Correlated mutations: Advances and limitations. A study on fusion proteins and on the Cohesin-Dockerin families

Proteins: Structure, Function and Genetics

Volumn 63, Issue 4, 2006, Pages 832-845

  Halperin, Inbal ^a   Wolfson, Haim ^a   Nussinov, Ruth ^a,b,c  

^a TEL AVIV UNIVERSITY   (Israel)

^b SAIC FREDERICK INC   (United States)

^c NATIONAL CANCER INSTITUTE   (United States)

Author keywords

Binding site; Correlated mutations; Fusion proteins; Protein protein interactions; Residue covariation

Indexed keywords

COHESIN; DNA; DNA POLYMERASE; DOCKERIN; HYBRID PROTEIN; PROTEIN; RNA; UNCLASSIFIED DRUG;

ARTICLE; BINDING SITE; MUTAGENESIS; MUTATION; PRIORITY JOURNAL; PROBABILITY; PROTEIN PROTEIN INTERACTION; PROTEIN RNA BINDING; SCORING SYSTEM; STATISTICAL ANALYSIS; THREE DIMENSIONAL IMAGING;

AMINO ACIDS; CELL CYCLE PROTEINS; CHEMISTRY, PHYSICAL; CHROMOSOMAL PROTEINS, NON-HISTONE; ENTROPY; MUTATION; NUCLEAR PROTEINS; PROTEIN SUBUNITS; RECOMBINANT FUSION PROTEINS;

EID: 33646766064     PISSN: 08873585     EISSN: 10970134     Source Type: Journal    
DOI: 10.1002/prot.20933     Document Type: Article

References (69)

