Evolution of protein modularity

Current Opinion in Structural Biology

Volumn 19, Issue 3, 2009, Pages 335-340

  Trifonov, Edward N ^a,b   Frenkel, Zakharia M ^a  

^a UNIVERSITY OF HAIFA   (Israel)

^b MASARYK UNIVERSITY   (Czech Republic)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID SEQUENCE; CONSENSUS SEQUENCE; MOLECULAR EVOLUTION; PRIORITY JOURNAL; PROTEIN DOMAIN; PROTEIN FOLDING; PROTEIN FUNCTION; PROTEIN MOTIF; PROTEIN STRUCTURE; REVIEW; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS; SEQUENCE HOMOLOGY; THERMODYNAMICS;

AMINO ACID SEQUENCE; EVOLUTION, MOLECULAR; HUMANS; MOLECULAR SEQUENCE DATA; PROTEIN STRUCTURE, TERTIARY; PROTEINS;

EID: 66549085563     PISSN: 0959440X     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.sbi.2009.03.007     Document Type: Review

References (47)

1. Zeldovich K.B., and Shakhnovich E.I. Understanding protein evolution: from protein physics to Darwinian selection. Annu Rev Phys Chem 59 (2008) 105-127
2. Trifonov E.N. Sequence codes. In: Creighton T.E. (Ed). Encyclopedia of Molecular Biology (1999), John Wiley & Sons, Inc. 2324-2326
3. Helling R., Li H., Melin R., Miller J., Wingreen N., Zeng C., and Tang C. The designability of protein structures. J Mol Graph Model 19 (2001) 157-167
4. Ausiello G., Gherardini P.F., Marcatili P., Tramontano A., Via A., and Helmer-Citterich M. FunClust: a web server for the identification of structural motifs in a set of non-homologous protein structures. BMC Bioinform 9 (2008) Article No. S2
5. Frenkel Z.M., and Trifonov E.N. Walking through the protein sequence space: towards new generation of the homology modeling. Proteins-Struct Funct Bioinform 67 (2007) 271-284
6. Xia Y., and Levitt M. Simulating protein evolution in sequence and structure space. Curr Opin Struct Biol 14 (2004) 202-207
7. Voigt C.A., Kauffman S., and Wang Z.G. Rational evolutionary design: the theory of in vitro protein evolution. Adv Protein Chem 55 (2001) 79-160
8. BornbergBauer E. How are model protein structures distributed in sequence space?. Biophys J 73 (1997) 2393-2403
9. Papandreou N., Berezovsky I.N., Lopes A., Eliopoulos E., and Chomilier J. Universal positions in globular proteins - from observation to simulation. Eur J Biochem 271 (2004) 4762-4768. Dynamic Monte Carlo simulation of initial stages of protein chain folding (alpha-carbon lattice) generates clusters of most interacting residues (MIR), anchor residues for further protein folding. Comparison with known protein structures confirms that the MIRs largely correspond to the ends of TEF (closed loops).
10. Lonquety M., Lacroix Z., Papandreou N., and Chomilier J. SPROUTS: a database for the evaluation of protein stability upon point mutation. Nucleic Acids Res 37 (2009) D374-D379
11. Cheng G., Qian B., Samudrala R., and Baker D. Improvement in protein functional site prediction by distinguishing structural and functional constraints on protein family evolution using computational design. Nucleic Acids Res 33 (2005) 5861-5867
12. Kuhlman B., Dantas G., Ireton G.C., Varani G., Stoddard B.L., and Baker D. Design of a novel globular protein fold with atomic-level accuracy. Science 302 (2003) 1364-1368
13. Goldstein R.A. The structure of protein evolution and the evolution of protein structure. Curr Opin Struct Biol 18 (2008) 170-177
14. Deeds E.J., and Shakhnovich E.I. A structure-centric view of protein evolution, design, and adaptation. Adv Enzymol Relat Areas Mol Biol 75 (2007) 133-191 xi-xii. A comprehensive review of a large body of recent work illuminating the structural aspects of protein evolution. A number of theoretical models are considered that explain heterogeneity of protein populations. Problem of protein designability is addressed.
15. Brenner S. The molecular evolution of genes and proteins - a tale of 2 serines. Nature 334 (1988) 528-530
16. Trifonov E.N., Kirzhner A., Kirzhner V.M., and Berezovsky I.N. Distinct stages of protein evolution as suggested by protein sequence analysis. J Mol Evol 53 (2001) 394-401
17. Kelly D.R., and Roberts S.M. Oligopeptides as catalysts for asymmetric epoxidation. Biopolymers 84 (2006) 74-89
18. Sobolevsky Y., Frenkel Z.M., and Trifonov E.N. Combinations of ancestral modules in proteins. J Mol Evol 65 (2007) 640-650
19. Frenkel Z.M., and Trifonov E.N. From protein sequence space to elementary protein modules. Gene 408 (2008) 64-71. An original portrayal of proteins is developed, first of its kind, that allows to identify distinct sequence modules for any given protein sequence. The procedure is based exclusively on the protein sequence, and utilizes a whole wealth of information provided by formatted sequence space of virtually all natural proteins.
20. Holland T.A., Veretnik S., Shindyalov I.N., and Bourne P.E. Partitioning protein structures into domains: Why is it so difficult?. J Mol Biol 361 (2006) 562-590
21. Andreeva A., Howorth D., Chandonia J.M., Brenner S.E., Hubbard T.J.P., Chothia C., and Murzin A.G. Data growth and its impact on the SCOP database: new developments. Nucleic Acids Res 36 (2008) D419-D425
22. Chandonia J.M., Hon G., Walker N.S., Lo Conte L., Koehl P., Levitt M., and Brenner S.E. The ASTRAL compendium in 2004. Nucleic Acids Res 32 (2004) D189-D192
23. Koczyk G., and Berezovsky I.N. Domain hierarchy and closed Loops (DHcL): a server for exploring hierarchy of protein domain structure. Nucleic Acids Res 36 (2008) W239-W245
