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Free-Energy Landscape and Rate Estimation of the Aromatic Ring Flips in Basic Pancreatic Trypsin Inhibitors Using Metadynamics
[Image: see text] Aromatic side chains (phenylalanine and tyrosine) of a protein flip by 180° around the C(β)–C(γ) axis (χ(2) dihedral of the side chain), producing two symmetry-equivalent states. The study of ring flip dynamics with nuclear magnetic resonance (NMR) experiments helps to understand l...
Autores principales: | , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
American Chemical Society
2023
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Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10569046/ https://www.ncbi.nlm.nih.gov/pubmed/37698852 http://dx.doi.org/10.1021/acs.jctc.3c00460 |
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author | Kulkarni, Mandar Söderhjelm, Pär |
author_facet | Kulkarni, Mandar Söderhjelm, Pär |
author_sort | Kulkarni, Mandar |
collection | PubMed |
description | [Image: see text] Aromatic side chains (phenylalanine and tyrosine) of a protein flip by 180° around the C(β)–C(γ) axis (χ(2) dihedral of the side chain), producing two symmetry-equivalent states. The study of ring flip dynamics with nuclear magnetic resonance (NMR) experiments helps to understand local conformational fluctuations. Ring flips are categorized as slow (milliseconds and onward) or fast (nanoseconds to near milliseconds) based on timescales accessible to NMR experiments. In this study, we investigated the ability of the infrequent metadynamics approach to estimate the flip rate and discriminate between slow and fast ring flips for eight individual aromatic side chains (F4, Y10, Y21, F22, Y23, F33, Y35, and F45) of the basic pancreatic trypsin inhibitor. Well-tempered metadynamics simulations were performed to estimate the ring-flipping free-energy surfaces for all eight aromatic residues. The results indicate that χ(2) as a standalone collective variable (CV) is not sufficient to obtain computationally consistent results. Inclusion of a complementary CV, such as χ(1)(C(α)–C(β)), solved the problem for most residues and enabled us to classify fast and slow ring flips. This indicates the importance of librational motions in ring flips. Multiple pathways and mechanisms were observed for residues F4, Y10, and F22. Recrossing events were observed for residues F22 and F33, indicating a possible role of friction effects in ring flipping. The results demonstrate the successful application of infrequent metadynamics to estimate ring flip rates and identify certain limitations of the approach. |
format | Online Article Text |
id | pubmed-10569046 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2023 |
publisher | American Chemical Society |
record_format | MEDLINE/PubMed |
spelling | pubmed-105690462023-10-13 Free-Energy Landscape and Rate Estimation of the Aromatic Ring Flips in Basic Pancreatic Trypsin Inhibitors Using Metadynamics Kulkarni, Mandar Söderhjelm, Pär J Chem Theory Comput [Image: see text] Aromatic side chains (phenylalanine and tyrosine) of a protein flip by 180° around the C(β)–C(γ) axis (χ(2) dihedral of the side chain), producing two symmetry-equivalent states. The study of ring flip dynamics with nuclear magnetic resonance (NMR) experiments helps to understand local conformational fluctuations. Ring flips are categorized as slow (milliseconds and onward) or fast (nanoseconds to near milliseconds) based on timescales accessible to NMR experiments. In this study, we investigated the ability of the infrequent metadynamics approach to estimate the flip rate and discriminate between slow and fast ring flips for eight individual aromatic side chains (F4, Y10, Y21, F22, Y23, F33, Y35, and F45) of the basic pancreatic trypsin inhibitor. Well-tempered metadynamics simulations were performed to estimate the ring-flipping free-energy surfaces for all eight aromatic residues. The results indicate that χ(2) as a standalone collective variable (CV) is not sufficient to obtain computationally consistent results. Inclusion of a complementary CV, such as χ(1)(C(α)–C(β)), solved the problem for most residues and enabled us to classify fast and slow ring flips. This indicates the importance of librational motions in ring flips. Multiple pathways and mechanisms were observed for residues F4, Y10, and F22. Recrossing events were observed for residues F22 and F33, indicating a possible role of friction effects in ring flipping. The results demonstrate the successful application of infrequent metadynamics to estimate ring flip rates and identify certain limitations of the approach. American Chemical Society 2023-09-12 /pmc/articles/PMC10569046/ /pubmed/37698852 http://dx.doi.org/10.1021/acs.jctc.3c00460 Text en © 2023 The Authors. Published by American Chemical Society https://creativecommons.org/licenses/by/4.0/Permits the broadest form of re-use including for commercial purposes, provided that author attribution and integrity are maintained (https://creativecommons.org/licenses/by/4.0/). |
spellingShingle | Kulkarni, Mandar Söderhjelm, Pär Free-Energy Landscape and Rate Estimation of the Aromatic Ring Flips in Basic Pancreatic Trypsin Inhibitors Using Metadynamics |
title | Free-Energy Landscape
and Rate Estimation of the Aromatic
Ring Flips in Basic Pancreatic Trypsin Inhibitors Using Metadynamics |
title_full | Free-Energy Landscape
and Rate Estimation of the Aromatic
Ring Flips in Basic Pancreatic Trypsin Inhibitors Using Metadynamics |
title_fullStr | Free-Energy Landscape
and Rate Estimation of the Aromatic
Ring Flips in Basic Pancreatic Trypsin Inhibitors Using Metadynamics |
title_full_unstemmed | Free-Energy Landscape
and Rate Estimation of the Aromatic
Ring Flips in Basic Pancreatic Trypsin Inhibitors Using Metadynamics |
title_short | Free-Energy Landscape
and Rate Estimation of the Aromatic
Ring Flips in Basic Pancreatic Trypsin Inhibitors Using Metadynamics |
title_sort | free-energy landscape
and rate estimation of the aromatic
ring flips in basic pancreatic trypsin inhibitors using metadynamics |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10569046/ https://www.ncbi.nlm.nih.gov/pubmed/37698852 http://dx.doi.org/10.1021/acs.jctc.3c00460 |
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