Review Article
Mechanism of peptide bond formation on the ribosome
- Marina V. Rodnina, Malte Beringer, Wolfgang Wintermeyer
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- Published online by Cambridge University Press:
- 08 August 2006, pp. 203-225
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1. The ribosome 204
2. Peptide bond formation is catalyzed by RNA 205
3. Characteristics of the uncatalyzed reaction 207
4. Potential catalytic strategies of the ribosome 207
5. Experimental systems 208
6. Substrate binding in the PT center 210
7. Induced fit in the active site 211
8. pH dependence of peptide bond formation 212
9. Reaction with full-length aa-tRNA 214
10. Role of active-site residues 215
11. pH-dependent structural changes of the active site 216
12. Entropic catalysis 217
13. Role of 2′-OH of A76 in P-site tRNA 218
14. Catalysis by proton shuttling 219
15. Plasticity of the active site 220
16. Conclusions 221
17. Acknowledgments 222
18. References 222
Peptide bond formation is the fundamental reaction of ribosomal protein synthesis. The ribosome's active site – the peptidyl transferase center – is composed of rRNA, and thus the ribosome is the largest known RNA catalyst. The ribosome accelerates peptide bond formation by 107-fold relative to the uncatalyzed reaction. Recent progress of structural, biochemical and computational approaches has provided a fairly detailed picture of the catalytic mechanisms employed by the ribosome. Energetically, catalysis is entirely entropic, indicating an important role of solvent reorganization, substrate positioning, and/or orientation of the reacting groups within the active site. The ribosome provides a pre-organized network of electrostatic interactions that stabilize the transition state and facilitate proton shuttling involving ribose hydroxyl groups of tRNA. The catalytic mechanism employed by the ribosome suggests how ancient RNA-world enzymes may have functioned.
The architecture and function of the light-harvesting apparatus of purple bacteria: from single molecules to in vivo membranes
- Richard J. Cogdell, Andrew Gall, Jürgen Köhler
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- Published online by Cambridge University Press:
- 12 October 2006, pp. 227-324
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1. Introduction 229
2. Structures 234
2.1 The structure of LH2 234
2.2 Natural variants of peripheral antenna complexes 242
2.3 RC–LH1 complexes 242
3. Spectroscopy 249
3.1 Steady-state spectroscopy 249
3.2 Factors which affect the position of the Qy absorption band of Bchla 249
4. Regulation of biosynthesis and assembly 257
4.1 Regulation 257
4.1.1 Oxygen 257
4.1.2 Light 258
4.1.2.1 AppA: blue-light-mediated regulation 259
4.1.2.2 Bacteriophytochromes 259
4.1.3 From the RC to the mature PSU 261
4.2 Assembly 261
4.2.1 LH1 262
4.2.2 LH2 263
5. Frenkel excitons 265
5.1 General 265
5.2 B800 267
5.3 B850 267
5.4 B850 delocalization 273
6. Energy-transfer pathways: experimental results 274
6.1 Theoretical background 274
6.2 ‘Follow the excitation energy’ 276
6.2.1 Bchla→Bchla energy transfer 277
6.2.1.1 B800→B800 277
6.2.1.2 B800→B850 278
6.2.1.3 B850→B850 279
6.2.1.4 B850→B875 280
6.2.1.5 B875→RC 280
6.2.2 Car[harr ]Bchla energy transfer 281
7. Single-molecule spectroscopy 284
7.1 Introduction to single-molecule spectroscopy 284
7.2 Single-molecule spectroscopy on LH2 285
7.2.1 Overview 285
7.2.2 B800 286
7.2.2.1 General 286
7.2.2.2 Intra- and intercomplex disorder of site energies 287
7.2.2.3 Electron-phonon coupling 289
7.2.2.4 B800→B800 energy transfer revisited 290
7.2.3 B850 293
8. Quantum mechanics and the purple bacteria LH system 298
9. Appendix 299
9.1 A crash course on quantum mechanics 299
9.2 Interacting dimers 305
10. Acknowledgements 306
11. References 307
This review describes the structures of the two major integral membrane pigment complexes, the RC–LH1 ‘core’ and LH2 complexes, which together make up the light-harvesting system present in typical purple photosynthetic bacteria. The antenna complexes serve to absorb incident solar radiation and to transfer it to the reaction centres, where it is used to ‘power’ the photosynthetic redox reaction and ultimately leads to the synthesis of ATP. Our current understanding of the biosynthesis and assembly of the LH and RC complexes is described, with special emphasis on the roles of the newly described bacteriophytochromes. Using both the structural information and that obtained from a wide variety of biophysical techniques, the details of each of the different energy-transfer reactions that occur, between the absorption of a photon and the charge separation in the RC, are described. Special emphasis is given to show how the use of single-molecule spectroscopy has provided a more detailed understanding of the molecular mechanisms involved in the energy-transfer processes. We have tried, with the help of an Appendix, to make the details of the quantum mechanics that are required to appreciate these molecular mechanisms, accessible to mathematically illiterate biologists. The elegance of the purple bacterial light-harvesting system lies in the way in which it has cleverly exploited quantum mechanics.