G., Schneider, J., Koleini, M., Köppen, S., Meißner, R., Wright, L. B., Walsh, T. R. & Colombi Ciacchi, L. (2012) Ab initio derived force-field parameters for molecular dynamics simulations of deprotonated amorphous-SiO2/water interfaces. Physica Status Solidi (B) 249, 292305.
Calzolai, L., Franchini, F., Gilliland, D. & Rossi, F. (2010) Protein−nanoparticle interaction: identification of the ubiquitin−gold nanoparticle interaction site. Nano Letters 10, 31013105.
Calzolari, A., Cicero, G., Cavazzoni, C., Di Felice, R., Catellani, A. & Corni, S. (2010) Hydroxyl-rich β-sheet adhesion to the gold surface in water by first-principle simulations. Journal of the American Chemical Society 132, 47904795.
Camden, A. N., Barr, S. A. & Berry, R. J. (2013) Simulations of peptide-graphene interactions in explicit water. The Journal of Physical Chemistry B 117, 1069110697.
Cardone, A., Pant, H. & Hassan, S. A. (2013) Specific and non-specific protein association in solution: computation of solvent effects and prediction of first-encounter modes for efficient configurational bias Monte Carlo simulations. The Journal of Physical Chemistry B 117, 1236012374.
Carravetta, V. & Monti, S. (2006) Peptide−TiO2 surface interaction in solution by ab initio and molecular dynamics simulations. The Journal of Physical Chemistry B 110, 61606169.
Carravetta, V., Monti, S. & Zhang, W. (2009) Interaction of biomolecular systems with titanium-based materials: computational investigations. Theoretical Chemistry Accounts 123, 299309.
Carrillo-Parramon, O., Brancolini, G. & Corni, S. (2013) Simulation of protein–surface interactions by a coarse-grained method. BioNanoScience 3, 1220.
Casals, E., Bastus, N., Vázquez, S., Varon, M., Comenge, J. & Puntes, V. (2008) Inorganic nanoparticles and biology. Contributions to Science 4, 171176.
Castells, V., Yang, S. & Van Tassel, P. R. (2002) Surface-induced conformational changes in lattice model proteins by Monte Carlo simulation. Physical Review E 65, 031912.
Chaki, N. K. & Vijayamohanan, K. (2002) Self-assembled monolayers as a tunable platform for biosensor applications. Biosensors and Bioelectronics 17, 112.
Chen, H., Su, X., Neoh, K.-G. & Choe, W.-S. (2009a) Context-dependent adsorption behavior of cyclic and linear peptides on metal oxide surfaces. Langmuir 25, 15881593.
Chen, Q., Wang, Q., Liu, Y.-C., Wu, T., Kang, Y., Moore, J. D. & Gubbins, K. E. (2009b) Energetics investigation on encapsulation of protein/peptide drugs in carbon nanotubes. The Journal of Chemical Physics 131, 015101.
Chen, S.-K., Wang, B.-C., Huang, W.-Z. & Gao, S. (2010) Molecular dynamics simulation of the interaction between Maps and Cu(100) surface. In proceedings of The 2nd Conference on Environmental Science and Information Application Technology pp. 533536. IEEE.
Chen, Y., Cruz-Chu, E. R., Woodard, J. C., Gartia, M. R., Schulten, K. & Liu, L. (2012) Electrically induced conformational change of peptides on metallic nanosurfaces. ACS Nano 6, 88478856.
Chiu, C.-C., Moore, P. B., Shinoda, W. & Nielsen, S. O. (2009) Size-dependent hydrophobic to hydrophilic transition for nanoparticles: a molecular dynamics study. The Journal of Chemical Physics 131, 244706.
Choi, J.-W., Kim, J. S., Kim, S.-U. & Min, J. (2009) Charge storage in redox-active azurin monolayer on 11-MUA modified gold surface. Biochip Journal 3, 157163.
Cicero, G., Calzolari, A., Corni, S. & Catellani, A. (2011) Anomalous wetting layer at the Au(111) surface. The Journal of Physical Chemistry Letters 2, 25822586.
Clementi, C., Nymeyer, H. & Onuchic, J. N. (2000) Topological and energetic factors: what determines the structural details of the transition state ensemble and ‘en-route’ intermediates for protein folding? An investigation for small globular proteins. Journal of Molecular Biology 298, 937953.
Cohavi, O., Corni, S., De Rienzo, F., Di Felice, R., Gottschalk, K. E., Hoefling, M., Kokh, D., Molinari, E., Schreiber, G., Vaskevich, A. & Wade, R. C. (2010) Protein-surface interactions: challenging experiments and computations. Journal of Molecular Recognition 23, 259262.
Cohavi, O., Reichmann, D., Abramovich, R., Tesler, A. B., Bellapadrona, G., Kokh, D. B., Wade, R. C., Vaskevich, A., Rubinstein, I. & Schreiber, G. (2011) A quantitative, real-time assessment of binding of peptides and proteins to gold surfaces. Chemistry - A European Journal 17, 13271336.
Cole, D. J., Payne, M. C., Csányi, G., Mark Spearing, S. & Colombi Ciacchi, L. (2007) Development of a classical force field for the oxidized Si surface: application to hydrophilic wafer bonding. The Journal of Chemical Physics 127, 204704.
Collier, G., Vellore, N. A., Yancey, J. A., Stuart, S. J. & Latour, R. A. (2012) Comparison between empirical protein force fields for the simulation of the adsorption behavior of structured LK peptides on functionalized surfaces. Biointerphases 7, 24.
Colombi Ciacchi, L. & Payne, M. C. (2005) First-principles molecular-dynamics study of native oxide growth on Si(001). Physical Review Letters 95, 196101.
Coppage, R., Slocik, J. M., Briggs, B. D., Frenkel, A. I., Heinz, H., Naik, R. R. & Knecht, M. R. (2011) Crystallographic recognition controls peptide binding for bio-based nanomaterials. Journal of the American Chemical Society 133, 1234612349.
Coppage, R., Slocik, J. M., Ramezani-Dakhel, H., Bedford, N. M., Heinz, H., Naik, R. R. & Knecht, M. R. (2013) Exploiting localized surface binding effects to enhance the catalytic reactivity of peptide-capped nanoparticles. Journal of the American Chemical Society 135, 1104811054.
Cornell, W. D., Cieplak, P., Bayly, C. I., Gould, I. R., Merz, K. M., Ferguson, D. M., Spellmeyer, D. C., Fox, T., Caldwell, J. W. & Kollman, P. A. (1995) A second generation force field for the simulation of proteins, nucleic acids, and organic molecules. Journal of the American Chemical Society 117, 51795197.
Corni, S., Hnilova, M., Tamerler, C. & Sarikaya, M. (2013) Conformational behavior of genetically-engineered dodecapeptides as a determinant of binding affinity for gold. The Journal of Physical Chemistry C 117, 1699017003.
Costa, D., Garrain, P.-A. & Baaden, M. (2013) Understanding small biomolecule-biomaterial interactions: a review of fundamental theoretical and experimental approaches for biomolecule interactions with inorganic surfaces. Journal of Biomedical Materials Research Part A 101A, 12101222.
Cruz-Chu, E. R., Aksimentiev, A. & Schulten, K. (2006) Water−silica force field for simulating nanodevices. The Journal of Physical Chemistry B 110, 2149721508.
Cygan, R. T., Liang, J.-J. & Kalinichev, A. G. (2004) Molecular models of hydroxide, oxyhydroxide, and clay phases and the development of a general force field. The Journal of Physical Chemistry B 108, 12551266.
Dauber-Osguthorpe, P., Roberts, V. A., Osguthorpe, D. J., Wolff, J., Genest, M. & Hagler, A. T. (1988) Structure and energetics of ligand binding to proteins:Escherichia coli dihydrofolate reductase-trimethoprim, a drug-receptor system. Proteins: Structure, Function, and Genetics 4, 3147.
De la Torre, J. G., Hernández Cifre, J. G., Ortega, A., Schmidt, R. R., Fernandes, M. X., Pérez Sánchez, H. E. & Pamies, R. (2009) SIMUFLEX: Algorithms and tools for simulation of the conformation and dynamics of flexible molecules and nanoparticles in dilute solution. Journal of Chemical Theory and Computation 5, 26062618.
De Leeuw, N. H. (2010) Computer simulations of structures and properties of the biomaterial hydroxyapatite. Journal of Materials Chemistry 20, 53765389.
De Miranda Tomásio, S. & Walsh, T. R. (2007) Atomistic modelling of the interaction between peptides and carbon nanotubes. Molecular Physics 105, 221229.
Demann, E. T. K., Stein, P. S. & Haubenreich, J. E. (2005) Gold as an implant in medicine and dentistry. Journal of Long-Term Effects of Medical Implants 15, 687698.
Di Felice, R. & Corni, S. (2011) Simulation of peptide–surface recognition. The Journal of Physical Chemistry Letters 2, 15101519.
Di Felice, R. & Selloni, A. (2004) Adsorption modes of cysteine on Au(111): thiolate, amino-thiolate, disulfide. The Journal of Chemical Physics 120, 49064914.
Di Felice, R., Selloni, A. & Molinari, E. (2003) DFT study of cysteine adsorption on Au(111). The Journal of Physical Chemistry B 107, 11511156.
Diebold, U. (2003) The surface science of titanium dioxide. Surface Science Reports 48, 53229.
Ding, F., Radic, S., Chen, R., Chen, P., Geitner, N. K., Brown, J. M. & Ke, P. C. (2013) Direct observation of a single nanoparticle–ubiquitin corona formation. Nanoscale 5, 91629169.
Dion, M., Rydberg, H., Schröder, E., Langreth, D. C. & Lundqvist, B. I. (2004) Van der Waals density functional for general geometries. Physical Review Letters 92, 246401.
Dong, X., Wang, Q., Wu, T. & Pan, H. (2007) Understanding adsorption-desorption dynamics of BMP-2 on hydroxyapatite (001) surface. Biophysical Journal 93, 750759.
Dufort, S., Sancey, L. & Coll, J.-L. (2012) Physico-chemical parameters that govern nanoparticles fate also dictate rules for their molecular evolution. Advanced Drug Delivery Reviews 64, 179189.
Durdagi, S., Mavromoustakos, T., Chronakis, N. & Papadopoulos, M. G. (2008) Computational design of novel fullerene analogues as potential HIV-1 PR inhibitors: analysis of the binding interactions between fullerene inhibitors and HIV-1 PR residues using 3D QSAR, molecular docking and molecular dynamics simulations. Bioorganic & Medicinal Chemistry 16, 99579974.
