Actin filament remodeling by actin depolymerization factor/cofilin

Proceedings of the National Academy of Sciences of the United States of America

Volumn 107, Issue 16, 2010, Pages 7299-7304

  Pfaendtner, Jim ^a,d   De La Cruz, Enrique M ^b   Voth, Gregory A ^c,d  

^a University of Washington   (United States)

^b YALE UNIVERSITY   (United States)

^c UNIVERSITY OF CHICAGO   (United States)

^d UNIVERSITY OF UTAH   (United States)

Author keywords

Biopolymer; Coarse grained; Cytoskeleton; Mechanics; Molecular dynamics

Indexed keywords

ACTIN DEPOLYMERIZING FACTOR; BIOPOLYMER; COFILIN; DEOXYRIBONUCLEASE I; PROTEIN SUBUNIT;

ACTIN FILAMENT; ALLOSTERISM; ARTICLE; CONFORMATIONAL TRANSITION; HYDROPHOBICITY; MASS; MOLECULAR DYNAMICS; PRIORITY JOURNAL; PROTEIN BINDING; PROTEIN DOMAIN; PROTEIN INTERACTION; PROTEIN PROTEIN INTERACTION; PROTEIN STRUCTURE; RIGIDITY; THERMAL ANALYSIS;

ACTIN DEPOLYMERIZING FACTORS; ACTINS; ANIMALS; BIOCHEMISTRY; BIOPOLYMERS; CATTLE; COFILIN 1; COMPUTER SIMULATION; CYTOSKELETON; DEOXYRIBONUCLEASE I; HOT TEMPERATURE; MICROFILAMENTS; MODELS, MOLECULAR; MODELS, STATISTICAL; MOLECULAR CONFORMATION; PROTEIN BINDING; TEMPERATURE;

EID: 77952123773     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.0911675107     Document Type: Article

References (53)

