{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,14]],"date-time":"2026-03-14T03:03:56Z","timestamp":1773457436569,"version":"3.50.1"},"reference-count":44,"publisher":"MDPI AG","issue":"22","license":[{"start":{"date-parts":[[2022,11,10]],"date-time":"2022-11-10T00:00:00Z","timestamp":1668038400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"FCT, Portugal","award":["UID\/MULT I\/04046\/2020"],"award-info":[{"award-number":["UID\/MULT I\/04046\/2020"]}]},{"name":"FCT, Portugal","award":["SFRH\/BD\/144345\/2019"],"award-info":[{"award-number":["SFRH\/BD\/144345\/2019"]}]},{"name":"FCT, Portugal","award":["PTDC\/FIS-OUT\/28210\/2017"],"award-info":[{"award-number":["PTDC\/FIS-OUT\/28210\/2017"]}]},{"name":"FCT, Portugal","award":["CA17139"],"award-info":[{"award-number":["CA17139"]}]},{"name":"FCT, Portugal","award":["PID2019-106557GB-C21"],"award-info":[{"award-number":["PID2019-106557GB-C21"]}]},{"name":"COST Action","award":["UID\/MULT I\/04046\/2020"],"award-info":[{"award-number":["UID\/MULT I\/04046\/2020"]}]},{"name":"COST Action","award":["SFRH\/BD\/144345\/2019"],"award-info":[{"award-number":["SFRH\/BD\/144345\/2019"]}]},{"name":"COST Action","award":["PTDC\/FIS-OUT\/28210\/2017"],"award-info":[{"award-number":["PTDC\/FIS-OUT\/28210\/2017"]}]},{"name":"COST Action","award":["CA17139"],"award-info":[{"award-number":["CA17139"]}]},{"name":"COST Action","award":["PID2019-106557GB-C21"],"award-info":[{"award-number":["PID2019-106557GB-C21"]}]},{"name":"Spanish \u201cMinisterio de Ciencia e Innovaci\u00f3n\u201d","award":["UID\/MULT I\/04046\/2020"],"award-info":[{"award-number":["UID\/MULT I\/04046\/2020"]}]},{"name":"Spanish \u201cMinisterio de Ciencia e Innovaci\u00f3n\u201d","award":["SFRH\/BD\/144345\/2019"],"award-info":[{"award-number":["SFRH\/BD\/144345\/2019"]}]},{"name":"Spanish \u201cMinisterio de Ciencia e Innovaci\u00f3n\u201d","award":["PTDC\/FIS-OUT\/28210\/2017"],"award-info":[{"award-number":["PTDC\/FIS-OUT\/28210\/2017"]}]},{"name":"Spanish \u201cMinisterio de Ciencia e Innovaci\u00f3n\u201d","award":["CA17139"],"award-info":[{"award-number":["CA17139"]}]},{"name":"Spanish \u201cMinisterio de Ciencia e Innovaci\u00f3n\u201d","award":["PID2019-106557GB-C21"],"award-info":[{"award-number":["PID2019-106557GB-C21"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["IJMS"],"abstract":"<jats:p>Monte Carlo simulations are a powerful technique and are widely used in different fields. When applied to complex molecular systems with long chains, such as those in synthetic polymers and proteins, they have the advantage of providing a fast and computationally efficient way to sample equilibrium ensembles and calculate thermodynamic and structural properties under desired conditions. Conformational Monte Carlo techniques employ a move set to perform the transitions in the simulation Markov chain. While accepted conformations must preserve the sequential bonding of the protein chain model and excluded volume among its units, the moves themselves may take the chain across itself. We call this a break in linear topology preservation. In this manuscript, we show, using simple protein models, that there is no difference in equilibrium properties calculated with a move set that preserves linear topology and one that does not. However, for complex structures, such as those of deeply knotted proteins, the preservation of linear topology provides correct equilibrium results but only after long relaxation. In any case, to analyze folding pathways, knotting mechanisms and folding kinetics, the preservation of linear topology may be an unavoidable requirement.<\/jats:p>","DOI":"10.3390\/ijms232213871","type":"journal-article","created":{"date-parts":[[2022,11,10]],"date-time":"2022-11-10T19:16:23Z","timestamp":1668107783000},"page":"13871","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":9,"title":["A Note on the Effects of Linear Topology Preservation in Monte Carlo Simulations of Knotted Proteins"],"prefix":"10.3390","volume":"23","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-5476-5370","authenticated-orcid":false,"given":"Jo\u00e3o N. C.","family":"Especial","sequence":"first","affiliation":[{"name":"Departamento de F\u00edsica, BioISI-Biosystems and Integrative Sciences Institute, Faculdade de Ci\u00eancias, Universidade de Lisboa, 1749-016 Lisboa, Portugal"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8901-4198","authenticated-orcid":false,"given":"Antonio","family":"Rey","sequence":"additional","affiliation":[{"name":"Departamento de Qu\u00edmica F\u00edsica, Facultad de Ciencias Qu\u00edmicas, Universidad Complutense, 28040 Madrid, Spain"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2493-2748","authenticated-orcid":false,"given":"Patr\u00edcia F. N.","family":"Fa\u00edsca","sequence":"additional","affiliation":[{"name":"Departamento de F\u00edsica, BioISI-Biosystems and Integrative Sciences Institute, Faculdade de Ci\u00eancias, Universidade de Lisboa, 1749-016 Lisboa, Portugal"}]}],"member":"1968","published-online":{"date-parts":[[2022,11,10]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"495","DOI":"10.1038\/268495a0","article-title":"\u03b2-Sheet topology and the relatedness of proteins","volume":"268","author":"Richardson","year":"1977","journal-title":"Nature"},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"916","DOI":"10.1038\/35022623","article-title":"A deeply knotted protein structure and how it might fold","volume":"406","author":"Taylor","year":"2000","journal-title":"Nature"},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"533","DOI":"10.1042\/BST20120339","article-title":"Identifying knots in proteins","volume":"41","author":"Millett","year":"2013","journal-title":"Biochem. 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