CAPRI targets T29-42: Proving ground for new docking procedures

Proteins: Structure, Function and Bioinformatics

Volumn 78, Issue 15, 2010, Pages 3174-3181

  Eisenstein, Miriam ^a   Ben Shimon, Avraham ^a   Frankenstein, Ziv ^a   Kowalsman, Noga ^a,b  

^a WEIZMANN INSTITUTE OF SCIENCE   (Israel)

^b HEBREW UNIVERSITY OF JERUSALEM   (Israel)

Author keywords

Anchoring spots; Class specific filter; Enzyme centroid; Interface core; Interface propensities; MolFit; Normal modes analysis; Protein protein docking; Solvation; Weighted docking

Indexed keywords

COLICIN; GUANOSINE TRIPHOSPHATE; LEUCINE ZIPPER PROTEIN; NUCLEAR PROTEIN; PLEXIN; PROTEIN RND1; RAC1 PROTEIN; SUBTILISIN; TRYPSIN; UNCLASSIFIED DRUG;

ARTICLE; MOLECULAR DOCKING; PRIORITY JOURNAL; PROTEIN PROTEIN INTERACTION; SOLVATION; TETRATRICOPEPTIDE REPEAT;

COMPUTATIONAL BIOLOGY; MODELS, CHEMICAL; MODELS, MOLECULAR; MODELS, STATISTICAL; PROTEIN BINDING; PROTEIN CONFORMATION; PROTEIN INTERACTION MAPPING; PROTEINS; SOFTWARE;

EID: 77957933725     PISSN: 08873585     EISSN: 10970134     Source Type: Journal    
DOI: 10.1002/prot.22793     Document Type: Article

References (56)

