{"title":"Abstract Conformer Space","authors":"Gunnar Jeschke","doi":"10.1002/hlca.202500032","DOIUrl":null,"url":null,"abstract":"<p>Pairwise distance root mean square deviation defines a hyperspace where conformers with similar shape reside close to each other. The radius of gyration of protein ensembles in this abstract conformer space (ACS) converges at ensemble sizes between 50 and 500, depending on the extent of disorder. Upon further increase of ensemble size, the root mean square distance of conformers to their nearest neighbors decreases only slowly. Clustering in ACS can reveal distinct subensembles. For proteins that exist in two states, clustering in a common ACS reveals differences between the ensembles in the two states. The dimension of ACS can be reduced to 2D or 3D by multi-dimensional scaling or principal component analysis. Visualization in these lower-dimensional spaces also reveals differences between protein states or the existence of subensembles. The ratio between the gyration radius in ACS and its counterpart in real space is a global disorder parameter.</p>","PeriodicalId":12842,"journal":{"name":"Helvetica Chimica Acta","volume":"108 7","pages":""},"PeriodicalIF":1.8000,"publicationDate":"2025-05-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/hlca.202500032","citationCount":"0","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"Helvetica Chimica Acta","FirstCategoryId":"92","ListUrlMain":"https://onlinelibrary.wiley.com/doi/10.1002/hlca.202500032","RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q3","JCRName":"CHEMISTRY, MULTIDISCIPLINARY","Score":null,"Total":0}
引用次数: 0
Abstract
Pairwise distance root mean square deviation defines a hyperspace where conformers with similar shape reside close to each other. The radius of gyration of protein ensembles in this abstract conformer space (ACS) converges at ensemble sizes between 50 and 500, depending on the extent of disorder. Upon further increase of ensemble size, the root mean square distance of conformers to their nearest neighbors decreases only slowly. Clustering in ACS can reveal distinct subensembles. For proteins that exist in two states, clustering in a common ACS reveals differences between the ensembles in the two states. The dimension of ACS can be reduced to 2D or 3D by multi-dimensional scaling or principal component analysis. Visualization in these lower-dimensional spaces also reveals differences between protein states or the existence of subensembles. The ratio between the gyration radius in ACS and its counterpart in real space is a global disorder parameter.
期刊介绍：
Helvetica Chimica Acta, founded by the Swiss Chemical Society in 1917, is a monthly multidisciplinary journal dedicated to the dissemination of knowledge in all disciplines of chemistry (organic, inorganic, physical, technical, theoretical and analytical chemistry) as well as research at the interface with other sciences, where molecular aspects are key to the findings. Helvetica Chimica Acta is committed to the publication of original, high quality papers at the frontier of scientific research. All contributions will be peer reviewed with the highest possible standards and published within 3 months of receipt, with no restriction on the length of the papers and in full color.
求助内容：
应助结果提醒方式：
京公网安备 11010802042870号
