How to mark off paths on the protein energy landscape

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

Volumn 106, Issue 45, 2009, Pages 18879-18880

  Gruebele, Martin ^a  

^a UNIVERSITY OF ILLINOIS AT URBANA CHAMPAIGN   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BETA SHEET; MOLECULAR DYNAMICS; NOTE; PRIORITY JOURNAL; PROBABILITY; PROTEIN FOLDING; SIMULATION;

MODELS, CHEMICAL; PROTEIN CONFORMATION; PROTEIN FOLDING; PROTEINS;

EID: 73149122337     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.0910764106     Document Type: Note

References (21)

1. Ikai A, Tanford C (1971) Kinetic evidence for incorrectly folded intermediate states in the refolding of denatured proteins. Nature 230:100-102.
2. Jackson SE, Fersht AR (1991) Folding of chymotrypsin inhibitor-2. I. Evidence for a two-state transition. Biochemistry 30:10428-10435.
3. Yang WY, Gruebele M (2003) Folding at the speed limit. Nature 423:193-197.
4. Bryngelson JD, Onuchic JN, Socci ND, Wolynes PG (1995) Funnels, pathways, and the energy landscape of protein folding: A synthesis. Proteins Struct Funct Genet 21:167-195.
5. Noé F, Schütte C, Vanden-Eijnden E, Reich L, Weikl TR (2009) Constructing the equilibrium ensemble of folding pathways from short off-equilibrium simulations. Proc Natl Acad Sci USA 106:19011-19016.
6. Chodera JD, Singhal N, Pande VS, Dill KA, Swope WC (2007) Automatic discovery of metastable states for the construction of Markov models of macromolecular conformational dynamics. J Chem Phys 126:15501.
7. Singhal N, Snow CD, Pande VS (2004) Using path sampling to build better Markovian state models: Predicting the folding rate and mechanism of a tryptophan zipper beta hairpin. J Chem Phys 121:415-425.
8. Chodera JD, Dill KA, Swope WC, Pitera JW (2004) Constructing master equation models of protein folding and dynamics from atomistic simulation. Protein Sci 13(Suppl 1):101-102.
9. Berezhkovskii A, Hummer G, Szabo A (2009) Reactive flux and folding pathways in network models of coarse-grained protein dynamics. J Chem Phys 130:205102.
10. Noé F, Fischer S (2008) Transition networks for modeling the kinetics of conformational change in macromolecules. Curr Opin Struct Biol 18:154-162.
11. Jäger M, Nguyen H, Crane J, Kelly J, Gruebele M (2001) The folding mechanism of a β-sheet: The WW domain. J Mol Biol 311:373-393.
12. Liu F, et al. (2008) An experimental survey of the transition between two-state and downhill protein folding scenarios. Proc Natl Acad Sci USA 105:2369-2374.
13. Ensign DL, Pande VS (2009) The Fip35 WW domain folds with structural and mechanistic heterogeneity in molecular dynamics simulations. Biophys J 96:L53-L55.
14. Frauenfelder H, Sligar SG, Wolynes PG (1991) The energy landscapes and motions of proteins. Science 254:1598-1603.
15. Kubelka J, Chiu TK, Davies DR, Eaton WA, Hofrichter J (2006) Sub-microsecond protein folding. J Mol Biol 359:546-553.
16. Gruebele M (2005) Downhill protein folding: Evolution meets physics. Comptes Rendus Biol 328:701-712.
17. Alexander PA, He Y, Chen Y, Orban J (2007) The design and characterization of two proteins with 88% sequence identity but different structure and function. Proc Natl Acad Sci USA 104:11963-11968.
18. Kim SJ, Matsumura Y, Dumont C, Kihara H, Gruebele M (2009) Slowing down downhill folding: A three-probe study. Biophys J 97:295-302.
19. Shea J, Brooks CL (2001) From folding theories to folding proteins: A review and assessment of simulation studies of protein folding and unfolding. Annu Rev Phys Chem 52:499-535.
20. Klepeis JL, Lindorff-Larsen K, Dror RO, Shaw DE (2009) Long-time scale molecular dynamics simulations of protein structure and function. Curr Opin Struct Biol 19:120-127.
21. Moult J, et al. (2007) Critical assessment of methods of protein structure prediction: Round VII. Proteins Struct Funct Bioinform 69:3-9.