1. Janin J, Henrick K, Moult J, Eyck LT, Sternberg MJ, Vajda S, Vakser I, Wodak SJ. CAPRI: a Critical Assessment of PRedicted Interactions. Proteins 2003;52:2-9.
2. Kowalsman N, Eisenstein M. Combining interface core and whole interface descriptors in postscan processing of protein-protein docking models. Proteins 2009;77:297-318.
3. Chakrabarti P, Janin J. Dissecting protein-protein recognition sites. Proteins 2002;47:334-343.
4. Ben-Shimon A, Eisenstein M. Looking at enzymes from the inside out: the proximity of catalytic residues to the molecular centroid can be used for detection of active sites and enzyme-ligand interfaces. J Mol Biol 2005;351:309-326.
5. Katchalski-Katzir E, Shariv I, Eisenstein M, Friesem AA, Aflalo C, Vakser IA. Molecular surface recognition: determination of geometric fit between proteins and their ligands by correlation techniques. Proc Natl Acad Sci USA 1992;89:2195-2199.
6. Berchanski A, Shapira B, Eisenstein M. Hydrophobic complementarity in protein-protein docking. Proteins 2004;56:130-142.
7. Heifetz A, Katchalski-Katzir E, Eisenstein M. Electrostatics in protein-protein docking. Protein Sci 2002;11:571-587.
8. Ben-Zeev E, Eisenstein M. Weighted geometric docking: incorporating external information in the rotation-translation scan. Proteins 2003;52:24-27.
9. Leulliot N, Chaillet M, Durand D, Ulryck N, Blondeau K, van Tilbeurgh H. Structure of the yeast tRNA m7G methylation complex. Structure 2008;16:52-61.
10. Zegers I, Gigot D, van Vliet F, Tricot C, Aymerich S, Bujnicki JM, Kosinski J, Droogmans L. Crystal structure of Bacillus subtilis TrmB, the tRNA (m7G46) methyltransferase. Nucleic Acids Res 2006;34:1925-1934.
11. Tong Y, Chugha P, Hota PK, Alviani RS, Li M, Tempel W, Shen L, Park HW, Buck M. Binding of Rac1. Rnd1, and Rho D to a novel Rho GTPase interaction motif destabilizes dimerization of the plexin-B1 effector domain. J Biol Chem 2007;282:37215-37224.
12. Tong Y, Hughes D, Placanica L, Buck M. When monomers are preferred: a strategy for the identification and disruption of weakly oligomerized proteins. Structure 2005;13:7-15.
13. Oinuma I, Katoh H, Harada A, Negishi M. Direct interaction of Rnd1 with Plexin-B1 regulates PDZ-RhoGEF-mediated Rho activation by Plexin-B1 and induces cell contraction in COS-7 cells. J Biol Chem 2003;278:25671-25677.
14. Driessens MH, Hu H, Nobes CD, Self A, Jordens I, Goodman CS, Hall A. Plexin-B semaphorin receptors interact directly with active Rac and regulate the actin cytoskeleton by activating Rho. Curr Biol 2001;11:339-344.
15. Micheelsen PO, Vevodova J, De Maria L, Ostergaard PR, Friis EP, Wilson K, Skjot M. Structural and mutational analyses of the interaction between the barley alpha-amylase/subtilisin inhibitor and the subtilisin savinase reveal a novel mode of inhibition. J Mol Biol 2008;380:681-690.
16. Betzel C, Klupsch S, Papendorf G, Hastrup S, Branner S, Wilson KS. Crystal structure of the alkaline proteinase Savinase from Bacillus lentus at 1.4 A resolution. J Mol Biol 1992;223:427-445.
17. Vallee F, Kadziola A, Bourne Y, Juy M, Rodenburg KW, Svensson B, Haser R. Barley alpha-amylase bound to its endogenous protein inhibitor BASI: crystal structure of the complex at 1.9 A resolution. Structure 1998;6:649-659.
18. Pal GP, Kavounis CA, Jany KD, Tsernoglou D. The three-dimensional structure of the complex of proteinase K with its naturally occurring protein inhibitor, PKI3. FEBS Lett 1994;341:167-170.
19. Lebars I, Yoshizawa S, Stenholm AR, Guittet E, Douthwaite S, Fourmy D. Structure of 23S rRNA hairpin 35 and its interaction with the tylosin-resistance methyltransferase RlmAII. EMBO J 2003;22:183-192.
20. Lebars I, Husson C, Yoshizawa S, Douthwaite S, Fourmy D. Recognition elements in rRNA for the tylosin resistance methyltransferase RlmA(II). J Mol Biol 2007;372:525-534.
21. Das K, Acton T, Chiang Y, Shih L, Arnold E, Montelione GT. Crystal structure of RlmAI: implications for understanding the 23S rRNA G745/G748-methylation at the macrolide antibiotic-binding site. Proc Natl Acad Sci USA 2004;101:4041-4046.
22. Isabet T, Montagnac G, Regazzoni K, Raynal B, El Khadali F, England P, Franco M, Chavrier P, Houdusse A, Menetrey J. The structural basis of Arf effector specificity: the crystal structure of ARF6 in a complex with JIP4. EMBO J 2009;28:2835-2845.
23. O'Neal CJ, Jobling MG, Holmes RK, Hol WG. Structural basis for the activation of cholera toxin by human ARF6-GTP. Science 2005;309:1093-1096.
24. O'shea EK, Klemm JD, Kim PS, Alber T. X-ray structure of the GCN4 leucine zipper, a two-stranded, parallel coiled coil. Science 1991;254:539-544.
25. Bao R, Zhou CZ, Jiang C, Lin SX, Chi CW, Chen Y. The ternary structure of the double-headed arrowhead protease inhibitor API-A complexed with two trypsins reveals a novel reactive site conformation. J Biol Chem 2009;284:26676-26684.
26. Katz BA, Finer-Moore J, Mortezaei R, Rich DH, Stroud RM. Episelection: novel Ki approximately nanomolar inhibitors of serine proteases selected by binding or chemistry on an enzyme surface. Biochemistry 1995;34:8264-8280.
27. Huber R, Kukla D, Bode W, Schwager P, Bartels K, Deisenhofer J, Steigemann W. Structure of the complex formed by bovine trypsin and bovine pancreatic trypsin inhibitor. II. Crystallographic refinement at 1.9 A resolution. J Mol Biol 1974;89:73-101.
