Computational design, construction, and characterization of a set of specificity determining residues in protein-protein interactions

Proteins: Structure, Function and Bioinformatics

Volumn 80, Issue 10, 2012, Pages 2426-2436

  Nagao, Chioko ^a   Izako, Nozomi ^b,c   Soga, Shinji ^b   Khan, Samia Haseeb ^a,d   Kawabata, Shigeki ^b   Shirai, Hiroki ^b   Mizuguchi, Kenji ^a,d  

^a NATIONAL INSTITUTE OF BIOMEDICAL INNOVATION   (Japan)

^b ASTELLAS PHARMA INC   (Japan)

^c Hitachi Solutions   (Japan)

^d OSAKA UNIVERSITY   (Japan)

Author keywords

Charge complementary interactions; Interaction energy; Protein complex structures; Ras domain family; TGF_beta domain family

Indexed keywords

AMINO ACID;

AMINO ACID SEQUENCE; ARTICLE; COMPLEX FORMATION; CRYSTAL STRUCTURE; ENERGY; MATHEMATICAL COMPUTING; PRIORITY JOURNAL; PROTEIN DOMAIN; PROTEIN FAMILY; PROTEIN PROTEIN INTERACTION;

AMINO ACID SEQUENCE; ANIMALS; CLUSTER ANALYSIS; COMPUTATIONAL BIOLOGY; DATABASES, PROTEIN; HUMANS; MICE; MODELS, MOLECULAR; PROTEIN INTERACTION DOMAINS AND MOTIFS; PROTEIN INTERACTION MAPPING; PROTEINS; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, PROTEIN; THERMODYNAMICS; TRANSFORMING GROWTH FACTOR BETA;

EID: 84865973599     PISSN: 08873585     EISSN: 10970134     Source Type: Journal    
DOI: 10.1002/prot.24127     Document Type: Article

References (62)