Emami, F. S., Puddu, V., Berry, R. J., Varshney, V., Patwardhan, S. V., Perry, C. C. & Heinz, H. (2014a) Force field and a surface model database for silica to simulate interfacial properties in atomic resolution. Chemistry of Materials 26, 26472658.
Emami, F. S., Puddu, V., Berry, R. J., Varshney, V., Patwardhan, S. V., Perry, C. C. & Heinz, H. (2014b) Prediction of specific biomolecule adsorption on silica surfaces as a function of pH and particle size. Chemistry of Materials 26, 57255734.
Eralp, T., Shavorskiy, A. & Held, G. (2011) The adsorption geometry and chemical state of lysine on Cu{110}. Surface Science 605, 468472.
Euston, S. R., Hughes, P., Naser, M. A. & Westacott, R. E. (2008) Comparison of the adsorbed conformation of barley lipid transfer protein at the decane−water and vacuum−water interface: a molecular dynamics simulation. Biomacromolecules 9, 14431453.
Euston, S. R. & Naser, M. A. (2005) Simulating the equation of state of model globular proteins adsorbed at a surface. Langmuir 21, 42274235.
Evers, C. H. J., Andersson, T., Lund, M. & Skepö, M. (2012) Adsorption of unstructured protein β-casein to hydrophobic and charged surfaces. Langmuir 28, 1184311849.
Fajín, J. L. C., Gomes, J. R. B. & Cordeiro, M. N. D. S. (2013) DFT study of the adsorption of D-(L-)cysteine on flat and chiral stepped gold surfaces. Langmuir 29, 88568864.
Feng, J., Pandey, R. B., Berry, R. J., Farmer, B. L., Naik, R. R. & Heinz, H. (2011) Adsorption mechanism of single amino acid and surfactant molecules to Au {111} surfaces in aqueous solution: design rules for metal-binding molecules. Soft Matter 7, 2113.
Fenoglio, I., Fubini, B., Ghibaudi, E. M. & Turci, F. (2011) Multiple aspects of the interaction of biomacromolecules with inorganic surfaces. Advanced Drug Delivery Reviews 63, 11861209.
Finnis, M. W. (1991) The interaction of a point charge with an aluminium (111) surface. Surface Science 241, 6172.
Folliet, N., Gervais, C., Costa, D., Laurent, G., Babonneau, F., Stievano, L., Lambert, J.-F. & Tielens, F. (2013) A molecular picture of the adsorption of glycine in mesoporous silica through NMR experiments combined with DFT-D calculations. The Journal of Physical Chemistry C 117, 41044114.
Freeman, C. L., Asteriadis, I., Yang, M. & Harding, J. H. (2009) Interactions of organic molecules with calcite and magnesite surfaces. The Journal of Physical Chemistry C 113, 36663673.
Freeman, C. L., Harding, J. H., Cooke, D. J., Elliott, J. A., Lardge, J. S. & Duffy, D. M. (2007) New forcefields for modeling biomineralization processes. The Journal of Physical Chemistry C 111, 1194311951.
Freeman, C. L., Harding, J. H., Quigley, D. & Rodger, P. M. (2010) Structural control of crystal nuclei by an eggshell protein. Angewandte Chemie International Edition 49, 51355137.
Freeman, C. L., Harding, J. H., Quigley, D. & Rodger, P. M. (2011) Simulations of ovocleidin-17 binding to calcite surfaces and its implications for eggshell formation. The Journal of Physical Chemistry C 115, 81758183.
Frenkel, D. & Smit, B. (2001) Understanding Molecular Simulation: From Algorithms to Applications, 2nd edition. Academic Press, Orlando, FL, USA.
Friddle, R. W., Battle, K., Trubetskoy, V., Tao, J., Salter, E. A., Moradian-Oldak, J., De Yoreo, J. J. & Wierzbicki, A. (2011) Single-molecule determination of the face-specific adsorption of amelogenin's C-terminus on hydroxyapatite. Angewandte Chemie International Edition 50, 75417545.
Friedrichs, W., Köppen, S. & Langel, W. (2013) Titanium binding dodecapeptides and the impact of water structure. Surface Science 617, 4252.
Friedrichs, W. & Langel, W. (2014) Atomistic modeling of peptide adsorption on rutile (100) in the presence of water and of contamination by low molecular weight alcohols. Biointerphases 9, 031006.
Fukunishi, H., Watanabe, O. & Takada, S. (2002) On the Hamiltonian replica exchange method for efficient sampling of biomolecular systems: Application to protein structure prediction. The Journal of Chemical Physics 116, 90589067.
Gabdoulline, R. R. & Wade, R. C. (2002) Biomolecular diffusional association. Current Opinion in Structural Biology 12, 204213.
Gagner, J. E., Lopez, M. D., Dordick, J. S. & Siegel, R. W. (2011) Effect of gold nanoparticle morphology on adsorbed protein structure and function. Biomaterials 32, 72417252.
Gagner, J. E., Shrivastava, S., Qian, X., Dordick, J. S. & Siegel, R. W. (2012) Engineering nanomaterials for biomedical applications requires understanding the nano-bio interface: a perspective. The Journal of Physical Chemistry Letters 3, 31493158.
Garland, A., Shen, L. & Zhu, X. (2012) Mobile precursor mediated protein adsorption on solid surfaces. Progress in Surface Science 87, 122
Ghiringhelli, L. M., Hess, B., van der Vegt, N. F. A. & Delle Site, L. (2008) Competing adsorption between hydrated peptides and water onto metal surfaces: from electronic to conformational properties. Journal of the American Chemical Society 130, 1346013464.
Ghiringhelli, L. M., Schravendijk, P. & Delle Site, L. (2006) Adsorption of alanine on a Ni(111) surface: a multiscale modeling oriented density functional study. Physical Review B 74, 035437.
Ghosh, S., Jana, S. & Guchhait, N. (2012) Domain specific association of small fluorescent probe trans -3-(4-monomethylaminophenyl)-acrylonitrile (MMAPA) with bovine serum albumin (BSA) and its dissociation from protein binding sites by Ag nanoparticles: spectroscopic and molecular docking study. The Journal of Physical Chemistry B 116, 11551163.
Gibbs, D., Ocko, B. M., Zehner, D. M. & Mochrie, S. G. J. (1990) Structure and phases of the Au(001) surface: in-plane structure. Physical Review B 42, 73307344.
Gooding, J. J., Mearns, F., Yang, W. & Liu, J. (2003) Self-assembled monolayers into the 21st century: recent advances and applications. Electroanalysis 15, 8196.
Gorba, C. & Helms, V. (2003) Diffusional dynamics of cytochrome c molecules in the presence of a charged surface. Soft Materials 1, 185202.
Gray, J. J. (2004) The interaction of proteins with solid surfaces. Current Opinion in Structural Biology 14, 110115.
Griepernau, B., Hanke, C., Santen, L., B, R. A. Hansmann, U. H. E., Meinke, J. H., Mohanty, S. & Nadler, W. (2008) Coarse-grained simulations of protein adsorption on solid surfaces. In From Computational Biophysics to Systems Biology (CBSB08), Proceedings of the NIC Workshop (eds Hansmann, U. H. E., Meinke, J. H., Mohanty, S., Nadler, W. & Zimmermann, O.), pp. 223226. John von Neumann Institute for Computing, Julich, Germany.
Grimme, S. (2004) Accurate description of van der Waals complexes by density functional theory including empirical corrections. Journal of Computational Chemistry 25, 14631473.
Grimme, S., Antony, J., Ehrlich, S. & Krieg, H. (2010) A consistent and accurate ab initio parametrization of density functional dispersion correction (DFT-D) for the 94 elements H-Pu. The Journal of Chemical Physics 132, 154104.
Große Holthaus, S., Köppen, S., Frauenheim, T. & Colombi Ciacchi, L. (2012) Atomistic simulations of the  ZnO(12-10)/water interface: a comparison between first-principles, tight-binding, and empirical methods. Journal of Chemical Theory and Computation 8, 45174526.
Guldi, D. M., Rahman, G. M. A., Sgobba, V. & Ehli, C. (2006) Multifunctional molecular carbon materials—from fullerenes to carbon nanotubes. Chemical Society Reviews 35, 471487.
Guo, J., Yao, X., Ning, L., Wang, Q. & Liu, H. (2014) The adsorption mechanism and induced conformational changes of three typical proteins with different secondary structural features on graphene. RSC Advances 4, 9953.
Hagiwara, T., Sakiyama, T. & Watanabe, H. (2009) Molecular simulation of bovine β-lactoglobulin adsorbed onto a positively charged solid surface. Langmuir 25, 226234.
Hahm, J. (2014) Fundamentals of nanoscale polymer–protein interactions and potential contributions to solid-state nanobioarrays. Langmuir 30, 98919904.
Halgren, T. A. & Damm, W. (2001) Polarizable force fields. Current Opinion in Structural Biology 11, 236242.
Hamdi, M., Ferreira, A., Sharma, G. & Mavroidis, C. (2008) Prototyping bio-nanorobots using molecular dynamics simulation and virtual reality. Microelectronics Journal 39, 190201.
Hansmann, U. H. E. (1997) Parallel tempering algorithm for conformational studies of biological molecules. Chemical Physics Letters 281, 140150.
Hansmann, U. H. E. & Okamoto, Y. (1999) New Monte Carlo algorithms for protein folding. Current Opinion in Structural Biology 9, 177183.
Hassan, S. A. & Steinbach, P. J. (2011) Water-exclusion and liquid-structure forces in implicit solvation. The Journal of Physical Chemistry B 115, 1466814682.
Hauptmann, S., Dufner, H., Brickmann, J., Kast, S. M. & Berry, R. S. (2003) Potential energy function for apatites. Physical Chemistry Chemical Physics 5, 635639.
Heinz, H., Farmer, B. L., Pandey, R. B., Slocik, J. M., Patnaik, S. S., Pachter, R. & Naik, R. R. (2009) Nature of molecular interactions of peptides with gold, palladium, and Pd−Au bimetal surfaces in aqueous solution. Journal of the American Chemical Society 131, 97049714.
Heinz, H., Jha, K. C., Luettmer-Strathmann, J., Farmer, B. L. & Naik, R. R. (2011) Polarization at metal-biomolecular interfaces in solution. Journal of the Royal Society Interface 8, 220232.
Heinz, H., Lin, T.-J., Kishore Mishra, R. & Emami, F. S. (2013) Thermodynamically consistent force fields for the assembly of inorganic, organic, and biological nanostructures: the INTERFACE force field. Langmuir 29, 17541765.
