Analysis of Protein Sequence/Structure Similarity Relationships

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• 作者：Hin Hark Gan ; Rebecca A. Perlow ; Sharmili Roy ; Joy Ko ; Min Wu ; Jing Huang ; Shixiang Yan ; Angelo Nicoletta ; Jonathan Vafai ; Ding Sun ; Lihua Wang ; Joyce E. Noah ; Samuela Pasquali ; Tamar Schlick
• 刊名：Biophysical Journal
• 出版年：2002
• 出版时间：November 2002
• 年：2002
• 卷：83
• 期：5
• 页码：2781-2791
• 全文大小：1023 K

文摘

Current analyses of protein sequence/structure relationships have focused on expected similarity relationships for structurally similar proteins. To survey and explore the basis of these relationships, we present a general sequence/structure map that covers all combinations of similarity/dissimilarity relationships and provide novel energetic analyses of these relationships. To aid our analysis, we divide protein relationships into four categories: expected/unexpected similarity (S and S^?) and expected/unexpected dissimilarity (D and D^?) relationships. In the expected similarity region S, we show that trends in the sequence/structure relation can be derived based on the requirement of protein stability and the energetics of sequence and structural changes. Specifically, we derive a formula relating sequence and structural deviations to a parameter characterizing protein stiffness; the formula fits the data reasonably well. We suggest that the absence of data in region S^? (high structural but low sequence similarity) is due to unfavorable energetics. In contrast to region S, region D^? (high sequence but low structural similarity) is well-represented by proteins that can accommodate large structural changes. Our analyses indicate that there are several categories of similarity relationships and that protein energetics provide a basis for understanding these relationships.