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11 - Quantum biology of retinal
- from Part III - Quantum effects in higher organisms and applications
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- By Klaus Schulten, University of Illinois, Shigehiko Hayashi, Kyoto University
- Edited by Masoud Mohseni, Yasser Omar, Gregory S. Engel, University of Chicago, Martin B. Plenio, Universität Ulm, Germany
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- Book:
- Quantum Effects in Biology
- Published online:
- 05 August 2014
- Print publication:
- 07 August 2014, pp 237-263
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Summary
Introduction
Retinal is a biological chromophore ubiquitous in visual receptors of higher life forms, but serving also as an antenna in light energy transformation and phototaxis of bacteria. The chromophore arises in various retinal proteins, the best known two being the visual receptor rhodopsin and the light-driven proton pump bacteriorhodopsin. The ubiquitous nature of retinal in photobiology is most remarkable as the molecule shows an extremely wide adaptability of its spectral absorption characteristics and a precise selection of its photoproducts, both properties steered by retinal proteins.
Rhodopsin (Rh) is a membrane protein of the rod cells in the retina of animal eyes and contains a retinal molecule as a chromophore surrounded by the protein's seven transmembrane helices (Khorana, 1992), as shown in Figure 11.1. Rhodopsin serves as the receptor protein for monochromic vision, in particular, for vision in the dark. Analogous retinal proteins, called iodopsins, exist in the cone cells of the retina and serve as receptor proteins for colour vision in daylight (Nathans et al., 1986).
Retinal proteins also serve in certain bacteria as light-driven proton pumps that maintain the cell potential, as in case of bacteriorhodopsin (bR) (Schulten and Tavan, 1978), or as light sensors in bacterial phototaxis (Spudich and Jung, 2005).
All retinal proteins are structurally homologous, being composed of seven transmembrane helices with a retinal chromophore bound to a lysine side group. The photoactivation mechanisms of the proteins' retinal moieties are similar, but distinct from each other. The primary event of retinal photoactivation is a photoisomerization reaction (Birge, 1990).
10 - A chemical compass for bird navigation
- from Part III - Quantum effects in higher organisms and applications
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- By Ilia A. Solov'yov, University of Southern Denmark (SDU), Thorsten Ritz, Department of Physics and Astronomy, Irvine, CA, Klaus Schulten, University of Illinois, Peter J. Hore, University of Oxford
- Edited by Masoud Mohseni, Yasser Omar, Gregory S. Engel, University of Chicago, Martin B. Plenio, Universität Ulm, Germany
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- Book:
- Quantum Effects in Biology
- Published online:
- 05 August 2014
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- 07 August 2014, pp 218-236
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Summary
Introduction
Migratory birds travel spectacular distances each year, navigating and orienting by a variety of means, most of which are poorly understood. Among these is a remarkable ability to perceive the intensity and direction of the Earth's magnetic field (Mouritsen and Ritz, 2005; Wiltschko and Wiltschko, 2006; Johnsen and Lohmann, 2008). Biologically credible mechanisms for the detection of such a weak field (25–65 μT) are scarce, and in recent years just two proposals have emerged as front-runners. One, essentially classical, centers on clusters of magnetic iron-containing particles in the upper beak, which appear to act as a magnetometer for determining geographical position (Kirschvink and Gould, 1981; Kirschvink et al., 2001; Fleissner et al., 2007; Solov'yov and Greiner, 2007; Walker, 2008; Solov'yov and Greiner, 2009a, b; Falkenberg et al., 2010). The other relies on the quantum spin dynamics of transient photoinduced radical pairs (Schulten et al., 1978; Schulten, 1982; Schulten and Windemuth, 1986; Ritz et al., 2000b; Cintolesi et al., 2003; Möller et al., 2004; Mouritsen et al., 2004; Heyers et al., 2007; Liedvogel et al., 2007b, a; Solov'yov et al., 2007; Feenders et al., 2008; Maeda et al., 2008; Solov'yov and Schulten, 2009; Ritz et al., 2009; Rodgers and Hore, 2009; Zapka et al., 2009). Originally suggested by Schulten in 1978 (Schulten et al., 1978) as the basis of the avian magnetic compass sensor, this mechanism gained support from the subsequent observation that the compass is light dependent (Wiltschko et al., 1993) (for a review see e.g. (Wiltschko et al., 2010)).