Heinz, H., Vaia, R. A., Farmer, B. L. & Naik, R. R. (2008) Accurate simulation of surfaces and interfaces of face-centered cubic metals using 12–6 and 9–6 Lennard-Jones potentials. The Journal of Physical Chemistry C 112, 1728117290.
Henderson, M. (2002) The interaction of water with solid surfaces: fundamental aspects revisited. Surface Science Reports 46, 1308.
Hill, H. D., Vega, R. A. & Mirkin, C. A. (2007) Nonenzymatic detection of bacterial genomic DNA using the bio bar code assay. Analytical Chemistry 79, 92189223.
Hoefling, M., Iori, F., Corni, S. & Gottschalk, K.-E. (2010a) Interaction of amino acids with the Au(111) surface: adsorption free energies from molecular dynamics simulations. Langmuir 26, 83478351.
Hoefling, M., Iori, F., Corni, S. & Gottschalk, K.-E. (2010b) The conformations of amino acids on a gold(111) surface. ChemPhysChem 11, 17631767.
Hoefling, M., Monti, S., Corni, S. & Gottschalk, K. E. (2011) Interaction of β-sheet folds with a gold surface. PLoS ONE 6, e20925.
Hoffman, A. S. (2008) The origins and evolution of ‘controlled’ drug delivery systems. Journal of Controlled Release 132, 153163.
Hohenberg, P. & Kohn, W. (1964) Inhomogeneous electron gas. Physical Review 136, B864B871.
Hong, G., Heinz, H., Naik, R. R., Farmer, B. L. & Pachter, R. (2009) Toward understanding amino acid adsorption at metallic interfaces: a density functional theory study. ACS Applied Materials & Interfaces 1, 388392.
Horbett, T. A. & Brash, J. L. (1995) Proteins at Interfaces II. American Chemical Society, Washington, DC, USA.
Horinek, D., Serr, A., Bonthuis, D. J., Boström, M., Kunz, W. & Netz, R. R. (2008) Molecular hydrophobic attraction and ion-specific effects studied by molecular dynamics. Langmuir 24, 12711283.
Hou, T., Wang, J., Li, Y. & Wang, W. (2011) Assessing the performance of the MM/PBSA and MM/GBSA methods. 1. The accuracy of binding free energy calculations based on molecular dynamics simulations. Journal of Chemical Information and Modeling 51, 6982.
Hsu, H.-J., Sheu, S.-Y. & Tsay, R.-Y. (2008) Preferred orientation of albumin adsorption on a hydrophilic surface from molecular simulation. Colloids and Surfaces B: Biointerfaces 67, 183191.
Hu, Y., Das, A., Hecht, M. H. & Scoles, G. (2005) Nanografting de novo proteins onto gold surfaces. Langmuir 21, 91039109.
Huang, L., Gubbins, K. E., Li, L. & Lu, X. (2014) Water on titanium dioxide surface: a revisiting by reactive molecular dynamics simulations. Langmuir 30, 1483214840.
Huang, X., Hagen, M., Kim, B., Friesner, R. A., Zhou, R. & Berne, B. J. (2007) Replica exchange with solute tempering: efficiency in large scale systems. The Journal of Physical Chemistry B 111, 54055410.
Hughes, Z. E., Tomásio, S. M. & Walsh, T. R. (2014) Efficient simulations of the aqueous bio-interface of graphitic nanostructures with a polarisable model. Nanoscale 6, 54385448.
Hung, A., Mwenifumbo, S., Mager, M., Kuna, J. J., Stellacci, F., Yarovsky, I. & Stevens, M. M. (2011) Ordering surfaces on the nanoscale: implications for protein adsorption. Journal of the American Chemical Society 133, 14381450.
Imamura, K., Kawasaki, Y., Awadzu, T., Sakiyama, T. & Nakanishi, K. (2003) Contribution of acidic amino residues to the adsorption of peptides onto a stainless steel surface. Journal of Colloid and Interface Science 267, 294301.
Imamura, K., Kawasaki, Y., Nagayasu, T., Sakiyama, T. & Nakanishi, K. (2007) Adsorption characteristics of oligopeptides composed of acidic and basic amino acids on titanium surface. Journal of Bioscience and Bioengineering 103, 712.
Iori, F. & Corni, S. (2008) Including image charge effects in the molecular dynamics simulations of molecules on metal surfaces. Journal of Computational Chemistry 29, 16561666.
Iori, F., Corni, S. & Di Felice, R. (2008) Unraveling the interaction between histidine side chain and the Au(111) surface: a DFT study. The Journal of Physical Chemistry C 112, 1354013545.
Iori, F., Di Felice, R., Molinari, E. & Corni, S. (2009) GolP: An atomistic force-field to describe the interaction of proteins with Au(111) surfaces in water. Journal of Computational Chemistry 30, 14651476.
Iwamatsu, M. & Okabe, Y. (2004) Basin hopping with occasional jumping. Chemical Physics Letters 399, 396400.
Jackson, D. R., Omanovic, S. & Roscoe, S. G. (2000) Electrochemical studies of the adsorption behavior of serum proteins on titanium. Langmuir 16, 54495457.
Jain, P. K., Huang, X., El-Sayed, I. H. & El-Sayed, M. A. (2008) Noble metals on the nanoscale: optical and photothermal properties and some applications in imaging, sensing, biology, and medicine. Accounts of Chemical Research 41, 15781586.
Jarzynski, C. (1997) Nonequilibrium equality for free energy differences. Physical Review Letters 78, 26902693.
Jeyachandran, Y. L., Mielczarski, E., Rai, B. & Mielczarski, J. A. (2009) Quantitative and qualitative evaluation of adsorption/desorption of bovine serum albumin on hydrophilic and hydrophobic surfaces. Langmuir 25, 1161411620.
Jimenez-Izal, E., Chiatti, F., Corno, M., Rimola, A. & Ugliengo, P. (2012) Glycine adsorption at nonstoichiometric (010) hydroxyapatite surfaces: a B3LYP study. The Journal of Physical Chemistry C 116, 1456114567.
Jönsson, U., Fägerstam, L., Ivarsson, B., Johnsson, B., Karlsson, R., Lundh, K., Löfås, S., Persson, B., Roos, H. & Rönnberg, I. (1991) Real-time biospecific interaction analysis using surface plasmon resonance and a sensor chip technology. BioTechniques 11, 620627.
Jorgensen, W. L., Chandrasekhar, J., Madura, J. D., Impey, R. W. & Klein, M. L. (1983) Comparison of simple potential functions for simulating liquid water. The Journal of Chemical Physics 79, 926.
Jorgensen, W. L., Maxwell, D. S. & Tirado-Rives, J. (1996) Development and testing of the OPLS all-atom force field on conformational energetics and properties of organic liquids. Journal of the American Chemical Society 118, 1122511236.
Jose, J. C. & Sengupta, N. (2013) Molecular dynamics simulation studies of the structural response of an isolated Aβ1–42 monomer localized in the vicinity of the hydrophilic TiO2 surface. European Biophysics Journal 42, 487494.
Juffer, A. H., Argos, P. & de Vlieg, J. (1996) Adsorption of proteins onto charged surfaces: A Monte Carlo approach with explicit ions. Journal of Computational Chemistry 17, 17831803.
Kang, S., Huynh, T., Xia, Z., Zhang, Y., Fang, H., Wei, G. & Zhou, R. (2013) Hydrophobic interaction drives surface-assisted epitaxial assembly of amyloid-like peptides. Journal of the American Chemical Society 135, 31503157.
Kang, Y., Li, X., Tu, Y., Wang, Q. & Ågren, H. (2010) On the mechanism of protein adsorption onto hydroxylated and nonhydroxylated TiO2 surfaces. The Journal of Physical Chemistry C 114, 1449614502.
Kang, Y., Liu, Y.-C., Wang, Q., Shen, J.-W., Wu, T. & Guan, W.-J. (2009) On the spontaneous encapsulation of proteins in carbon nanotubes. Biomaterials 30, 28072815.
Kantarci, N., Tamerler, C., Sarikaya, M., Haliloglu, T. & Doruker, P. (2005) Molecular dynamics simulations on constraint metal binding peptides. Polymer 46, 43074313.
Kästner, J. & Thiel, W. (2005) Bridging the gap between thermodynamic integration and umbrella sampling provides a novel analysis method: ‘Umbrella integration’. The Journal of Chemical Physics 123, 144104.
Katti, D. R., Ghosh, P., Schmidt, S. & Katti, K. S. (2005a) Mechanical properties of the sodium montmorillonite interlayer intercalated with amino acids. Biomacromolecules 6, 32763282.
Katti, D. R., Schmidt, S. R., Ghosh, P. & Katti, K. S. (2005b) Modeling the response of pyrophyllite interlayer to applied stress using steered molecular dynamics. Clays and Clay Minerals 53, 171178.
Khlebtsov, N. G. & Dykman, L. A. (2010) Optical properties and biomedical applications of plasmonic nanoparticles. Journal of Quantitative Spectroscopy and Radiative Transfer 111, 135.
Kievit, F. M. & Zhang, M. (2011) Surface engineering of iron oxide nanoparticles for targeted cancer therapy. Accounts of Chemical Research 44, 853862.
Kim, M. S., Khang, G. & Lee, H. B. (2008) Gradient polymer surfaces for biomedical applications. Progress in Polymer Science 33, 138164.
Kim, S.-Y., Kumar, N., Persson, P., Sofo, J., van Duin, A. C. T. & Kubicki, J. D. (2013) Development of a ReaxFF reactive force field for titanium dioxide/water systems. Langmuir 29, 78387846.
Klimeš, J., Bowler, D. R. & Michaelides, A. (2010) Chemical accuracy for the van der Waals density functional. Journal of Physics: Condensed Matter 22, 022201.
Klimeš, J., Bowler, D. R. & Michaelides, A. (2011) Van der Waals density functionals applied to solids. Physical Review B 83, 195131.
Knotts, T. A., Rathore, N. & de Pablo, J. J. (2005) Structure and stability of a model three-helix-bundle protein on tailored surfaces. Proteins: Structure, Function, and Bioinformatics 61, 385397.
Knotts, T. A., Rathore, N. & de Pablo, J. J. (2008) An entropic perspective of protein stability on surfaces. Biophysical Journal 94, 44734483.
Koch, R., Lipton, A. S., Filipek, S. & Renugopalakrishnan, V. (2011) Arginine interactions with anatase TiO2 (100) surface and the perturbation of 49Ti NMR chemical shifts – a DFT investigation: relevance to Renu-Seeram bio solar cell. Journal of Molecular Modeling 17, 14671472.
