Analysis of Conformations of Amino Acid Residues and Prediction of Backbone Topography in Proteins
Analysis of Conformations of Amino Acid Residues and Prediction of Backbone Topography in Proteins
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蛋白质中氨基酸残基的构象分析和主链形貌的预测
DOI：
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发表时间：
1974
期刊：
影响因子：
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通讯作者：
H. Scheraga
中科院分区：
文献类型：
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作者：
A. Burgess;P. Ponnuswamy;H. Scheraga
描述蛋白质中氨基酸残基的离散构象状态的方法，并用于研究链折叠的拓扑结构。短程，中程和长程相互作用的相对重要性进行了讨论，在光的构象状态的分析，为不同的氨基酸残基在8个蛋白质的已知结构。一个预测算法，它分配四个状态的蛋白质链的每个残基（α-螺旋，延伸结构，弯曲，或线圈），已开发出从短期和中期相互作用的考虑，并应用于已知的三维结构的13个蛋白质。该预测算法应用简单，α-螺旋和扩展结构的分配明显优于大多数其他预测方案。链反转或弯曲区域的预测也优于以前的算法，但这些分配不如α-螺旋和延伸结构。该算法的发展的动机不仅是为了证明短距离和长距离相互作用的相对重要性，但更重要的是，开始开发程序，获得一个近似的起始构象，随后的能量最小化，以预测蛋白质的三维结构。这个程序，以及其他各种方法的预测的骨干拓扑结构和构象状态的蛋白质中的残基的氨基酸序列，已被审查和评估的成功的方法进行比较，预期从随机分配的构象状态的成功。
Methods for describing a discrete number of conformational states of amino acid residues in proteins are presented and used to investigate the topography of chain folding. The relative importance of short-range, medium-range and long-range interactions is discussed in the light of an analysis of the conformational states for the different amino acid residues in eight proteins of known structure. A prediction algorithm, which assigns four states to each residue of a protein chain (α-helix, extended structure, bend, or coil), has been developed from a consideration of both short- and medium-range interactions and applied to thirteen proteins of known three-dimensional structure. The prediction algorithm is simple to apply, and the assignment of α-helix and extended structure is considerably better than in most other predictive schemes. The prediction of chain reversal or bend regions was also better than with previous algorithms, but these assignments were not as good as those for α-helix and extended structure. The motivation for the development of this algorithm is not only to demonstrate the relative importance of short- and longer-range interactions but, more important, to begin to develop procedures for obtaining an approximate starting conformation for subsequent energy minimization to predict the three-dimensional structure of a protein. This procedure, as well as various other methods for the prediction of the backbone topography and conformational states of residues in proteins from the amino acid sequence, have been reviewed and evaluated by comparing the success of the methods to the success expected from a random assignment of conformational states.