24. Berezovsky I.N., Esipova N.G., and Tumanyan V.G. Definition of energetically significant parts of globule and hierarchy of domain structure of macromolecule of protein. Biofizika 42 (1997) 567-576. Partition of the protein globules into hierarchy of protein parts, by calculating van der Waals interactions between the domains and subdomains of crystallized proteins. The interaction energy partition allows unique identification of the subdomains consistent with other ways of partition, and provides a unified quantitative approach to the domain definition.
25. Berezovsky I.N. Discrete structure of van der Waals domains in globular proteins. Protein Eng 16 (2003) 161-167
26. Berezovsky I.N., Grosberg A.Y., and Trifonov E.N. Closed loops of nearly standard size: common basic element of protein structure. FEBS Lett 466 (2000) 283-286. The polymer-statistical structural element of the size dictated by chain flexibility - closed loop of 25-30 aa - is introduced for the first time into the field of protein structure. Consequentially, many chapters of protein science, especially protein folding and evolution, undergo now a gradual revision.
27. Lamarine M., Mornon J.P., Berezovsky I.N., and Chomilier J. Distribution of tightened end fragments of globular proteins statistically matches that of topohydrophobic positions: towards an efficient punctuation of protein folding?. Cell Mol Life Sci 58 (2001) 492-498
28. Dokholyan N.V., and Shakhnovich E.I. Understanding hierarchical protein evolution from first principles. J Mol Biol 312 (2001) 289-307
29. Trifonov E.N., and Berezovsky I.N. Evolutionary aspects of protein structure and folding. Curr Opin Struct Biol 13 (2003) 110-114
30. Yew B.K., Chintapalli S.V., Upton G.G.C., and Reynolds C.A. Conservation of closed loops. J Mol Graph Modell 26 (2007) 652-655
31. Gribskov M., McLachlan A.D., and Eisenberg D. Profile analysis - detection of distantly related proteins. Proc Natl Acad Sci U S A 84 (1987) 4355-4358
32. Henikoff J.G., Pietrokovski S., McCallum C.M., and Henikoff S. Blocks-based methods for detecting protein homology. Electrophoresis 21 (2000) 1700-1706
33. Su Q.J.J., Lu L., Saxonov S., and Brutlag D.L. eBLOCKs: enumerating conserved protein blocks to achieve maximal sensitivity and specificity. Nucleic Acids Res 33 (2005) D178-D182
34. Bornberg-Bauer E., and Chan H.S. Modeling evolutionary landscapes: mutational stability, topology, and superfunnels in sequence space. Proc Natl Acad Sci U S A 96 (1999) 10689-10694
35. Meyerguz L., Kleinberg J., and Elber R. The network of sequence flow between protein structures. Proc Natl Acad Sci U S A 104 (2007) 11627-11632. A directed graph of sequences and structures of proteins from the Protein Data Bank is computed. At native energies the graph can connect the sequences from different folds [because of common modules in different folds? (ET and ZF)]. The sequence flows in the 'structural' graphs correlate with respective numbers of matching genomic sequences. Strength of connections between the nodes is found to reflect structural similarity between the proteins.
36. Dokholyan N.V. The architecture of the protein domain universe. Gene 347 (2005) 199-206
37. Shakhnovich B.E., Deeds E., Delisi C., and Shakhnovich E. Protein structure and evolutionary history determine sequence space topology. Genome Res 15 (2005) 385-392
38. Xia Y., and Levitt M. Funnel-like organization in sequence space determines the distributions of protein stability and folding rate preferred by evolution. Proteins-Struct Funct Bioinform 55 (2004) 107-114
39. Frenkel Z.M., and Trifonov E.N. Walking through protein sequence space. J Theor Biol 244 (2007) 77-80. The formatted (same length fragments) natural protein sequence space is introduced that covers very large number of available protein sequences. Connecting pair-wise the fragments with high sequence match results in the formation of networks that contain often rather dissimilar fragments (connected via long walks). Since the fragments making the networks, essentially, share the same functions and structures, the fragments with dissimilar sequences, thus, can be classified as relatives. This substantially expands the possibilities of 'homology searches' and provides strong evolutionary clues.
40. Frenkel Z.M., and Trifonov E.N. Evolutionary networks in the formatted protein sequence space. J Comput Biol 14 (2007) 1044-1057
41. Frenkel Z.M. Does protein relatedness require sequence matching? Alignment via networks in sequence space. J Biomol Struct Dyn 26 (2008) 215-222
42. Altschul S.F., Madden T.L., Schaffer A.A., Zhang J.H., Zhang Z., Miller W., and Lipman D.J. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25 (1997) 3389-3402
43. Altschul S.F., Wootton J.C., Gertz E.M., Agarwala R., Morgulis A., Schaffer A.A., and Yu Y.K. Protein database searches using compositionally adjusted substitution matrices. FEBS J 272 (2005) 5101-5109
44. Blake J.D., and Cohen F.E. Pairwise sequence alignment below the twilight zone. J Mol Biol 307 (2001) 721-735
45. Watts D.J., and Strogatz S.H. Collective dynamics of 'small-world' networks. Nature 393 (1998) 440-442
46. Goldberg A.V., and Tarjan R.E. A new approach to the maximum-flow problem. J ACM 35 (1988) 921-940
47. Milo R., Shen-Orr S., Itzkovitz S., Kashtan N., Chklovskii D., and Alon U. Network motifs: simple building blocks of complex networks. Science 298 (2002) 824-827