Mapping side chain interactions at protein helix termini
نویسندگان
چکیده
منابع مشابه
Steric interactions determine side-chain conformations in protein cores.
We investigate the role of steric interactions in defining side-chain conformations in protein cores. Previously, we explored the strengths and limitations of hard-sphere dipeptide models in defining sterically allowed side-chain conformations and recapitulating key features of the side-chain dihedral angle distributions observed in high-resolution protein structures. Here, we show that modelin...
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Three-dimensional structures of proteins are the support of their biological functions. Their folds are stabilized by contacts between residues. Inner protein contacts are generally described through direct atomic contacts, i.e. interactions between side-chain atoms, while contact prediction methods mainly used inter-Calpha distances. In this paper, we have analyzed the protein contacts on a re...
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Transmembrane helices are no longer believed to be just hydrophobic segments that exist solely to anchor proteins to a lipid bilayer, but rather they appear to have the capacity to specify function and structure. Specific interactions take place between hydrophobic segments within the lipid bilayer whereby subtle mutations that normally would be considered innocuous can result in dramatic struc...
متن کاملSide-chain interactions in the C-peptide helix: Phe 8 ... His 12+.
Previous studies have demonstrated that His 12 plays a major role in the pH-dependent stability of the helix formed by the isolated C-peptide (residues 1-13 of ribonuclease A). Here, amino acid replacement experiments show that His 12+ stabilizes the C-peptide helix chiefly by interacting with Phe 8. The Phe 8 ... His 12+ ring interaction is specific for the protonated form of His 12 (His 12+) ...
متن کاملHelix propensities of the amino acids measured in alanine-based peptides without helix-stabilizing side-chain interactions.
Helix propensities of the amino acids have been measured in alanine-based peptides in the absence of helix-stabilizing side-chain interactions. Fifty-eight peptides have been studied. A modified form of the Lifson-Roig theory for the helix-coil transition, which includes helix capping (Doig AJ, Chakrabartty A, Klingler TM, Baldwin RL, 1994, Biochemistry 33:3396-3403), was used to analyze the re...
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ژورنال
عنوان ژورنال: BMC Bioinformatics
سال: 2015
ISSN: 1471-2105
DOI: 10.1186/s12859-015-0671-4