Prediction and Dissection of Widely-Varying Association Rate Constants of Actin-Binding Proteins

PLoS Computational Biology

Volumn 8, Issue 10, 2012, Pages

  Pang, Xiaodong ^a   Zhou, Kenneth H ^b   Qin, Sanbo ^a   Zhou, Huan Xiang ^a  

^a Florida State University   (United States)

^b Lawton Chiles High School   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ASSOCIATION REACTIONS; COMPUTATION THEORY; ELECTROSTATICS; POLYMERIZATION; PROTEINS;

ACTIN POLYMERIZATION; ACTIN-BINDING PROTEINS; ASSOCIATION RATE CONSTANTS; COMPLEX THEORY; EUKARYOTIC CYTOSKELETON; PROTEIN ASSOCIATIONS; REGULATORY FUNCTIONS; RELATIVE ORIENTATION; THREE ORDERS OF MAGNITUDE; TRANSIENT COMPLEXES;

RATE CONSTANTS;

EID: 84868120066     PISSN: 1553734X     EISSN: 15537358     Source Type: Journal    
DOI: 10.1371/journal.pcbi.1002696     Document Type: Article

References (44)

1. Drenckhahn D, Pollard TD, (1986) Elongation of actin filaments is a diffusion-limited reaction at the barbed end and is accelerated by inert macromolecules. J Biol Chem 261: 12754-12758.
2. Sept D, Elcock AH, McCammon JA, (1999) Computer simulations of actin polymerization can explain the barbed-pointed end asymmetry. J Mol Biol 294: 1181-1189.
3. Bryan J, (1988) Gelsolin has three actin-binding sites. J Cell Biol 106: 1553-1562.
4. Mc Leod JF, Kowalski MA, Haddad JG Jr, (1989) Interactions among serum vitamin D binding protein, monomeric actin, profilin, and profilactin. J Biol Chem 264: 1260-1267.
5. Kinosian HJ, Selden LA, Gershman LC, Estes JE, (2000) Interdependence of profilin, cation, and nucleotide binding to vertebrate non-muscle actin. Biochemistry 39: 13176-13188.
6. Marchand JB, Kaiser DA, Pollard TD, Higgs HN, (2001) Interaction of WASP/Scar proteins with actin and vertebrate Arp2/3 complex. Nat Cell Biol 3: 76-82.
7. Ojala PJ, Paavilainen VO, Vartiainen MK, Tuma R, Weeds AG, et al. (2002) The two ADF-H domains of twinfilin play functionally distinct roles in interactions with actin monomers. Mol Biol Cell 13: 3811-3821.
8. Hertzog M, van Heijenoort C, Didry D, Gaudier M, Coutant J, et al. (2004) The β-thymosin/WH2 domain: structural basis for the switch from inhibition to promotion of actin assembly. Cell 117: 611-623.
9. Au JK, Olivares AO, Henn A, Cao W, Safer D, et al. (2008) Widely distributed residues in thymosin beta4 are critical for actin binding. Biochemistry 47: 4181-4188.
10. Qin S, Pang X, Zhou HX, (2011) Automated prediction of protein association rate constants. Structure 19: 1744-1751.
11. Machesky LM, Insall RH, (1998) Scar1 and the related Wiskott Aldrich syndrome protein, WASP, regulate the actin cytoskeleton through the Arp2/3 complex. Curr Biol 8: 1347-1356.
12. Robinson RC, Turbedsky K, Kaiser DA, Marchand JB, Higgs HN, et al. (2001) Crystal structure of Arp2/3 complex. Science 294: 1679-1684.
13. Vinson VK, De La Cruz EM, Higgs HN, Pollard TD, (1998) Interactions of Acanthamoeba profilin with actin and nucleotides bound to actin. Biochemistry 37: 10871-10880.
14. Carlier MF, Jean C, Rieger KJ, Lenfant M, Pantaloni D, (1993) Modulation of the interaction between G-actin and thymosin β4 by the ATP/ADP ratio: possible implication in the regulation of actin dynamics. Proc Natl Acad Sci U S A 90: 5034-5038.
15. Pollard TD, Blanchoin L, Mullins RD, (2000) Molecular mechanisms controlling actin filament dynamics in nonmuscle cells. Annu Rev Biophys Biomol Struct 29: 545-576.
16. McLaughlin PJ, Gooch JT, Mannherz HG, Weeds AG, (1993) Structure of gelsolin segment 1-actin complex and the mechanism of filament severing. Nature 364: 685-692.
17. Schutt CE, Myslik JC, Rozycki MD, Goonesekere NC, Lindberg U, (1993) The structure of crystalline profilin-beta-actin. Nature 365: 810-816.
18. Otterbein LR, Cosio C, Graceffa P, Dominguez R, (2002) Crystal structures of the vitamin D-binding protein and its complex with actin: structural basis of the actin-scavenger system. Proc Natl Acad Sci U S A 99: 8003-8008.
19. Irobi E, Aguda AH, Larsson M, Guerin C, Yin HL, et al. (2004) Structural basis of actin sequestration by thymosin-β4: implications for WH2 proteins. EMBO J 23: 3599-3608.
