Simulations of protein folding and unfolding

Current Opinion in Structural Biology

Volumn 8, Issue 2, 1998, Pages 222-226

  Brooks III, Charles L ^a  

^a SCRIPPS RESEARCH INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

KINETICS; MOLECULAR DYNAMICS; PRIORITY JOURNAL; PROTEIN CONFORMATION; PROTEIN FOLDING; REVIEW; STATISTICAL ANALYSIS; THERMODYNAMICS;

EID: 0032053619     PISSN: 0959440X     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0959-440X(98)80043-2     Document Type: Article

References (40)

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3. Brooks CL III. Molecular simulations of peptide and protein unfolding: in quest of a molten globule. Curr Opin Struct Biol. 3:1993;92-98.
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5. Onuchic JN, Luthey-Schulten Z, Wolynes PG. Theory of protein folding: the energy landscape perspective. of outstanding interest Ann Rev Phys Chem. 48:1997;545-600 The authors provide a relatively extensive overview of the landscape analysis approach to protein folding theory and simulations. Its emphasis is the work on the landscape perspective that has been developed by Wolynes and his collaborators over the past eight years. It also provides a review of open questions in this area and discusses connections to both experiment and molecular simulation studies.
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8. Dobson CM, Sali A, Karplus M. Protein folding: a perspective from theory and experiment. of outstanding interest Angew Chem. 1998; This review contrasts the 'chemical perspective' of folding with the new landscape viewpoint. It contains a good discussion of the theoretical developments from Karplus and his collaborators, as well as reviewing recent and exciting advances in experimental protein folding, particularly those by NMR spectroscopy.
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13. Boczko EM, Brooks CL III. First principles calculation of the folding free energy of a three-helix bundle protein. Science. 269:1995;393-396.
14. Lazaridis T, Karplus M. New view of protein folding reconciled with the old through multiple unfolding simulations. of outstanding interest Science. 278:1997;1928-1931 This short account provides an excellent discussion of the methods used to explore unfolding pathways using nonequilibrium unfolding experiments. The work presented indicates that one can extract information regarding unfolding (and possibly) folding pathways from statistical analyses of unfolding trajectories. Also of note in this study is the combined use of an implicit solvent model with molecular dynamics.
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18. Bond CJ, Wong K-B, Clarke J, Fersht AR, Daggett V. Characterization of residual structure in the thermally denatured state of barnase by simulation and experiment: description of the folding pathway. of outstanding interest Proc Natl Acad Sci USA. 94:1997;13409-13413 Simulated structures of denatured barnase were used together with rudimentary NMR data to bootstrap to a more complete picture of the folding of barnase. This combination of experiment and simulation provides an excellent example of the complementary (and possibly essential) role simulation will play in producing a detailed picture of the protein folding process in particular systems.
19. Li A, Daggett V. Molecular dynamics simulation of the unfolding of barnase: characterization of the major intermediate. of special interest J Mol Biol. 275:1998;677-694 The authors use molecular dynamics to unfold barnase and explore the correlation between the structures populated during unfolding and the NMR-characterized folding intermediate. Agreement with experiment is found for a number of hydrophobic clusters and an α helix.
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26. Kazmirski SL, Daggett V. Simulations of the structural and dynamical properties of denatured proteins: the 'molten coil' state of bovine pancreatic trypsin inhibitor. J Mol Biol. 1998;. in press.
27. Guo Z, Boczko EM, Brooks CL III. Exploring the folding free energy surface of a three-helix bundle protein. of special interest Proc Natl Acad Sci USA. 94:1997;10161-10166 This study extends the earlier work of Boczko and Brooks [13] by examining the free energy landscape for the folding of the protein as it projects onto coordinates that describe the native contacts, the native helical hydrogen bonds and the radius of gyration. Insights into the mechanism of folding are also discussed.
28. Sheinerman FB, Brooks CL III. Molecular picture of folding of a small α/β protein. of special interest Proc Natl Acad Sci USA. 95:1998;1562-1567 Sheinerman and Brooks describe the folding landscape and aspects of the folding mechanism for a mixed α/β topology protein. The calculations described in this work used explicit representation of solvent and molecular dynamics. Connections to experiments on this system, and further interpretations of experimental observations are discussed.
29. Sheinerman FB, Brooks CL III. Calculations on folding of segment B1 of streptococcal protein G. of outstanding interest J Mol Biol. 277:1998; This paper provides a lengthy discussion of the methodologies involved in computations of folding free energy landscapes. Details of techniques and protocols are given. Analysis of the folding of the protein G fragment is also presented. This is the most comprehensive paper on folding free energy calculation methodology, and is a good starting point for researchers interested in working in this area.
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36. Okamoto Y. Protein folding problem studied by new simulation algorithms. of special interest Dev Pure Appl Chem. 2:1998;1-23 Okamoto provides a short, concise review of a number of the sampling methods that are available for studies of protein folding when implicit solvent models are used. Such methods are also applicable to more 'minimalist' representations of proteins and folding studies on these models.
37. Mohanty D, Elber R, Thirumalai D, Beglov D, Roux B. Kinetics of peptide folding: computer simulations of SYPFDV and peptide variants in water. J Mol Biol. 272:1997;423-442.
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