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12 - Life on earth: the role of proteins

Published online by Cambridge University Press:  18 December 2009

By
Jayanth R. Banavar  and
Amos Maritan
Edited by
John D. Barrow ,
Simon Conway Morris ,
Stephen J. Freeland  and
Charles L. Harper, Jr
Jayanth R. Banavar
Affiliation:
Pennsylvania State University
Amos Maritan
Affiliation:
Instituto Nazionale per la Fisica della Materia, Dipartimento da Fisica G. Galilei, Universita di Padova
John D. Barrow
Affiliation:
University of Cambridge
Simon Conway Morris
Affiliation:
University of Cambridge
Stephen J. Freeland
Affiliation:
University of Maryland, Baltimore
Charles L. Harper, Jr
Affiliation:
John Templeton Foundation
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Summary

Introduction

It is now believed that our universe was created around 13.8 billion years ago. Our planet earth came into existence around 4.5 billion years ago. For nearly a billion years or so after it was formed, the earth was stark and bereft of life. The matter contained on earth was inorganic with relatively small molecules. There were endless rock formations, oceans, and an atmosphere.

And then there was life.

The problem of how life was created is a fascinating one. Our focus is on looking at life on earth and asking how it works. The lessons we learn provide hints to the answer to the deep and fundamental question pondered by our ancients: Was life on earth inevitable? Then there are the questions posed by Henderson [1]: Is the nature of our physical world biocentric? Is there a need for fine-tuning in biochemistry to provide for the fitness of life in the cosmos – or, even less ambitiously, for life here on earth? Surprisingly, as we will show, a physics approach turns out to be valuable for thinking about these questions.

All living organisms have a genetic map consisting of a one-dimensional string of information encoded in the DNA molecule. An essential question that one seeks to answer is how an organism converts that information into a three-dimensional living being.

Life has many common patterns. All living cells follow certain simple “universal” themes.

Type
Chapter
Information
Fitness of the Cosmos for Life
Biochemistry and Fine-Tuning
 , pp. 225 - 255
Publisher: Cambridge University Press
Print publication year: 2007