1. Pollard TD, Blanchoin L, Mullins RD (2000) Molecular mechanisms controlling actin filament dynamics in nonmuscle cells. Annu Rev Biophys Biomol Struct 29:545-576. (Pubitemid 30599604)
2. Geeves MA, Holmes KC (1999) Structural mechanism of muscle contraction. Annu Rev Biochem 68:687-728.
3. Pollard TD (2007) Regulation of actin filament assembly by Arp2/3 complex and formins. Annu Rev Biophys Biomol Struct 36:451-477.
4. De La Cruz EM (2009) How cofilin severs an actin filament. Biophysical Reviews 1:51-59.
5. Hawkins M, Pope B, Maciver SK,Weeds AG (1993) Human actin depolymerizing factor mediates a pH-sensitive destruction of actin filaments. Biochemistry 32:9985-9993. (Pubitemid 23312424)
6. Hayden SM, Miller PS, Brauweiler A, Bamburg JR (1993) Analysis of the interactions of actin depolymerizing factor with G- and F-actin. Biochemistry 32:9994-10004. (Pubitemid 23312425)
7. McGough A, Pope B, Chiu W, Weeds A (1997) Cofilin changes the twist of F-actin: Implications for actin filament dynamics and cellular function. J Cell Biol 138:771-781. (Pubitemid 27365041)
8. De La Cruz EM (2005) Cofilin binding to muscle and non-muscle actin filaments: Isoform-dependent cooperative interactions. J Mol Biol 346:557-564.
9. Bobkov AA, et al. (2006) Cooperative effects of cofilin (ADF) on actin structure suggest allosteric mechanism of cofilin function. J Mol Biol 356:325-334.
10. Paavilainen V, 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. (Pubitemid 352008621)
11. McGough A, Chiu W (1999) ADF/cofilin weakens lateral contacts in the actin filament. J Mol Biol 291:513-519. (Pubitemid 29392629)
12. Galkin VE, Orlova A, Lukoyanova N, Wriggers W, Egelman EH (2001) Actin depolymerizing factor stabilizes an existing state of F-actin and can change the tilt of F-actin subunits. J Cell Biol 153:75-86. (Pubitemid 34280195)
13. Prochniewicz E, Janson N, Thomas D, De La Cruz EM (2005) Cofilin increases the torsional flexibility and dynamics of actin filaments. J Mol Biol 353:990-1000. (Pubitemid 41503267)
14. McCullough B, Blanchoin L, Martiel J, De La Cruz EM (2008) Cofilin increases the bending flexibility of actin filaments: Implications for severing and cell mechanics. J Mol Biol 381:550-558.
15. Galkin VE, et al. (2003) ADF/cofilin use an intrinsic mode of F-actin instability to disrupt actin filaments. J Cell Biol 163:1057-1066.
16. Grintsevich EE, et al. (2008) Mapping the cofilin binding site on yeast G-actin by chemical cross-linking. J Mol Biol 377:395-409.
17. Pfaendtner J, Lyman E, Pollard TD, Voth GA (2010) Structure and dynamics of the actin filament. J Mol Biol 396:252-263.
18. Pfaendtner J, Branduardi D, Parrinello M, Pollard TD, Voth GA (2009) Nucleotide-dependent conformational states of actin. Proc Natl Acad Sci USA 106:12723-12728.
19. Chu JW, Voth GA (2005) Allostery of actin filaments: Molecular dynamics simulations and coarse-grained analysis. Proc Natl Acad Sci USA 102:13111-13116. (Pubitemid 41324987)
20. Oztug Durer ZA, Diraviyam K, Sept D, Kudryashov DS, Reisler E (2010) F-actin structure destabilization and DNase I binding loop fluctuations: mutational cross-linking and electron microscopy analysis of loop states and effects on F-actin. J Mol Biol 395:544-557.
21. Wriggers W, Schulten K (1997) Stability and dynamics of G-actin: Back-door water diffusion and behavior of a subdomain 3/4 loop. Biophys J 73:624-639. (Pubitemid 27337600)
22. Zheng X, Diraviyam K, Sept D (2007) Nucleotide effects on the structure and dynamics of actin. Biophys J 93:1277-1283. (Pubitemid 47330907)
23. Dalhaimer P, Pollard TD, Nolen BJ (2008) Nucleotide-mediated conformational changes of monomeric actin and Arp3 studied by molecular dynamics simulations. J Mol Biol 376:166-183.
24. Wriggers W, Tang JX, Azuma T, Marks PW, Janmey PA (1998) Cofilin and gelsolin segment-1: Molecular dynamics simulation and biochemical analysis predict a similar actin binding mode. J Mol Biol 282:921-932. (Pubitemid 28468193)
25. Pfaendtner J, Voth GA (2008) Molecular dynamics simulation and coarse-grained analysis of the Arp2/3 complex. Biophys J 95:5324-5333.
26. Oda T, Iwasa M, Aihara T, Maeda Y, Narita A (2009) The nature of the globular- to fibrous-actin transition. Nature 457:441-445.
