Dataset Information

Populations of the Minor ?-Conformation in AcGXGNH2 and the ?-Helical Nucleation Propensities.

ABSTRACT: Intrinsic backbone conformational preferences of different amino acids are important for understanding the local structure of unfolded protein chains. Recent evidence suggests ?-structure is relatively minor among three major backbone conformations for unfolded proteins. The ?-helices are the dominant structures in many proteins. For these proteins, how could the ?-structures occur from the least in unfolded to the most in folded states? Populations of the minor ?-conformation in model peptides provide vital information. Reliable determination of populations of the ?-conformers in these peptides that exist in multiple equilibriums of different conformations remains a challenge. Combined analyses on data from AcGXPNH2 and AcGXGNH2 peptides allow us to derive the populations of PII, ? and ? in AcGXGNH2. Our results show that on average residue X in AcGXGNH2 adopt PII, ?, and ? 44.7%, 44.5% and 10.8% of time, respectively. The contents of ?-conformations for different amino acids define an ?-helix nucleation propensity scale. With derived PII, ? and ?-contents, we can construct a free energy-conformation diagram on each AcGXGNH2 in aqueous solution for the three major backbone conformations. Our results would have broad implications on early-stage events of protein folding.

SUBMITTER: Zhou Y

PROVIDER: S-EPMC4891685 | biostudies-literature | 2016 Jun

REPOSITORIES: biostudies-literature

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Populations of the Minor α-Conformation in AcGXGNH2 and the α-Helical Nucleation Propensities.

Zhou Yanjun Y He Liu L Zhang Wenwen W Hu Jingjing J Shi Zhengshuang Z

Scientific reports 20160603

Intrinsic backbone conformational preferences of different amino acids are important for understanding the local structure of unfolded protein chains. Recent evidence suggests α-structure is relatively minor among three major backbone conformations for unfolded proteins. The α-helices are the dominant structures in many proteins. For these proteins, how could the α-structures occur from the least in unfolded to the most in folded states? Populations of the minor α-conformation in model peptides ...[more]

PMID: 27256621

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Project description:BACKGROUND: A large number of studies have been carried out to obtain amino acid propensities for ?-helices and ?-sheets. The obtained propensities for ?-helices are consistent with each other, and the pair-wise correlation coefficient is frequently high. On the other hand, the ?-sheet propensities obtained by several studies differed significantly, indicating that the context significantly affects ?-sheet propensity. RESULTS: We calculated amino acid propensities for ?-helices and ?-sheets for 39 and 24 protein folds, respectively, and addressed whether they correlate with the fold. The propensities were also calculated for exposed and buried sites, respectively. Results showed that ?-helix propensities do not differ significantly by fold, but ?-sheet propensities are diverse and depend on the fold. The propensities calculated for exposed sites and buried sites are similar for ?-helix, but such is not the case for the ?-sheet propensities. We also found some fold dependence on amino acid frequency in ?-strands. Folds with a high Ser, Thr and Asn content at exposed sites in ?-strands tend to have a low Leu, Ile, Glu, Lys and Arg content (correlation coefficient = -0.90) and to have flat ?-sheets. At buried sites in ?-strands, the content of Tyr, Trp, Gln and Ser correlates negatively with the content of Val, Ile and Leu (correlation coefficient = -0.93). "All-?" proteins tend to have a higher content of Tyr, Trp, Gln and Ser, whereas "?/?" proteins tend to have a higher content of Val, Ile and Leu. CONCLUSIONS: The ?-helix propensities are similar for all folds and for exposed and buried residues. However, ?-sheet propensities calculated for exposed residues differ from those for buried residues, indicating that the exposed-residue fraction is one of the major factors governing amino acid composition in ?-strands. Furthermore, the correlations we detected suggest that amino acid composition is related to folding properties such as the twist of a ?-strand or association between two ? sheets.

Dataset Information

Populations of the Minor ?-Conformation in AcGXGNH2 and the ?-Helical Nucleation Propensities.

Publications

Populations of the Minor α-Conformation in AcGXGNH2 and the α-Helical Nucleation Propensities.

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