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References

Henderson, L. J.. The Fitness of the Environment: An Inquiry into the Biological Significance of the Properties of Matter. New York: Macmillan (1913). Repr. Boston, MA: Beacon Press (1958); Gloucester, MA: Peter Smith (1970).Google Scholar
Hoagland, M. and Dodson, B.. The Way Life Works. New York, NY: Random House (1995).Google Scholar
Alberts, B.et al. Molecular Biology of the Cell. New York, NY: Garland Science Publishing (2002); Voet, D. and Voet, J. G.. Biochemistry. New York, NY: John Wiley and Sons (2003).Google Scholar
Watson, J. D. and Crick, F. H. C.. Molecular structure of nucleic acids – a structure for deoxyribose nucleic acid. Nature, 171 (1953), 737.CrossRefGoogle ScholarPubMed
Kimura, M.. Population Genetics, Molecular Evolution and the Neutral Theory. Chicago, IL: University of Chicago Press (1994).Google Scholar
Fersht, A.. Structure and Mechanism in Protein Science: A Guide to Enzyme Catalysis and Protein Folding. New York, NY: W. H. Freeman and Company (1999).Google Scholar
Finkelstein, A. V. and Ptistyn, O.. Protein Physics: A Course of Lectures. New York, NY: Academic Press (2002).Google Scholar
Kornberg, A.. For the Love of Enzymes. Cambridge, MA: Harvard University Press (1989).Google Scholar
For a brief review of computational approaches to the protein-folding problem, see Banavar, J. R. and Maritan, A.. Computational approach to the protein-folding problem. Proteins, 42 (2001), 433.3.0.CO;2-S>CrossRefGoogle ScholarPubMed
Pauling, L., Corey, R. B. and Branson, H. R.. The structure of proteins – 2 hydrogen-bonded helical configurations of the polypeptide chain. Proceedings of the National Academy of Sciences, USA, 37 (1951), 205.CrossRefGoogle Scholar
Pauling, L. and Corey, R. B.. Configurations of polypeptide chains with favored orientations around single bonds – 2 new pleated sheets. Proceedings of the National Academy of Sciences, USA, 37 (1951), 729.CrossRefGoogle Scholar
Eisenberg, D.. The discovery of the ά-helix and β-sheet, the principal structural features of proteins. Proceedings of the National Academy of Sciences, USA, 100 (2003), 11207.CrossRefGoogle ScholarPubMed
Lightman, A. P.. Great Ideas in Physics. New York, NY: McGraw-Hill (2000).Google Scholar
Creighton, T. E.. Proteins: Structures and Molecular Properties. New York, NY: W. H. Freeman and Company (1993).Google Scholar
Kelly, J. W.. The alternative conformations of amyloidogenic proteins and their multi-step assembly pathways. Current Opinions in Structural Biology, 8 (1998), 101.CrossRefGoogle ScholarPubMed
Dobson, C. M.. Protein folding and disease: a view from the first Horizon Symposium. National Review of Drug Discoveries, 2 (2003), 154.CrossRefGoogle ScholarPubMed
Chaikin, P. M. and Lubensky, T. C.. Principles of Condensed Matter Physics. Cambridge, UK: Cambridge University Press (2000).Google Scholar
Szpiro, G. G.. Kepler's Conjecture. New York, NY: John Wiley (2003).Google Scholar
Banavar, J. R., Gonzalez, O., Maddocks, J. H.et al.Self-interactions of strands and sheets. Journal of Statistical Physics, 110 (2003), 35.CrossRefGoogle Scholar
A theorem proved by Gonzalez, O. and Maddocks, J. (Global curvature, thickness, and the ideal shapes of knots. Proceedings of the National Academy of Sciences, USA, 96 [1999], 4769) in the context of knot topologies shows the remarkable connection between the three-point recipe and the tube thickness.CrossRefGoogle ScholarPubMed
Banavar, J. R., Flammini, A., Marenduzzo, D.et al.Geometry of compact tubes and protein structures. ComPlexUs, 1 (2003), 4.CrossRefGoogle Scholar
Gennes, P. G. and Prost, J.. The Physics of Liquid Crystals. Oxford: Oxford University Press (1995).Google Scholar
Chandrasekhar, S.. Liquid Crystals. Cambridge, UK: Cambridge University Press (1977).Google Scholar
Chothia, C. and Finkelstein, A. V.. The classifications and origins of protein folding patterns. Annual Review of Biochemistry, 59 (1990), 1007.CrossRefGoogle ScholarPubMed
Chothia, C.. Proteins – 1000 families for the molecular biologist. Nature, 357 (1992), 543.CrossRefGoogle Scholar
Przytycka, T., Srinivasan, R. and Rose, G. D.. Recursive domains in proteins. Protein Science, 2 (2002), 409.Google Scholar
Chothia, C., Gough, J., Vogel, C.et al.Evolution of the protein repertoire. Science, 300 (2003), 1701.CrossRefGoogle ScholarPubMed
Denton, M. and Marshall, C.. Laws of form revisited. Nature, 410 (2001), 417.CrossRefGoogle ScholarPubMed
