Premium
De novo predictions of the quaternary structure of leucine zippers and other coiled coils
Author(s) -
Skolnick Jeffrey,
Kolinski Andrzej,
Mohanty Debasisa
Publication year - 1999
Publication title -
international journal of quantum chemistry
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.484
H-Index - 105
eISSN - 1097-461X
pISSN - 0020-7608
DOI - 10.1002/(sici)1097-461x(1999)75:3<165::aid-qua6>3.0.co;2-q
Subject(s) - leucine zipper , coiled coil , chemistry , protein quaternary structure , monte carlo method , helix (gastropod) , crystallography , thermodynamics , statistical physics , physics , transcription factor , biochemistry , mathematics , ecology , statistics , protein subunit , biology , snail , gene
Coiled coils possess a quaternary structure comprised of the side‐by‐side arrangement of α‐helices. Due their inherent structural simplicity, they are ideal model systems for both theoretical and experimental studies. Among the coiled coils are the leucine zippers, which play an important role in the activation of DNA transcription. In contrast to the large amount of available experimental data, an overview of which is presented, there are very few theoretical studies. To address this need, the status of existing theoretical approaches to predict coiled coil quaternary structure is described. Furthermore, to treat the conformational equilibria inherent in these systems, an extension of entropy sampling Monte Carlo simulations is developed that can treat multimers. Here, the approach is applied to GCN4 leucine zippers in the context of a reduced protein model. Not only is the native conformation successfully predicted, but the model also reproduces the experimentally observed helix content in the denatured state and the observed two‐state thermodynamic behavior. Such two‐state behavior arises from the dissociation of highly helical dimeric chains to form monomers of low, isolated chain helix content. ©1999 John Wiley & Sons, Inc. Int J Quant Chem 75: 165–176, 1999