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Average and extreme multi-atom Van der Waals interactions: Strong coupling of multi-atom Van der Waals interactions with covalent bonding

BACKGROUND: The prediction of ligand binding or protein structure requires very accurate force field potentials – even small errors in force field potentials can make a 'wrong' structure (from the billions possible) more stable than the single, 'correct' one. However, despite hug...

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Detalles Bibliográficos
Autor principal: Finkelstein, Alexei V
Formato: Texto
Lenguaje:English
Publicado: BioMed Central 2007
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1988792/
https://www.ncbi.nlm.nih.gov/pubmed/17880673
http://dx.doi.org/10.1186/1752-153X-1-21
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author Finkelstein, Alexei V
author_facet Finkelstein, Alexei V
author_sort Finkelstein, Alexei V
collection PubMed
description BACKGROUND: The prediction of ligand binding or protein structure requires very accurate force field potentials – even small errors in force field potentials can make a 'wrong' structure (from the billions possible) more stable than the single, 'correct' one. However, despite huge efforts to optimize them, currently-used all-atom force fields are still not able, in a vast majority of cases, even to keep a protein molecule in its native conformation in the course of molecular dynamics simulations or to bring an approximate, homology-based model of protein structure closer to its native conformation. RESULTS: A strict analysis shows that a specific coupling of multi-atom Van der Waals interactions with covalent bonding can, in extreme cases, increase (or decrease) the interaction energy by about 20–40% at certain angles between the direction of interaction and the covalent bond. It is also shown that on average multi-body effects decrease the total Van der Waals energy in proportion to the square root of the electronic component of dielectric permittivity corresponding to dipole-dipole interactions at small distances, where Van der Waals interactions take place. CONCLUSION: The study shows that currently-ignored multi-atom Van der Waals interactions can, in certain instances, lead to significant energy effects, comparable to those caused by the replacement of atoms (for instance, C by N) in conventional pairwise Van der Waals interactions.
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spelling pubmed-19887922007-09-21 Average and extreme multi-atom Van der Waals interactions: Strong coupling of multi-atom Van der Waals interactions with covalent bonding Finkelstein, Alexei V Chem Cent J Research Article BACKGROUND: The prediction of ligand binding or protein structure requires very accurate force field potentials – even small errors in force field potentials can make a 'wrong' structure (from the billions possible) more stable than the single, 'correct' one. However, despite huge efforts to optimize them, currently-used all-atom force fields are still not able, in a vast majority of cases, even to keep a protein molecule in its native conformation in the course of molecular dynamics simulations or to bring an approximate, homology-based model of protein structure closer to its native conformation. RESULTS: A strict analysis shows that a specific coupling of multi-atom Van der Waals interactions with covalent bonding can, in extreme cases, increase (or decrease) the interaction energy by about 20–40% at certain angles between the direction of interaction and the covalent bond. It is also shown that on average multi-body effects decrease the total Van der Waals energy in proportion to the square root of the electronic component of dielectric permittivity corresponding to dipole-dipole interactions at small distances, where Van der Waals interactions take place. CONCLUSION: The study shows that currently-ignored multi-atom Van der Waals interactions can, in certain instances, lead to significant energy effects, comparable to those caused by the replacement of atoms (for instance, C by N) in conventional pairwise Van der Waals interactions. BioMed Central 2007-07-30 /pmc/articles/PMC1988792/ /pubmed/17880673 http://dx.doi.org/10.1186/1752-153X-1-21 Text en Copyright © 2007 Finkelstein et al
spellingShingle Research Article
Finkelstein, Alexei V
Average and extreme multi-atom Van der Waals interactions: Strong coupling of multi-atom Van der Waals interactions with covalent bonding
title Average and extreme multi-atom Van der Waals interactions: Strong coupling of multi-atom Van der Waals interactions with covalent bonding
title_full Average and extreme multi-atom Van der Waals interactions: Strong coupling of multi-atom Van der Waals interactions with covalent bonding
title_fullStr Average and extreme multi-atom Van der Waals interactions: Strong coupling of multi-atom Van der Waals interactions with covalent bonding
title_full_unstemmed Average and extreme multi-atom Van der Waals interactions: Strong coupling of multi-atom Van der Waals interactions with covalent bonding
title_short Average and extreme multi-atom Van der Waals interactions: Strong coupling of multi-atom Van der Waals interactions with covalent bonding
title_sort average and extreme multi-atom van der waals interactions: strong coupling of multi-atom van der waals interactions with covalent bonding
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1988792/
https://www.ncbi.nlm.nih.gov/pubmed/17880673
http://dx.doi.org/10.1186/1752-153X-1-21
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