The Effect of a Knot on the Thermal Stability of Protein MJ0366: Insights from Molecular Dynamics and Monte Carlo Simulations

Protein MJ0366 is a hypothetical protein from Methanocaldococcus jannaschii that has a rare and complex knot in its structure. The knot is a right-handed trefoil knot that involves about half of the protein's residues. In this article, we investigate the thermal stability of protein MJ0366 usin...

Full description

Saved in:
Bibliographic Details
Published in:arXiv.org 2024-11
Main Authors: Begun, A M, Korneev, A A, Zorina, A V
Format: Article
Language:English
Subjects:
Biological activity
Biological effects
Computer simulation
Dynamic structural analysis
High temperature
Knots
Molecular dynamics
Molecular structure
Monte Carlo simulation
Proteins
Thermal stability
Online Access:Get full text
Tags: Add Tag
No Tags, Be the first to tag this record!
cited_by
cites
container_end_page
container_issue
container_start_page
container_title arXiv.org
container_volume
creator Begun, A M
Korneev, A A
Zorina, A V
description Protein MJ0366 is a hypothetical protein from Methanocaldococcus jannaschii that has a rare and complex knot in its structure. The knot is a right-handed trefoil knot that involves about half of the protein's residues. In this article, we investigate the thermal stability of protein MJ0366 using numerical simulations based on molecular dynamics and Monte Carlo methods. We compare the results with those of a similar unknotted protein and analyze the effects of the knot on the folding and unfolding processes. We show that the knot in protein MJ0366 increases its thermal stability by creating a topological barrier that prevents the protein from unfolding at high temperatures. We also discuss the possible biological implications of the knot for the function and evolution of protein MJ0366.
format article
fullrecord <record><control><sourceid>proquest</sourceid><recordid>TN_cdi_proquest_journals_3126151568</recordid><sourceformat>XML</sourceformat><sourcesystem>PC</sourcesystem><sourcerecordid>3126151568</sourcerecordid><originalsourceid>FETCH-proquest_journals_31261515683</originalsourceid><addsrcrecordid>eNqNisFqAjEURYMgVHT-4YHrgZmkE8XtaKkVoeDsJR2TGsm81yZvFi76703BD-jqXs45EzGTStXl-lnKJ1GkdKuqSuqVbBo1Ez_d1cLOOdszkAMDB6T8EDjz7OJgApzYfPjg-f6XvEdi6xGOb5XSegN7TP7zyglcpAGOFGw_BhNhe0cz-D6BwUvGyBZaEwPByQ85YE-YFmLqTEi2eOxcLF92XftafkX6Hm3i843GiFmdVS113dSNXqv_Vb-W4U18</addsrcrecordid><sourcetype>Aggregation Database</sourcetype><iscdi>true</iscdi><recordtype>article</recordtype><pqid>3126151568</pqid></control><display><type>article</type><title>The Effect of a Knot on the Thermal Stability of Protein MJ0366: Insights from Molecular Dynamics and Monte Carlo Simulations</title><source>Publicly Available Content Database</source><creator>Begun, A M ; Korneev, A A ; Zorina, A V</creator><creatorcontrib>Begun, A M ; Korneev, A A ; Zorina, A V</creatorcontrib><description>Protein MJ0366 is a hypothetical protein from Methanocaldococcus jannaschii that has a rare and complex knot in its structure. The knot is a right-handed trefoil knot that involves about half of the protein's residues. In this article, we investigate the thermal stability of protein MJ0366 using numerical simulations based on molecular dynamics and Monte Carlo methods. We compare the results with those of a similar unknotted protein and analyze the effects of the knot on the folding and unfolding processes. We show that the knot in protein MJ0366 increases its thermal stability by creating a topological barrier that prevents the protein from unfolding at high temperatures. We also discuss the possible biological implications of the knot for the function and evolution of protein MJ0366.