5 - Structure, function, and quantum dynamics of pigment–protein complexes
- from Part II - Quantum effects in bacterial photosynthetic energy transfer
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- By Ioan Kosztin, University of Missouri, Klaus Schulten, University of Illinois
- Edited by Masoud Mohseni, Yasser Omar, Gregory S. Engel, University of Chicago, Martin B. Plenio, Universität Ulm, Germany
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- Book:
- Quantum Effects in Biology
- Published online:
- 05 August 2014
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- 07 August 2014, pp 123-143
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Summary
Introduction
Photosynthesis is fundamental to life on Earth as it establishes access to the main energy source of the biosphere, sunlight (Blankenship, 2002). Photosynthesis is based on the interaction between living matter and the sun's radiation field, mainly visible light. This interaction involves the electrons of biological macromolecules and, accordingly, the process of light absorption is governed by quantum physics. During the course of biological evolution, photosynthetic lifeforms learned to exploit quantum physics in ingenious ways, in particular, under the circumstances of physiological temperature. A description of quantum phenomena under the influence of strong thermal effects as arise under these circumstances is challenging. Indeed, the quantum biology of photosynthesis is an active and fascinating research area.
Photosynthesis, in general, is understood to encompass the various processes in living cells by which lifeforms utilize sunlight to drive chemical synthesis. This involves primary processes of light-harvesting, transformation of electronic excitation energy into a membrane potential, as well as the splitting of water into oxygen, abstracting electrons that are added to molecules of nicotinamide adenine dinucleotide phosphate (NADPH+) at a high redox potential. The membrane potential drives the synthesis of adenosine triphosphate (ATP) which is used to fuel many processes in living cells. In plant photosynthesis NADPH+ and ATP are needed for the synthesis of sugar and starch, the most widely known products of photosynthesis. Because of its fundamental importance in cellular energetics, photosynthesis has been the subject of great evolutionary pressure such that, amidst a deep overall similarity, many variants have developed in the competition for habitats and efficiency.
Chapter 8 - Viewing the Mechanisms of Translation through the Computational Microscope
- Edited by Joachim Frank, Columbia University, New York
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- Molecular Machines in Biology
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- 05 January 2012
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- 19 December 2011, pp 142-157
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Summary
Introduction
Biological molecular machines span a range of sizes, from the 80-Å-sized helicases (e.g., PcrA) (Dittrich and Schulten, 2006; Dittrich et al., 2006), to the 250-Å-sized ATP synthase (Aksimentiev et al., 2004), to the 10-μm-long Bacterial flagellum (Arkhipov et al., 2006; Kitao et al., 2006). The machines all share certain traits, particularly the ability to utilize energy to perform useful work. Like macroscopic machines, those on the molecular scale are typically comprised of different components that carry out a cycle of well-regulated steps. Unlike macroscopic machines, however, molecular machines must contend with, and even take advantage of, thermal fluctuations that are omnipresent at their scale.
A quintessential example of a large molecular machine, the ribosome, is found in all organisms and in all cells. It is a large (2.5–4.5 MDa) nucleo-protein complex responsible for translating a cell's genetic information into proteins (Korostelev et al., 2008; Steitz, 2008; Schmeing and Ramakrishnan, 2009; Frank and Gonzalez, Jr., 2010). The ribosome is composed of a multitude of interacting components (more than fifty) that assemble into two subunits, denoted large and small. Translation can be broken down into four fundamental stages, initiation, elongation, termination and recycling, each composed of multiple steps and requiring the involvement of additional specialized components. In the first stage (step 1), the two ribosomal subunits join together with a messenger RNA (mRNA) strand to initiate its translation. Initiation is followed by elongation (step 2) of the nascent protein, enabled via the delivery of each amino acid by a transfer RNA (tRNA) in complex with elongation factor Tu (EF-Tu) (Agirrezabala and Frank, 2009). The translocation of tRNAs through the ribosome also occurs in discrete steps, brought about by a large-scale ratchet-like motion of the two ribosomal subunits (Frank and Agrawal, 2000; Dunke and Cate, 2010). The nascent protein leaves the ribosome through an exit tunnel, which is not merely a passive conduit but can play a regulatory role. Some nascent proteins control their own translation through specific protein-tunnel interactions that halt translation or recruit other factors to the ribosome. For example, proteins not destined for immediate extrusion into the cytoplasm can direct the ribosome to a protein-conducting translocon, the SecY/Sec61 complex, which then aids the proper localization of the nascent protein (Rapoport, 2007). After elongation is completed, translation is terminated (step 3) and the ribosomal components are all recycled (step 4), making them available for the next mRNA.
