{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,26]],"date-time":"2026-02-26T20:34:41Z","timestamp":1772138081495,"version":"3.50.1"},"reference-count":17,"publisher":"Oxford University Press (OUP)","issue":"12","license":[{"start":{"date-parts":[[2017,2,13]],"date-time":"2017-02-13T00:00:00Z","timestamp":1486944000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/about_us\/legal\/notices"}],"funder":[{"DOI":"10.13039\/100000001","name":"National Science Foundation","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2017,6,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Motivation<\/jats:title>\n                    <jats:p>Protein loops show rich conformational dynamics properties on a wide range of timescales as they play an essential role for many cellular functions during protein\u2013protein interactions and recognition processes. However, little is known about the detail behavior of loops upon protein binding including allostery.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>We report the loop motions and their dominant timescales for a library of 230 proteins that form protein\u2013protein complexes using the ToeLoop predictor of loop dynamics. We applied the analysis to proteins in both their complex and free state and relate specific loop properties to their role in protein recognition. We observe a strong tendency of loops that move on relatively slow timescales of tens of ns to sub-\u03bcs to be directly involved in binding and recognition processes. Complex formation leads to a significant reduction in loop flexibility at the binding interface, but in a number of cases it can also trigger increased flexibility in distal loops in response to allosteric conformational changes. The importance of loop dynamics and allostery is highlighted by a case study of an antibody-antigen complex. Furthermore, we explored the relationship between loop dynamics and experimental binding affinities and found that a prevalence of high loop rigidity at the binding interface is an indicator of increased binding strength.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and Implementation<\/jats:title>\n                    <jats:p>http:\/\/spin.ccic.ohio-state.edu\/index.php\/toeloopppi<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Supplementary information<\/jats:title>\n                    <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btx070","type":"journal-article","created":{"date-parts":[[2017,2,15]],"date-time":"2017-02-15T03:58:08Z","timestamp":1487131088000},"page":"1814-1819","source":"Crossref","is-referenced-by-count":5,"title":["Statistical database analysis of the role of loop dynamics for protein\u2013protein complex formation and allostery"],"prefix":"10.1093","volume":"33","author":[{"given":"Yina","family":"Gu","sequence":"first","affiliation":[{"name":"Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Da-Wei","family":"Li","sequence":"additional","affiliation":[{"name":"Campus Chemical Instrument Center, The Ohio State University, Columbus, OH, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Rafael","family":"Br\u00fcschweiler","sequence":"additional","affiliation":[{"name":"Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH, USA"},{"name":"Campus Chemical Instrument Center, The Ohio State University, Columbus, OH, USA"},{"name":"Department of Biological Chemistry and Pharmacology, The Ohio State University, Columbus, OH, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2017,2,13]]},"reference":[{"key":"2023020301104778800_btx070-B1","doi-asserted-by":"crossref","first-page":"D315","DOI":"10.1093\/nar\/gkt1189","article-title":"ArchDB 2014: structural classification of loops in proteins","volume":"42","author":"Bonet","year":"2014","journal-title":"Nucleic Acids Res"},{"key":"2023020301104778800_btx070-B2","doi-asserted-by":"crossref","first-page":"6267","DOI":"10.1021\/acs.chemrev.5b00718","article-title":"Advances in NMR methods to map allosteric sites: from models to translation","volume":"116","author":"Boulton","year":"2016","journal-title":"Chem Rev"},{"key":"2023020301104778800_btx070-B3","doi-asserted-by":"crossref","first-page":"633","DOI":"10.1016\/1074-5521(95)90023-3","article-title":"Let's get specific: the relationship between specificity and affinity","volume":"2","author":"Eaton","year":"1995","journal-title":"Chem. 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