20. Chereau D, Kerff F, Graceffa P, Grabarek Z, Langsetmo K, et al. (2005) Actin-bound structures of Wiskott-Aldrich syndrome protein (WASP)-homology domain 2 and the implications for filament assembly. Proc Natl Acad Sci U S A 102: 16644-16649.
21. Paavilainen VO, Oksanen E, Goldman A, Lappalainen P, (2008) Structure of the actin-depolymerizing factor homology domain in complex with actin. J Cell Biol 182: 51-59.
22. Panchal SC, Kaiser DA, Torres E, Pollard TD, Rosen MK, (2003) A conserved amphipathic helix in WASP/Scar proteins is essential for activation of Arp2/3 complex. Nat Struct Biol 10: 591-598.
23. Kelly AE, Kranitz H, Dotsch V, Mullins RD, (2006) Actin binding to the central domain of WASP/Scar proteins plays a critical role in the activation of the Arp2/3 complex. J Biol Chem 281: 10589-10597.
24. Domanski M, Hertzog M, Coutant J, Gutsche-Perelroizen I, Bontems F, et al. (2004) Coupling of folding and binding of thymosin beta4 upon interaction with monomeric actin monitored by nuclear magnetic resonance. J Biol Chem 279: 23637-23645.
25. Alsallaq R, Zhou HX, (2008) Electrostatic rate enhancement and transient complex of protein-protein association. Proteins 71: 320-335.
26. Gabdoulline RR, Wade RC, (2001) Protein-protein association: investigation of factors influencing association rates by Brownian dynamics simulations. J Mol Biol 306: 1139-1155.
27. Schreiber G, Haran G, Zhou H-X, (2009) Fundamental aspects of protein-protein association kinetics. Chem Rev 109: 839-860.
28. Pang X, Qin S, Zhou HX, (2011) Rationalizing 5,000-fold differences in receptor-binding rate constants of four cytokines. Biophys J 101: 1175-1183.
29. Zhou HX, (1990) Kinetics of diffusion-influenced reactions studied by Brownian dynamics. J Phys Chem 94: 8794-8800.
30. Perelroizen I, Marchand JB, Blanchoin L, Didry D, Carlier MF, (1994) Interaction of profilin with G-actin and poly(L-proline). Biochemistry 33: 8472-8478.
31. Burtnick LD, Koepf EK, Grimes J, Jones EY, Stuart DI, et al. (1997) The crystal structure of plasma gelsolin: implications for actin severing, capping, and nucleation. Cell 90: 661-670.
32. Kim AS, Kakalis LT, Abdul-Manan N, Liu GA, Rosen MK, (2000) Autoinhibition and activation mechanisms of the Wiskott-Aldrich syndrome protein. Nature 404: 151-158.
33. Zhou HX, (2001) The affinity-enhancing roles of flexible linkers in two-domain DNA-binding proteins. Biochemistry 40: 15069-15073.
34. Zhou HX, Pang X, Cai L, (2012) Rate constants and mechanisms of intrinsically disordered proteins binding to structured targets. Phys Chem Chem Phys 14: 10466-76.
35. Didry D, Cantrelle FX, Husson C, Roblin P, Moorthy AM, et al. (2012) How a single residue in individual β-thymosin/WH2 domains controls their functions in actin assembly. EMBO J 31: 1000-1013.
36. Suhre K, Sanejouand YH, (2004) ElNemo: a normal mode web server for protein movement analysis and the generation of templates for molecular replacement. Nucleic Acids Res 32: W610-W614.
37. Lal AA, Brenner SL, Korn ED, (1984) Preparation and polymerization of skeletal muscle ADP-actin. J Biol Chem 259: 13061-13065.
38. Lee FS, Auld DS, Vallee BL, (1989) Tryptophan fluorescence as a probe of placental ribonuclease inhibitor binding to angiogenin. Biochemistry 28: 219-224.
39. Shoup D, Lipari G, Szabo A, (1981) Diffusion-controlled bimolecular reaction rates. The effect of rotational diffusion and orientation constraints. Biophys J 36: 697-714.
40. Northrup SH, Erickson HP, (1992) Kinetics of protein-protein association explained by Brownian dynamics computer simulation. Proc Natl Acad Sci U S A 89: 3338-3342.
41. Zhou HX, (2010) Rate theories for biologists. Q Rev Biophys 43: 219-293.
42. Qin S, Zhou HX, (2009) Dissection of the high rate constant for the binding of a ribotoxin to the ribosome. Proc Natl Acad Sci U S A 106: 6974-6979.
43. Mouilleron S, Guettler S, Langer CA, Treisman R, McDonald NQ, (2008) Molecular basis for G-actin binding to RPEL motifs from the serum response factor coactivator MAL. EMBO J 27: 3198-3208.
44. Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA, (2001) Electrostatics of nanosystems: Application to microtubules and the ribosome. Proc Natl Acad Sci U S A 98: 10037-10041.