Evolutionary aspects of protein structure and folding

Current Opinion in Structural Biology

Volumn 13, Issue 1, 2003, Pages 110-114

  Trifonov, Edward N ^a   Berezovsky, Igor N ^b  

^a UNIVERSITY OF HAIFA   (Israel)

^b WEIZMANN INSTITUTE OF SCIENCE   (Israel)

Author keywords

[No Author keywords available]

Indexed keywords

CIRCULAR DNA; DNA; GLOBULAR PROTEIN; POLYMER; POLYPEPTIDE; PROTEIN;

AMINO ACID SEQUENCE; CRYSTAL STRUCTURE; MOLECULAR DYNAMICS; MOLECULAR EVOLUTION; PRIORITY JOURNAL; PROTEIN FOLDING; PROTEIN STRUCTURE; REVIEW;

EID: 0037308797     PISSN: 0959440X     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0959-440X(03)00005-8     Document Type: Review

References (59)

1. Fersht A.R. Transition-state structure as a unifying basis in protein-folding mechanisms: contact order, chain topology, stability, and the extended nucleus mechanism. Proc. Natl. Acad. Sci. USA. 97:2000;1525-1529.
2. Mayor U., Johnson C.M., Daggett V., Fersht A.R. Protein folding and unfolding in microseconds to nanoseconds by experiment and simulation. Proc. Natl. Acad. Sci. USA. 97:2000;13518-13522.
3. Dokholyan N.V., Shakhnovich E.I. Understanding hierarchical protein evolution from first principles. J. Mol. Biol. 312:2001;289-307.
4. Liu Y., Eisenberg D. 3D domain swapping: as domains continue to swap. Protein Sci. 11:2002;1285-1299.
5. Apic G., Gough J., Teichmann S.A. Domain combinations in archaeal, eubacterial and eukaryotic proteomes. J. Mol. Biol. 310:2001;311-325 The general concept of the combinatorial fusion of a limited repertoire of protein domains is amply illustrated by a survey of domain combinations through species and kingdoms. The most common domain families are also the most frequent contributors to the recombination events. A significant proportion of the protein domains remain solitary.
6. Todd A.E., Orengo C.A., Thornton J.M. Evolution of function in protein superfamilies, from a structural perspective. J. Mol. Biol. 307:2001;1113-1143.
7. Kussell E., Shimada J., Shakhnovich E.I. A structure-based method for derivation of all-atom potentials for protein folding. Proc. Natl. Acad. Sci. USA. 99:2002;5343-5348.
8. Bonneau R., Ruczinski I., Tsai J., Baker D. Contact order and ab initio protein structure prediction. Protein Sci. 11:2002;1937-1944.
9. Koehl P., Levitt M. Protein topology and stability define the space of allowed sequences. Proc. Natl. Acad. Sci. USA. 99:2002;1280-1285.
10. Todd A.E., Orengo C.A., Thornton J.M. Plasticity of enzyme active sites. Trends Biochem. Sci. 27:2002;419-426 Components of active sites that exhibit a given enzymatic activity are not necessarily positioned along the sequence in a similar way. The active groups, which are also not necessarily identical, may be brought to the active centers by diverse three-dimensional arrangements. There are thus many evolutionary ways to converge to the same enzymatic activity.
11. Teichmann S.A., Murzin A.G., Chothia C. Determination of protein function, evolution and interactions by structural genomics. Curr. Opin. Struct. Biol. 11:2001;354-363.
12. Fersht A.R., Daggett V. Protein folding and unfolding at atomic resolution. Cell. 108:2002;573-582 Folding and unfolding simulations, well supported by experimental evidence, display in a very appealing way the detailed picture of transitions between the structural extremes. These series of 'snapshots' are insightful and highly recommended for viewing.
13. Aravind L., Mazumder R., Vasudevan S., Koonin E.V. Trends in protein evolution inferred from sequence and structure analysis. Curr. Opin. Struct. Biol. 12:2002;392-399.
