{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,11]],"date-time":"2026-09-11T01:20:09Z","timestamp":1789089609035,"version":"build-2803163510"},"reference-count":21,"publisher":"MDPI AG","issue":"24","license":[{"start":{"date-parts":[[2025,12,16]],"date-time":"2025-12-16T00:00:00Z","timestamp":1765843200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100008982","name":"Qatar National Research Fund","doi-asserted-by":"publisher","award":["NPRP14S-0406-210150"],"award-info":[{"award-number":["NPRP14S-0406-210150"]}],"id":[{"id":"10.13039\/100008982","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100004252","name":"Qatar University","doi-asserted-by":"publisher","award":["QUST-1-CPH-2025-247"],"award-info":[{"award-number":["QUST-1-CPH-2025-247"]}],"id":[{"id":"10.13039\/501100004252","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Molecules"],"abstract":"<jats:p>Sestrin2 (SESN2) is a highly conserved stress-inducible protein that serves as a central hub for integrating cellular responses to nutrient availability, oxidative stress, and endoplasmic reticulum (ER) stress. A key function of SESN2 is its role as a direct sensor for the branched-chain amino acid (BCAA) leucine, which modulates the activity of the mechanistic target of rapamycin complex 1 (mTORC1), a master regulator of cell growth and metabolism. While the functional link between leucine and SESN2 is well-established, the precise molecular determinants that confer its high specificity for leucine over other BCAAs, such as isoleucine and valine, remain poorly understood. This study employs an integrated computational approach, spanning atomic interactions to global protein dynamics, combining molecular docking, extensive all-atom molecular dynamics (MD) simulations, and binding free energy calculations, to elucidate the structural and dynamic basis of BCAA-SESN2 recognition. Our thermodynamic analysis reveals a distinct binding affinity hierarchy (Leucine &gt; Isoleucine &gt; Valine), which is primarily driven by superior van der Waals interactions and the shape complementarity of leucine\u2019s isobutyl side chain within the protein\u2019s hydrophobic pocket. Critically, a quantitative analysis of the conformational ensemble reveals that leucine induces a dramatic collapse of the protein\u2019s structural heterogeneity. This \u201cconformational locking\u201d mechanism funnels the flexible, high-entropy unbound protein\u2014which samples 35 distinct conformations\u2014into a sharply restricted ensemble of just 9 stable states. This four-fold reduction in conformational freedom is accompanied by a kinetic trapping effect, which significantly lowers the rate of transitions between states. This process of conformational selection stabilizes a well-defined, signaling-competent structure, providing a comprehensive, atom-to-global-scale model of SESN2\u2019s function. In the context of these findings, this work provides a critical framework for understanding SESN2\u2019s complex role in disease and offers a clear rationale for the design of next-generation allosteric therapeutics.<\/jats:p>","DOI":"10.3390\/molecules30244791","type":"journal-article","created":{"date-parts":[[2025,12,16]],"date-time":"2025-12-16T11:00:26Z","timestamp":1765882826000},"page":"4791","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":1,"title":["Allosteric Conformational Locking of Sestrin2 by Leucine: An Integrated Computational Analysis of Branched-Chain Amino Acid Recognition and Specificity"],"prefix":"10.3390","volume":"30","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-7222-6776","authenticated-orcid":false,"given":"Muhammad Ammar","family":"Zahid","sequence":"first","affiliation":[{"name":"Department of Pharmaceutical Sciences, College of Pharmacy, QU Health, Qatar University, Doha P.O. Box 2713, Qatar"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Abbas","family":"Khan","sequence":"additional","affiliation":[{"name":"Department of Pharmaceutical Sciences, College of Pharmacy, QU Health, Qatar University, Doha P.O. Box 2713, Qatar"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5140-2531","authenticated-orcid":false,"given":"Mona A.","family":"Sawali","sequence":"additional","affiliation":[{"name":"Department of Pharmaceutical Sciences, College of Pharmacy, QU Health, Qatar University, Doha P.O. Box 2713, Qatar"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0002-2769-3508","authenticated-orcid":false,"given":"Osama Aboubakr","family":"Mohamed","sequence":"additional","affiliation":[{"name":"Department of Pharmaceutical Sciences, College of Pharmacy, QU Health, Qatar University, Doha P.O. Box 2713, Qatar"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0007-1323-2053","authenticated-orcid":false,"given":"Ahmed Mohammad","family":"Gharaibeh","sequence":"additional","affiliation":[{"name":"Department of Pharmaceutical Sciences, College of Pharmacy, QU Health, Qatar University, Doha P.O. Box 2713, Qatar"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8363-1582","authenticated-orcid":false,"given":"Abdelali","family":"Agouni","sequence":"additional","affiliation":[{"name":"Department of Pharmaceutical Sciences, College of Pharmacy, QU Health, Qatar University, Doha P.O. Box 2713, Qatar"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2025,12,16]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1016\/j.celrep.2014.09.014","article-title":"The Sestrins Interact with GATOR2 to Negatively Regulate the Amino-Acid-Sensing Pathway Upstream of mTORC1","volume":"9","author":"Chantranupong","year":"2014","journal-title":"Cell Rep."},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"e997113","DOI":"10.1080\/23723556.2014.997113","article-title":"SESTRINs Regulate mTORC1 via RRAGs: The Riddle of GATOR","volume":"2","author":"Budanov","year":"2015","journal-title":"Mol. Cell. Oncol."},{"key":"ref_3","doi-asserted-by":"crossref","unstructured":"Haidurov, A., and Budanov, A.V. (2024). Locked in Structure: Sestrin and GATOR\u2014A Billion-Year Marriage. 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