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In the so-called <jats:italic>loop<\/jats:italic> model, the ICL3 region that is missing in available crystal structures was modeled as an unstructured loop of 32-residues length, whereas in the <jats:italic>clipped<\/jats:italic> model, the two open ends were covalently bonded to each other. The latter model without ICL3 was taken as a reference, which has also been commonly used in recent computational studies. Each model was embedded into POPC bilayer membrane with explicit water and subjected to a 1 \u03bcs molecular dynamics (MD) simulation at 310\u00a0K.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Results<\/jats:title>\n            <jats:p>After around 600\u00a0ns, the <jats:italic>loop<\/jats:italic> model started a transition to a \u201cvery inactive\u201d conformation, which is characterized by a further movement of the intracellular half of transmembrane helix 6 (TM6) towards the receptor core, and a close packing of ICL3 underneath the membrane completely blocking the G-protein\u2019s binding site. Concurrently, the binding site at the extracellular part of the receptor expanded slightly with the Ser207-Asp113 distance increasing to 18\u00a0\u00c5 from 11\u00a0\u00c5, which was further elaborated by docking studies.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Conclusions<\/jats:title>\n            <jats:p>The essential dynamics analysis indicated a strong coupling between the extracellular and intracellular parts of the intact receptor, implicating a functional relevance for allosteric regulation. In contrast, no such transition to the \u201cvery inactive\u201d state, nor any structural correlation, was observed in the <jats:italic>clipped<\/jats:italic> model without ICL3. Furthermore, elastic network analysis using different conformers for the <jats:italic>loop<\/jats:italic> model indicated a consistent picture on the specific ICL3 conformational change being driven by global modes.<\/jats:p>\n          <\/jats:sec>","DOI":"10.1186\/1472-6807-13-29","type":"journal-article","created":{"date-parts":[[2013,11,9]],"date-time":"2013-11-09T22:00:53Z","timestamp":1384034453000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":31,"title":["Effect of intracellular loop 3 on intrinsic dynamics of human \u03b22-adrenergic receptor"],"prefix":"10.1186","volume":"13","author":[{"given":"Ozer","family":"Ozcan","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Arzu","family":"Uyar","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Pemra","family":"Doruker","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ebru Demet","family":"Akten","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2013,11,9]]},"reference":[{"key":"465_CR1","doi-asserted-by":"publisher","first-page":"739","DOI":"10.1126\/science.289.5480.739","volume":"289","author":"K Palczewski","year":"2000","unstructured":"Palczewski K, Kumasaka T, Hori T, Behnke CA, Motoshima H, Fox BA, Trong IL, Teller DC, Okada T, Stenkamp RE, Yamamoto M, Miyano M: Crystal structure of rhodopsin: a G protein-coupled receptor. 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