1. Moreira IS, Fernandes PA, Ramos MJ.Hot spots-a review of the protein-protein interface determinant amino-acid residues.Proteins 2007;68:803-812.
2. Bogan AA, Thorn KS.Anatomy of hot spots in protein interfaces.J Mol Biol 1998;280:1-9.
3. Capra JA, Singh M.Characterization and prediction of residues determining protein functional specificity.Bioinformatics 2008;24:1473-1480.
4. Donald JE, Shakhnovich EI.SDR: a database of predicted specificity-determining residues in proteins.Nucleic Acids Res 2009;37:D191-D194.
5. Rausell A, Juan D, Pazos F, Valencia A.Protein interactions and ligand binding: from protein subfamilies to functional specificity.Proc Natl Acad Sci USA 2010;107:1995-2000.
6. Reva B, Antipin Y, Sander C.Determinants of protein function revealed by combinatorial entropy optimization.Genome Biol 2007;8:R232.
7. Lichtarge O, Bourne HR, Cohen FE.An evolutionary trace method defines binding surfaces common to protein families.J Mol Biol 1996;257:342-358.
8. Pei J, Cai W, Kinch LN, Grishin NV.Prediction of functional specificity determinants from protein sequences using log-likelihood ratios.Bioinformatics 2006;22:164-171.
9. Chakrabarti S, Bryant SH, Panchenko AR.Functional specificity lies within the properties and evolutionary changes of amino acids.J Mol Biol 2007;373:801-810.
10. Kalinina OV, Novichkov PS, Mironov AA, Gelfand MS, Rakhmaninova AB.SDPpred: a tool for prediction of amino acid residues that determine differences in functional specificity of homologous proteins.Nucleic Acids Res 2004;32:W424-W428.
11. Ye K, Feenstra KA, Heringa J, Ijzerman AP, Marchiori E.Multi-RELIEF: a method to recognize specificity determining residues from multiple sequence alignments using a Machine-Learning approach for feature weighting.Bioinformatics 2008;24:18-25.
12. Clackson T, Wells JA.A hot spot of binding energy in a hormone-receptor interface.Science 1995;267:383-386.
13. Guharoy M, Pal A, Dasgupta M, Chakrabarti P.PRICE (PRotein Interface Conservation and Energetics): a server for the analysis of protein-protein interfaces.J Struct Funct Genomics 2011;12:33-41.
14. Li X, Keskin O, Ma B, Nussinov R, Liang J.Protein-protein interactions: hot spots and structurally conserved residues often locate in complemented pockets that pre-organized in the unbound states: implications for docking.J Mol Biol 2004;344:781-795.
15. Ben-Shimon A, Eisenstein M.Computational mapping of anchoring spots on protein surfaces.J Mol Biol 2010;402:259-277.
16. Berman H, Henrick K, Nakamura H.Announcing the worldwide Protein Data Bank.Nat Struct Biol 2003;10:980.
17. Finn RD, Mistry J, Tate J, Coggill P, Heger A, Pollington JE, Gavin OL, Gunasekaran P, Ceric G, Forslund K, Holm L, Sonnhammer EL, Eddy SR, Bateman A.The Pfam protein families database.Nucleic Acids Res 2010;38:D211-D222.
18. Li W, Godzik A.Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences.Bioinformatics 2006;22:1658-1659.
19. Stein A, Ceol A, Aloy P.3did: identification and classification of domain-based interactions of known three-dimensional structure.Nucleic Acids Res 2011;39:D718-D723.
20. Velankar S, McNeil P, Mittard-Runte V, Suarez A, Barrell D, Apweiler R, Henrick K.E-MSD: an integrated data resource for bioinformatics.Nucleic Acids Res 2005;33:D262-265.
21. Hu Z-L, Bao J, Reecy JM.CateGOrizer: a web-based program to batch analyze gene ontology classification categories.Online J Bioinformatics 2008;9:108-112.
22. MOE (The Molecular Operating Environment), Virsion 2009.1: Chemical Computins Group; 2009.
23. Wang J, Cieplak P, Kollman PA.How well does a Restrained Electrostatic Potential (RESP) model perform in calculating conformational energies of organic and biological molecules?J Comput Chem 2000;21:1049-1074.
24. Valdar WS.Scoring residue conservation.Proteins 2002;48:227-241.
25. Mihalek I, Res I, Lichtarge O.A family of evolution-entropy hybrid methods for ranking protein residues by importance.J Mol Biol 2004;336:1265-1282.
26. Morgan DH, Kristensen DM, Mittelman D, Lichtarge O.ET viewer: an application for predicting and visualizing functional sites in protein structures.Bioinformatics 2006;22:2049-2050.
27. Mizuguchi K, Deane CM, Blundell TL, Johnson MS, Overington JP.JOY: protein sequence-structure representation and analysis.Bioinformatics 1998;14:617-623.
28. R Development Core Team.R: A language and environment for statistical computing.Vienna, Austria:R Foundation for Statistical Computing;2008.
29. Chakrabarti P, Janin J.Dissecting protein-protein recognition sites.Proteins 2002;47:334-343.
30. Hubbard SJ, Thornton JM.'NACCESS', computer program.University College London: Department of Biochemistry and Molecular Biology;1993.
31. Guerois R, Nielsen JE, Serrano L.Predicting changes in the stability of proteins and protein complexes: a study of more than 1000 mutations.J Mol Biol 2002;320:369-387.
32. Schymkowitz J, Borg J, Stricher F, Nys R, Rousseau F, Serrano L.The FoldX web server: an online force field.Nucleic Acids Res 2005;33:W382-W388.
33. Massova I, Kollman PA.Computational alanine scanning to probe protein-protein interactions: a novel approach to evaluate binding free energies.J Am Chem Soc 1999;121:8133-8143.
34. Bradshaw RT, Patel BH, Tate EW, Leatherbarrow RJ, Gould IR.Comparing experimental and computational alanine scanning techniques for probing a prototypical protein-protein interaction.Protein Eng Des Sel 2011;24:197-207.