Privalov, P. L.. Stability of proteins: proteins which do not present a single cooperative system. Advances in Protein Chemistry, 35 (1982), 1.CrossRefGoogle ScholarPubMed
Maritan, A., Micheletti, C., Trovato, A.et al.Optimal shapes of compact strings. Nature, 406 (2000), 287.CrossRefGoogle ScholarPubMed
Ginsburg, A. and Carroll, W. R.. Some specific ion effects on the conformation and thermal stability of ribonuclease. Biochemistry-US, 4 (1965), 2159.CrossRefGoogle Scholar
Anfinsen, C. B.. Principles that govern folding of protein chains. Science, 181 (1973), 223.CrossRefGoogle ScholarPubMed
Jackson, S. E.. How do small single-domain proteins fold?Folding and Design, 3 (1998), R81.CrossRefGoogle ScholarPubMed
Baldwin, R. L. and Rose, G. D.. Is protein folding hierarchic? I. Local structure and peptide folding. Trends in Biochemical Science, 24 (1999), 26.CrossRefGoogle ScholarPubMed
Baker, D.. A surprising simplicity to protein folding. Nature, 405 (2002), 39.CrossRefGoogle Scholar
Banavar, J. R., Maritan, A., Micheletti, C.et al.Geometry and physics of proteins. Proteins, 47 (2002), 315.CrossRefGoogle ScholarPubMed
Ramachandran, G. N. and Sasisekharan, V.. Conformation of polypeptides and proteins. Advances in Protein Chemistry, 23 (1968), 283.CrossRefGoogle ScholarPubMed
Srinivasan, R. and Rose, G. D.. LINUS: a hierarchic procedure to predict the fold of a protein. Proteins, 22 (1995), 81.CrossRefGoogle ScholarPubMed
Stanley, H. E.. Scaling, universality, and renormalization: three pillars of modern critical phenomena. Reviews of Modern Physics, 71 (1999), S358.CrossRefGoogle Scholar
Jacobs, D. J., Rader, A. J., Kuhn, L. A.et al.Protein flexibility predictions using graph theory. Proteins, 44 (2001), 150; A. J. Rader, B. M. Hespenheide, L. A. Kuhn et al. Protein unfolding: rigidity lost. Proceedings of the National Academy of Sciences, USA, 99 (2002), 3540.CrossRefGoogle ScholarPubMed
Englander, S. W., Downer, N. W. and Teitelbaum, H.. Hydrogen exchange. Annual Review of Biochemistry, 41 (1972), 903; Woodward, C. K. and Hilton, B. D.. Hydrogen exchange kinetics and internal motions in proteins and nucleic acids. Annual Review of Biophysics and Biomolecular Structure, 8 (1979), 99; Udgaonkar, J. B. and Baldwin, R. L.. NMR evidence for an early framework intermediate on the folding pathway of ribonuclease A. Nature, 335 (1988), 694; Matouschek, A., Kellis, J. T. Jr., Serrano, L.et al.Transient folding intermediates characterized by protein engineering. Nature, 346 (1990), 440; Radford, S. E. and Dobson, C. M.. Insights into protein folding using physical techniques: studies of lysozyme and alpha-lactalbumin. Philosophical Transactions of the Royal Society of London, B 348 (1995), 17; Fersht, A. R.. Characterizing transition states in protein folding: an essential step in the puzzle. Current Opinion in Structural Biology, 5 (1995), 79.CrossRefGoogle ScholarPubMed
Hoang, T. X., Trovato, A., Seno, F.et al.Geometry and symmetry presculpt the free-energy landscape of proteins. Proceedings of the National Academy of Sciences, USA, 101 (2004), 7960.CrossRefGoogle ScholarPubMed
Berman, H. M.et al.The Protein Data Bank. Nucleic Acids Research, 28 (2000), 235.CrossRefGoogle ScholarPubMed
Zhou, Y., Hall, C. K. and Karplus, M.. First-order disorder-to-order transition in an isolated homopolymer model. Physical Review Letters, 77 (1996), 2822.CrossRefGoogle Scholar
Wilkinson, K. D. and Meyer, A. N.. Alcohol-induced conformational changes of ubiquitin. Archives of Biochemistry and Biophysics, 250 (1986), 390; Dufour, E. and Haertle, T.. Alcohol-induced changes of beta-lactoglobulin-retinol-binding stoichiometry. Protein Engineering, 4 (1990), 185; Harding, M. M., Williams, D. H. and Woolfson, D. N.. Characterization of a partially denatured state of a protein by two-dimensional NMR: reduction of the hydrophobic interactions in ubiquitin. Biochemistry-US, 30 (1991), 3120; Fan, P., Bracken, C. and Baum, J.. Structural characterization of monellin in the alcohol-denatured state by NMR: evidence for beta-sheet to alpha-helix conversion. Biochemistry-US, 32 (1993), 1573; Shiraki, K., Nishikawa, K. and Goto, Y.. Trifluoroethanol-induced stabilization of the alpha-helical structure of beta-lactoglobulin: implication for non-hierarchical protein folding. Journal of Molecular Biology, 245 (1995), 180.CrossRefGoogle ScholarPubMed
Bryngelson, J. D. and Wolynes, P. G.. Spin-glasses and the statistical-mechanics of protein folding. Proceedings of the National Academy of Sciences, USA, 84 (1987), 7524.CrossRefGoogle ScholarPubMed
