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Prediction of the folding pathways and structure of the GCN4 leucine zipper.
J Mol Biol. 1994 Apr 08; 237(4):361-7.JM

Abstract

A hierarchical approach is described for the prediction of the three-dimensional structure and folding pathway of the GCN4 leucine zipper. Dimer assembly is simulated by Monte Carlo dynamics. The resulting lowest energy structures undergo cooperative rearrangement of their hydrophobic core leading to side-chain fixation. The coarse-grained structures are further refined using a molecular dynamics annealing protocol. This produces full atom models with a backbone root-mean-square deviation from the crystal structure of 0.81 A. Thus, we demonstrate the predictive ability of our approach to yield high resolution structures of small coiled coils from their sequence.

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Authors+Show Affiliations

Vieth M
Department of Molecular Biology, Scripps Research Institute, La Jolla, CA 92037.
Kolinski A
No affiliation info available
Brooks CL
No affiliation info available
Skolnick J
No affiliation info available

MeSH

Amino Acid SequenceCrystallography, X-RayDNA-Binding ProteinsFungal ProteinsLeucine ZippersModels, MolecularMolecular Sequence DataMonte Carlo MethodProtein FoldingProtein KinasesProtein Structure, SecondarySaccharomyces cerevisiae Proteins

Pub Type(s)

Journal Article
Research Support, U.S. Gov't, P.H.S.

Language

eng

PubMed ID

8151697

Citation

Vieth, M, et al. "Prediction of the Folding Pathways and Structure of the GCN4 Leucine Zipper." Journal of Molecular Biology, vol. 237, no. 4, 1994, pp. 361-7.
Vieth M, Kolinski A, Brooks CL, et al. Prediction of the folding pathways and structure of the GCN4 leucine zipper. J Mol Biol. 1994;237(4):361-7.
Vieth, M., Kolinski, A., Brooks, C. L., & Skolnick, J. (1994). Prediction of the folding pathways and structure of the GCN4 leucine zipper. Journal of Molecular Biology, 237(4), 361-7.
Vieth M, et al. Prediction of the Folding Pathways and Structure of the GCN4 Leucine Zipper. J Mol Biol. 1994 Apr 8;237(4):361-7. PubMed PMID: 8151697.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Prediction of the folding pathways and structure of the GCN4 leucine zipper. AU - Vieth,M, AU - Kolinski,A, AU - Brooks,C L,3rd AU - Skolnick,J, PY - 1994/4/8/pubmed PY - 2001/3/28/medline PY - 1994/4/8/entrez SP - 361 EP - 7 JF - Journal of molecular biology JO - J Mol Biol VL - 237 IS - 4 N2 - A hierarchical approach is described for the prediction of the three-dimensional structure and folding pathway of the GCN4 leucine zipper. Dimer assembly is simulated by Monte Carlo dynamics. The resulting lowest energy structures undergo cooperative rearrangement of their hydrophobic core leading to side-chain fixation. The coarse-grained structures are further refined using a molecular dynamics annealing protocol. This produces full atom models with a backbone root-mean-square deviation from the crystal structure of 0.81 A. Thus, we demonstrate the predictive ability of our approach to yield high resolution structures of small coiled coils from their sequence. SN - 0022-2836 UR - https://www.unboundmedicine.com/medline/citation/8151697/Prediction_of_the_folding_pathways_and_structure_of_the_GCN4_leucine_zipper_ L2 - https://linkinghub.elsevier.com/retrieve/pii/S0022-2836(84)71239-3 DB - PRIME DP - Unbound Medicine ER -