35. Zoete V, Michielin O.Comparison between computational alanine scanning and per-residue binding free energy decomposition for protein-protein association using MM-GBSA: application to the TCR-p-MHC complex.Proteins 2007;67:1026-1047.
36. Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, Harris MA, Hill DP, Issel-Tarver L, Kasarskis A, Lewis S, Matese JC, Richardson JE, Ringwald M, Rubin GM, Sherlock G.Gene ontology: tool for the unification of biology. The Gene Ontology Consortium.Nat Genet 2000;25:25-29.
37. Shirai H, Mokrab Y, Mizuguchi K.The guanidino-group modifying enzymes: structural basis for their diversity and commonality.Proteins 2006;64:1010-1023.
38. Shirai H, Kidera A, Nakamura H.H3-rules: identification of CDR-H3 structures in antibodies.FEBS Lett 1999;455:188-197.
39. Sekhon JS.Multivariate and propensity score matching software with automated balance optimization: the matching package for R.J Stat Software 2011;42:1-52.
40. Koenig BB, Cook JS, Wolsing DH, Ting J, Tiesman JP, Correa PE, Olson CA, Pecquet AL, Ventura F, Grant RA, Chen G-X, Wrana JL, Massagué J, Rosenbaum JS. Characterization and cloning of a receptor for BMP-2 and BMP-4 from NIH 3T3 cells. Mol Cell Biol 1994;14:5961-5974.
41. Allendorph GP, Vale WW, Choe S.Structure of the ternary signaling complex of a TGF-beta superfamily member.Proc Natl Acad Sci USA 2006;103:7643-7648.
42. Kirsch T, Nickel J, Sebald W.BMP-2 antagonists emerge from alterations in the low-affinity binding epitope for receptor BMPR-II.EMBO J 2000;19:3314-3324.
43. Rehmann H, Arias-Palomo E, Hadders MA, Schwede F, Llorca O, Bos JL. Structure of Epac2 in complex with a cyclic AMP analogue and RAP1B. Nature 2008;455:124-127.
44. Fukai S, Matern HT, Jagath JR, Scheller RH, Brunger AT.Structural basis of the interaction between RalA and Sec5, a subunit of the sec6/8 complex.EMBO J 2003;22:3267-3278.
45. Bugg TDH.Introduction to enzyme and coenzyme chemistry, 2nd Edition.Oxford, UK:Blackwell Publishing Ltd.;2004. pp 304.
46. Perona JJ, Evnin LB, Craik CS.A genetic selection elucidates structural determinants of arginine versus lysine specificity in trypsin.Gene 1993;137:121-126.
47. Xu S, Rall K, Bordusa F.Enzymatic coupling of specific peptides at nonspecific ligation sites: effect of Asp189Glu mutation in trypsin on substrate mimetic-mediated reactions.J Org Chem 2001;66:1627-1632.
48. Graf L, Jancso A, Szilagyi L, Hegyi G, Pinter K, Naray-Szabo G, Hepp J, Medzihradszky K, Rutter WJ.Electrostatic complementarity within the substrate-binding pocket of trypsin.Proc Natl Acad Sci USA 1988;85:4961-4965.
49. Grunberg R, Domgall I, Gunther R, Rall K, Hofmann HJ, Bordusa F.Peptide bond formation mediated by substrate mimetics. Structure-guidedoptimization of trypsin for synthesis.Eur J Biochem 2000;267:7024-7030.
50. McGrath ME, Hines WM, Sakanari JA, Fletterick RJ, Craik CS.The sequence and reactive site of ecotin. A general inhibitor of pancreatic serine proteases from Escherichia coli.J Biol Chem 1991;266:6620-6625.
51. Yang SQ, Wang CI, Gillmor SA, Fletterick RJ, Craik CS.Ecotin: a serine protease inhibitor with two distinct and interacting binding sites.J Mol Biol 1998;279:945-957.
52. Slep KC, Kercher MA, He W, Cowan CW, Wensel TG, Sigler PB.Structural determinants for regulation of phosphodiesterase by a G protein at 2.0 A.Nature 2001;409:1071-1077.
53. Himanen JP, Goldgur Y, Miao H, Myshkin E, Guo H, Buck M, Nguyen M, Rajashankar KR, Wang B, Nikolov DB.Ligand recognition by A-class Eph receptors: crystal structures of the EphA2 ligand-binding domain and the EphA2/ephrin-A1 complex.EMBO Rep 2009;10:722-728.
54. Chrencik JE, Brooun A, Kraus ML, Recht MI, Kolatkar AR, Han GW, Seifert JM, Widmer H, Auer M, Kuhn P.Structural and biophysical characterization of the EphB4*ephrinB2 protein-protein interaction and receptor specificity.J Biol Chem 2006;281:28185-28192.
55. Govindarajan S, Ness JE, Kim S, Mundorff EC, Minshull J, Gustafsson C.Systematic variation of amino acid substitutions for stringent assessment of pairwise covariation.J Mol Biol 2003;328:1061-1069.
56. Rohl CA, Strauss CE, Misura KM, Baker D.Protein structure prediction using Rosetta.Methods Enzymol 2004;383:66-93.
57. Normanno N, De Luca A, Bianco C, Strizzi L, Mancino M, Maiello MR, Carotenuto A, De Feo G, Caponigro F, Salomon DS.Epidermal growth factor receptor (EGFR) signaling in cancer.Gene 2006;366:2-16.
58. Locksley RM, Killeen N, Lenardo MJ.The TNF and TNF receptor superfamilies: integrating mammalian biology.Cell 2001;104:487-501.
59. Keeble AH, Joachimiak LA, Mate MJ, Meenan N, Kirkpatrick N, Baker D, Kleanthous C.Experimental and computational analyses of the energetic basis for dual recognition of immunity proteins by colicin endonucleases.J Mol Biol 2008;379:745-759.
60. Meenan NA, Sharma A, Fleishman SJ, Macdonald CJ, Morel B, Boetzel R, Moore GR, Baker D, Kleanthous C.The structural and energetic basis for high selectivity in a high-affinity protein-protein interaction.Proc Natl Acad Sci USA 2010;107:10080-10085.
61. Stark C, Breitkreutz BJ, Chatr-Aryamontri A, Boucher L, Oughtred R, Livstone MS, Nixon J, Van Auken K, Wang X, Shi X, Reguly T, Rust JM, Winter A, Dolinski K, Tyers M.The BioGRID interaction database: 2011 update.Nucleic Acids Res 2011;39: D698-D704.
62. Murakami Y, Mizuguchi K.Applying the Naive Bayes classifier with kernel density estimation to the prediction of protein-protein interaction sites.Bioinformatics 2010;26:1841-1848.