Leopold, P. E., Montal, M. and Onuchic, J. N.. Protein folding funnels: a kinetic approach to the sequence-structure relationship. Proceedings of the National Academy of Sciences, USA, 89 (1992), 8271; Wolynes, P. G., Onuchic, J. N. and Thirumalai, D.. Navigating the folding routes. Science, 267 (1995), 1619; Dill, K. A. and Chan, H. S.. From Levinthal to pathways to funnels. Nature Structural Biology, 4 (1997), 10.CrossRefGoogle ScholarPubMed
Banavar, J. R. and Maritan, A.. Colloquium: geometrical approach to protein folding – a tube picture. Reviews of Modern Physics, 75 (2003), 23.CrossRefGoogle Scholar
Bernal, J. D.. Structure of proteins. Nature, 143 (1939), 663.CrossRefGoogle Scholar
Perl, D., Welker, C., Schindler, T.et al.Conservation of rapid two-state folding in mesophilic, thermophilic and hyperthermophilic cold shock proteins. Nature Structural Biology, 5 (1998), 229.CrossRefGoogle ScholarPubMed
Riddle, D. S., Santiago, J. V., Bray, S. T.et al.Functional rapidly folding proteins from simplified amino acid sequences. Nature Structural Biology, 4 (1997), 805; Kim, D. E., Gu, H. and Baker, D.. The sequences of small proteins are not extensively optimized for rapid folding by natural selection. Proceedings of the National Academy of Sciences USA, 95 (1998), 4982.CrossRefGoogle ScholarPubMed
Villegas, V., Martinez, J. C., Aviles, F. X.et al.Structure of the transition state in the folding process of human procarboxypeptidase A2 activation domain. Journal of Molecular Biology, 283 (1998), 1027; Chiti, F., Taddei, N., White, P. M.et al.Mutational analysis of acylphosphatase suggests the importance of topology and contact order in protein folding. Nature Structural Biology, 6 (1999), 1005.CrossRefGoogle Scholar
Martinez, J. C. and Serrano, L.. Obligatory steps in protein folding and the conformational diversity of the transition state. Nature Structural Biology, 6 (1999), 1010; Riddle, D. S., Grantcharova, V. P., Santiago, J. V.et al.Experiment and theory highlight role of native state topology in SH3 folding. Nature Structural Biology, 6 (1999), 1016.Google Scholar
Richardson, J. S. and Richardson, D. C.. The de novo design of protein structures. Trends in Biochemical Science, 14 (1989), 304; DeGrado, W. F., Wasserman, Z. R. and Lear, J. D.. Protein design, a minimalist approach. Science, 243 (1989), 622; Hecht, M. H., Richardson, J. S., Richardson, D. C.et al.De novo design, expression, and characterization of felix – a 4-helix bundle protein of native-like sequence. Science, 249 (1990), 884; Hill, C. P., Anderson, D. H., Wesson, L.et al.Crystal-structure of alpha-1 – implications for protein design. Science, 249 (1990), 343; Sander, C. and Schneider, R.. Database of homology-derived protein structures and the structural meaning of sequence alignment. Proteins, 9 (1991), 56; Kamtekar, S., Schiffer, J. M., Xiong, H. Y.et al.Protein design by binary patterning of polar and nonpolar amino-acids. Science, 262 (1993), 1680; Brunet, A. P., Huang, E. S., Huffine, M. E.et al.The role of turns in the structure of an alpha-helical protein. Nature, 364 (1993), 355; Davidson, A. R. and Sauer, R. T.. Folded proteins occur frequently in libraries of random amino-acid-sequences. Proceedings of the National Academy of Sciences USA, 91 (1994), 2146; West, M. W., Wang, W. X., Patterson, J.et al.De novo amyloid proteins from designed combinatorial libraries. Proceedings of the National Academy of Sciences, USA, 96 (1999), 11211; Wei, Y., Kim, S., Fela, D.et al.Solution structure of a de novo protein from a designed combinatorial library. Proceedings of the National Academy of Sciences, USA, 100 (2003), 13270.CrossRefGoogle Scholar
Rose, G. D., Geselowitz, A. R., Lesser, G. J.et al.Hydrophobicity of amino acid residues in globular proteins. Science, 229 (1985), 834; Miller, S., Janin, J., Lesk, A. M.et al.Interior and surface of monomeric proteins. Journal of Molecular Biology, 196 (1987), 641; Lawrence, C., Auger, I. and Mannella, C.. Distribution of accessible surfaces of amino acids in globular proteins. Proteins, 2 (1987), 153.CrossRefGoogle ScholarPubMed
Bowie, J. U., Reidhaar-Olson, J. F., Lim, W. A.et al.Deciphering the message in protein sequences – tolerance to amino-acid substitutions. Science, 247 (1990), 1306; Lim, W. A. and Sauer, R. T.. The role of internal packing interactions in determining the structure and stability of a protein. Journal of Molecular Biology, 219 (1991), 359; Heinz, D. W., Baase, W. A. and Matthews, B. W.. Folding and function of a t4 lysozyme containing 10 consecutive alanines illustrate the redundancy of information in an amino-acid-sequence. Proceedings of the National Academy of Sciences, USA, 89 (1992), 3751; Matthews, B. W.. Structural and genetic analysis of protein stability. Annual Review of Biochemistry, 62 (1993), 139.CrossRefGoogle ScholarPubMed