Kohn, W. & Sham, L. J. (1965) Self-consistent equations including exchange and correlation effects. Physical Review 140, A1133A1138.
Kokh, D. B., Corni, S., Winn, P. J., Hoefling, M., Gottschalk, K. E. & Wade, R. C. (2010) ProMetCS: An atomistic force field for modeling protein−metal surface interactions in a continuum aqueous solvent. Journal of Chemical Theory and Computation 6, 17531768.
Kollman, P. A., Massova, I., Reyes, C., Kuhn, B., Huo, S., Chong, L., Lee, M., Lee, T., Duan, Y., Wang, W., Donini, O., Cieplak, P., Srinivasan, J., Case, D. A. & Cheatham, T. E. (2000) Calculating structures and free energies of complex molecules: combining molecular mechanics and continuum models. Accounts of Chemical Research 33, 889897.
Köppen, S., Bronkalla, O. & Langel, W. (2008) Adsorption configurations and energies of amino acids on anatase and rutile surfaces. The Journal of Physical Chemistry C 112, 1360013606.
Köppen, S. & Langel, W. (2010) Simulation of adhesion forces and energies of peptides on titanium dioxide surfaces. Langmuir 26, 1524815256.
Korzeniewski, C., Climent, V. & Feliu, J. M. (2011) Electrochemistry at platinum single crystal electrodes. In Electroanalytical Chemistry (eds Bard, C. & Zoski, A. J.), pp. 75170. CRC Press, Boca Raton, FL, USA.
Kraszewski, S., Tarek, M., Treptow, W. & Ramseyer, C. (2010) Affinity of C60 neat fullerenes with membrane proteins: a computational study on potassium channels. ACS Nano 4, 41584164.
Kubiak-Ossowska, K. & Mulheran, P. A. (2010a) What governs protein adsorption and immobilization at a charged solid surface? Langmuir 26, 76907694.
Kubiak-Ossowska, K. & Mulheran, P. A. (2010b) Mechanism of hen egg white lysozyme adsorption on a charged solid surface. Langmuir 26, 1595415965.
Kubiak-Ossowska, K. & Mulheran, P. A. (2012) Protein diffusion and long-term adsorption states at charged solid surfaces. Langmuir 28, 1557715585.
Kumar, S., Rosenberg, J. M., Bouzida, D., Swendsen, R. H. & Kollman, P. A. (1992) The weighted histogram analysis method for free-energy calculations on biomolecules. I. The method. Journal of Computational Chemistry 13, 10111021.
Lacerda, S. H. D. P., Park, J. J., Meuse, C., Pristinski, D., Becker, M. L., Karim, A. & Douglas, J. F. (2010) Interaction of gold nanoparticles with common human blood proteins. ACS Nano 4, 365379.
Laera, S., Ceccone, G., Rossi, F., Gilliland, D., Hussain, R., Siligardi, G. & Calzolai, L. (2011) Measuring protein structure and stability of protein–nanoparticle systems with synchrotron radiation circular dichroism. Nano Letters 11, 44804484.
Laio, A. & Gervasio, F. L. (2008) Metadynamics: a method to simulate rare events and reconstruct the free energy in biophysics, chemistry and material science. Reports on Progress in Physics 71, 126601.
Laio, A. & Parrinello, M. (2002) Escaping free-energy minima. Proceedings of the National Academy of Sciences 99, 1256212566.
Lal, M., Plummer, M., Richmond, N. J. & Smith, W. (2004) Solvation of metal nanoparticles in a subcritical — supercritical fluid: a computer simulation study. The Journal of Physical Chemistry B 108, 60526061.
Lal, M., Plummer, M. & Smith, W. (2006) Solvent density effects on the solvation behavior and configurational structure of bare and passivated 38-atom gold nanoparticle in supercritical ethane. The Journal of Physical Chemistry B 110, 2087920888.
Landau, D. P. & Binder, K. (2009) A Guide to Monte Carlo Simulations in Statistical Physics. Cambridge University Press, Cambridge, UK.
Latour, R. A. (2008) Molecular simulation of protein-surface interactions: benefits, problems, solutions, and future directions (Review). Biointerphases 3, FC2FC12.
Lee, K., Murray, É.D., Kong, L., Lundqvist, B. I. & Langreth, D. C. (2010) Higher-accuracy van der Waals density functional. Physical Review B 82, 081101.
Lee, S.-S., Kim, B. & Lee, S. (2014) Structures and bonding properties of gold–Arg-Cys complexes: DFT study of simple peptide-coated metal. The Journal of Physical Chemistry C 118, 2084020847.
Li, C., Monti, S., Ågren, H. & Carravetta, V. (2014) Cysteine on TiO2 (110): a theoretical study by reactive dynamics and photoemission spectra simulation. Langmuir 30, 88198828.
Li, C., Monti, S. & Carravetta, V. (2012) Journey toward the surface: how glycine adsorbs on titania in water solution. The Journal of Physical Chemistry C 116, 1831818326.
Li, H., Luo, Y., Derreumaux, P. & Wei, G. (2011) Carbon nanotube inhibits the formation of β-sheet-rich oligomers of the Alzheimer's amyloid-β(16-22) peptide. Biophysical Journal 101, 22672276.
Li, J., Liu, T., Li, X., Ye, L., Chen, H., Fang, H., Wu, Z. & Zhou, R. (2005) Hydration and dewetting near graphite−CH3 and graphite−COOH plates. The Journal of Physical Chemistry B 109, 1363913648.
Li, Y. & Gu, N. (2010) Thermodynamics of charged nanoparticle adsorption on charge-neutral membranes: a simulation study. The Journal of Physical Chemistry B 114, 27492754.
Li, Z. & Scheraga, H. (1987) Monte Carlo-minimization approach to the multiple-minima problem in protein folding. Proceedings of the National Academy of Sciences 84, 66116615.
Liang, J., Fieg, G., Keil, F. J. & Jakobtorweihen, S. (2012) Adsorption of proteins onto ion-exchange chromatographic media: a molecular dynamics study. Industrial & Engineering Chemistry Research 51, 1604916058.
Liao, C., Xie, Y. & Zhou, J. (2014) Computer simulations of fibronectin adsorption on hydroxyapatite surfaces. RSC Advances 4, 15759.
Liao, C. & Zhou, J. (2014) Replica-exchange molecular dynamics simulation of basic fibroblast growth factor adsorption on hydroxyapatite. The Journal of Physical Chemistry B 118, 58435852.
Liu, H. & Chakrabarti, A. (1999) Molecular dynamics study of adsorption and spreading of a polymer chain onto a flat surface. Polymer 40, 72857293.
Liu, J., Liao, C. & Zhou, J. (2013) Multiscale simulations of protein G B1 adsorbed on charged self-assembled monolayers. Langmuir 29, 1136611374.
Liu, P., Kim, B., Friesner, R. A. & Berne, B. J. (2005) Replica exchange with solute tempering: A method for sampling biological systems in explicit water. Proceedings of the National Academy of Sciences 102, 1374913754.
Liu, X., Chu, P. & Ding, C. (2004) Surface modification of titanium, titanium alloys, and related materials for biomedical applications. Materials Science and Engineering: R: Reports 47, 49121.
Liu, Y., Wu, M., Feng, X., Shao, X. & Cai, W. (2012) Adsorption behavior of hydrophobin proteins on polydimethylsiloxane substrates. The Journal of Physical Chemistry B 116, 1222712234.
Liu, Z. & Liang, X.-J. (2012) Nano-carbons as theranostics. Theranostics 2, 235237.
Lopes, P. E. M., Murashov, V., Tazi, M., Demchuk, E. & MacKerell, A. D. (2006) Development of an empirical force field for silica. Application to the quartz−water interface. The Journal of Physical Chemistry B 110, 27822792.
Love, J. C., Estroff, L. A., Kriebel, J. K., Nuzzo, R. G. & Whitesides, G. M. (2005) Self-assembled monolayers of thiolates on metals as a form of nanotechnology. Chemical Reviews 105, 11031170.
Lu, D. R., Lee, S. J. & Park, K. (1992) Calculation of solvation interaction energies for protein adsorption on polymer surfaces. Journal of Biomaterials Science, Polymer Edition 3, 127147.
Lund, M., Åkesson, T. & Jönsson, B. (2005) Enhanced protein adsorption due to charge regulation. Langmuir 21, 83858388.
Lundqvist, M., Sethson, I. & Jonsson, B.-H. (2004) Protein adsorption onto silica nanoparticles: conformational changes depend on the particles’ curvature and the protein stability. Langmuir 20, 1063910647.
MacKerell, A. D., Bashford, D., Bellott, M., Dunbrack, R. L., Evanseck, J. D., Field, M. J., Fischer, S., Gao, J., Guo, H., Ha, S., Joseph-McCarthy, D., Kuchnir, L., Kuczera, K., Lau, F. T. K., Mattos, C., Michnick, S., Ngo, T., Nguyen, D. T., Prodhom, B., Reiher, W. E., Roux, B., Schlenkrich, M., Smith, J. C., Stote, R., Straub, J., Watanabe, M., Wiórkiewicz-Kuczera, J., Yin, D. & Karplus, M. (1998) All-atom empirical potential for molecular modeling and dynamics studies of proteins. The Journal of Physical Chemistry B 102, 35863616.
Madura, J. D., Davist, M. E., Gilson, M. K., Wade, R. C., Luty, B. A. & McCammon, J. A. (1994) Biological applications of electrostatic calculations and Brownian dynamics simulations. In Reviews in Computational Chemistry, Volume 5 (eds Lipkowitz, K. B. & Boyd, D. B.), pp. 229267. John Wiley & Sons, Inc., New York, NY, USA.
Mahmoudi, M., Lynch, I., Ejtehadi, M. R., Monopoli, M. P., Bombelli, F. B. & Laurent, S. (2011) Protein−nanoparticle interactions: opportunities and challenges. Chemical Reviews 111, 56105637.
Mahon, E., Salvati, A., Baldelli Bombelli, F., Lynch, I. & Dawson, K. A. (2012) Designing the nanoparticle–biomolecule interface for ‘targeting and therapeutic delivery’. Journal of Controlled Release 161, 164174.
Mandal, D., Nasrolahi Shirazi, A. & Parang, K. (2014) Self-assembly of peptides to nanostructures. Organic & Biomolecular Chemistry 12, 35443561.
