Simulating Polyproline II-Helix-Rich Peptides with the Latest Kirkwood–Buff Force Field: A Direct Comparison with AMBER and CHARMM

We simulated the dynamics of a set of peptides characterized by ensembles rich in PPII-helical content, to assess the ability of the most recent Kirkwood–Buff force field (KBFF20) to sample this conformational peculiarity. KBFF has been previously shown to capably reproduce experimental dimensions o...

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Veröffentlicht in:	The journal of physical chemistry. B 2022-10, Vol.126 (40), p.7833-7846
Hauptverfasser:	McIvor, Jordan A. P., Larsen, Danaé S., Mercadante, Davide
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Sprache:	eng
Schlagworte:	B: Biophysical and Biochemical Systems and Processes Intrinsically Disordered Proteins Molecular Conformation Molecular Dynamics Simulation Peptides - chemistry
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container_title	The journal of physical chemistry. B
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creator	McIvor, Jordan A. P. Larsen, Danaé S. Mercadante, Davide
description	We simulated the dynamics of a set of peptides characterized by ensembles rich in PPII-helical content, to assess the ability of the most recent Kirkwood–Buff force field (KBFF20) to sample this conformational peculiarity. KBFF has been previously shown to capably reproduce experimental dimensions of disordered proteins, while being limited in confidently sampling structured proteins. Further development of the force field bridged this gap. It is however still unknown what are the main differences between KBFF and AMBER/CHARMM force fields. A direct comparison is now possible as both AMBER/CHARMM force fields have been used to sample peptides rich in PPII-helical content. We found that KBFF20 samples’ PPII-helical content qualitatively matches both AMBER and CHARMM force fields, with the main difference being the KBFF ability to populate the αR region of the Ramachandran plot in the set of simulated peptides. Overall, KBFF20 is a well-balanced force field, able to sample the dynamics of both structured and unstructured proteins.
doi_str_mv	10.1021/acs.jpcb.2c03837
format	Article
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P.</creatorcontrib><creatorcontrib>Larsen, Danaé S.</creatorcontrib><creatorcontrib>Mercadante, Davide</creatorcontrib><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>MEDLINE - Academic</collection><jtitle>The journal of physical chemistry. B</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>McIvor, Jordan A. P.</au><au>Larsen, Danaé S.</au><au>Mercadante, Davide</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Simulating Polyproline II-Helix-Rich Peptides with the Latest Kirkwood–Buff Force Field: A Direct Comparison with AMBER and CHARMM</atitle><jtitle>The journal of physical chemistry. B</jtitle><addtitle>J. Phys. Chem. B</addtitle><date>2022-10-13</date><risdate>2022</risdate><volume>126</volume><issue>40</issue><spage>7833</spage><epage>7846</epage><pages>7833-7846</pages><issn>1520-6106</issn><eissn>1520-5207</eissn><abstract>We simulated the dynamics of a set of peptides characterized by ensembles rich in PPII-helical content, to assess the ability of the most recent Kirkwood–Buff force field (KBFF20) to sample this conformational peculiarity. KBFF has been previously shown to capably reproduce experimental dimensions of disordered proteins, while being limited in confidently sampling structured proteins. Further development of the force field bridged this gap. It is however still unknown what are the main differences between KBFF and AMBER/CHARMM force fields. A direct comparison is now possible as both AMBER/CHARMM force fields have been used to sample peptides rich in PPII-helical content. 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subjects	B: Biophysical and Biochemical Systems and Processes Intrinsically Disordered Proteins Molecular Conformation Molecular Dynamics Simulation Peptides - chemistry
title	Simulating Polyproline II-Helix-Rich Peptides with the Latest Kirkwood–Buff Force Field: A Direct Comparison with AMBER and CHARMM
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