journal article Nov 06, 2003

Ab Initio Folding of Helix Bundle Proteins Using Molecular Dynamics Simulations

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References
60
[1]
Nolting B. (1999) 10.1007/978-3-662-03966-3
[2]
Fersht A, R (1999)
[3]
Berne B. J. Curr. Opin. Struct. Biol. (1997) 10.1016/s0959-440x(97)80023-1
[4]
FROMFOLDINGTHEORIES TOFOLDINGPROTEINS: A Review and Assessment of Simulation Studies of Protein Folding and Unfolding

Joan-Emma Shea, Charles L Brooks III

Annual Review of Physical Chemistry 2001 10.1146/annurev.physchem.52.1.499
[5]
Protein Structure Prediction and Structural Genomics

David Baker, Andrej Šali

Science 2001 10.1126/science.1065659
[6]
Onuchic J. N. Adv. Protein Chem. (2000)
[7]
Screen Savers of the World Unite!

Michael Shirts, Vijay S. Pande

Science 2001 10.1126/science.290.5498.1903
[8]
Navigating the Folding Routes

Peter G. Wolynes, José N. Onuchic, D. Thirumalai

Science 1995 10.1126/science.7886447
[9]
Theoretical studies of protein folding and unfolding

Martin Karplus, Andrej Šali

Current Opinion in Structural Biology 1995 10.1016/0959-440x(95)80010-x
[10]
Study of the stability and unfolding mechanism of BBA1 by molecular dynamics simulations at different temperatures

Lu Wang, Yong Duan, Rebecca Shortle et al.

Protein Science 1999 10.1110/ps.8.6.1292
[11]
Finkelstein A. V. Protein Eng. (1997) 10.1093/protein/10.8.843
[12]
Weak temperature dependence of the free energy surface and folding pathways of structured peptides

Andrea Cavalli, Philippe Ferrara, Amedeo Caflisch

Proteins: Structure, Function, and Bioinformatics 2002 10.1002/prot.10041
[13]
All-Atom Structure Prediction and Folding Simulations of a Stable Protein

Carlos Simmerling, Bentley Strockbine, Adrian E. Roitberg

Journal of the American Chemical Society 2002 10.1021/ja0273851
[14]
Constanciel R. Theor. Chim. Acta (1984) 10.1007/bf02427575
[15]
The GB/SA Continuum Model for Solvation. A Fast Analytical Method for the Calculation of Approximate Born Radii

Di Qiu, Peter S. Shenkin, Frank P. Hollinger et al.

The Journal of Physical Chemistry A 1997 10.1021/jp961992r
[16]
Still W. C. J. Am. Chem. Soc. (1990) 10.1021/ja00172a038
[17]
Pairwise solute descreening of solute charges from a dielectric medium

Gregory D. Hawkins, Christopher J. Cramer, Donald G. Truhlar

Chemical Physics Letters 1995 10.1016/0009-2614(95)01082-k
[18]
Edinger S. R. J. Phys. Chem. B (1997) 10.1021/jp962156k
[19]
Dominy B. H. J. Phys. Chem. B (1999) 10.1021/jp984440c
[20]
Application of a pairwise generalized Born model to proteins and nucleic acids: inclusion of salt effects

Jayashree Srinivasan, Megan W. Trevathan, Paul Beroza et al.

Theoretical Chemistry Accounts 1999 10.1007/s002140050460
[21]
Bursulaya B. D. J. Am. Chem. Soc. (1999) 10.1021/ja991764l
[22]
Molecular Dynamics Study of Peptides in Implicit Water:  Ab Initio Folding of β-Hairpin, β-Sheet, and ββα-motif

Soonmin Jang, Seokmin Shin, Youngshang Pak

Journal of the American Chemical Society 2002 10.1021/ja025675b
[23]
Brescher A. Proc. Natl. Acad. Sci. U.S.A. (1979) 10.1073/pnas.76.5.2321
[24]
Bottomley S. P. Protein Eng. (1994) 10.1093/protein/7.12.1463
[25]
A Thermostable 35-Residue Subdomain within Villin Headpiece

James C. McKnight, Don S. Doering, Paul T. Matsudaira et al.

