Protein dynamics investigated by inherent structure analysis

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

Volumn 107, Issue 20, 2010, Pages 9152-9157

  Rao, Francesco ^a   Karplus, Martin ^a,b  

^a UNIVERSITÉ DE STRASBOURG   (France)

^b HARVARD UNIVERSITY   (United States)

Author keywords

Complex networks; Conformational dynamics; Energy landscapes; Molecular dynamics simulations

Indexed keywords

ARTICLE; CONTROLLED STUDY; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN CONFORMATION; PROTEIN DOMAIN; PROTEIN STRUCTURE; ROOM TEMPERATURE; SIMULATION; STRUCTURE ANALYSIS; SURFACE PROPERTY; THERMODYNAMICS;

KINETICS; MOLECULAR DYNAMICS SIMULATION; PROTEIN CONFORMATION; PROTEINS; THERMODYNAMICS;

EID: 77952738461     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.0915087107     Document Type: Article

References (52)

1. Schuler B, Eaton WA (2008) Protein folding studied by single-molecule FRET. Curr Opin Struct Biol 18:16-26.
2. Colletier JP, et al. (2008) Shoot-and-Trap: Use of specific x-ray damage to study structural protein dynamics by temperature-controlled cryo-crystallography. Proc Natl Acad Sci USA 105:11742-11747.
3. Boehr DD, McElheny D, Dyson HJ, Wright PE (2006) The dynamic energy landscape of dihydrofolate reductase catalysis. Science 313:1638-1642. (Pubitemid 44414038)
4. Goldstein M (1969) Viscous liquids and glass transition: A potential energy barrier picture. J Chem Phys 51:3728-3739.
5. Frauenfelder H, Sligar S, Wolynes P (1991) The energy landscapes and motions of proteins. Science 254:1598-1603.
6. Elber R, Karplus M (1987) Multiple conformational states of proteins: A molecular dynamics analysis of myoglobin. Science 235:318-321. (Pubitemid 17232557)
7. Zagrovic B, Snow CD, Shirts MR, Pande VS (2002) Simulation of folding of a small alpha-helical protein in atomistic detail using worldwide-distributed computing. J Mol Biol 323:927-937. (Pubitemid 35341065)
8. Karplus M, Kuriyan J (2005) Molecular dynamics and protein function. Proc Natl Acad Sci USA 102:6679-6685.
9. Dror RO, et al. (2009) Identification of two distinct inactive conformations of the beta2-adrenergic receptor reconciles structural and biochemical observations. Proc Natl Acad Sci USA 106:4689-4694.
10. Klepeis J, Lindorff-Larsen K, Dror R, Shaw D (2009) Long-timescale molecular dynamics simulations of protein structure and function. Cur Opin Struc Biol 19:120-127.
11. Rao F, Caflisch A (2004) The protein folding network. J Mol Biol 342:299-306.
12. Krivov S, Karplus M (2004) Hidden complexity of free energy surfaces for peptide (protein) folding. Proc Natl Acad Sci USA 101:14766-14770. (Pubitemid 39410749)
13. Caflisch A (2006) Network and graph analyses of folding free energy surfaces. Curr Opin Struct Biol 16:71-78.
14. Gfeller D, De Los Rios P, Caflisch A, Rao F (2007) Complex network analysis of free-energy landscapes. Proc Natl Acad Sci USA 104:1817-1822. (Pubitemid 46239862)
15. Settanni G, Fersht AR (2008) High temperature unfolding simulations of the TRPZ1 peptide. Biophys J 94:4444-4453.
16. Yang S, Roux B (2008) Src kinase conformational activation: Thermodynamics, pathways, and mechanisms. PLOS Comput Biol 4(3):e1000047. (Pubitemid 351497520)
17. Prada-Gracia D, Gomez-Gardenes J, Echenique P, Falo F (2009) Exploring the free energy landscape: From dynamics to networks and back. PLOS Comput Biol 5:e1000415.
18. Li CB, Yang H, Komatsuzaki T (2008) Multiscale complex network of protein conformational fluctuations in single-molecule time series. Proc Natl Acad Sci USA 105:536-541. (Pubitemid 351171743)
19. Ihalainen JA, et al. (2007) Folding and unfolding of a photoswitchable peptide from picoseconds to microseconds. Proc Natl Acad Sci USA 104:5383-5388.
20. Ihalainen JA, et al. (2008) Alpha-helix folding in the presence of structural constraints. Proc Natl Acad Sci USA 105:9588-9593.
21. Bowman GR, Beauchamp KA, Boxer G, Pande VS (2009) Progress and challenges in the automated construction of Markov state models for full protein systems. J Chem Phys 131:124101.
22. Noé F, et al. (2009) Constructing the equilibrium ensemble of folding pathways from short off-equilibrium simulations. Proc Nat Acad Sci USA 106:19011-19016.
23. Stillinger FH, Weber TA (1982) Hidden structure in liquids. Phys Rev A 25:978-989.