Photosynthetic apparatus of purple bacteria
- Xiche Hu, Thorsten Ritz, Ana Damjanović, Felix Autenrieth, Klaus Schulten
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- Journal:
- Quarterly Reviews of Biophysics / Volume 35 / Issue 1 / February 2002
- Published online by Cambridge University Press:
- 09 May 2002, pp. 1-62
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1. Introduction 2
2. Structure of the bacterial PSU 5
2.1 Organization of the bacterial PSU 5
2.2 The crystal structure of the RC 9
2.3 The crystal structures of LH-II 11
2.4 Bacteriochlorophyll pairs in LH-II and the RC 13
2.5 Models of LH-I and the LH-I-RC complex 15
2.6 Model for the PSU 17
3. Excitation transfer in the PSU 18
3.1 Electronic excitations of BChls 22
3.1.1 Individual BChls 22
3.1.2 Rings of BChls 22
3.1.2.1 Exciton states 22
3.1.3 Effective Hamiltonian 24
3.1.4 Optical properties 25
3.1.5 The effect of disorder 26
3.2 Theory of excitation transfer 29
3.2.1 General theory 29
3.2.2 Mechanisms of excitation transfer 32
3.2.3 Approximation for long-range transfer 34
3.2.4 Transfer to exciton states 35
3.3 Rates for transfer processes in the PSU 37
3.3.1 Car→BChl transfer 37
3.3.1.1 Mechanism of Car→BChl transfer 39
3.3.1.2 Pathways of Car→BChl transfer 40
3.3.2 Efficiency of Car→BChl transfer 40
3.3.3 B800-B850 transfer 44
3.3.4 LH-II→LH-II transfer 44
3.3.5 LH-II→LH-I transfer 45
3.3.6 LH-I→RC transfer 45
3.3.7 Excitation migration in the PSU 46
3.3.8 Genetic basis of PSU assembly 49
4. Concluding remarks 53
5. Acknowledgments 55
6. References 55
Life as we know it today exists largely because of photosynthesis, the process through which light energy is converted into chemical energy by plants, algae, and photosynthetic bacteria (Priestley, 1772; Barnes, 1893; Wurmser, 1925; Van Niel, 1941; Clayton & Sistrom, 1978; Blankenship et al. 1995; Ort & Yocum, 1996). Historically, photosynthetic organisms are grouped into two classes. When photosynthesis is carried out in the presence of air it is called oxygenic photosynthesis (Ort & Yocum, 1996). Otherwise, it is anoxygenic (Blankenship et al. 1995). Higher plants, algae and cyanobacteria perform oxygenic photosynthesis, which involves reduction of carbon dioxide to carbohydrate and oxidation of water to produce molecular oxygen. Some photosynthetic bacteria, such as purple bacteria, carry out anoxygenic photosynthesis that involves oxidation of molecules other than water. In spite of these differences, the general principles of energy transduction are the same in anoxygenic and oxygenic photosynthesis (Van Niel, 1931, 1941; Stanier, 1961; Wraight, 1982; Gest, 1993). The primary processes of photosynthesis involve absorption of photons by light-harvesting complexes (LHs), transfer of excitation energy from LHs to the photosynthetic reaction centers (RCs), and the primary charge separation across the photosynthetic membrane (Sauer, 1975; Knox, 1977; Fleming & van Grondelle, 1994; van Grondelle et al. 1994). In this article, we will focus on the anoxygenic photosynthetic process in purple bacteria, since its photosynthetic system is the most studied and best characterized during the past 50 years.
Quasiparticle Excitations in Polyenes and Polyacetylene
- Paul Tavan, Klaus Schulten
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- Journal:
- MRS Online Proceedings Library Archive / Volume 109 / 1987
- Published online by Cambridge University Press:
- 25 February 2011, 163
- Print publication:
- 1987
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We apply the Pariser-Parr-Pople Hamiltonian to study many-electron excitations in polyenes and polyacetylene. The excited singlet states of polyenes, calculated by a multireference double excitation expansion, are classified as quasi-particle excitations, namely as triplet-triplet magnons and particle-hole excitons. From finite polyene spectra we derive approximate dispersion relations for these quasi-particles in the infinite polyene, i.e. polyacetylene.