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Correlation between knowledge‐based and detailed atomic potentials: Application to the unfolding of the GCN4 leucine zipper
Author(s) -
Mohanty Debasisa,
Dominy Brian N.,
Kolinski Andrzej,
Brooks Charles L.,
Skolnick Jeffrey
Publication year - 1999
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/(sici)1097-0134(19990601)35:4<447::aid-prot8>3.0.co;2-o
Subject(s) - solvation , zipper , leucine zipper , molecular dynamics , atom (system on chip) , chemistry , chemical physics , crystallography , implicit solvation , computational chemistry , molecule , computer science , algorithm , biochemistry , organic chemistry , peptide sequence , gene , embedded system
Abstract The relationship between the unfolding pseudo free energies of reduced and detailed atomic models of the GCN4 leucine zipper is examined. Starting from the native crystal structure, a large number of conformations ranging from folded to unfolded were generated by all‐atom molecular dynamics unfolding simulations in an aqueous environment at elevated temperatures. For the detailed atomic model, the pseudo free energies are obtained by combining the CHARMM all‐atom potential with a solvation component from the generalized Born, surface accessibility, GB/SA, model. Reduced model energies were evaluated using a knowledge‐based potential. Both energies are highly correlated. In addition, both show a good correlation with the root mean square deviation, RMSD, of the backbone from native. These results suggest that knowledge‐based potentials are capable of describing at least some of the properties of the folded as well as the unfolded states of proteins, even though they are derived from a database of native protein structures. Since only conformations generated from an unfolding simulation are used, we cannot assess whether these potentials can discriminate the native conformation from the manifold of alternative, low‐energy misfolded states. Nevertheless, these results also have significant implications for the development of a methodology for multiscale modeling of proteins that combines reduced and detailed atomic models. Proteins 1999;35:447–452. © 1999 Wiley‐Liss, Inc.