Conformational changes associated with protein-protein interactions

Current Opinion in Structural Biology

Volumn 14, Issue 1, 2004, Pages 104-109

  Goh, Chern Sing ^a   Milburn, Duncan ^a   Gerstein, Mark ^a,b  

^a YALE UNIVERSITY   (United States)

^b Yale University   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ACTIN; CALMODULIN; CALMODULIN BINDING PROTEIN; CBL PROTEIN; CHAPERONIN; CHEA KINASE; CHEMOKINE RECEPTOR CCR4; COLICIN; CYCLIN A; CYCLIN DEPENDENT KINASE 2; EPIDERMAL GROWTH FACTOR RECEPTOR 2; ERYTHROPOIETIN; ERYTHROPOIETIN RECEPTOR; G PROTEIN COUPLED RECEPTOR KINASE 2; GLYCOPROTEIN GP 130; HLA A2 ANTIGEN; IMMUNOGLOBULIN F(AB) FRAGMENT; KARYOPHERIN BETA; LEUKEMIA INHIBITORY FACTOR; MYOSIN; PEROXISOME PROLIFERATOR ACTIVATED RECEPTOR GAMMA; POLYDEOXYRIBONUCLEOTIDE SYNTHASE; PROTEIN G; PROTEIN KINASE ZAP 70; PROTON TRANSPORTING ADENOSINE TRIPHOSPHATE SYNTHASE; RAN PROTEIN; STEROID RECEPTOR COACTIVATOR 1; THROMBIN; TUMOR NECROSIS FACTOR RECEPTOR ASSOCIATED FACTOR 6; UNINDEXED DRUG;

AMINO TERMINAL SEQUENCE; CRYSTAL STRUCTURE; ELECTRON MICROSCOPY; HYDROPHOBICITY; PRIORITY JOURNAL; PROTEIN BINDING; PROTEIN CONFORMATION; PROTEIN DOMAIN; PROTEIN MOTIF; PROTEIN PHOSPHORYLATION; PROTEIN PROTEIN INTERACTION; PROTEIN SECRETION; PROTEIN STRUCTURE; REVIEW;

EID: 1342302339     PISSN: 0959440X     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.sbi.2004.01.005     Document Type: Review

References (45)