28. Meenan NA, Sharma A, Fleishman SJ, MacDonald C, 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.
29. Krachler AM, Sharma A, Kleanthous C. Self-association of TPR domains: natural and engineered. Proteins 2010;78:2131-2143.
30. Mendez R, Leplae R, Lensink MF, Wodak SJ. Assessment of CAPRI predictions in rounds 3-5 shows progress in docking procedures. Proteins 2005;60:150-169.
31. Alexandrov A, Martzen MR, Phizicky EM. Two proteins that form a complex are required for 7-methylguanosine modification of yeast tRNA. RNA 2002;8:1253-1266.
32. Alexandrov A, Grayhack EJ, Phizicky EM. tRNA m7G methyltransferase Trm8p/Trm82p: evidence linking activity to a growth phenotype and implicating Trm82p in maintaining levels of active Trm8p. RNA 2005;11:821-830.
33. Oinuma I, Katoh H, Negishi M. Molecular dissection of the semaphorin 4D receptor plexin-B1-stimulated R-Ras GTPase-activating protein activity and neurite remodeling in hippocampal neurons. J Neurosci 2004;24:11473-11480.
34. Vikis HG, Li W, He Z, Guan KL. The semaphorin receptor plexin-B1 specifically interacts with active Rac in a ligand-dependent manner. Proc Natl Acad Sci USA 2000;97:12457-12462.
35. Hu H, Marton TF, Goodman CS. Plexin B mediates axon guidance in Drosophila by simultaneously inhibiting active Rac and enhancing RhoA signaling. Neuron 2001;32:39-51.
36. Zanata SM, Hovatta I, Rohm B, Puschel AW. Antagonistic effects of Rnd1 and RhoD GTPases regulate receptor activity in Semaphorin 3A-induced cytoskeletal collapse. J Neurosci 2002;22:471-477.
37. Dalpe G, Zhang LW, Zheng H, Culotti JG. Conversion of cell movement responses to Semaphorin-1 and Plexin-1 from attraction to repulsion by lowered levels of specific RAC GTPases in C. elegans. Development 2004;131:2073-2088.
38. Toyofuku T, Yoshida J, Sugimoto T, Zhang H, Kumanogoh A, Hori M, Kikutani H. FARP2 triggers signals for Sema3A-mediated axonal repulsion. Nat Neurosci 2005;8:1712-1719.
39. Chardin P. Function and regulation of Rnd proteins. Nat Rev Mol Cell Biol 2006;7:54-62.
40. Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE. The Protein Data Bank. Nucleic Acids Res 2000;28:235-242.
41. Charnock SJ, Bolam DN, Turkenburg JP, Gilbert HJ, Ferreira LM, Davies GJ, Fontes CM. The X6 "thermostabilizing" domains of xylanases are carbohydrate-binding modules: structure and biochemistry of the Clostridium thermocellum X6b domain. Biochemistry 2000;39:5013-5021.
42. Thacker E, Kearns B, Chapman C, Hammond J, Howell A, Theibert A. The arf6 GAP centaurin alpha-1 is a neuronal actin-binding protein which also functions via GAP-independent activity to regulate the actin cytoskeleton. Eur J Cell Biol 2004;83:541-554.
43. Venkateswarlu K, Hanada T, Chishti AH. Centaurin-alpha1 interacts directly with kinesin motor protein KIF13B. J Cell Sci 2005;118:2471-2484.
44. Mahajan A, Yuan C, Lee H, Chen ES, Wu PY, Tsai MD. Structure and function of the phosphothreonine-specific FHA domain. Sci Signal 2008;1:re12.
45. Horiguchi K, Hanada T, Fukui Y, Chishti AH. Transport of PIP3 by GAKIN, a kinesin-3 family protein, regulates neuronal cell polarity. J Cell Biol 2006;174:425-436.
46. Jiang C, Bao R, Chen Y. Expression, purification, crystallization and preliminary X-ray diffraction analysis of Sagittaria sagittifolia arrowhead protease inhibitor API-A in complex with bovine trypsin. Acta Crystallogr Sect F Struct Biol Cryst Commun 2008;64:1060-1062.
47. Xie ZW, Luo MJ, Xu WF, Chi CW. Two reactive site locations and structure-function study of the arrowhead proteinase inhibitors, A and B, using mutagenesis Biochemistry 1997;36:5846-5852.
48. 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.
49. Keeble AH, Kirkpatrick N, Shimizu S, Kleanthous C. Calorimetric dissection of colicin DNase-immunity protein complex specificity. Biochemistry 2006;45:3243-3254.
50. Kuhlmann UC, Pommer AJ, Moore GR, James R, Kleanthous C. Specificity in protein-protein interactions: the structural basis for dual recognition in endonuclease colicin-immunity protein complexes. J Mol Biol 2000;301:1163-1178.
51. Osborne MJ, Breeze AL, Lian LY, Reilly A, James R, Kleanthous C, Moore GR. Three-dimensional solution structure and 13C nuclear magnetic resonance assignments of the colicin E9 immunity protein Im9. Biochemistry 1996;35:9505-9512.
52. Suhre K, Sanejouand YH. ElNemo: a normal mode web server for protein movement analysis and the generation of templates for molecular replacement. Nucleic Acids Res 2004;32:W610-W614.
53. Krebs WG, Alexandrov V, Wilson CA, Echols N, Yu H, Gerstein M. Normal mode analysis of macromolecular motions in a database framework: developing mode concentration as a useful classifying statistic. Proteins 2002;48:682-695.
54. Delarue M, Sanejouand YH. Simplified normal mode analysis of conformational transitions in DNA-dependent polymerases: the elastic network model. J Mol Biol 2002;320:1011-1024.
55. Main ER, Xiong Y, Cocco MJ, D'Andrea L, Regan L. Design of stable alpha-helical arrays from an idealized TPR motif. Structure 2003;11:497-508.
56. Han D, Kim K, Kim Y, Kang Y, Lee JY. Crystal structure of the N-terminal domain of anaphase-promoting complex subunit 7. J Biol Chem 2009;284:15137-15146.