14. Grishin N.V. Fold change in evolution of protein structures. J. Struct. Biol. 134:2001;167-185 It is commonly accepted that different sequences can form very similar structures. As this review concludes, the reverse is true as well - homologous proteins may possess thoroughly distinct structures. This paradoxical duality is a serious challenge to understanding the sequence/structure connection.
15. Kinch L.N., Grishin N.V. Evolution of protein structures and functions. Curr. Opin. Struct. Biol. 12:2002;400-408.
16. Lupas A.N., Ponting C.P., Russell R.B. On the evolution of protein folds: are similar motifs in different protein folds the result of convergence, insertion, or relics of an ancient peptide world? J. Struct. Biol. 134:2001;191-203.
17. Trifonov E.N., Berezovsky I.N. Molecular evolution from abiotic scratch. FEBS Lett. 527:2002;1-4 A minireview on the early evolution of proteins traceable in contemporary sequences and structures. Distinct early stages of protein evolution are outlined on the basis of reconstructed codon chronology, the loop fold structure of proteins and the optimal DNA ring closure size.
18. Svedberg T. Mass and size of protein molecules. Nature. 123:1929;871.
19. Jones S., Stewart M., Michie A., Swindells M.B., Orengo C., Thornton J.M. Domain assignment for protein structures using a consensus approach: characterization and analysis. Protein Sci. 7:1998;233-242.
20. Gerstein M. How representative are the known structures of the proteins in a complete genome? A comprehensive structural census. Fold Des. 3:1998;497-512.
21. Wheelan S.J., Marchler-Bauer A., Bryant S.H. Domain size distribution can predict domain boundaries. Bioinformatics. 16:2000;613-618.
22. •] and design.
23. Berezovsky I.N., Trifonov E.N. Loop fold nature of globular proteins. Protein Eng. 14:2001;403-407.
24. Berezovsky I.N., Kirzhner A., Kirzhner V.M., Trifonov E.N. Protein folding: looping from the hydrophobic nuclei. Proteins. 45:2001;346-350.
25. Trifonov E.N., Kirzhner A., Kirzhner V.M., Berezovsky I.N. Distinct stages of protein evolution as suggested by protein sequence analysis. J. Mol. E. 53:2001;394-401.
26. Berezovsky I.N., Trifonov E.N. Protein structure and folding: a new start. J. Biomol. Struct. Dyn. 19:2001;397-403.
27. Grosberg A, Khokhlov A: Statistical Physics of Macromolecules. New York: AIP Press; 1994.
28. Flory P: Statistical Mechanics of Chain Molecules. New York: Interscience; 1969.
29. Borochov N., Eisenberg H., Kam Z. Dependence of DNA conformation on the concentration of salt. Biopolymers. 20:1981;231-235.
30. Shimada J., Yamakawa H. Ring-closure probabilities for twisted wormlike chains. Application to DNA. Macromolecules. 17:1984;689-698.
31. De Gennes PG: Introduction to Polymer Dynamics. Cambridge: Cambridge University Press; 1990.
32. Shore D., Langowski J., Baldwin R.L. DNA flexibility studied by covalent closure of short fragments into circles. Proc. Natl. Acad. Sci. USA. 78:1981;4833-4837.
33. Lamarine M., Mornon J.-P., Berezovsky I.N., Chomilier J. Distribution of tightened end fragments of globular proteins statistically match that of topohydrophobic positions: towards an efficient punctuation of protein folding? Cell Mol. Life Sci. 58:2001;492-498.
34. Chin J.W., Schepartz A. Concerted evolution of structure and function in a miniature protein. J. Am. Chem. Soc. 123:2001;2929-2930.
35. Neidigh J.W., Fesinmeyer R.M., Andersen N.H. Designing a 20-residue protein. Nat. Struct. Biol. 9:2002;425-430.
36. Berezovsky I.N., Trifonov E.N. Van der Waals locks: loop-n-lock structure of globular proteins. J. Mol. Biol. 307:2001;1419-1426 The loop fold nature of proteins suggests a new specific role for van der Waals interactions in globular proteins. They bring the ends of the closed loops together in forming loop-n-lock elements. These elements are readily detected by analyzing clusters of close contacts between amino acid residues in the crystallized proteins. The interacting van der Waals locks form well-defined hydrophobic cores in the globular proteins.