Journal of Molecular Biology 1996 10.1006/jmbi.1996.0387
[26]
NMR structure of the 35-residue villin headpiece subdomain

C. James McKnight, Paul T. Matsudaira, Peter S. Kim

Nature Structural Biology 1997 10.1038/nsb0397-180
[27]
Bai Y. Protein Sci. (1997) 10.1002/pro.5560060709
[28]

Jeffrey K. Myers, Terrence G. Oas

Nature Structural Biology 2001 10.1038/88626
[29]
Dynamic NMR Line-Shape Analysis Demonstrates that the Villin Headpiece Subdomain Folds on the Microsecond Time Scale

Minghui Wang, Yuefeng Tang, Satoshi Sato et al.

Journal of the American Chemical Society 2003 10.1021/ja028752b
[30]
Pathways to a Protein Folding Intermediate Observed in a 1-Microsecond Simulation in Aqueous Solution

Yong Duan, Peter A. Kollman

Science 1998 10.1126/science.282.5389.740
[31]
The early stage of folding of villin headpiece subdomain observed in a 200-nanosecond fully solvated molecular dynamics simulation

Yong Duan, Lu Wang, Peter A. Kollman

Proceedings of the National Academy of Sciences 1998 10.1073/pnas.95.17.9897
[32]
All‐atom fast protein folding simulations: The villin headpiece

Min‐yi Shen, Karl F. Freed

Proteins: Structure, Function, and Bioinformatics 2002 10.1002/prot.10230
[33]
Simulation of Folding of a Small Alpha-helical Protein in Atomistic Detail using Worldwide-distributed Computing

Bojan Zagrovic, Christopher D. Snow, Michael R. Shirts et al.

Journal of Molecular Biology 2002 10.1016/s0022-2836(02)00997-x
[34]
Foldability and the funnel of HP-36 protein sequence: Use of hydropathy scale in protein folding

Goundla Srinivas, Biman Bagchi

The Journal of Chemical Physics 2002 10.1063/1.1467341
[35]
Large-Scale Context in Protein Folding:  Villin Headpiece

Ariel Fernández, Min-Yi Shen, Andrés Colubri et al.

Biochemistry 2003 10.1021/bi026510i
[36]
Berriz G. F. J. Mol. Biol. (2001) 10.1006/jmbi.2001.4792
[37]
Zhou Y. J. Mol. Biol. (1999) 10.1006/jmbi.1999.2936
[38]
Kolinski A. J. Chem. Phys. (1998) 10.1063/1.475646
[39]
Shea J.-E. J. Chem. Phys. (2000) 10.1063/1.1313792
[40]
Favrin G. Proteins (2002) 10.1002/prot.10072
[41]
Kussell E. (2002)
[42]
Alonso D. O. V. Proc. Natl. Acad. Sci. U.S.A. (2000) 10.1073/pnas.97.1.133
[43]
Exploring the folding free energy surface of a three-helix bundle protein

Zhuyan Guo, Charles L. Brooks, Erik M. Boczko

Proceedings of the National Academy of Sciences 1997 10.1073/pnas.94.19.10161
[44]
First-Principles Calculation of the Folding Free Energy of a Three-Helix Bundle Protein

Erik M. Boczko, Charles L. Brooks

Science 1995 10.1126/science.7618103
[45]
Zhou Y. Nature (1999)
[46]
Smith A. V. J. Chem. Phys. (2000) 10.1063/1.1320824
[47]
Linhananta A. J. Chem. Phys. (2002) 10.1063/1.1514574
[48]
Linhananta A. Protein Sci. (2002) 10.1110/ps.0205002
[49]
Ghosh A. Proc. Natl. Acad. Sci. U.S.A. (2002) 10.1073/pnas.142288099
[50]
Elber R. J. Chem. Phys. (2000) 10.1063/1.481131

Showing 50 of 60 references

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