Exceptional pairs of amino acid neighbors in α-helices
نویسندگان
چکیده
منابع مشابه
Prediction of protein crystallization using collocation of amino acid pairs.
While above 80% of protein structures in PDB were determined using X-ray crystallography, in some cases only 42% of soluble purified proteins yield crystals. Since experimental verification of protein's ability to crystallize is relatively expensive and time-consuming, we propose a new in silico prediction system, called CRYSTALP, which is based on the protein's sequence. CRYSTALP uses a novel ...
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In order to study the tendency of amino acid neighbors in helical structures, proteins with known structures were carefully analyzed. The studied helical positions: N , Ncap, N1, N2, N3, N4, M, C4, C3, C2, C1, Ccap, C and their doublet counterparts: N Ncap, NcapN1, N1N2, N2N3, N3N4, M1M2, M2M3, C4C3, C3C2, C2C1, C1Ccap, CcapC were carefully analyzed. The propensity for all amino acids i...
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Using a new representation for interactions in protein sequences based on correlations between pairs of amino acids, we have examined α-helical segments from known protein structures for important interactions. Traditional techniques for representing protein sequences usually make an explicit assumption of conditional independence of residues in the sequences. Protein structure analyses, howeve...
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Molecular dynamics (MD) is a valuable tool for the investigation of functional elements in biomolecules, providing information on dynamic properties and processes. Previous work by our group has characterized static geometric properties of the two MHC α-helices comprising the peptide binding region recognized by T cells. We build upon this work and used several spline models to approximate the ...
متن کاملOrientation of TOAC amino-acid spin labels in a-helices and b-strands
The orientation of a-helices or b-strands, e.g., in membranes, can be determined from EPR order parameters of (2,2,6,6-tetramethylpiperidine-1-oxy-4-amino-4-carboxylic acid) TOAC amino-acid spin labels incorporated in the polypeptide backbone. This requires knowledge of the inclination of the nitroxide axes, relative to the a-helix or b-strand axis. Crystal structures of TOAC-containing peptide...
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ژورنال
عنوان ژورنال: FEBS Letters
سال: 2003
ISSN: 0014-5793
DOI: 10.1016/s0014-5793(03)00105-4