Holm, L. and Sander, C.. An evolutionary treasure: unification of a broad set of amidohydrolases related to urease. Proteins, 28 (1997), 72.3.0.CO;2-L>CrossRefGoogle ScholarPubMed
Jones, D. T., Taylor, W. R. and Thornton, J. M.. A new approach to protein fold recognition. Nature, 358 (1992), 86.CrossRefGoogle ScholarPubMed
Radford, S. E. and Dobson, C. M.. From computer simulations to human disease: emerging themes in protein folding. Cell, 97 (1999), 291; Bucciantini, M., Giannoni, E., Chiti, F.et al.Inherent toxicity of aggregates implies a common mechanism for protein misfolding diseases. Nature, 416 (2002), 507; Dumoulin, M., Last, A. M., Desmyter, A.et al.A camelid antibody fragment inhibits the formation of amyloid fibrils by human lysozyme. Nature, 424 (2003), 783; Chiti, F., Stefani, M., Taddei, N.et al.Rationalization of the effects of mutations on peptide and protein aggregation rates. Nature, 424 (2003), 805.CrossRefGoogle ScholarPubMed
Prusiner, S. B.. Prions. Proceedings of the National Academy of Sciences, USA, 95 (1998), 13363.CrossRefGoogle ScholarPubMed
Aggeli, A., Nyrkova, I. A., Bell, M.et al.Hierarchical self-assembly of chiral rod-like molecules as a model for peptide beta-sheet tapes, ribbons, fibrils, and fibers. Proceedings of the National Academy of Sciences, USA, 98 (2001), 11857.CrossRefGoogle ScholarPubMed
Horwich, A. L., Weber-Ban, E. U. and Finley, D.. Chaperone rings in protein folding and degradation. Proceedings of the National Academy of Sciences, USA, 96 (1999), 11033.CrossRefGoogle ScholarPubMed
Fandrich, M. and Dobson, C. M.. The behaviour of polyamino acids reveals an inverse side chain effect in amyloid structure formation. EMBO Journal, 21 (2002), 5682.CrossRefGoogle ScholarPubMed
Smith, J. Maynard. Natural selection and concept of a protein space. Nature, 225 (1970), 563.CrossRefGoogle ScholarPubMed
Kimura, M.. Evolutionary rate at the molecular level. Nature, 217 (1968), 624.CrossRefGoogle ScholarPubMed
King, J. L. and Jukes, T. H.. Non-Darwinian evolution. Science, 164 (1969), 788.CrossRefGoogle ScholarPubMed
Kimura, M.. How genes evolve: a population geneticist's view. Annales de Génétique–Paris, 19 (1976), 153.Google ScholarPubMed
Mering, C., Krause, R., Snel, B.et al.Comparative assessment of large-scale data sets of protein–protein interactions. Nature, 417 (2002), 399.CrossRefGoogle Scholar
Thornton, J. M., Todd, A. E., Milburn, D.et al.From structure to function: approaches and limitations. Nature Structural Biology, 7 (2000), 991 (suppl. S).CrossRefGoogle ScholarPubMed
Orengo, C. A., Todd, A. E. and Thornton, J. M.. From protein structure to function. Current Opinion in Structural Biology, 9 (1999), 374.CrossRefGoogle ScholarPubMed
Gavin, A. C., Bösche, M., Krause, R.et al.Functional organization of the yeast proteome by systematic analysis of protein complexes. Nature, 415 (2002), 141; Ho, Y., Gruhler, A., Heilbut, A.et al.Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry. Nature, 415 (2002), 180.CrossRefGoogle ScholarPubMed
Hopfield, J. J.. Neural networks and physical systems with emergent collective computational abilities. Proceedings of the National Academy of Sciences, USA, 79 (1982), 2554.CrossRefGoogle ScholarPubMed
Anderson, P. W.. Suggested model for prebiotic evolution – the use of chaos. Proceedings of the National Academy of Sciences, USA, 80 (1983), 3386.CrossRefGoogle Scholar
Eigen, M., Schuster, P., Gardiner, W.et al.The origin of genetic information. Scientific American, 244 (1981), 78.CrossRefGoogle ScholarPubMed
Binder, K. and Young, A. P.. Spin glasses: experimental facts, theoretical concepts, and open questions. Reviews of Modern Physics, 58 (1986), 801; Mezard, M., Parisi, G. and Virasoro, M., Spin Glass Theory and Beyond. Singapore: World Scientific (1987).Google Scholar
Bryngelson, J. D., Onuchic, J. N., Socci, N. D.et al.Funnels, pathways, and the energy landscape of protein-folding – a synthesis. Proteins, 21 (1995), 167; Klimov, D. K. and Thirumalai, D.. Criterion that determines the foldability of proteins. Physical Review Letters, 76 (1996), 4070; Chan, H. S. and Dill, K. A.. Protein folding in the landscape perspective: chevron plots and non-arrhenius kinetics. Proteins, 30 (1998), 2.CrossRefGoogle ScholarPubMed

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