Manecka, G. M., Labrash, J., Rouxel, O., Dubot, P., Lalevée, J., Andaloussi, S. A., Renard, E., Langlois, V. & Versace, D. L. (2014) Green photoinduced modification of natural poly(3-hydroxybutyrate- co -3-hydroxyvalerate) surface for antibacterial applications. ACS Sustainable Chemistry & Engineering 2, 9961006.
Marcus, R. A. & Sutin, N. (1985) Electron transfers in chemistry and biology. Biochimica et Biophysica Acta (BBA) - Reviews on Bioenergetics 811, 265322.
Marrink, S. J., Risselada, H. J., Yefimov, S., Tieleman, D. P. & de Vries, A. H. (2007) The MARTINI force field: coarse grained model for biomolecular simulations. The Journal of Physical Chemistry B 111, 78127824.
Martin, R. M. (2004) Electronic structure: basic theory and practical methods. Cambridge University Press, Cambridge, UK.
Marx, D. & Hutter, J. (2000) Ab initio molecular dynamics: theory and implementation. In Modern Methods and Algorithms of Quantum Chemistry (ed Grotendorst, J.), pp. 301449. Forschungszentrum Jülich, Jülich, Germany.
Matsui, M. & Akaogi, M. (1991) Molecular dynamics simulation of the structural and physical properties of the four polymorphs of TiO2. Molecular Simulation 6, 239244.
Meißner, R. H., Schneider, J., Schiffels, P. & Colombi Ciacchi, L. (2014) Computational prediction of circular dichroism spectra and quantification of helicity loss upon peptide adsorption on silica. Langmuir 30, 34873494.
Mereghetti, P. & Wade, R. C. (2011) Diffusion of hydrophobin proteins in solution and interactions with a graphite surface. BMC Biophysics 4, 2.
Metropolis, N., Rosenbluth, A. W., Rosenbluth, M. N., Teller, A. H. & Teller, E. (1953) Equation of state calculations by fast computing machines. The Journal of Chemical Physics 21, 10871092.
Mijajlovic, M., Penna, M. J. & Biggs, M. J. (2013) Free energy of adsorption for a peptide at a liquid/solid interface via nonequilibrium molecular dynamics. Langmuir 29, 29192926.
Millo, D., Pandelia, M.-E., Utesch, T., Wisitruangsakul, N., Mroginski, M. A., Lubitz, W., Hildebrandt, P. & Zebger, I. (2009) Spectroelectrochemical study of the [NiFe] hydrogenase from Desulfovibrio vulgaris Miyazaki F in solution and immobilized on biocompatible gold surfaces. The Journal of Physical Chemistry B 113, 1534415351.
Mirau, P. A., Naik, R. R. & Gehring, P. (2011) Structure of peptides on metal oxide surfaces probed by NMR. Journal of the American Chemical Society 133, 1824318248.
Mishra, R. K., Flatt, R. J. & Heinz, H. (2013) Force field for tricalcium silicate and insight into nanoscale properties: cleavage, initial hydration, and adsorption of organic molecules. The Journal of Physical Chemistry C 117, 1041710432.
Mongan, J. & Case, D. A. (2005) Biomolecular simulations at constant pH. Current Opinion in Structural Biology 15, 157163.
Monti, S. (2007) RAD16II β-sheet filaments onto titanium dioxide: dynamics and adsorption properties. Journal of Physical Chemistry C 111, 1696216973.
Monti, S., Carravetta, V., Battocchio, C., Iucci, G. & Polzonetti, G. (2008) Peptide/TiO2 surface interaction: a theoretical and experimental study on the structure of adsorbed ALA-GLU and ALA-LYS. Langmuir 24, 32053214.
Mori, T., Hamers, R. J., Pedersen, J. A. & Cui, Q. (2013) An explicit consideration of desolvation is critical to binding free energy calculations of charged molecules at ionic surfaces. Journal of Chemical Theory and Computation 9, 50595069.
Motta, A., Gaigeot, M.-P. & Costa, D. (2012) AIMD evidence of inner sphere adsorption of glycine on a stepped (101) boehmite AlOOH surface. The Journal of Physical Chemistry C 116, 2341823427.
Mücksch, C. & Urbassek, H. M. (2011) Molecular dynamics simulation of free and forced BSA adsorption on a hydrophobic graphite surface. Langmuir 27, 1293812943.
Muir, J. M. R., Costa, D. & Idriss, H. (2014) DFT computational study of the RGD peptide interaction with the rutile TiO2 (110) surface. Surface Science 624, 814.
Nada, H. (2014) Difference in the conformation and dynamics of aspartic acid on the flat regions, step edges, and kinks of a calcite surface: a molecular dynamics study. The Journal of Physical Chemistry C 118, 1433514345.
Nadler, R. & Sanz, J. F. (2012) Effect of dispersion correction on the Au(1 1 1)-H2O interface: a first-principles study. The Journal of Chemical Physics 137, 114709.
Nawrocki, G. & Cieplak, M. (2013) Amino acids and proteins at ZnO–water interfaces in molecular dynamics simulations. Physical Chemistry Chemical Physics 15, 1362813636.
Nazmutdinov, R. R., Manyurov, I. R., Zinkicheva, T. T., Jang, J. & Ulstrup, J. (2007) Cysteine adsorption on the Au(111) surface and the electron transfer in configuration of a scanning tunneling microscope: a quantum-chemical approach. Russian Journal of Electrochemistry 43, 328341.
Neves, R. S., Motheo, A. J., Fartaria, R. P. S. & Silva Fernandes, F. M. S. (2007) Modelling water adsorption on Au(210) surfaces. I. A force field for water–Au interactions by DFT. Journal of Electroanalytical Chemistry 609, 140146.
Nie, Z. & Kumacheva, E. (2008) Patterning surfaces with functional polymers. Nature Materials 7, 277290.
Nie, Z., Petukhova, A. & Kumacheva, E. (2010) Properties and emerging applications of self-assembled structures made from inorganic nanoparticles. Nature Nanotechnology 5, 1525.
Nonella, M. & Seeger, S. (2008) Investigating alanine–silica interaction by means of first-principles molecular-dynamics simulations. ChemPhysChem 9, 414421.
Noon, W. H., Kong, Y. & Ma, J. (2002) Molecular dynamics analysis of a buckyball-antibody complex. Proceedings of the National Academy of Sciences 99, 64666470.
Notman, R. & Walsh, T. R. (2009) Molecular dynamics studies of the interactions of water and amino acid analogues with quartz surfaces. Langmuir 25, 16381644.
Novoselov, K. S. (2004) Electric field effect in atomically thin carbon films. Science 306, 666669.
Nowinski, A. K., Sun, F., White, A. D., Keefe, A. J. & Jiang, S. (2012) Sequence, structure, and function of peptide self-assembled monolayers. Journal of the American Chemical Society 134, 60006005.
O'Brien, C. P., Stuart, S. J., Bruce, D. A. & Latour, R. A. (2008) Modeling of peptide adsorption interactions with a poly(lactic acid) surface. Langmuir 24, 1411514124.
O'Mahony, S., O'Dwyer, C., Nijhuis, C. A., Greer, J. C., Quinn, A. J. & Thompson, D. (2013) Nanoscale dynamics and protein adhesivity of alkylamine self-assembled monolayers on graphene. Langmuir 29, 72717282.
Oberle, M., Yigit, C., Angioletti-Uberti, S., Dzubiella, J. & Ballauff, M. (2015) Competitive protein adsorption to soft polymeric layers: binary mixtures and comparison to theory. The Journal of Physical Chemistry B 119, 32503258.
Oostenbrink, C., Villa, A., Mark, A. E. & Van Gunsteren, W. F. (2004) A biomolecular force field based on the free enthalpy of hydration and solvation: the GROMOS force-field parameter sets 53A5 and 53A6. Journal of Computational Chemistry 25, 16561676.
Oren, E. E., Notman, R., Kim, I. W., Evans, J. S., Walsh, T. R., Samudrala, R., Tamerler, C. & Sarikaya, M. (2010) Probing the molecular mechanisms of quartz-binding peptides. Langmuir 26, 1100311009.
Oren, E. E., Tamerler, C. & Sarikaya, M. (2005) Metal recognition of septapeptides via polypod molecular architecture. Nano Letters 5, 415419.
Otsuka, H., Nagasaki, Y. & Kataoka, K. (2003) PEGylated nanoparticles for biological and pharmaceutical applications. Advanced Drug Delivery Reviews 55, 403419.
Palafox-Hernandez, J. P., Tang, Z., Hughes, Z. E., Li, Y., Swihart, M. T., Prasad, P. N., Walsh, T. R. & Knecht, M. R. (2014) Comparative study of materials-binding peptide interactions with gold and silver surfaces and nanostructures: a thermodynamic basis for biological selectivity of inorganic materials. Chemistry of Materials 26, 49604969.
Pan, H., Qin, M., Meng, W., Cao, Y. & Wang, W. (2012) How do proteins unfold upon adsorption on nanoparticle surfaces? Langmuir 28, 1277912787.
Park, S. Y., Lytton-Jean, A. K. R., Lee, B., Weigand, S., Schatz, G. C. & Mirkin, C. A. (2008) DNA-programmable nanoparticle crystallization. Nature 451, 553556.
Parks, G. A. (1965) The isoelectric points of solid oxides, solid hydroxides, and aqueous hydroxo complex systems. Chemical Reviews 65, 177198.
Patwardhan, S. V., Emami, F. S., Berry, R. J., Jones, S. E., Naik, R. R., Deschaume, O., Heinz, H. & Perry, C. C. (2012) Chemistry of aqueous silica nanoparticle surfaces and the mechanism of selective peptide adsorption. Journal of the American Chemical Society 134, 62446256.
Penna, M. J., Mijajlovic, M. & Biggs, M. J. (2014) Molecular-level understanding of protein adsorption at the interface between water and a strongly interacting uncharged solid surface. Journal of the American Chemical Society 136, 53235331.
Pincus, D. L., Cho, S. S., Hyeon, C. & Thirumalai, D. (2008) Minimal models for proteins and RNA: from folding to function. In Progress in molecular biology and translational science (ed Conn, P. M.), pp. 203250. Academic Press, San Diego, CA, USA.
Praprotnik, M., Site, L. D. & Kremer, K. (2008) Multiscale simulation of soft matter: from scale bridging to adaptive resolution. Annual Review of Physical Chemistry 59, 545571.
Předota, M., Bandura, A. V., Cummings, P. T., Kubicki, J. D., Wesolowski, D. J., Chialvo, A. A. & Machesky, M. L. (2004) Electric double layer at the rutile (110) surface. 1. Structure of surfaces and interfacial water from molecular dynamics by use of ab initio potentials. The Journal of Physical Chemistry B 108, 1204912060.