1. Gerstein M., Krebs W. A database of macromolecular motions. Nucleic Acids Res. 26:1998;4280-4290.
2. Echols N., Milburn D., Gerstein M. MolMovDB: analysis and visualization of conformational change and structural flexibility. Nucleic Acids Res. 31:2003;478-482.
3. Krebs W.G., Gerstein M. The morph server: a standardized system for analyzing and visualizing macromolecular motions in a database framework. Nucleic Acids Res. 28:2000;1665-1675.
4. Koshland D. Application of a theory of enzyme specificity to protein synthesis. Proc. Natl. Acad. Sci. U.S.A. 44:1958;98-104.
5. Tsai C.J., Kumar S., Ma B., Nussinov R. Folding funnels, binding funnels, and protein function. Protein Sci. 8:1999;1181-1190.
6. Frauenfelder H., Sligar S.G., Wolynes P.G. The energy landscapes and motions of proteins. Science. 254:1991;1598-1603.
7. Bryngelson J.D., Onuchic J.N., Socci N.D., Wolynes P.G. Funnels, pathways, and the energy landscape of protein folding: a synthesis. Proteins. 21:1995;167-195.
8. Karplus M. The Levinthal paradox: yesterday and today. Fold Des. 2:1997;S69-S75.
9. Dill K.A., Chan H.S. From Levinthal to pathways to funnels. Nat. Struct. Biol. 4:1997;10-19.
10. Monod J., Wyman J., Changeux J. On the allosteric transitions: a plausible model. J. Mol. Biol. 12:1965;88-118.
11. Koshland D.E. Jr., Hamadani K. Proteomics and models for enzyme cooperativity. J. Biol. Chem. 277:2002;46841-46844.
12. Koshland D.E. Jr., Nemethy G., Filmer D. Comparison of experimental binding data and theoretical models in proteins containing subunits. Biochemistry. 5:1966;365-385.
13. Freire E. The propagation of binding interactions to remote sites in proteins: analysis of the binding of the monoclonal antibody D1.3 to lysozyme. Proc. Natl. Acad. Sci. U.S.A. 96:1999;10118-10122.
14. Holmes K.C., Angert I., Kull F.J., Jahn W., Schroder R.R. Electron cryo-microscopy shows how strong binding of myosin to actin releases nucleotide. Nature. 425:2003;423-427 Cryo-EM of the myosin-actin complex reveals a conformational change upon binding. These studies suggest that the closing of the actin-binding cleft is structurally linked to the opening of the nucleotide-binding pocket.
15. Rayment I., Holden H.M., Whittaker M., Yohn B.C., Lorenz M., Holmes K.C., Milligan R.A. Structure of the actin-myosin complex and its implications for muscle contraction. Science. 261:1993;58-65.
16. Yengo C.M., De La Cruz E.M., Chrin L.R., Gaffney D.P. II, Berger C.L. Actin-induced closure of the actin-binding cleft of smooth muscle myosin. J. Biol. Chem. 277:2002;24114-24119.
17. Conibear P.B., Bagshaw C.R., Fajer P.G., Kovacs M., Malnasi-Csizmadia A. Myosin cleft movement and its coupling to actomyosin dissociation. Nat. Struct. Biol. 10:2003;831-835.
18. Evdokimov A.G., Phan J., Tropea J.E., Routzahn K.M., Peters H.K., Pokross M., Waugh D.S. Similar modes of polypeptide recognition by export chaperones in flagellar biosynthesis and type III secretion. Nat. Struct. Biol. 10:2003;789-793 The first crystallographic structure of a flagellar export chaperone, Aquifex aeolicus FliS, and its complex with FliC (flagellin).
19. Aldridge P., Hughes K.T. Regulation of flagellar assembly. Curr. Opin. Microbiol. 5:2002;160-165.
20. Fraser G.M., Bennett J.C., Hughes C. Substrate-specific binding of hook-associated proteins by FlgN and FliT, putative chaperones for flagellum assembly. Mol. Microbiol. 32:1999;569-580.
21. Auvray F., Thomas J., Fraser G.M., Hughes C. Flagellin polymerisation control by a cytosolic export chaperone. J. Mol. Biol. 308:2001;221-229.
22. Bennett J.C., Hughes C. From flagellum assembly to virulence: the extended family of type III export chaperones. Trends Microbiol. 8:2000;202-204.
23. Page A.L., Parsot C. Chaperones of the type III secretion pathway: jacks of all trades. Mol. Microbiol. 46:2002;1-11.
24. i1·GDP). The structure reveals the conformational changes that preclude concurrent Gβγ binding to the complex.
25. Siderovski D.P., Diverse-Pierluissi M., De Vries L. The GoLoco motif: a Galphai/o binding motif and potential guanine-nucleotide exchange factor. Trends Biochem. Sci. 24:1999;340-341.
26. Takesono A., Cismowski M.J., Ribas C., Bernard M., Chung P., Hazard S. III, Duzic E., Lanier S.M. Receptor-independent activators of heterotrimeric G-protein signaling pathways. J. Biol. Chem. 274:1999;33202-33205.
27. De Vries L., Fischer T., Tronchere H., Brothers G.M., Strockbine B., Siderovski D.P., Farquhar M.G. Activator of G protein signaling 3 is a guanine dissociation inhibitor for Galpha i subunits. Proc. Natl. Acad. Sci. U.S.A. 97:2000;14364-14369.
28. Natochin M., Lester B., Peterson Y.K., Bernard M.L., Lanier S.M., Artemyev N.O. AGS3 inhibits GDP dissociation from galpha subunits of the Gi family and rhodopsin-dependent activation of transducin. J. Biol. Chem. 275:2000;40981-40985.
29. Natochin M., Gasimov K.G., Artemyev N.O. Inhibition of GDP/GTP exchange on G alpha subunits by proteins containing G-protein regulatory motifs. Biochemistry. 40:2001;5322-5328.
30. Schaefer M., Petronczki M., Dorner D., Forte M., Knoblich J.A. Heterotrimeric G proteins direct two modes of asymmetric cell division in the Drosophila nervous system. Cell. 107:2001;183-194.
31. Eaton W.A., Henry E.R., Hofrichter J., Mozzarelli A. Is cooperative oxygen binding by hemoglobin really understood? Nat. Struct. Biol. 6:1999;351-358.
32. James L.C., Roversi P., Tawfik D.S. Antibody multispecificity mediated by conformational diversity. Science. 299:2003;1362-1367 This study reports the crystal structures of two different conformations of the unbound antibody Spe7. The two conformations are found to bind structurally distinct ligands using very different binding sites. The conformation that binds the antigen is flat with a shallow groove, whereas the conformation that binds to haptens is a deep hole.
33. Oldstone M.B. Molecular mimicry and autoimmune disease. Cell. 50:1987;819-820.
34. ••].
35. ••].
36. Marchese P., Murata M., Mazzucato M., Pradella P., De Marco L., Ware J., Ruggeri Z.M. Identification of three tyrosine residues of glycoprotein Ib alpha with distinct roles in von Willebrand factor and alpha-thrombin binding. J. Biol. Chem. 270:1995;9571-9578.
37. Volkman B.F., Lipson D., Wemmer D.E., Kern D. Two-state allosteric behavior in a single-domain signaling protein. Science. 291:2001;2429-2433.
38. Malmendal A., Evenas J., Forsen S., Akke M. Structural dynamics in the C-terminal domain of calmodulin at low calcium levels. J. Mol. Biol. 293:1999;883-899.
39. Martinez K.L., Gohon Y., Corringer P.J., Tribet C., Merola F., Changeux J.P., Popot J.L. Allosteric transitions of Torpedo acetylcholine receptor in lipids, detergent and amphipols: molecular interactions vs. physical constraints. FEBS Lett. 528:2002;251-256 Kinetic experiments reveal two conformational states for the unbound Torpedo acetylcholine receptor.
40. Nevo R., Stroh C., Kienberger F., Kaftan D., Brumfeld V., Elbaum M., Reich Z., Hinterdorfer P. A molecular switch between alternative conformational states in the complex of Ran and importin beta1. Nat. Struct. Biol. 10:2003;553-557 Dynamic force spectroscopy analysis of the Ran-importin β1 complex reveals two distinct bound states.
41. Barak R., Eisenbach M. Correlation between phosphorylation of the chemotaxis protein CheY and its activity at the flagellar motor. Biochemistry. 31:1992;1821-1826.
42. Wyman C., Rombel I., North A.K., Bustamante C., Kustu S. Unusual oligomerization required for activity of NtrC, a bacterial enhancer-binding protein. Science. 275:1997;1658-1661.
43. James L.C., Tawfik D.S. Conformational diversity and protein evolution-a 60-year-old hypothesis revisited. Trends Biochem. Sci. 28:2003;361-368 This interesting discussion focuses on the hypothesis that a given protein sequence can adopt multiple structures and functions.
44. The PyMOL Molecular Graphics System on World Wide Web URL: http://www.pymol.org.
45. Sadler J.E. Structural biology. A menage a trois in two configurations. Science. 301:2003;177-179.