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Monte carlo simulations of protein folding. II. Application to protein A, ROP, and crambin
Author(s) -
Kolinski Andrzej,
Skolnick Jeffrey
Publication year - 1994
Publication title -
proteins: structure, function, and bioinformatics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.699
H-Index - 191
eISSN - 1097-0134
pISSN - 0887-3585
DOI - 10.1002/prot.340180406
Subject(s) - monte carlo method , protein folding , native state , dimer , crystallography , chemistry , lattice protein , protein structure , folding (dsp implementation) , protein structure prediction , statistical physics , physics , mathematics , biochemistry , statistics , organic chemistry , electrical engineering , engineering
The 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.