Dictionary of protein secondary structure: Pattern recognition of hydrogen‐bonded and geometrical features

化学 扭转(腹足类) 曲率 回路建模 蛋白质二级结构 球状蛋白 结晶学 氢键 蛋白质结构 分子 几何学 生物化学 数学 蛋白质结构预测 有机化学 医学 外科
作者
Wolfgang Kabsch,Christian Sander
出处
期刊:Biopolymers [Wiley]
卷期号:22 (12): 2577-2637 被引量:14994
标识
DOI:10.1002/bip.360221211
摘要

For a successful analysis of the relation between amino acid sequence and protein structure, an unambiguous and physically meaningful definition of secondary structure is essential. We have developed a set of simple and physically motivated criteria for secondary structure, programmed as a pattern-recognition process of hydrogen-bonded and geometrical features extracted from x-ray coordinates. Cooperative secondary structure is recognized as repeats of the elementary hydrogen-bonding patterns "turn" and "bridge." Repeating turns are "helices," repeating bridges are "ladders," connected ladders are "sheets." Geometric structure is defined in terms of the concepts torsion and curvature of differential geometry. Local chain "chirality" is the torsional handedness of four consecutive Cα positions and is positive for right-handed helices and negative for ideal twisted β-sheets. Curved pieces are defined as "bends." Solvent "exposure" is given as the number of water molecules in possible contact with a residue. The end result is a compilation of the primary structure, including SS bonds, secondary structure, and solvent exposure of 62 different globular proteins. The presentation is in linear form: strip graphs for an overall view and strip tables for the details of each of 10.925 residues. The dictionary is also available in computer-readable form for protein structure prediction work.
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