</description><identifier>EISSN: 2331-8422</identifier><language>eng</language><publisher>Ithaca: Cornell University Library, arXiv.org</publisher><subject>Biological activity ; Biological effects ; Computer simulation ; Dynamic structural analysis ; High temperature ; Knots ; Molecular dynamics ; Molecular structure ; Monte Carlo simulation ; Proteins ; Thermal stability</subject><ispartof>arXiv.org, 2024-11</ispartof><rights>2024. This work is published under http://creativecommons.org/licenses/by/4.0/ (the “License”). Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.</rights><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktohtml>$$Uhttps://www.proquest.com/docview/3126151568?pq-origsite=primo$$EHTML$$P50$$Gproquest$$Hfree_for_read</linktohtml><link.rule.ids>776,780,25733,36991,44569</link.rule.ids></links><search><creatorcontrib>Begun, A M</creatorcontrib><creatorcontrib>Korneev, A A</creatorcontrib><creatorcontrib>Zorina, A V</creatorcontrib><title>The Effect of a Knot on the Thermal Stability of Protein MJ0366: Insights from Molecular Dynamics and Monte Carlo Simulations</title><title>arXiv.org</title><description>Protein MJ0366 is a hypothetical protein from Methanocaldococcus jannaschii that has a rare and complex knot in its structure. The knot is a right-handed trefoil knot that involves about half of the protein's residues. In this article, we investigate the thermal stability of protein MJ0366 using numerical simulations based on molecular dynamics and Monte Carlo methods. We compare the results with those of a similar unknotted protein and analyze the effects of the knot on the folding and unfolding processes. We show that the knot in protein MJ0366 increases its thermal stability by creating a topological barrier that prevents the protein from unfolding at high temperatures. We also discuss the possible biological implications of the knot for the function and evolution of protein MJ0366.</description><subject>Biological activity</subject><subject>Biological effects</subject><subject>Computer simulation</subject><subject>Dynamic structural analysis</subject><subject>High temperature</subject><subject>Knots</subject><subject>Molecular dynamics</subject><subject>Molecular structure</subject><subject>Monte Carlo simulation</subject><subject>Proteins</subject><subject>Thermal stability</subject><issn>2331-8422</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2024</creationdate><recordtype>article</recordtype><sourceid>PIMPY</sourceid><recordid>eNqNisFqAjEURYMgVHT-4YHrgZmkE8XtaKkVoeDsJR2TGsm81yZvFi76703BD-jqXs45EzGTStXl-lnKJ1GkdKuqSuqVbBo1Ez_d1cLOOdszkAMDB6T8EDjz7OJgApzYfPjg-f6XvEdi6xGOb5XSegN7TP7zyglcpAGOFGw_BhNhe0cz-D6BwUvGyBZaEwPByQ85YE-YFmLqTEi2eOxcLF92XftafkX6Hm3i843GiFmdVS113dSNXqv_Vb-W4U18</recordid><startdate>20241107</startdate><enddate>20241107</enddate><creator>Begun, A M</creator><creator>Korneev, A A</creator><creator>Zorina, A V</creator><general>Cornell University Library, arXiv.org</general><scope>8FE</scope><scope>8FG</scope><scope>ABJCF</scope><scope>ABUWG</scope><scope>AFKRA</scope><scope>AZQEC</scope><scope>BENPR</scope><scope>BGLVJ</scope><scope>CCPQU</scope><scope>DWQXO</scope><scope>HCIFZ</scope><scope>L6V</scope><scope>M7S</scope><scope>PIMPY</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>PRINS</scope><scope>PTHSS</scope></search><sort><creationdate>20241107</creationdate><title>The Effect of a Knot on the Thermal Stability of Protein MJ0366: Insights from Molecular Dynamics and Monte Carlo Simulations</title><author>Begun, A M ; Korneev, A A ; Zorina, A V</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-proquest_journals_31261515683</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2024</creationdate><topic>Biological activity</topic><topic>Biological effects</topic><topic>Computer simulation</topic><topic>Dynamic structural analysis</topic><topic>High temperature</topic><topic>Knots</topic><topic>Molecular dynamics</topic><topic>Molecular structure</topic><topic>Monte Carlo