{"title":"同源蛋白的同步和耦合能量优化:结构预测的新工具","authors":"Chen Keasar , Ron Elber , Jeffrey Skolnick","doi":"10.1016/S1359-0278(97)00033-3","DOIUrl":null,"url":null,"abstract":"<div><p><strong>Background:</strong> Homology-based modeling and global optimization of energy are two complementary approaches to prediction of protein structures. A combination of the two approaches is proposed in which a novel component is added to the energy and forces similarity between homologous proteins.</p><p><strong>Results:</strong> The combination was tested for two families: pancreatic hormones and homeodomains. The simulated lowest-energy structure of the pancreatic hormones is a reasonable approximation to the native fold. The lowest-energy structure of the homeodomains has 80% of the native contacts, but the helices are not packed correctly. The fourth lowest energy structure of the homeodomains has the correct helix packing (RMS 5.4 Å and 82% of the correct contacts). Optimizations of a single protein of the family yield considerably worse structures.</p><p><strong>Conclusions:</strong> Use of coupled homologous proteins in the search for the native fold is more successful than the folding of a single protein in the family.</p></div>","PeriodicalId":79488,"journal":{"name":"Folding & design","volume":"2 4","pages":"Pages 247-259"},"PeriodicalIF":0.0000,"publicationDate":"1997-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/S1359-0278(97)00033-3","citationCount":"16","resultStr":"{\"title\":\"Simultaneous and coupled energy optimization of homologous proteins: a new tool for structure prediction\",\"authors\":\"Chen Keasar , Ron Elber , Jeffrey Skolnick\",\"doi\":\"10.1016/S1359-0278(97)00033-3\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<div><p><strong>Background:</strong> Homology-based modeling and global optimization of energy are two complementary approaches to prediction of protein structures. A combination of the two approaches is proposed in which a novel component is added to the energy and forces similarity between homologous proteins.</p><p><strong>Results:</strong> The combination was tested for two families: pancreatic hormones and homeodomains. The simulated lowest-energy structure of the pancreatic hormones is a reasonable approximation to the native fold. The lowest-energy structure of the homeodomains has 80% of the native contacts, but the helices are not packed correctly. The fourth lowest energy structure of the homeodomains has the correct helix packing (RMS 5.4 Å and 82% of the correct contacts). Optimizations of a single protein of the family yield considerably worse structures.</p><p><strong>Conclusions:</strong> Use of coupled homologous proteins in the search for the native fold is more successful than the folding of a single protein in the family.</p></div>\",\"PeriodicalId\":79488,\"journal\":{\"name\":\"Folding & design\",\"volume\":\"2 4\",\"pages\":\"Pages 247-259\"},\"PeriodicalIF\":0.0000,\"publicationDate\":\"1997-08-01\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"https://sci-hub-pdf.com/10.1016/S1359-0278(97)00033-3\",\"citationCount\":\"16\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"Folding & design\",\"FirstCategoryId\":\"1085\",\"ListUrlMain\":\"https://www.sciencedirect.com/science/article/pii/S1359027897000333\",\"RegionNum\":0,\"RegionCategory\":null,\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"\",\"PubModel\":\"\",\"JCR\":\"\",\"JCRName\":\"\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"Folding & design","FirstCategoryId":"1085","ListUrlMain":"https://www.sciencedirect.com/science/article/pii/S1359027897000333","RegionNum":0,"RegionCategory":null,"ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"","JCRName":"","Score":null,"Total":0}
Simultaneous and coupled energy optimization of homologous proteins: a new tool for structure prediction
Background: Homology-based modeling and global optimization of energy are two complementary approaches to prediction of protein structures. A combination of the two approaches is proposed in which a novel component is added to the energy and forces similarity between homologous proteins.
Results: The combination was tested for two families: pancreatic hormones and homeodomains. The simulated lowest-energy structure of the pancreatic hormones is a reasonable approximation to the native fold. The lowest-energy structure of the homeodomains has 80% of the native contacts, but the helices are not packed correctly. The fourth lowest energy structure of the homeodomains has the correct helix packing (RMS 5.4 Å and 82% of the correct contacts). Optimizations of a single protein of the family yield considerably worse structures.
Conclusions: Use of coupled homologous proteins in the search for the native fold is more successful than the folding of a single protein in the family.