{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,13]],"date-time":"2026-01-13T02:07:12Z","timestamp":1768270032627,"version":"3.49.0"},"reference-count":45,"publisher":"Oxford University Press (OUP)","issue":"12","license":[{"start":{"date-parts":[[2020,3,14]],"date-time":"2020-03-14T00:00:00Z","timestamp":1584144000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"DOI":"10.13039\/100017019","name":"Leir foundation","doi-asserted-by":"crossref","id":[{"id":"10.13039\/100017019","id-type":"DOI","asserted-by":"crossref"}]},{"name":"Ginzburg foundation"},{"name":"Foulkes Foundation fellowship"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2020,6,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>Polyproline II (PPII) is a common conformation, comparable to \u03b1-helix and \u03b2-sheet. PPII, recently termed with a more generic name\u2014\u03ba-helix, adopts a left-handed structure with 3-fold rotational symmetry. Lately, a new type of binding mechanism\u2014the helical lock and key model was introduced in SH3-domain complexes, where the interaction is characterized by a sliding helical pattern. However, whether this binding mechanism is unique only to SH3 domains is unreported.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>Here, we show that the helical binding pattern is a universal feature of the \u03ba-helix conformation, present within all the major target families\u2014SH3, WW, profilin, MHC-II, EVH1 and GYF domains. Based on a geometric analysis of 255 experimentally solved structures, we found that they are characterized by a distinctive rotational angle along the helical axis. Furthermore, we found that the range of helical pitch varies between different protein domains or peptide orientations and that the interaction is also represented by a rotational displacement mimicking helical motion. The discovery of rotational interactions as a mechanism, reveals a new dimension in the realm of protein\u2013protein interactions, which introduces a new layer of information encoded by the helical conformation. Due to the extensive involvement of the conformation in functional interactions, we anticipate our model to expand the current molecular understanding of the relationship between protein structure and function.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>We have implemented the proposed methods in an R package freely available at https:\/\/github.com\/Grantlab\/bio3d.<\/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\/btaa186","type":"journal-article","created":{"date-parts":[[2020,3,13]],"date-time":"2020-03-13T12:36:35Z","timestamp":1584102995000},"page":"3726-3732","source":"Crossref","is-referenced-by-count":12,"title":["\u03ba-helix and the helical lock and key model: a pivotal way of looking at polyproline II"],"prefix":"10.1093","volume":"36","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-5011-5477","authenticated-orcid":false,"given":"Tomer","family":"Meirson","sequence":"first","affiliation":[{"name":"Drug Discovery Laboratory , The Azrieli Faculty of Medicine, Bar-Ilan University, Safed 1311502, Israel"},{"name":"Ella Lemelbaum Institute for Immuno-oncology , Sheba Medical Center, Ramat-Gan 526260, Israel"}]},{"given":"David","family":"Bomze","sequence":"additional","affiliation":[{"name":"Sackler Faculty of Medicine , Tel Aviv University, Tel Aviv 6997801, Israel"}]},{"given":"Gal","family":"Markel","sequence":"additional","affiliation":[{"name":"Ella Lemelbaum Institute for Immuno-oncology , Sheba Medical Center, Ramat-Gan 526260, Israel"},{"name":"Department of Clinical Microbiology and Immunology , Sackler Faculty of Medicine, Tel Aviv University, Tel-Aviv 6997801, Israel"}]},{"given":"Abraham O","family":"Samson","sequence":"additional","affiliation":[{"name":"Drug Discovery Laboratory , The Azrieli Faculty of Medicine, Bar-Ilan University, Safed 1311502, Israel"}]}],"member":"286","published-online":{"date-parts":[[2020,3,14]]},"reference":[{"key":"2023063011065952400_btaa186-B1","doi-asserted-by":"crossref","first-page":"472","DOI":"10.1006\/jmbi.1993.1047","article-title":"Left-handed polyproline II helices commonly occur in globular proteins","volume":"229","author":"Adzhubei","year":"1993","journal-title":"J. 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