Puddu, V. & Perry, C. C. (2012) Peptide adsorption on silica nanoparticles: evidence of hydrophobic interactions. ACS Nano 6, 63566363.
Qin, L., Banholzer, M. J., Millstone, J. E. & Mirkin, C. A. (2007a) Nanodisk codes. Nano Letters 7, 38493853.
Qin, L., Banholzer, M. J., Xu, X., Huang, L. & Mirkin, C. A. (2007b) Rational design and synthesis of catalytically driven nanorotors. Journal of the American Chemical Society 129, 1487014871.
Qin, Z. & Buehler, M. J. (2014) Molecular mechanics of mussel adhesion proteins. Journal of the Mechanics and Physics of Solids 62, 1930.
Qu, Z. G., He, X. C., Lin, M., Sha, B. Y., Shi, X. H., Lu, T. J. & Xu, F. (2013) Advances in the understanding of nanomaterial–biomembrane interactions and their mathematical and numerical modeling. Nanomedicine 8, 9951011.
Rabe, M., Verdes, D. & Seeger, S. (2011) Understanding protein adsorption phenomena at solid surfaces. Advances in Colloid and Interface Science 162, 87106.
Raffaini, G. & Ganazzoli, F. (2003) Simulation study of the interaction of some albumin subdomains with a flat graphite surface. Langmuir 19, 34033412.
Raffaini, G. & Ganazzoli, F. (2004a) Molecular dynamics simulation of the adsorption of a fibronectin module on a graphite surface. Langmuir 20, 33713378.
Raffaini, G. & Ganazzoli, F. (2004b) Surface ordering of proteins adsorbed on graphite. The Journal of Physical Chemistry B 108, 1385013854.
Raffaini, G. & Ganazzoli, F. (2006) Adsorption of charged albumin subdomains on a graphite surface. Journal of Biomedical Materials Research Part A 76A, 638645.
Raffaini, G. & Ganazzoli, F. (2007) Understanding the performance of biomaterials through molecular modeling: crossing the bridge between their intrinsic properties and the surface adsorption of proteins. Macromolecular Bioscience 7, 552566.
Raffaini, G. & Ganazzoli, F. (2010) Protein adsorption on a hydrophobic surface: a molecular dynamics study of lysozyme on graphite. Langmuir 26, 56795689.
Raffaini, G. & Ganazzoli, F. (2012) Molecular modelling of protein adsorption on the surface of titanium dioxide polymorphs. Philosophical Transactions of the Royal Society A 370, 14441462.
Raffaini, G. & Ganazzoli, F. (2013) Surface topography effects in protein adsorption on nanostructured carbon allotropes. Langmuir 29, 48834893.
Ravichandran, S., Madura, J. D. & Talbot, J. (2001) A Brownian dynamics study of the initial stages of hen egg-white lysozyme adsorption at a solid interface. The Journal of Physical Chemistry B 105, 36103613.
Ravichandran, S. & Talbot, J. (2000) Mobility of adsorbed proteins: a Brownian dynamics study. Biophysical Journal 78, 110120.
Rechendorff, K., Hovgaard, M. B., Foss, M., Zhdanov, V. P. & Besenbacher, F. (2006) Enhancement of protein adsorption induced by surface roughness. Langmuir 22, 1088510888.
Ren, P. & Ponder, J. W. (2002) Consistent treatment of inter- and intramolecular polarization in molecular mechanics calculations. Journal of Computational Chemistry 23, 14971506.
Ren, P. & Ponder, J. W. (2003) Polarizable atomic multipole water model for molecular mechanics simulation. The Journal of Physical Chemistry B 107, 59335947.
Rick, S. W., Stuart, S. J. & Berne, B. J. (1994) Dynamical fluctuating charge force fields: application to liquid water. The Journal of Chemical Physics 101, 6141.
Rimola, A., Aschi, M., Orlando, R. & Ugliengo, P. (2012) Does adsorption at hydroxyapatite surfaces induce peptide folding? Insights from large-scale B3LYP calculations. Journal of the American Chemical Society 134, 1089910910.
Rimola, A., Costa, D., Sodupe, M., Lambert, J.-F. & Ugliengo, P. (2013) Silica surface features and their role in the adsorption of biomolecules: computational modeling and experiments. Chemical Reviews 113, 42164313.
Rimola, A., Sodupe, M. & Ugliengo, P. (2009) Affinity scale for the interaction of amino acids with silica surfaces. The Journal of Physical Chemistry C 113, 57415750.
Roach, P., Farrar, D. & Perry, C. C. (2006) Surface tailoring for controlled protein adsorption: effect of topography at the nanometer scale and chemistry. Journal of the American Chemical Society 128, 39393945.
Roman, T., Diño, W. A., Nakanishi, H. & Kasai, H. (2006) Amino acid adsorption on single-walled carbon nanotubes. The European Physical Journal D 38, 117120.
Rosa, M., Corni, S. & Di Felice, R. (2012) A density functional theory study of cytosine on Au(111). The Journal of Physical Chemistry C 116, 2136621373.
Rosa, M., Corni, S. & Di Felice, R. (2014a) Enthalpy–entropy tuning in the adsorption of nucleobases at the Au(111) surface. Journal of Chemical Theory and Computation 10, 17071716.
Rosa, M., Corni, S. & Di Felice, R. (2014b) van der Waals effects at molecule-metal interfaces. Physical Review B 90, 125448.
Salata, O. (2004) Applications of nanoparticles in biology and medicine. Journal of Nanobiotechnology 2, 3.
Saptarshi, S. R., Duschl, A. & Lopata, A. L. (2013) Interaction of nanoparticles with proteins: relation to bio-reactivity of the nanoparticle. Journal of Nanobiotechnology 11, 26.
Schlick, T. (2002) Molecular Modeling and Simulation. Springer, New York, NY, USA.
Schneider, J. & Colombi Ciacchi, L. (2010) First principles and classical modeling of the oxidized titanium (0001) surface. Surface Science 604, 11051115.
Schneider, J. & Colombi Ciacchi, L. (2011) A classical potential to model the adsorption of biological molecules on oxidized titanium surfaces. Journal of Chemical Theory and Computation 7, 473484.
Schneider, J. & Colombi Ciacchi, L. (2012) Specific material recognition by small peptides mediated by the interfacial solvent structure. Journal of the American Chemical Society 134, 24072413.
Schreiber, F. (2004) Self-assembled monolayers: from simple model systems to biofunctionalized interfaces. Journal of Physics: Condensed Matter 16, R881R900.
Schyman, P. & Jorgensen, W. L. (2013) Exploring adsorption of water and ions on carbon surfaces using a polarizable force field. The Journal of Physical Chemistry Letters 4, 468474.
Scida, K., Stege, P. W., Haby, G., Messina, G. A. & García, C. D. (2011) Recent applications of carbon-based nanomaterials in analytical chemistry: critical review. Analytica Chimica Acta 691, 617.
Senaratne, W., Andruzzi, L. & Ober, C. K. (2005) Self-assembled monolayers and polymer brushes in biotechnology: current applications and future perspectives. Biomacromolecules 6, 24272448.
Seo, M., Rauscher, S., Pomès, R. & Tieleman, D. P. (2012) Improving internal peptide dynamics in the coarse-grained MARTINI model: toward large-scale simulations of amyloid- and elastin-like peptides. Journal of Chemical Theory and Computation 8, 17741785.
Sethuraman, A. & Belfort, G. (2005) Protein structural perturbation and aggregation on homogeneous surfaces. Biophysical Journal 88, 13221333.
Shaw, C. P., Middleton, D. A., Volk, M. & Lévy, R. (2012) Amyloid-derived peptide forms self-assembled monolayers on gold nanoparticle with a curvature-dependent β-sheet structure. ACS Nano 6, 14161426.
Shelley, J. C., Patey, G. N., Bérard, D. R. & Torrie, G. M. (1997) Modeling and structure of mercury-water interfaces. The Journal of Chemical Physics 107, 2122.
Shemetov, A. A., Nabiev, I. & Sukhanova, A. (2012) Molecular interaction of proteins and peptides with nanoparticles. ACS Nano 6, 45854602.
Shen, J., Wu, T., Wang, Q. & Pan, H. (2008) Molecular simulation of protein adsorption and desorption on hydroxyapatite surfaces. Biomaterials 29, 513532.
Shin, H., Jo, S. & Mikos, A. G. (2003) Biomimetic materials for tissue engineering. Biomaterials 24, 43534364.
Siepmann, J. I. & Sprik, M. (1995) Influence of surface topology and electrostatic potential on water/electrode systems. The Journal of Chemical Physics 102, 511.
Singh, N. & Warshel, A. (2010) Absolute binding free energy calculations: on the accuracy of computational scoring of protein-ligand interactions. Proteins: Structure, Function, and Bioinformatics 78, 17051723.
Siwko, M. E. & Corni, S. (2013) Cytochrome c on a gold surface: investigating structural relaxations and their role in protein–surface electron transfer by molecular dynamics simulations. Physical Chemistry Chemical Physics 15, 59455956.
Skelton, A. A., Fenter, P., Kubicki, J. D., Wesolowski, D. J. & Cummings, P. T. (2011) Simulations of the quartz(1011)/water interface: a comparison of classical force fields, ab initio molecular dynamics, and x-ray reflectivity experiments. The Journal of Physical Chemistry C 115, 20762088.
Skepö, M. (2008) Model simulations of the adsorption of statherin to solid surfaces: effects of surface charge and hydrophobicity. The Journal of Chemical Physics 129, 185101185111.
Skepö, M., Linse, P. & Arnebrant, T. (2006) Coarse-grained modeling of proline rich protein 1 (PRP-1) in bulk solution and adsorbed to a negatively charged surface. The Journal of Physical Chemistry B 110, 1214112148.
Slocik, J. M., Govorov, A. O. & Naik, R. R. (2011) Plasmonic circular dichroism of peptide-functionalized gold nanoparticles. Nano Letters 11, 701705.
Smith, N. V., Chen, C. T. & Weinert, M. (1989) Distance of the image plane from metal surfaces. Physical Review B 40, 75657573.
Snyder, J. A., Abramyan, T., Yancey, J. A., Thyparambil, A. A., Wei, Y., Stuart, S. J. & Latour, R. A. (2012) Development of a tuned interfacial force field parameter set for the simulation of protein adsorption to silica glass. Biointerphases 7, 56.
Snyder, J. A. & Madura, J. D. (2008) Interaction of the phospholipid head group with representative quartz and aluminosilicate structures: an ab initio study. The Journal of Physical Chemistry B 112, 70957103.