37. Pace C.N., Horn G., Hebert E.J., Bechert J., Shaw K., Urbanikova L., Scholtz J.M., Sevcik J. Tyrosine hydrogen bonds make a large contribution to protein stability. J. Mol. Biol. 312:2001;393-404 This paper demonstrates that, in the case of tyrosine, not only hydrogen bonds but also van der Waals interactions contribute to protein stability.
38. Hendsch Z.S., Tidor B. Do salt bridges stabilize proteins? A continuum electrostatic analysis. Protein Sci. 3:1994;211-226.
39. Qian B., Goldstein R.A. Distribution of Indel lengths. Proteins. 45:2001;102-104.
40. ••,25].
41. Roy S.W., Nosaka M., de Souza S.J., Gilbert W. Centripetal modules and ancient introns. Gene. 238:1999;85-91.
42. Sato Y., Niimura Y., Yura K., Go M. Module-intron correlation and intron sliding in family F/10 xylanase genes. Gene. 238:1999;93-101.
43. Angelov B., Sadoc J.F., Jullien R., Soyer A., Mornon J.P., Chomilier J. Nonatomic solvent-driven Voronoi tessellation of proteins: an open tool to analyze protein folds. Proteins. 49:2002;446-456.
44. Berezovsky I.N., Trifonov E.N. Flowering buds of globular proteins: transpiring simplicity of protein organization. Compar. Funct. Genom. 3:2002;525-534.
45. Goryushin I.Y., Kil Y.V., Reznikoff W.S. DNA length, bending and twisting constraints on IS50 transposition. Proc. Natl. Acad. Sci. USA. 91:1994;10834-10838.
46. Bresler S.E., Talmud D.L. On the nature of globular proteins. Compt. Rend. Acad. Sci. URSS. 43:1944;310-314.
47. Trifonov E.N. Segmented structure of protein sequences and early evolution of genome by combinatorial fusion of DNA elements. J. Mol. Evol. 40:1995;337-342.
48. Fersht A: Structure and Mechanism in Protein Science. A Guide to Enzyme Catalysis and Protein Folding. New York: WH Freeman and Company; 1999.
49. Berezovskii I.N., Esipova N.G., Tumanyan V.G. Isolation of the energy-significant parts of the globule and the hierarchy of the domain structure of the protein macromolecule. Biophysics. 42:1997;557-565.
50. Abkevich V.I., Gutin A.M., Shakhnovich E.I. Specific nucleus as the transition state for protein folding: evidence from the lattice model. Biochemistry. 33:1994;10026-10036.
51. Panchenko A.R., Luthey-Schulten Z., Cole R., Wolynes P.G. The foldon universe: a survey of structural similarity and self-recognition of independently folding units. J. Mol. Biol. 272:1997;95-105.
52. Galzitskaya O.V., Ivankov D.N., Finkelstein A.V. Folding nuclei in proteins. FEBS Lett. 489:2001;113-118.
53. Berezovsky I.N., Trifonov E.N. Loop fold structure of proteins: resolution of Levinthal's paradox. J. Biomol. Struct. Dyn. 20:2002;5-6 The size of the polypeptide chain that would search through all its possible conformations during observed times of protein synthesis and folding is estimated to be 23-31 residues. This is in good agreement with the observed typical closed loop size (25-30 residues).
54. Finkelstein A.V. Cunning simplicity of a hierarchical folding. J. Biomol. Struct. Dyn. 20:2002;311-313.
55. Berezovsky I.N., Trifonov E.N. Back to units of protein folding. J. Biomol. Struct. Dyn. 20:2002;315-316.
56. Grosberg A. A few disconnected notes related to Levinthal paradox. J. Biomol. Struct. Dyn. 20:2002;317-321.
57. Kloczkowski A., Jernigan R.L. Loop folds in proteins and evolutionary conservation of folding nuclei. J. Biomol. Struct. Dyn. 20:2002;323-325.
58. Rooman M., Dehouck Y., Kwasigroch J.M., Biot C., Gilis D. What is paradoxical about Levinthal Paradox? J. Biomol. Struct. Dyn. 20:2002;327-329.
59. Fernandez A., Belinky A., Boland M.M. Protein folding: where is the paradox? J. Biomol. Struct. Dyn. 20:2002;331-332.