DOI: 10.1002/prot.340180406. Monte carlo simulations of protein folding. II. Application to protein A, ROP, and crambin

Monte carlo simulations of protein folding. II. Application to protein A, ROP, and crambin

10.1002/prot.340180406

Crossref journal-article

Wiley

Proteins: Structure, Function, and Bioinformatics (311)

Abstract

AbstractThe hierarchy of lattice Monte Carlo models described in the accompanying paper (Kolinski, A., Skolnick, J. Monte Carlo simulations of protein folding. I. Lattice model and interaction scheme. Proteins 18:338–352, 1994) is applied to the simulation of protein folding and the prediction of 3‐dimensional structure. Using sequence information alone, three proteins have been successfully folded: the B domain of staphylococcal protein A, a 120 residue, monomeric version of ROP dimer, and crambin. Starting from a random expanded conformation, the model proteins fold along relatively well‐defined folding pathways. These involve a collection of early intermediates, which are followed by the final (and rate‐determining) transition from compact intermediates closely resembling the molten globule state to the native‐like state. The predicted structures are rather unique, with native‐like packing of the side chains. The accuracy of the predicted native conformations is better than those obtained in previous folding simulations. The best (but by no means atypical) folds of protein A have a coordinate rms of 2.25 Å from the native Cα trace, and the best coordinate rms from crambin is 3.18 Å. For ROP monomer, the lowest coordinate rms from equivalent Cαs of ROP dimer is 3.65 Å. Thus, for two simple helical proteins and a small α/β protein, the ability to predict protein structure from sequence has been demonstrated. © 1994 John Wiley & Sons, Inc.

Bibliography

Kolinski, A., & Skolnick, J. (1994). Monte carlo simulations of protein folding. II. Application to protein A, ROP, and crambin. Proteins: Structure, Function, and Bioinformatics, 18(4), 353â366. Portico.

Authors 2

Andrzej Kolinski (first)
Jeffrey Skolnick (additional)

References 31 Referenced 124

10.1002/prot.340180405
{'key': 'e_1_2_1_3_2', 'first-page': 'A265', 'article-title': 'A designed 4‐helical bundle shows characteristics of both molten globule and native states of proteins', 'volume': '61', 'author': 'Handel T.', 'year': '1992', 'journal-title': 'Biophysical J.'} / Biophysical J. / A designed 4‐helical bundle shows characteristics of both molten globule and native states of proteins by Handel T. (1992)
10.1021/ja00051a061
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Sander C.Private communication 1993.
Rey A. Kolinski A. Skolnick J. Application of a discretized protein model to secondary structure prediction in preparation.
10.1007/BF02337559
10.1016/0960-9822(93)90348-R
10.1002/prot.340060202
10.1126/science.8346440
10.1016/0014-5793(90)80143-7
{'key': 'e_1_2_1_16_2', 'first-page': '2099', 'article-title': 'From independent modules to molten globules: Observations on the nature of protein folding intermediates', 'volume': '90', 'author': 'Skolnick J.', 'year': '1993', 'journal-title': 'J. Mol. Biol.'} / J. Mol. Biol. / From independent modules to molten globules: Observations on the nature of protein folding intermediates by Skolnick J. (1993)
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{'key': 'e_1_2_1_29_2', 'first-page': '45', 'article-title': 'Prediction of protein secondary structure', 'volume': '47', 'author': 'Chou P. Y.', 'year': '1978', 'journal-title': 'Adv. Enzymol.'} / Adv. Enzymol. / Prediction of protein secondary structure by Chou P. Y. (1978)
10.1002/jcc.540130407
10.1073/pnas.83.11.3801
PDB Quarterly Newsletter No. 63 January1993.

Dates

Type	When
Created	20 years, 3 months ago (May 28, 2005, 9:33 p.m.)
Deposited	1 year, 10 months ago (Oct. 24, 2023, 10:47 a.m.)
Indexed	1 year ago (Aug. 12, 2024, 4:32 a.m.)
Issued	31 years, 4 months ago (April 1, 1994)
Published	31 years, 4 months ago (April 1, 1994)
Published Online	21 years, 6 months ago (Feb. 3, 2004)
Published Print	31 years, 4 months ago (April 1, 1994)

Funders 0

None

BibTeX

@article{Kolinski_1994, title={Monte carlo simulations of protein folding. II. Application to protein A, ROP, and crambin}, volume={18}, ISSN={1097-0134}, url={http://dx.doi.org/10.1002/prot.340180406}, DOI={10.1002/prot.340180406}, number={4}, journal={Proteins: Structure, Function, and Bioinformatics}, publisher={Wiley}, author={Kolinski, Andrzej and Skolnick, Jeffrey}, year={1994}, month=apr, pages={353–366} }

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