1. Fraser HB, Hirsh AE, Steinmetz LM, Scharfe C, Feldman MW. Evolutionary rate in the protein interaction network. Science 2002;296:750-752.
2. Moyle WR, Campbell RK, Myers RV, Bernard MP, Han Y, Wang X. Co-evolution of ligand-receptor pairs. Nature 1994;368:251-255.
3. van Kesteren RE, Tensen CP, Smit AB, van Minnen J, Kolakowski LF, Meyerhof W, Richter D, van Heerikhuizen H, Vreugdenhil E, Geraerts WP. Co-evolution of ligand-receptor pairs in the vasopressin/oxytocin superfamily of bioactive peptides. J Biol Chem 1996; 271:3619-3626.
4. Hughes AL, Yeager M. Coevolution of the mammalian chemokines and their receptors. Immunogenetics 1999;49:115-124.
5. Koretke KK, Lupas AN, Warren PV, Rosenberg M, Brown JR. Evolution of two-component signal transduction. Mol Biol Evol 2000;17:1956-1970.
6. Giver CR, Grosovsky AJ. Single and coincident intragenic mutations attributable to gene conversion in a human cell line. Genetics 1997;146:1429-1439.
7. Goodman MF. Error-prone repair DNA polymerases in prokaryotes and eukaryotes. Annu Rev Biochem 2002;71:17-50.
8. Ninio J. Gene conversion as a focusing mechanism for correlated mutations: a hypothesis. Mol Gen Genet 1996;251:503-508.
9. Mitchell GF. Co-evolution of parasites and adaptive immune responses. Immunol Today 1991;12:A2-A5.
10. Chen Y, Carlini DB, Baines JF, Parsch J, Braverman JM, Tanda S, Stephan W. RNA secondary structure and compensatory evolution. Genes Genet Syst 1999;74:271-286.
11. Gutell RR, Power A, Hertz GZ, Putz EJ, Stormo GD. Identifying constraints on the higher-order structure of RNA: continued development and application of comparative sequence analysis methods. Nucleic Acid. Res 1992;20:5785-5795.
12. Williamson CL, Desai NM, Burkel JM. Compensatory mutations demonstrate that P8 and P6 are RNA secondary structure elements important for processing of a group I intron. Nucleic Acid Res 1989;17:675-689.
13. Osuna J, Soberno X, Morett E. A proposed architecture for the Central domain of the bacterial enhancer-binding proteins based on secondary structure prediction and fold recognition. Protein Sci 1997;6:6543-6555.
14. Fariselli P, Casadio R. A neural network based predictor of residue contacts in proteins. Protein Eng 1999;12:15-21.
15. Larson SM, Di-Nardo AA, Davidson AR. Analysis of covariation in an SH3 domain sequence alignment: applications in tertiary contact prediction and the design of compensating hydrophobic core substitutions. J Mol Biol 2000;303:433-446.
16. Ortiz AR, Kolinski A, Skolnick J. Fold assembly of small proteins using Monte Carlo simulations driven by restraints derived from multiple sequence alignment. J Mol Biol 1998;277:419-448.
17. Lockless SW, Ranganathan R. Evolutionarily conserved pathways of energetic connectivity in protein families. Science 1999;286:295-299.
18. Olmea O, Rost B, Valencia A. Effective use of sequence correlation and conservation in fold recognition. J Mol Biol 1999;293:1221-1239.
19. Rigden DJ. Use of covariance analysis for the prediction of structural domain boundaries from multiple protein sequence alignments. Protein Eng 2002;15:65-77.
20. Kass I, Horovitz A. Mapping pathways of allosteric communication in GroEL by analysis of correlated mutations. Proteins 2002;48:611-617.
21. Fariselli P, Olmea O, Valencia A, Casadio R. Prediction of contact maps with neural networks and correlated mutations. Protein Eng 2001;14:835-843.
22. Fariselli P, Olmea O, Valencia A, Casadio R. Progress in predicting inter-residue contacts of proteins with neural networks and correlated mutations. Proteins 2001;S5:157-162.
23. Pazos F, Helmer-Citterich M, Ausiello G, Valencia A. Correlated mutations contain information about protein-protein interaction. J Mol Biol 1997;271:511-523.
24. Valdar WSJ. Scoring residue conservation. Proteins 2002;48:227-241.
25. Gobel U, Sander C, Schneider R, Valencia A. Correlated mutations and residue contacts in proteins. Proteins 1994;18:309-317.
26. Pollock DD, Taylor WR. Effectiveness of correlation analysis in identifying residues undergoing correlated evolution. Protein Eng 1997;10:647-657.
27. Neher E. How frequent are correlated changes in families of protein sequences? Proc Natl Acad Sci USA 1994;91:98-102.
28. Taylor WR, Hatrick K. Compensating changes in protein multiple sequence alignments. Protein Eng 1994;7:341-348.
29. Fodor AA, Aldrich RW. Influence of conservation on calculations of amino acid covariance in multiple sequence alignments. Proteins 2004;56:211-221.
30. Cover TM, Thomas JA. Elements of information theory. New York: Wiley; 1992.
31. Clarke ND. Covariation of residues in the homeodomain sequence family. Protein Sci 1995;4:2269-2278.
32. Atchley WR, Wollenberg ICR, Fitch WM, Terhalle W, Dress AW. Correlations among amino acid sites in bHLH protein domains: an information theoretic analysis. Mol Biol Evol 2000;17:164-178.
33. Galitsky B. Revealing the set of mutually correlated positions for the protein families of immunoglobulin fold. In Silico Biol 2002;3: 241-264.
34. Miyata T, Miyazawa S, Yasunaga T. Two types of amino acid substitutions in protein evolution. J Mol Evol 1979;12:219-236.
35. McLachlan AD. Tests for comparing related amino acid sequences. J Mol Biol 1971;61:409-424.
36. Galitsky B, Gelfand IM, Kister AE. Class-defining characteristics in the mouse heavy chains of variable domains. Protein Eng 1999;12:919-925.