24. Stillinger F, Weber T (1983) Dynamics of structural transitions in liquids. Phys Rev A 28:2408-2416.
25. Denny R, Reichman D, Bouchaud J (2003) Trap models and slow dynamics in super-cooled liquids. Phys Rev Lett 90(2):025503.
26. Berthier L, Garrahan J (2003) Nontopographic description of inherent structure dynamics in glassformers. J Chem Phys 119(8):4367-4371.
27. Caves LS, Evanseck JD, Karplus M (1998) Locally accessible conformations of proteins: Multiple molecular dynamics simulations of crambin. Protein Sci 7:649-666
28. Baumketner A, Shea JE, Hiwatari Y (2003) Glass transition in an off-lattice protein model studied by molecular dynamics simulations. Phys Rev E 67:011912.
29. Nakagawa N, PeyrardM(2006) the inherent structure landscape of a protein. Proc Nat Acad Sci USA 103(14):5279-5284.
30. Kim J, Keyes T (2007) Inherent structure analysis of protein folding. J Phys Chem B 111:2647-2657. (Pubitemid 46548749)
31. Kim J, Keyes T, Straub J (2009) Relationship between protein folding thermodynamics and the energy landscape. Phys Rev E 79(3):030902.
32. Krivov SV, Chekmarev SF, Karplus M (2002) Potential energy surfaces and conformational transitions in biomolecules: A successive confinement approach applied to a solvated tetrapeptide. Phys Rev Lett 88:038101.
33. Rao F, Caflisch A (2003) Replica exchange molecular dynamics simulations of reversible folding. J Chem Phys 119:4035-4042.
34. Krivov SV, KarplusM(2006) One-dimensional free-energy profiles of complex systems: Progress variables that preserve the barriers. J Phys Chem B 110:12689-12698.
35. Debenedetti PG, Stillinger FH (2001) Supercooled liquids and the glass transition. Nature 410:259-267.
36. Gfeller D, de Lachapelle DM, De Los Rios P, Caldarelli G, Rao F (2007) Uncovering the topology of configuration space networks. Phys Rev E 76:026113. (Pubitemid 47358013)
37. Ferrara P, Caflisch A (2000) Folding simulations of a three-stranded antiparallel betasheet peptide. Proc Natl Acad Sci USA 97:10780-10785.
38. Krivov SV, Muff S, Caflisch A, Karplus M (2008) One-dimensional barrier-preserving free-energy projections of a beta-sheet miniprotein: New insights into the folding process. J Phys Chem B 112:8701-8714.
39. Muff S, Caflisch A (2009) Identification of the protein folding transition state from molecular dynamics trajectories. J Chem Phys 130:125104-125111.
40. Chekmarev SF, Krivov SV, Karplus M (2005) Folding time distributions as an approach to protein folding kinetics. J Phys Chem B 109:5312-5330. (Pubitemid 40407753)
41. Rao F, Settanni G, Guarnera E, Caflisch A (2005) Estimation of protein folding probability from equilibrium simulations. J Chem Phys 122:184901-184905.
42. Kong Y, Karplus M (2008) Signaling pathways of PDZ2 domain: A molecular dynamics interaction correlation analysis. Proteins: Struct Funct Bioinformatics 74:145-154
43. Hamm P, Lim M, Hochstrasser RM (1998) Structure of the amide I band of peptides measured by femtosecond nonlinear-infrared spectroscopy. J Phys Chem B 102:6123-6138. (Pubitemid 128581186)
44. Kolano C, et al. (2006) Watching hydrogen-bond dynamics in a beta-turn by transient two-dimensional infrared spectroscopy. Nature 444:469-472. (Pubitemid 44809061)
45. Bagchi S, Falvo C, Mukamel S, Hochstrasser RM (2009) 2D-IR experiments and simulations of the coupling between amide-I and ionizable side chains in proteins: Application to the Villin headpiece. J Phys Chem B 113:11260-11273.
46. Brooks BR, et al. (1983) Charmm: A program for macromolecular energy, minimization, and dynamics calculations. J Comput Chem 4:187-217.
47. Brooks BR, et al. (2009) CHARMM: The biomolecular simulation program. J Comput Chem 30:1545-1614.
48. Ferrara P, Apostolakis J, Caflisch A (2002) Evaluation of a fast implicit solvent model for molecular dynamics simulations. Proteins: Struct Funct Genet 46:24-33. (Pubitemid 34033573)
49. Hartigan J (1975) Clustering Algorithms (Wiley, New York).
50. Seeber M, Cecchini M, Rao F, Settanni G, Caflisch A (2007) Wordom: A program for efficient analysis of molecular dynamics simulations. Bioinformatics 23:2625-2627. (Pubitemid 350048368)
51. Allen LR, Krivov SV, Paci E (2009) Analysis of the free-energy surface of proteins from reversible folding simulations. PLOS Comput Biol 5:e1000428.
52. Guarnera E, Pellarin R, Caflisch A (2009) How does a simplified-sequence protein fold?. Biophys J 97(6):1737-1746.