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Prediction of polyelectrolyte polypeptide structures using Monte Carlo conformational search methods with implicit solvation modeling

Evans, John Spencer and Chan, Sunney I. and Goddard, William A., III (1995) Prediction of polyelectrolyte polypeptide structures using Monte Carlo conformational search methods with implicit solvation modeling. Protein Science, 4 (10). pp. 2019-2031. ISSN 0961-8368. PMCID PMC2142998. doi:10.1002/pro.5560041007. https://resolver.caltech.edu/CaltechAUTHORS:20190227-091746936

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Abstract

Many interesting proteins possess defined sequence stretches containing negatively charged amino acids. At present, experimental methods (X‐ray crystallography, NMR) have failed to provide structural data for many of these sequence domains. We have applied the dihedral probability grid‐Monte Carlo (DPG‐MC) conformational search algorithm to a series of N‐ and C‐capped polyelectrolyte peptides, (Glu)_(20), (Asp)_(20). (PSer)_(20), and (PSer‐Asp)_(10), that represent polyanionic regions in a number of important proteins, such as parathymosin, calsequestrin, the sodium channel protein, and the acidic biomineralization proteins. The atomic charges were estimated from charge equilibration and the valence and van der Waals parameters are from DREIDING. Solvation of the carboxylate and phosphate groups was treated using sodium counterions for each charged side chain (one Na^+ for COO^−; two Na for CO(PO_3)^(−2)) plus a distance‐dependent (shielded) dielectric constant, ϵ = ϵ_0R, to simulate solvent water. The structures of these polyelectrolyte polypeptides were obtained by the DPG‐MC conformational search with ϵ_0 = 10, followed by calculation of solvation energies for the lowest energy conformers using the protein dipole‐Langevin dipole method of Warshel.


Item Type:Article
Related URLs:
URLURL TypeDescription
https://doi.org/10.1002/pro.5560041007DOIArticle
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2142998PubMed CentralArticle
ORCID:
AuthorORCID
Chan, Sunney I.0000-0002-5348-2723
Goddard, William A., III0000-0003-0097-5716
Additional Information:© 1995 The Protein Society. Manuscript accepted: 11 July 1995; Manuscript received: 17 April 1995. We thank Dr. Siddharth Dasgupta for his helpful advice during the course of this study. J.S.E. acknowledges a Postdoctoral National Research Service Award from the NIH (NIDR 1F32-DE-05445) and a fellowship award from AMGEN Pharmaceuticals. These studies were supported by a grant from DOE-AICD, using facilities supported also by NSF-CHE, NSF-GCAG, Aramco, Asahi Glass, Asahi Chemical, BP Chemical, Chevron Petroleum Technology Co., Oronite, Vestar, Hughes Research Labs, Xerox, and Beckman Institute.
Funders:
Funding AgencyGrant Number
NIH Postdoctoral FellowshipNIDR 1F32-DE-05445
AmgenUNSPECIFIED
Department of Energy (DOE)UNSPECIFIED
NSFUNSPECIFIED
AramcoUNSPECIFIED
Asahi GlassUNSPECIFIED
Asahi ChemicalUNSPECIFIED
BP ChemicalUNSPECIFIED
Chevron Petroleum Technology Co.UNSPECIFIED
OroniteUNSPECIFIED
VestarUNSPECIFIED
Hughes Research LaboratoriesUNSPECIFIED
XeroxUNSPECIFIED
Caltech Beckman InstituteUNSPECIFIED
Subject Keywords:computational chemistry; counterion condensation; dihedral angles; internal coordinate method; Monte Carlo; peptide conformation; polyanionic sequences; protein conformation; protein folding
Issue or Number:10
PubMed Central ID:PMC2142998
DOI:10.1002/pro.5560041007
Record Number:CaltechAUTHORS:20190227-091746936
Persistent URL:https://resolver.caltech.edu/CaltechAUTHORS:20190227-091746936
Official Citation:Evans, J. S., Chan, S. I. and Goddard, W. A. (1995), Prediction of polyelectrolyte polypeptide structures using Monte Carlo conformational search methods with implicit solvation modeling. Protein Science, 4: 2019-2031. doi:10.1002/pro.5560041007
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:93292
Collection:CaltechAUTHORS
Deposited By: Tony Diaz
Deposited On:27 Feb 2019 17:28
Last Modified:16 Nov 2021 16:56

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