{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,27]],"date-time":"2026-02-27T06:16:43Z","timestamp":1772173003274,"version":"3.50.1"},"update-to":[{"DOI":"10.1371\/journal.pcbi.1010119","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2022,5,27]],"date-time":"2022-05-27T00:00:00Z","timestamp":1653609600000}}],"reference-count":76,"publisher":"Public Library of Science (PLoS)","issue":"5","license":[{"start":{"date-parts":[[2022,5,17]],"date-time":"2022-05-17T00:00:00Z","timestamp":1652745600000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100004281","name":"Narodowe Centrum Nauki","doi-asserted-by":"publisher","award":["DEC-2013\/10\/E\/NZ1\/00649"],"award-info":[{"award-number":["DEC-2013\/10\/E\/NZ1\/00649"]}],"id":[{"id":"10.13039\/501100004281","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["www.ploscompbiol.org"],"crossmark-restriction":false},"short-container-title":["PLoS Comput Biol"],"abstract":"<jats:p>\n                    The evolutionary variability of a protein\u2019s residues is highly dependent on protein region and function. Solvent-exposed residues, excluding those at interaction interfaces, are more variable than buried residues whereas active site residues are considered to be conserved. The abovementioned rules apply also to \u03b1\/\u03b2-hydrolase fold proteins\u2014one of the oldest and the biggest superfamily of enzymes with buried active sites equipped with tunnels linking the reaction site with the exterior. We selected soluble epoxide hydrolases as representative of this family to conduct the first systematic study on the evolution of tunnels. We hypothesised that tunnels are lined by mostly conserved residues, and are equipped with a number of specific variable residues that are able to respond to evolutionary pressure. The hypothesis was confirmed, and we suggested a general and detailed way of the tunnels\u2019 evolution analysis based on entropy values calculated for tunnels\u2019 residues. We also found three different cases of entropy distribution among tunnel-lining residues. These observations can be applied for protein reengineering mimicking the natural evolution process. We propose a \u2018perforation\u2019 mechanism for new tunnels design\n                    <jats:italic>via<\/jats:italic>\n                    the merging of internal cavities or protein surface perforation. Based on the literature data, such a strategy of new tunnel design could significantly improve the enzyme\u2019s performance and can be applied widely for enzymes with buried active sites.\n                  <\/jats:p>","DOI":"10.1371\/journal.pcbi.1010119","type":"journal-article","created":{"date-parts":[[2022,5,17]],"date-time":"2022-05-17T13:56:36Z","timestamp":1652795796000},"page":"e1010119","update-policy":"https:\/\/doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":9,"title":["Evolution of tunnels in \u03b1\/\u03b2-hydrolase fold proteins\u2014What can we learn from studying epoxide hydrolases?"],"prefix":"10.1371","volume":"18","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-6802-8753","authenticated-orcid":true,"given":"Maria","family":"Bz\u00f3wka","sequence":"first","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0183-0845","authenticated-orcid":true,"given":"Karolina","family":"Mitusi\u0144ska","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1884-3669","authenticated-orcid":true,"given":"Agata","family":"Raczy\u0144ska","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6059-8663","authenticated-orcid":true,"given":"Tomasz","family":"Skalski","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6372-8125","authenticated-orcid":true,"given":"Aleksandra","family":"Samol","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1749-8514","authenticated-orcid":true,"given":"Weronika","family":"Bagrowska","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2904-6788","authenticated-orcid":true,"given":"Tomasz","family":"Magdziarz","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2530-6957","authenticated-orcid":true,"given":"Artur","family":"G\u00f3ra","sequence":"additional","affiliation":[]}],"member":"340","published-online":{"date-parts":[[2022,5,17]]},"reference":[{"issue":"7","key":"pcbi.1010119.ref001","doi-asserted-by":"crossref","first-page":"2848","DOI":"10.1073\/pnas.71.7.2848","article-title":"On 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