{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,17]],"date-time":"2026-09-17T14:01:51Z","timestamp":1789653711734,"version":"4.0.0"},"reference-count":138,"publisher":"American Chemical Society (ACS)","issue":"37","license":[{"start":{"date-parts":[[2026,9,4]],"date-time":"2026-09-04T00:00:00Z","timestamp":1788480000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000057","name":"National Institute of General Medical Sciences","doi-asserted-by":"publisher","award":["R35-GM150409"],"award-info":[{"award-number":["R35-GM150409"]}],"id":[{"id":"10.13039\/100000057","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2026,9,17]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Collagen is the primary constituent of the supramolecular fibers found in connective tissues. To be able to predict collagen\u2019s properties, we need rigorous characterization at the molecular scale. In this work, we focus on collagen-mimetic peptides (CMPs) that are composed of short sequences of (PPG) tripeptides folded into a triple helix. We use molecular dynamics simulations with the AMOEBA polarizable force field to model these CMPs at physiological temperature. We show that AMOEBA captures length-dependent fraying of the triple helix, consistent with experimental observations. We also introduce new metrics to quantify the deformation of the triple helix and hydration dynamics. This enables a systematic quantification of CMPs under a variety of conditions, which was missing in the field. We apply our approach to mutated CMPs and CMPs in the presence of d-glucose. We find that translational diffusion anisotropy is a molecular signature of CMP structural integrity.<\/jats:p>","DOI":"10.1021\/acs.jpcb.6c02718","type":"journal-article","created":{"date-parts":[[2026,9,4]],"date-time":"2026-09-04T09:02:16Z","timestamp":1788512536000},"page":"9481-9495","source":"Crossref","is-referenced-by-count":0,"title":["Using AMOEBA to\nUncover Deformation and Hydration\nAnisotropy in Collagen-Mimetic Peptides"],"prefix":"10.1021","volume":"130","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-4393-018X","authenticated-orcid":true,"given":"Ronnie","family":"Mondal","sequence":"first","affiliation":[{"name":"Virginia Tech , , , ,","place":["Blacksburg, Virginia, United States, 24061"]},{"name":"Virginia Tech , , , ,","place":["Blacksburg, Virginia, United States, 24061"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0834-4441","authenticated-orcid":true,"given":"Valerie","family":"Vaissier Welborn","sequence":"additional","affiliation":[{"name":"Virginia Tech , , , ,","place":["Blacksburg, Virginia, United States, 24061"]},{"name":"Virginia Tech , , , ,","place":["Blacksburg, Virginia, United States, 24061"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"316","published-online":{"date-parts":[[2026,9,4]]},"reference":[{"key":"2026091708475137500_cit1","doi-asserted-by":"publisher","first-page":"2784","DOI":"10.1021\/acs.biomac.4c01735","article-title":"Water and collagen: A mystery yet to unfold","volume":"26","author":"Giannetti","year":"2025","journal-title":"Biomacromolecules"},{"key":"2026091708475137500_cit2","doi-asserted-by":"publisher","first-page":"2557","DOI":"10.3390\/ijms18122557","article-title":"Probing protein\nglycation\nby chromatography and mass spectrometry: analysis of glycation adducts","volume":"18","author":"Soboleva","year":"2017","journal-title":"Int. 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G.\n          \n          Investigations into\nEffects of Modified Prolines on Cis-Trans Isomers and Polypeptide\nSecondary Structure & Prediction of Spectroscopic Properties of\nPhthalonitriles for Characterization Doctoral dissertation, Seton Hall University, 2021."},{"key":"2026091708475137500_cit43","doi-asserted-by":"publisher","first-page":"118","DOI":"10.32974\/mse.2022.012","article-title":"Investigating\ncollagen\nas a bio-material by molecular dynamics simulations","volume":"47","author":"Zakaraia","year":"2023","journal-title":"Hung. Mater. Chem.Sc. And Eng."},{"key":"2026091708475137500_cit44","doi-asserted-by":"publisher","first-page":"39","DOI":"10.1007\/s10822-022-00489-8","article-title":"Molecular and thermodynamic\ninsights into interfacial interactions\nbetween colla- gen and cellulose investigated by molecular dynamics\nsimulation and umbrella sampling","volume":"37","author":"Ma","year":"2023","journal-title":"J. Comput.-Aided\nMol. 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