Interaction of Charged Amino-Acid Side Chains with Ions: An Optimization Strategy for Classical Force Fields

Publication type:
Journal article
Metadata:
Autoren
  • Jens Kahlen
  • Leila Salimi
  • Marialore Sulpizi
  • Christine Peter
  • Davide Donadio
Autoren-URL
https://www.webofscience.com/api/gateway?GWVersion=2&SrcApp=fis-test-1&SrcAuth=WosAPI&KeyUT=WOS:000334572900021&DestLinkType=FullRecord&DestApp=WOS_CPL
DOI
10.1021/jp412490c
eISSN
1520-5207
Externe Identifier
  • Clarivate Analytics Document Solution ID: AF2WJ
  • PubMed Identifier: 24649981
ISSN
1520-6106
Ausgabe der Veröffentlichung
14
Zeitschrift
JOURNAL OF PHYSICAL CHEMISTRY B
Paginierung
3960 - 3972
Datum der Veröffentlichung
2014
Status
Published
Titel
Interaction of Charged Amino-Acid Side Chains with Ions: An Optimization Strategy for Classical Force Fields
Sub types
  • Article
Ausgabe der Zeitschrift
118

Data source: Web of Science (Lite)

Other metadata sources:
Autoren
  • Jens Kahlen
  • Leila Salimi
  • Marialore Sulpizi
  • Christine Peter
  • Davide Donadio
DOI
10.1021/jp412490c
eISSN
1520-5207
ISSN
1520-6106
Ausgabe der Veröffentlichung
14
Zeitschrift
The Journal of Physical Chemistry B
Sprache
en
Online publication date
2014
Paginierung
3960 - 3972
Datum der Veröffentlichung
2014
Status
Published
Herausgeber
American Chemical Society (ACS)
Herausgeber URL
http://dx.doi.org/10.1021/jp412490c
Datum der Datenerfassung
2023
Titel
Interaction of Charged Amino-Acid Side Chains with Ions: An Optimization Strategy for Classical Force Fields
Ausgabe der Zeitschrift
118

Data source: Crossref

Abstract
Many well-established classical biomolecular force fields, fitted on the solvation properties of single ions, do not necessarily describe all the details of ion pairing accurately, especially for complex polyatomic ions. Depending on the target application, it might not be sufficient to reproduce the thermodynamics of ion pairing, but it may also be necessary to correctly capture structural details, such as the coordination mode. In this work, we analyzed how classical force fields can be optimized to yield a realistic description of these different aspects of ion pairing. Given the prominent role of the interactions of negatively charged amino-acid side chains and divalent cations in many biomolecular systems, we chose calcium acetate as a benchmark system to devise a general optimization strategy that we applied to two popular force fields, namely, GROMOS and OPLS-AA. Using experimental association constants and first-principles molecular dynamics simulations as a reference, we found that small modifications of the van der Waals ion-ion interaction parameters allow a systematic improvement of the essential thermodynamic and structural properties of ion pairing.
Addresses
  • Max Planck Institute for Polymer Research , Ackermannweg 10, 55128 Mainz, Germany.
Autoren
  • Jens Kahlen
  • Leila Salimi
  • Marialore Sulpizi
  • Christine Peter
  • Davide Donadio
DOI
10.1021/jp412490c
eISSN
1520-5207
Externe Identifier
  • PubMed Identifier: 24649981
Open access
false
ISSN
1520-6106
Ausgabe der Veröffentlichung
14
Zeitschrift
The journal of physical chemistry. B
Schlüsselwörter
  • Calcium Compounds
  • Ions
  • Water
  • Acetates
  • Amino Acids
  • Hydrogen Bonding
  • Thermodynamics
  • Static Electricity
  • Molecular Dynamics Simulation
Sprache
eng
Medium
Print-Electronic
Online publication date
2014
Paginierung
3960 - 3972
Datum der Veröffentlichung
2014
Status
Published
Datum der Datenerfassung
2014
Titel
Interaction of charged amino-acid side chains with ions: an optimization strategy for classical force fields.
Sub types
  • Research Support, Non-U.S. Gov't
  • Journal Article
Ausgabe der Zeitschrift
118

Data source: Europe PubMed Central

Abstract
Many well-established classical biomolecular force fields, fitted on the solvation properties of single ions, do not necessarily describe all the details of ion pairing accurately, especially for complex polyatomic ions. Depending on the target application, it might not be sufficient to reproduce the thermodynamics of ion pairing, but it may also be necessary to correctly capture structural details, such as the coordination mode. In this work, we analyzed how classical force fields can be optimized to yield a realistic description of these different aspects of ion pairing. Given the prominent role of the interactions of negatively charged amino-acid side chains and divalent cations in many biomolecular systems, we chose calcium acetate as a benchmark system to devise a general optimization strategy that we applied to two popular force fields, namely, GROMOS and OPLS-AA. Using experimental association constants and first-principles molecular dynamics simulations as a reference, we found that small modifications of the van der Waals ion-ion interaction parameters allow a systematic improvement of the essential thermodynamic and structural properties of ion pairing.
Autoren
  • Jens Kahlen
  • Leila Salimi
  • Marialore Sulpizi
  • Christine Peter
  • Davide Donadio
Autoren-URL
https://www.ncbi.nlm.nih.gov/pubmed/24649981
DOI
10.1021/jp412490c
eISSN
1520-5207
Ausgabe der Veröffentlichung
14
Zeitschrift
J Phys Chem B
Schlüsselwörter
  • Acetates
  • Amino Acids
  • Calcium Compounds
  • Hydrogen Bonding
  • Ions
  • Molecular Dynamics Simulation
  • Static Electricity
  • Thermodynamics
  • Water
Sprache
eng
Country
United States
Paginierung
3960 - 3972
Datum der Veröffentlichung
2014
Status
Published
Datum, an dem der Datensatz öffentlich gemacht wurde
2015
Titel
Interaction of charged amino-acid side chains with ions: an optimization strategy for classical force fields.
Sub types
  • Journal Article
  • Research Support, Non-U.S. Gov't
Ausgabe der Zeitschrift
118

Data source: PubMed

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