Somorjai, G. A. & Li, Y. (2011) Impact of surface chemistry. Proceedings of the National Academy of Sciences 108, 917924.
Souaille, M. & Roux, B. (2001) Extension to the weighted histogram analysis method: combining umbrella sampling with free energy calculations. Computer Physics Communications 135, 4057.
Spohr, E. (1995) Computer modeling of interfaces between aqueous and metallic phases. Acta Chemica Scandinavica 49, 189202.
Srinivasan, J., Cheatham, T. E., Cieplak, P., Kollman, P. A. & Case, D. A. (1998) Continuum solvent studies of the stability of DNA, RNA, and phosphoramidate−DNA helices. Journal of the American Chemical Society 120, 94019409.
Steckbeck, S., Schneider, J., Wittig, L., Rischka, K., Grunwald, I. & Colombi Ciacchi, L. (2014) Identification of materials’ binding peptide sequences guided by a MALDI-ToF MS depletion assay. Analytical Methods 6, 15011509.
Strodel, B. & Wales, D. J. (2008) Implicit solvent models and the energy landscape for aggregation of the amyloidogenic KFFE peptide. Journal of Chemical Theory and Computation 4, 657672.
Stuart, D. A., Haes, A. J., Yonzon, C. R., Hicks, E. M. & Van Duyne, R. P. (2005) Biological applications of localised surface plasmonic phenomenae. IEE Proceedings - Nanobiotechnology 152, 1332.
Stuart, M. A. C., Huck, W. T. S., Genzer, J., Müller, M., Ober, C., Stamm, M., Sukhorukov, G. B., Szleifer, I., Tsukruk, V. V, Urban, M., Winnik, F., Zauscher, S., Luzinov, I. & Minko, S. (2010) Emerging applications of stimuli-responsive polymer materials. Nature Materials 9, 101113.
Sugita, Y. & Okamoto, Y. (1999) Replica-exchange molecular dynamics method for protein folding. Chemical Physics Letters 314, 141151.
Sugiyama, N., Masuda, T., Shinoda, K., Nakamura, A., Tomita, M. & Ishihama, Y. (2007) Phosphopeptide enrichment by aliphatic hydroxy acid-modified metal oxide chromatography for nano-LC-MS/MS in proteomics applications. Molecular & Cellular Proteomics 6, 11031109.
Sumper, M. & Brunner, E. (2008) Silica biomineralisation in diatoms: the model organism Thalassiosira pseudonana. ChemBioChem 9, 11871194.
Sun, C., Liu, L.-M., Selloni, A., Lu, G. Q. (Max) & Smith, S. C. (2010) Titania-water interactions: a review of theoretical studies. Journal of Materials Chemistry 20, 10319.
Sun, H. (1998) COMPASS: An ab initio force-field optimized for condensed-phase applications–overview with details on alkane and benzene compounds. The Journal of Physical Chemistry B 102, 73387364.
Sun, T., Han, G., Lindgren, M., Shen, Z. & Laaksonen, A. (2014a) Adhesion of lactoferrin and bone morphogenetic protein-2 to a rutile surface: dependence on the surface hydrophobicity. Biomaterials Science 2, 10901099.
Sun, X., Feng, Z., Hou, T. & Li, Y. (2014b) Mechanism of graphene oxide as an enzyme inhibitor from molecular dynamics simulations. ACS Applied Materials & Interfaces 6, 71537163.
Sun, Y., Dominy, B. N. & Latour, R. A. (2007) Comparison of solvation-effect methods for the simulation of peptide interactions with a hydrophobic surface. Journal of Computational Chemistry 28, 18831892.
Sun, Y. & Latour, R. A. (2006) Comparison of implicit solvent models for the simulation of protein–surface interactions. Journal of Computational Chemistry 27, 19081922.
Sun, Y., Welsh, W. J. & Latour, R. A. (2005) Prediction of the orientations of adsorbed protein using an empirical energy function with implicit solvation. Langmuir 21, 56165626.
Suttiponparnit, K., Jiang, J., Sahu, M., Suvachittanont, S., Charinpanitkul, T. & Biswas, P. (2010) Role of surface area, primary particle size, and crystal phase on titanium dioxide nanoparticle dispersion properties. Nanoscale Research Letters 6, 27.
Swanson, J. M. J., Henchman, R. H. & McCammon, J. A. (2004) Revisiting free energy calculations: a theoretical connection to MM/PBSA and direct calculation of the association free energy. Biophysical Journal 86, 6774.
Swendsen, R. H. & Wang, J.-S. (1986) Replica Monte Carlo simulation of spin-glasses. Physical Review Letters 57, 26072609.
Szott, L. M. & Horbett, T. A. (2011) Protein interactions with surfaces: computational approaches and repellency. Current Opinion in Chemical Biology 15, 683689.
Tallury, S. S. & Pasquinelli, M. A. (2010) Molecular dynamics simulations of flexible polymer chains wrapping single-walled carbon nanotubes. The Journal of Physical Chemistry B 114, 41224129.
Tang, Z., Palafox-Hernandez, J. P., Law, W.-C., E. Hughes, Z., Swihart, M. T., Prasad, P. N., Knecht, M. R. & Walsh, T. R. (2013) Biomolecular recognition principles for bionanocombinatorics: an integrated approach to elucidate enthalpic and entropic factors. ACS Nano 7, 96329646.
Tavanti, F., Pedone, A. & Menziani, M. C. (2015) A closer look into the ubiquitin corona on gold nanoparticles by computational studies. New Journal of Chemistry 39, 24742482.
Taylor, R. D., Jewsbury, P. J. & Essex, J. W. (2002) A review of protein-small molecule docking methods. Journal of Computer-Aided Molecular Design 16, 151166.
Tkatchenko, A., Romaner, L., Hofmann, O. T., Zojer, E., Ambrosch-Draxl, C. & Scheffler, M. (2010) Van der Waals interactions between organic adsorbates and at organic/inorganic interfaces. MRS Bulletin 35, 435442.
Todorova, N., Chiappini, C., Mager, M., Simona, B., Patel, I. I., Stevens, M. M. & Yarovsky, I. (2014) Surface presentation of functional peptides in solution determines cell internalization efficiency of TAT conjugated nanoparticles. Nano Letters 14, 52295237.
Todorova, N., Makarucha, A. J., Hine, N. D. M., Mostofi, A. A. & Yarovsky, I. (2013) Dimensionality of carbon nanomaterials determines the binding and dynamics of amyloidogenic peptides: multiscale theoretical simulations. PLoS Computational Biology 9, e1003360.
Tomásio, S. M. & Walsh, T. R. (2009) Modeling the binding affinity of peptides for graphitic surfaces. Influences of aromatic content and interfacial shape. The Journal of Physical Chemistry C 113, 87788785.
Tomba, G., Colombi Ciacchi, L. & De Vita, A. (2009) Atomic-level studies of molecular self-assembly on metallic surfaces. Advanced Materials 21, 10551066.
Torrie, G. M. & Valleau, J. P. (1974) Monte Carlo free energy estimates using non-Boltzmann sampling: application to the sub-critical Lennard-Jones fluid. Chemical Physics Letters 28, 578581.
Torrie, G. M. & Valleau, J. P. (1977) Nonphysical sampling distributions in Monte Carlo free-energy estimation: umbrella sampling. Journal of Computational Physics 23, 187199.
Tosaka, R., Yamamoto, H., Ohdomari, I. & Watanabe, T. (2010) Adsorption mechanism of ribosomal protein L2 onto a silica surface: a molecular dynamics simulation study. Langmuir 26, 99509955.
Tozzini, V. (2005) Coarse-grained models for proteins. Current Opinion in Structural Biology 15, 144150.
Utesch, T., Daminelli, G. & Mroginski, M. A. (2011) Molecular dynamics simulations of the adsorption of bone morphogenetic protein-2 on surfaces with medical relevance. Langmuir 27, 1314413153.
Utesch, T., Millo, D., Castro, M. A., Hildebrandt, P., Zebger, I. & Mroginski, M. A. (2013) Effect of the protonation degree of a self-assembled monolayer on the immobilization dynamics of a [NiFe] hydrogenase. Langmuir 29, 673682.
Utesch, T., Sezer, M., Weidinger, I. M. & Mroginski, M. A. (2012) Adsorption of sulfite oxidase on self-assembled monolayers from molecular dynamics simulations. Langmuir 28, 57615769.
Vallee, A., Humblot, V. & Pradier, C.-M. (2010) Peptide interactions with metal and oxide surfaces. Accounts of Chemical Research 43, 12971306.
Van Beest, B. W. H., Kramer, G. J. & van Santen, R. A. (1990) Force fields for silicas and aluminophosphates based on ab initio calculations. Physical Review Letters 64, 19551958.
Van Duin, A. C. T., Dasgupta, S., Lorant, F. & Goddard, W. A. (2001) ReaxFF: a reactive force field for hydrocarbons. The Journal of Physical Chemistry A 105, 93969409.
Vashishta, P., Kalia, R. K., Rino, J. P. & Ebbsjö, I. (1990) Interaction potential for SiO2: A molecular-dynamics study of structural correlations. Physical Review B 41, 1219712209.
Velasco-Velez, J.-J., Wu, C. H., Pascal, T. A., Wan, L. F., Guo, J., Prendergast, D. & Salmeron, M. (2014) The structure of interfacial water on gold electrodes studied by x-ray absorption spectroscopy. Science 346, 831834.
Vellore, N. A., Yancey, J. A., Collier, G., Latour, R. A. & Stuart, S. J. (2010) Assessment of the transferability of a protein force field for the simulation of peptide-surface interactions. Langmuir 26, 73967404.
Venkat, A. S., Corni, S. & Di Felice, R. (2007) Electronic coupling between azurin and gold at different protein/substrate orientations. Small 3, 14311437.
Vertegel, A. A., Siegel, R. W. & Dordick, J. S. (2004) Silica nanoparticle size influences the structure and enzymatic activity of adsorbed lysozyme. Langmuir 20, 68006807.
Vigmond, S. J., Iwakura, M., Mizutani, F. & Katsura, T. (1994) Site-specific immobilization of molecularly engineered dihydrofolate reductase to gold surfaces. Langmuir 10, 28602862.
Vila Verde, A., Acres, J. M. & Maranas, J. K. (2009) Investigating the specificity of peptide adsorption on gold using molecular dynamics simulations. Biomacromolecules 10, 21182128.
