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Helix packing in proteins: prediction and energetic analysis of dimeric, trimeric, and tetrameric GCN4 coiled coil structures.
Proteins. 1994 Oct; 20(2):105-23.P

Abstract

A simulated annealing method for atomic resolution structure prediction of alpha-helical coiled coil proteins is described which draws upon knowledge of the oligomerization state, the helix directionality, and the properties of heptad repeat sequences. Unknown structural parameters, such as the coiled coil twist angle and the side chain conformations, are heavily sampled while allowing for flexibility in the helix backbone geometry. Structures of the wild-type GCN4 dimer [O'Shea et al., Science 254:539-544, 1991] and a mutant tetramer [Harbury et al., Science 292:1401-1407, 1993] have been generated and compared with the X-ray crystal structures. The wild-type dimer model has a root mean square coordinate deviation from the crystal structure of 0.73 A for nonhydrogen atoms in the dimerization interface. Structures of a mutant dimer and a mutant trimer have been predicted. Packing energetics were analyzed for core leucine and isoleucine side chains in dimeric and tetrameric coiled coils. Strong packing preferences were found in the dimers but not in the tetramers. Thus, packing in the dimer may be responsible for the switch from a two-stranded to a four-stranded coiled coil caused by the GCN4 leucine zipper mutations.

Authors+Show Affiliations

DeLano WL
Howard Hughes Medical Institute, Yale University, New Haven, Connecticut 06520.
Brünger AT
No affiliation info available

MeSH

Amino Acid SequenceComputer SimulationDNA-Binding ProteinsFungal ProteinsIsoleucineLeucineModels, MolecularMolecular Sequence DataPeptidesProtein KinasesProtein Structure, TertiarySaccharomyces cerevisiae Proteins

Pub Type(s)

Journal Article

Language

eng

PubMed ID

7846022

Citation

DeLano, W L., and A T. Brünger. "Helix Packing in Proteins: Prediction and Energetic Analysis of Dimeric, Trimeric, and Tetrameric GCN4 Coiled Coil Structures." Proteins, vol. 20, no. 2, 1994, pp. 105-23.
DeLano WL, Brünger AT. Helix packing in proteins: prediction and energetic analysis of dimeric, trimeric, and tetrameric GCN4 coiled coil structures. Proteins. 1994;20(2):105-23.
DeLano, W. L., & Brünger, A. T. (1994). Helix packing in proteins: prediction and energetic analysis of dimeric, trimeric, and tetrameric GCN4 coiled coil structures. Proteins, 20(2), 105-23.
DeLano WL, Brünger AT. Helix Packing in Proteins: Prediction and Energetic Analysis of Dimeric, Trimeric, and Tetrameric GCN4 Coiled Coil Structures. Proteins. 1994;20(2):105-23. PubMed PMID: 7846022.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Helix packing in proteins: prediction and energetic analysis of dimeric, trimeric, and tetrameric GCN4 coiled coil structures. AU - DeLano,W L, AU - Brünger,A T, PY - 1994/10/1/pubmed PY - 1994/10/1/medline PY - 1994/10/1/entrez SP - 105 EP - 23 JF - Proteins JO - Proteins VL - 20 IS - 2 N2 - A simulated annealing method for atomic resolution structure prediction of alpha-helical coiled coil proteins is described which draws upon knowledge of the oligomerization state, the helix directionality, and the properties of heptad repeat sequences. Unknown structural parameters, such as the coiled coil twist angle and the side chain conformations, are heavily sampled while allowing for flexibility in the helix backbone geometry. Structures of the wild-type GCN4 dimer [O'Shea et al., Science 254:539-544, 1991] and a mutant tetramer [Harbury et al., Science 292:1401-1407, 1993] have been generated and compared with the X-ray crystal structures. The wild-type dimer model has a root mean square coordinate deviation from the crystal structure of 0.73 A for nonhydrogen atoms in the dimerization interface. Structures of a mutant dimer and a mutant trimer have been predicted. Packing energetics were analyzed for core leucine and isoleucine side chains in dimeric and tetrameric coiled coils. Strong packing preferences were found in the dimers but not in the tetramers. Thus, packing in the dimer may be responsible for the switch from a two-stranded to a four-stranded coiled coil caused by the GCN4 leucine zipper mutations. SN - 0887-3585 UR - https://www.unboundmedicine.com/medline/citation/7846022/Helix_packing_in_proteins:_prediction_and_energetic_analysis_of_dimeric_trimeric_and_tetrameric_GCN4_coiled_coil_structures_ L2 - https://doi.org/10.1002/prot.340200202 DB - PRIME DP - Unbound Medicine ER -