simulation</topic><topic>Proteins</topic><topic>Thermal stability</topic><toplevel>online_resources</toplevel><creatorcontrib>Begun, A M</creatorcontrib><creatorcontrib>Korneev, A A</creatorcontrib><creatorcontrib>Zorina, A V</creatorcontrib><collection>ProQuest SciTech Collection</collection><collection>ProQuest Technology Collection</collection><collection>Materials Science &amp; Engineering Collection</collection><collection>ProQuest Central (Alumni)</collection><collection>ProQuest Central</collection><collection>ProQuest Central Essentials</collection><collection>ProQuest Central</collection><collection>Technology Collection</collection><collection>ProQuest One Community College</collection><collection>ProQuest Central</collection><collection>SciTech Premium Collection</collection><collection>ProQuest Engineering Collection</collection><collection>Engineering Database</collection><collection>Publicly Available Content Database</collection><collection>ProQuest One Academic Eastern Edition (DO NOT USE)</collection><collection>ProQuest One Academic</collection><collection>ProQuest One Academic UKI Edition</collection><collection>ProQuest Central China</collection><collection>Engineering Collection</collection></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Begun, A M</au><au>Korneev, A A</au><au>Zorina, A V</au><format>book</format><genre>document</genre><ristype>GEN</ristype><atitle>The Effect of a Knot on the Thermal Stability of Protein MJ0366: Insights from Molecular Dynamics and Monte Carlo Simulations</atitle><jtitle>arXiv.org</jtitle><date>2024-11-07</date><risdate>2024</risdate><eissn>2331-8422</eissn><abstract>Protein MJ0366 is a hypothetical protein from Methanocaldococcus jannaschii that has a rare and complex knot in its structure. The knot is a right-handed trefoil knot that involves about half of the protein's residues. In this article, we investigate the thermal stability of protein MJ0366 using numerical simulations based on molecular dynamics and Monte Carlo methods. We compare the results with those of a similar unknotted protein and analyze the effects of the knot on the folding and unfolding processes. We show that the knot in protein MJ0366 increases its thermal stability by creating a topological barrier that prevents the protein from unfolding at high temperatures. We also discuss the possible biological implications of the knot for the function and evolution of protein MJ0366.</abstract><cop>Ithaca</cop><pub>Cornell University Library, arXiv.org</pub><oa>free_for_read</oa></addata></record>
fulltext fulltext
identifier EISSN: 2331-8422
ispartof arXiv.org, 2024-11
issn 2331-8422
language eng
recordid cdi_proquest_journals_3126151568
source Publicly Available Content Database
subjects Biological activity
Biological effects
Computer simulation
Dynamic structural analysis
High temperature
Knots
Molecular dynamics
Molecular structure
Monte Carlo simulation
Proteins
Thermal stability
title The Effect of a Knot on the Thermal Stability of Protein MJ0366: Insights from Molecular Dynamics and Monte Carlo Simulations
url http://sfxeu10.hosted.exlibrisgroup.com/loughborough?ctx_ver=Z39.88-2004&ctx_enc=info:ofi/enc:UTF-8&ctx_tim=2025-01-27T22%3A25%3A09IST&url_ver=Z39.88-2004&url_ctx_fmt=infofi/fmt:kev:mtx:ctx&rfr_id=info:sid/primo.exlibrisgroup.com:primo3-Article-proquest&rft_val_fmt=info:ofi/fmt:kev:mtx:book&rft.genre=document&rft.atitle=The%20Effect%20of%20a%20Knot%20on%20the%20Thermal%20Stability%20of%20Protein%20MJ0366:%20Insights%20from%20Molecular%20Dynamics%20and%20Monte%20Carlo%20Simulations&rft.jtitle=arXiv.org&rft.au=Begun,%20A%20M&rft.date=2024-11-07&rft.eissn=2331-8422&rft_id=info:doi/&rft_dat=%3Cproquest%3E3126151568%3C/proquest%3E%3Cgrp_id%3Ecdi_FETCH-proquest_journals_31261515683%3C/grp_id%3E%3Coa%3E%3C/oa%3E%3Curl%3E%3C/url%3E&rft_id=info:oai/&rft_pqid=3126151568&rft_id=info:pmid/&rfr_iscdi=true