37. Suel GM, Lockless SW, Wall MA, Ranganathan R. Evolutionary conserved networks of residues mediate allosteric communication in proteins. Nat Struct Biol 2003;10:59-69.
38. Dekker JP, Fodor A, Aldrich RW, Yellen G. A perturbation-based method for calculating explicit likelihood of evolutionary covariance in multiple sequence alignments. Bioinformatics 2004;20: 1565-1572.
39. Fodor AA, Aldrich RW. On evolutionary conservation of thermodynamic coupling in proteins. J Biol Chem 2004;279:19046-19050.
40. Pollock DD, Taylor WR, Goldman N. Coevolving protein residues: maximum likelihood identification and relashionship to structure. J Mol Biol 1999;287:187-198.
41. Fukami-Kobayashi K, Schreiber DR, Benner SA. Detecting compensatory covariation signals in protein evolution using reconstructed ancestral sequences. J Mol Biol 2002;319:729-743.
42. Fleishman SJ, Yifrach O, Ben-Tal N. An evolutionarily conserved network of amino acids mediates gating in voltage dependent potassium channels. J Mol Biol 2004;340:307-318.
43. Tan SH, Zhang Z, Ng SK. ADVICE: automated detection and validation of interaction by co-evolution. Nucleic Acid Res 2004;32: W69-W72.
44. Jespers L, Lijnen HR, Vanwetswinkel S, Van Hoef B, Brepoels K, Collen D, De Maeyer M. Guiding a docking mode by phage display: selection of correlated mutations at the staphylokinase-plasmin interface. J Mol Biol 1999;290:471-479.
45. Jucovic M, Hartley RW. Protein-protein interaction: a genetic selection for compensating mutations at the barnase-barstar interface. Proc Natl Acad Sci USA 1996;93:2343-2347.
46. Kummerfeld SK, Vogel C, Madera M, Pacoldl M, Teichmann SA. Evolution of multi-domain proteins by gene fusion and fission. Trends Genet 2005;21:25-30.
47. Vicatos S, Reddy BV, Kaznessis Y. Prediction of distant residue contacts with the use of evolutionary information. Proteins 2005; 58:935-949.
48. Pazos F, Valencia A. In silico two-hybrid system for the selection of physically interacting protein pairs. Proteins 2002;47:219-227.
49. Halperin I, Ma B, Wolfson H, Nussinov R. Principles of docking: an overview of search algorithms and a guide to scoring functions. Proteins 2002;49:409-443.
50. Wodak SJ, Mendez R. Prediction of protein-protein interactions: the CAPRI experiment, its evaluation and implications. Curr Opin Struct Biol 2004;14:242-249.
51. Suhre K, Claverie JM. FusionDB: a database for in-depth analysis of prokaryotic events. Nucleic Acid Res 2004;32:D273-D276.
52. Tatusov RL, Natale DA, Garkavtsev IV, Tatusova TA, Shankavaram UT, Rao BS, Kiryutin B, Galperin MY, Fedorova ND, Koonin EV. The COG database: new developments in phylogenetic classification of proteins from complete genomes. Nucleic Acid Res 2001;29:23-28.
53. Lichtarge O, Bourne HR, Cohen FE. An evolutionary trace method defines binding surfaces common to protein families. J Mol Biol 1996;257:342-358.
54. Glaser F, Pupko T, Paz I, Bell RE, Bechor-Shental D, Martz E, Ben-Tal N. ConSurf: identification of functional regions in proteins by surface-mapping of phylogenetic information. Bioinformatics 2003;19:163-164.
55. Madabushi S, Yao H, Marsh M, Kristensen DM, Philippi A, Sowa ME, Lichtarge O. Structural clusters of evolutionary trace residues are statistically significant and common in proteins. J Mol Biol 2002;316:139-154.
56. Edgar RC. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acid Res 2004;32:1792-1797.
57. Glaser F, Steinberg DM, Vakser IA, Ben-Tal N. Residue frequencies and pairing preferences at protein-protein interfaces. Proteins 2001;43:89-102.
58. Lu H, Lu L, Skolnick J. Development of unified statistical potentials describing protein-protein interactions. Biophys J 2003; 84:1895-1901.
59. Taylor WR. The classification of amino acid conservation. J Theor Biol 1986;119:205-218.
60. Tavares GA, Beguin P, Alzari M. The crystal structure of a type I Cohesin domain at 1.7 Å resolution. J Mol Biol 1997;273:701-713.
61. Shimon LJ, Bayer EA, Morag E, Lamed R, Yaron S, Shoham Y, Frolow F. A cohesin domain from Clostridium thermocellum: the crystal structure provides new insights into cellulosome assembly. Structure 1997;5:381-390.
62. Bateman A, Coin L, Durbin R, Finn RD, Hollich V, Griffiths-Jones S, Khanna A, Marshall M, Moxon S, Sonnhammer ELL, Studholme DJ, Yeats C, Eddy SR. The Pfam protein families database. Nucleic Acid Res 2004;32:D138-D141.
63. Jindou S, Soda A, Karita S, Kajino T, Beguin P, Wu JH, Inagaki M, Kimura T, Sakka K, Ohmiya K. Cohesin-dockerin interactions within and between Clostridium josui and Clostridium thermocellum: binding selectivity between cognate dockerin and cohesin domains and species specificity. J Biol Chem 2004;279:9867-9874.
64. Inbar Y, Schneidman-Duhovny D, Halperin I, Oron A, Nussinov R, Wolfson HJ. Approaching the CAPRI challenge with an efficient geometry based docking. Proteins 2005.
65. Yamano T, A possible extension of Shannon's information theory. Entropy 2001;3:280-292.
66. Petes TD. Meiotic recombination hot spots and cold spots. Nat Rev Genet 2001;2:360-369.
67. Thompson JD, Higgins DG, Gibson TJ. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acid Res 1994;22:4673-4680.
68. Connolly M. Solvent-accessible surfaces of proteins and nucleic acids. Science 1983;221:709-713.
69. Shannon CE. A mathematical theory of communication. Bell Syst Tech J 1948;27:379-423.