27. Orlova A, et al. (2004) Actin-destabilizing factors disrupt filaments by means of a time reversal of polymerization. Proc Natl Acad Sci USA 101:17664-17668. (Pubitemid 40051943)
28. Galkin VE, Orlova A, Cherepanova O, Lebart MC, Egelman EH (2008) High-resolution cryo-EM structure of the F-actin-fimbrin/plastin ABD2 complex. Proc Natl Acad Sci USA 105:1494-1498. (Pubitemid 351346542)
29. De La Cruz EM, Sept D (2010) The kinetics of cooperative cofilin binding reveals two states of the cofilin-actin filament. Biophys J, in press.
30. Orlova A, Egelman EH (1993) A conformational change in the actin subunit can change the flexibility of the actin filament. J Mol Biol 232:334-341. (Pubitemid 23251162)
31. Orlova A, Egelman EH (1992) Structural basis for the destabilization of F-actin by phosphate release following ATP hydrolysis. J Mol Biol 227:1043-1053.
32. Scoville D, et al. (2009) Effects of binding factors on structural elements in F-actin. Biochemistry 48:370-378.
33. Muhlrad A, Ringel I, Pavlov D, Peyser YM, Reisler E (2006) Antagonistic effects of cofilin, beryllium fluoride complex, and phalloidin on subdomain 2 and nucleotide-binding cleft in F-actin. Biophys J 91:4490-4499. (Pubitemid 44904233)
34. Bobkov AA, et al. (2002) Structural effects of cofilin on longitudinal contacts in F-actin. J Mol Biol 323:739-750. (Pubitemid 36160227)
35. Muhlrad A, et al. (2004) Cofilin induced conformational changes in F-actin expose subdomain 2 to proteolysis. J Mol Biol 342:1559-1567. (Pubitemid 39208678)
36. Fedorov AA, Lappalainen P, Fedorov EV, Drubin DG, Almo SC (1997) Structure determination of yeast cofilin. Nat Struct Mol Biol 4:366-369.
37. Chu JW, Voth GA (2006) Coarse-grained modeling of the actin filament derived from atomistic-scale simulations. Biophys J 90:1572-1582.
38. Milano G, Goudeau S, Mueller-Plathe F (2005) Multicentered Gaussian-based potentials for coarse-grained polymer simulations: Linking atomistic and mesoscopic scales. J Polym Sci Pol Phys 43:871-885. (Pubitemid 40567141)
39. Cao W, Goodarzi JP, De La Cruz EM (2006) Energetics and kinetics of cooperative cofilin-actin filament interactions. J Mol Biol 361:257-267. (Pubitemid 44092784)
40. Otterbein LR, Graceffa P, Dominguez R (2001) The crystal structure of uncomplexed actin in the ADP state. Science 293:708-711. (Pubitemid 32728675)
41. Schutt CE, Myslik JC, Rozycki MD, Goonesekere NC, Lindberg U (1993) The structure of crystalline profilin-beta-actin. Nature 365:810-816.
42. Strokopytov BV, et al. (2005) Phased translation function revisited: structure solution of the cofilin-homology domain from yeast actin-binding protein 1 using six-dimensional searches. Acta Crystallogr D 61:285-293.
43. Jorgensen WL, Chandrasekhar J, Madura JD, Impey RW, Klein ML (1983) Comparison of simple potential functions for simulating liquid water. J Chem Phys 79:926-935.
44. Humphrey W, Dalke A, Schulten K (1996) VMD: Visual molecular dynamics. J Mol Graphics 14:33-38.
45. Phillips JC, Braun R, Wang W, Gumbart J (2005) Scalable molecular dynamics with NAMD. J Comput Chem 26:1781-1802.
46. MacKerell AD, et al. (1998) All-atom empirical potential for molecular modeling and dynamics studies of proteins. J Phys Chem B 102:3586-3616. (Pubitemid 128576688)
47. Darden T, York D, Pedersen L (1993) Particle mesh Ewald: An N•log(N) method for ewald sums in large systems. J Chem Phys 98:10089-10092.
48. Ryckaert JP, Ciccotti G, Berendsen HJC (1977) Numerical integration of cartesian equations of motion of a system with constraints: molecular-dynamics of n-alkanes. J Comput Phys 23:327-341.
49. Feller SE, Zhang YH, Pastor RW, Brooks BR (1995) Constant-pressure molecular-dynamics simulation - The Langevin piston method. J Chem Phys 103:4613-4621.
50. Martyna GJ, Tobias DJ, Klein ML (1994) Constant-pressure molecular-dynamics algorithms. J Chem Phys 101:4177-4189.
51. Flyvbjerg H, Petersen HG (1989) Error-estimates on averages of correlated data. J Chem Phys 91:461-466.
52. Frenkel D, Smit B (2002) Understanding Molecular Simulation: From Algorithms to Applications (MPG Books, Bodman).
53. Isambert H, et al. (1995) Flexibility of actin filaments derived from thermal fluctuations. Effect of bound nucleotide, phalloidin, and muscle regulatory proteins. J Biol Chem 270:11437-11444.