Vila Verde, A., Beltramo, P. J. & Maranas, J. K. (2011) Adsorption of homopolypeptides on gold investigated using atomistic molecular dynamics. Langmuir 27, 59185926.
Voicescu, M., Ionescu, S. & Angelescu, D. G. (2012) Spectroscopic and coarse-grained simulation studies of the BSA and HSA protein adsorption on silver nanoparticles. Journal of Nanoparticle Research 14, 1174.
Voskerician, G., Shive, M. S., Shawgo, R. S., von Recum, H., Anderson, J. M., Cima, M. J. & Langer, R. (2003) Biocompatibility and biofouling of MEMS drug delivery devices. Biomaterials 24, 19591967.
Wales, D. J. & Doye, J. P. K. (1997) Global optimization by basin-hopping and the lowest energy structures of Lennard-Jones clusters containing up to 110 atoms. The Journal of Physical Chemistry A 101, 51115116.
Walsh, T. R. (2008) Modelling the nanoscale patterning of nucleic acid base pairs deposited on graphite. Molecular Physics 106, 16131619.
Walther, J. H., Jaffe, R., Halicioglu, T. & Koumoutsakos, P. (2001) Carbon nanotubes in water: structural characteristics and energetics. The Journal of Physical Chemistry B 105, 99809987.
Wang, D., Nap, R. J., Lagzi, I., Kowalczyk, B., Han, S., Grzybowski, B. A. & Szleifer, I. (2011) How and why nanoparticle's curvature regulates the apparent pKa of the coating ligands. Journal of the American Chemical Society 133, 21922197.
Wang, F., Stuart, S. J. & Latour, R. A. (2008) Calculation of adsorption free energy for solute-surface interactions using biased replica-exchange molecular dynamics. Biointerphases 3, 918.
Wang, M., Guo, Y., Wang, Q., Zhang, X., Huang, J., Lu, X., Wang, K., Zhang, H. & Leng, Y. (2014) Density functional theory study of interactions between glycine and TiO2/graphene nanocomposites. Chemical Physics Letters 599, 8691.
Wang, Q., Zhao, C., Zhao, J., Wang, J., Yang, J.-C., Yu, X. & Zheng, J. (2010a) Comparative molecular dynamics study of Aβ adsorption on the self-assembled monolayers. Langmuir 26, 33083316.
Wang, Q., Zhao, J., Yu, X., Zhao, C., Li, L. & Zheng, J. (2010b) Alzheimer Aβ 1–42 monomer adsorbed on the self-assembled monolayers. Langmuir 26, 1272212732.
Wang, S., Humphreys, E. S., Chung, S.-Y., Delduco, D. F., Lustig, S. R., Wang, H., Parker, K. N., Rizzo, N. W., Subramoney, S., Chiang, Y.-M. & Jagota, A. (2003) Peptides with selective affinity for carbon nanotubes. Nature Materials 2, 196200.
Wei, Q., Becherer, T., Angioletti-Uberti, S., Dzubiella, J., Wischke, C., Neffe, A. T., Lendlein, A., Ballauff, M. & Haag, R. (2014) Protein interactions with polymer coatings and biomaterials. Angewandte Chemie International Edition 53, 80048031.
Wei, T., Carignano, M. A. & Szleifer, I. (2011) Lysozyme adsorption on polyethylene surfaces: why are long simulations needed? Langmuir 27, 1207412081.
Wei, Y. & Latour, R. A. (2010) Correlation between desorption force measured by atomic force microscopy and adsorption free energy measured by surface plasmon resonance spectroscopy for peptide − surface interactions. Langmuir 26, 1885218861.
Wei, Y. & Latour, R. A. (2009) Benchmark experimental data set and assessment of adsorption free energy for peptide−surface interactions. Langmuir 25, 56375646.
Whaley, S. R., English, D. S., Hu, E. L., Barbara, P. F. & Belcher, A. M. (2000) Selection of peptides with semiconductor binding specificity for directed nanocrystal assembly. Nature 405, 665668.
Wierzbicki, A., Sikes, C. S., Madura, J. D. & Drake, B. (1994) Atomic force microscopy and molecular modeling of protein and peptide binding to calcite. Calcified Tissue International 54, 133141.
Wilt, F. H. (1999) Matrix and mineral in the sea urchin larval skeleton. Journal of Structural Biology 126, 216226.
Wright, L. B., Rodger, P. M., Corni, S. & Walsh, T. R. (2013a) GolP-CHARMM: First-principles based force fields for the interaction of proteins with Au(111) and Au(100). Journal of Chemical Theory and Computation 9, 16161630.
Wright, L. B., Rodger, P. M., Walsh, T. R. & Corni, S. (2013b) First-principles-based force field for the interaction of proteins with Au(100)(5×1): an extension of GolP-CHARMM. The Journal of Physical Chemistry C 117, 2429224306.
Wright, L. B. & Walsh, T. R. (2012) First-principles molecular dynamics simulations of NH4(+) and CH3COO(−) adsorption at the aqueous quartz interface. The Journal of Chemical Physics 137, 224702.
Wright, L. B. & Walsh, T. R. (2013) Efficient conformational sampling of peptides adsorbed onto inorganic surfaces: insights from a quartz binding peptide. Physical Chemistry Chemical Physics 15, 47154726.
Wu, C., Chen, M., Skelton, A. A., Cummings, P. T. & Zheng, T. (2013) Adsorption of arginine-glycine-aspartate tripeptide onto negatively charged rutile (110) mediated by cations: the effect of surface hydroxylation. ACS Applied Materials & Interfaces 5, 25672579.
Wu, X. & Narsimhan, G. (2008) Effect of surface concentration on secondary and tertiary conformational changes of lysozyme adsorbed on silica nanoparticles. Biochimica et Biophysica Acta 1784, 16941701.
Wu, X. & Narsimhan, G. (2009) Coarse grain molecular dynamics simulation for the prediction of tertiary conformation of lysozyme adsorbed on silica surface. Molecular Simulation 35, 974985.
Wu, X., Vargas, M. C., Nayak, S., Lotrich, V. & Scoles, G. (2001) Towards extending the applicability of density functional theory to weakly bound systems. The Journal of Chemical Physics 115, 8748.
Xie, L., Luo, Y., Lin, D., Xi, W., Yang, X. & Wei, G. (2014) The molecular mechanism of fullerene-inhibited aggregation of Alzheimer's β-amyloid peptide fragment. Nanoscale 6, 97529762.
Xie, Y., Liu, M. & Zhou, J. (2012) Molecular dynamics simulations of peptide adsorption on self-assembled monolayers. Applied Surface Science 258, 81538159.
Xie, Y., Zhou, J. & Jiang, S. (2010) Parallel tempering Monte Carlo simulations of lysozyme orientation on charged surfaces. The Journal of Chemical Physics 132, 065101.
Xu, Y., Cao, Q., Svec, F. & Fréchet, J. M. J. (2010) Porous polymer monolithic column with surface-bound gold nanoparticles for the capture and separation of cysteine-containing peptides. Analytical Chemistry 82, 33523358.
Xu, Z., Yang, X. & Yang, Z. (2008) On the mechanism of surfactant adsorption on solid surfaces: free-energy investigations. The Journal of Physical Chemistry B 112, 1380213811.
Xu, Z. P., Zeng, Q. H., Lu, G. Q. & Yu, A. B. (2006) Inorganic nanoparticles as carriers for efficient cellular delivery. Chemical Engineering Science 61, 10271040.
Yancey, J. A., Vellore, N. A., Collier, G., Stuart, S. J. & Latour, R. A. (2010) Development of molecular simulation methods to accurately represent protein-surface interactions: the effect of pressure and its determination for a system with constrained atoms. Biointerphases 5, 8595.
Yang, J. A., Johnson, B. J., Wu, S., Woods, W. S., George, J. M. & Murphy, C. J. (2013) Study of wild-type α-synuclein binding and orientation on gold nanoparticles. Langmuir 29, 46034615.
Yang, Z. & Zhao, Y.-P. (2006) QM/MM and classical molecular dynamics simulation of histidine-tagged peptide immobilization on nickel surface. Materials Science and Engineering: A 423, 8491.
Yang, Z. & Zhao, Y.-P. (2007) Adsorption of His-tagged peptide to Ni, Cu and Au (100) surfaces: molecular dynamics simulation. Engineering Analysis with Boundary Elements 31, 402409.
Yu, J., Becker, M. L. & Carri, G. A. (2012a) The influence of amino acid sequence and functionality on the binding process of peptides onto gold surfaces. Langmuir 28, 14081417.
Yu, J., Wei, W., Danner, E., Ashley, R. K., Israelachvili, J. N. & Waite, J. H. (2011) Mussel protein adhesion depends on interprotein thiol-mediated redox modulation. Nature Chemical Biology 7, 588590.
Yu, X., Wang, Q., Lin, Y., Zhao, J., Zhao, C. & Zheng, J. (2012b) Structure, orientation, and surface interaction of Alzheimer amyloid-β peptides on the graphite. Langmuir 28, 65956605.
Zahn, D. & Hochrein, O. (2003) Computational study of interfaces between hydroxyapatite and water. Physical Chemistry Chemical Physics 5, 40044007.
Zanetti-Polzi, L., Daidone, I., Bortolotti, C. A. & Corni, S. (2014) Surface packing determines the redox potential shift of cytochrome c adsorbed on gold. Journal of the American Chemical Society 136, 1292912937.
Zhang, L. & Sun, Y. (2010) Molecular simulation of adsorption and its implications to protein chromatography: a review. Biochemical Engineering Journal 48, 408415.
Zhang, L., Zhao, G. & Sun, Y. (2009a) Molecular insight into protein conformational transition in hydrophobic charge induction chromatography: a molecular dynamics simulation. The Journal of Physical Chemistry B 113, 68736880.
Zhang, Z., Chen, S., Feng, Y., Ding, Y., Zhou, J. & Jia, H. (2009b) Electrochemical and molecular simulation studies on the corrosion inhibition of L-glutamine monolayers on an iron surface. Journal of the Serbian Chemical Society 74, 407415.
Zhdanov, V. P. & Kasemo, B. (2000a) Monte Carlo simulation of diffusion of adsorbed proteins. Proteins: Structure, Function, and Genetics 39, 7681.
Zhdanov, V. P. & Kasemo, B. (2000b) Ordering of adsorbed proteins. Proteins: Structure, Function, and Genetics 40, 539542.
Zhou, J., Zheng, J. & Jiang, S. (2004) Molecular simulation studies of the orientation and conformation of cytochrome c adsorbed on self-assembled monolayers. The Journal of Physical Chemistry B 108, 1741817424.