Pairwise calculation of protein solvent-accessible surface areas

Arthur G. Street , Stephen L. Mayo
{"title":"Pairwise calculation of protein solvent-accessible surface areas","authors":"Arthur G. Street ,&nbsp;Stephen L. Mayo","doi":"10.1016/S1359-0278(98)00036-4","DOIUrl":null,"url":null,"abstract":"<div><p><strong>Background:</strong> The tractability of many algorithms for determining the energy state of a system depends on the pairwise nature of an energy expression. Some energy terms, such as the standard implementation of the van der Waals potential, satisfy this criterion whereas others do not. One class of important potentials that are not pairwise involves benefits and penalties for burying hydrophobic and/or polar surface areas. It has been found previously that, in some cases, a pairwise approximation to these surface areas correlates with the true surface areas. We set out to generalize the applicability of this approximation.</p><p><strong>Results:</strong> We develop a pairwise expression with one scalable parameter that closely reproduces both the true buried and the true exposed solvent-accessible surface areas. We then refit our previously published coiled-coil stability data to give solvation parameters of 26 cal/mol å<sup>2</sup> favoring hydrophobic burial and 100 cal/mol å<sup>2</sup> opposing polar burial.</p><p><strong>Conclusions:</strong>An accurate pairwise approximation to calculate exposed and buried protein solvent-accessible surface area is achieved.</p></div>","PeriodicalId":79488,"journal":{"name":"Folding & design","volume":"3 4","pages":"Pages 253-258"},"PeriodicalIF":0.0000,"publicationDate":"1998-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/S1359-0278(98)00036-4","citationCount":"152","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"Folding & design","FirstCategoryId":"1085","ListUrlMain":"https://www.sciencedirect.com/science/article/pii/S1359027898000364","RegionNum":0,"RegionCategory":null,"ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"","JCRName":"","Score":null,"Total":0}
引用次数: 152

Abstract

Background: The tractability of many algorithms for determining the energy state of a system depends on the pairwise nature of an energy expression. Some energy terms, such as the standard implementation of the van der Waals potential, satisfy this criterion whereas others do not. One class of important potentials that are not pairwise involves benefits and penalties for burying hydrophobic and/or polar surface areas. It has been found previously that, in some cases, a pairwise approximation to these surface areas correlates with the true surface areas. We set out to generalize the applicability of this approximation.

Results: We develop a pairwise expression with one scalable parameter that closely reproduces both the true buried and the true exposed solvent-accessible surface areas. We then refit our previously published coiled-coil stability data to give solvation parameters of 26 cal/mol å2 favoring hydrophobic burial and 100 cal/mol å2 opposing polar burial.

Conclusions:An accurate pairwise approximation to calculate exposed and buried protein solvent-accessible surface area is achieved.

蛋白质溶剂可及表面积的两两计算
背景:许多用于确定系统能量状态的算法的可跟踪性取决于能量表达式的两两性质。一些能量项,如范德华势的标准实现,满足这个标准,而另一些则不满足。一类重要的非成对电位涉及埋没疏水和/或极性表面积的利与弊。以前已经发现,在某些情况下,对这些表面积的两两近似与真正的表面积相关。我们着手推广这个近似的适用性。结果:我们开发了一个具有一个可扩展参数的成对表达式,该表达式紧密地再现了真实的埋藏和真实的暴露溶剂可及表面积。然后,我们修改了之前发表的线圈稳定性数据,给出了26 cal/mol 2有利于疏水埋藏和100 cal/mol 2相反极性埋藏的溶剂化参数。结论:实现了精确的两两近似计算暴露和埋藏的蛋白质溶剂可及表面积。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
求助全文
约1分钟内获得全文 求助全文
来源期刊
自引率
0.00%
发文量
0
×
引用
GB/T 7714-2015
复制
MLA
复制
APA
复制
导出至
BibTeX EndNote RefMan NoteFirst NoteExpress
×
提示
您的信息不完整,为了账户安全,请先补充。
现在去补充
×
提示
您因"违规操作"
具体请查看互助需知
我知道了
×
提示
确定
请完成安全验证×
copy
已复制链接
快去分享给好友吧!
我知道了
右上角分享
点击右上角分享
0
联系我们:info@booksci.cn Book学术提供免费学术资源搜索服务,方便国内外学者检索中英文文献。致力于提供最便捷和优质的服务体验。 Copyright © 2023 布克学术 All rights reserved.
京ICP备2023020795号-1
ghs 京公网安备 11010802042870号
Book学术文献互助
Book学术文献互助群
群 号:481959085
Book学术官方微信