Extending the Nonbonded Cationic Dummy Model to Account for Ion-Induced Dipole Interactions
Liao, Qinghua ; Pabis, Anna ; Strodel, Birgit and Kamerlin, Shina Caroline Lynn LU
(2017)
In The Journal of Physical Chemistry Letters
8(21).
p.5408-5414
- Abstract
Modeling metalloproteins often requires classical molecular dynamics (MD) simulations in order to capture their relevant motions, which in turn necessitates reliable descriptions of the metal centers involved. One of the most successful approaches to date is provided by the "cationic dummy model", where the positive charge of the metal ion is transferred toward dummy particles that are bonded to the central metal ion in a predefined coordination geometry. While this approach allows for ligand exchange, and captures the correct electrostatics as demonstrated for different divalent metal ions, current dummy models neglect ion-induced dipole interactions. In the present work, we resolve this weakness by taking advantage of the recently... (More)
Modeling metalloproteins often requires classical molecular dynamics (MD) simulations in order to capture their relevant motions, which in turn necessitates reliable descriptions of the metal centers involved. One of the most successful approaches to date is provided by the "cationic dummy model", where the positive charge of the metal ion is transferred toward dummy particles that are bonded to the central metal ion in a predefined coordination geometry. While this approach allows for ligand exchange, and captures the correct electrostatics as demonstrated for different divalent metal ions, current dummy models neglect ion-induced dipole interactions. In the present work, we resolve this weakness by taking advantage of the recently introduced 12-6-4 type Lennard-Jones potential to include ion-induced dipole interactions. We revise our previous dummy model for Mg2+ and demonstrate that the resulting model can simultaneously reproduce the experimental solvation free energy and metal-ligand distances without the need for artificial restraints or bonds. As ion-induced dipole interactions become particularly important for highly charged metal ions, we develop dummy models for the biologically relevant ions Al3+, Fe3+, and Cr3+. Finally, the effectiveness of our new models is demonstrated in MD simulations of several diverse (and highly challenging to simulate) metalloproteins.
(Less)
- author
- Liao, Qinghua
; Pabis, Anna
; Strodel, Birgit
and Kamerlin, Shina Caroline Lynn
LU
- publishing date
- 2017-11-02
- type
- Contribution to journal
- publication status
- published
- in
- The Journal of Physical Chemistry Letters
- volume
- 8
- issue
- 21
- pages
- 7 pages
- publisher
- The American Chemical Society (ACS)
- external identifiers
-
- scopus:85032825505
- pmid:29022713
- ISSN
- 1948-7185
- DOI
- 10.1021/acs.jpclett.7b02358
- language
- English
- LU publication?
- no
- id
- 27798b62-df4b-449a-ba5c-611c9a5415c0
- date added to LUP
- 2025-01-11 21:21:34
- date last changed
- 2025-07-13 18:46:18
@article{27798b62-df4b-449a-ba5c-611c9a5415c0,
abstract = {{<p>Modeling metalloproteins often requires classical molecular dynamics (MD) simulations in order to capture their relevant motions, which in turn necessitates reliable descriptions of the metal centers involved. One of the most successful approaches to date is provided by the "cationic dummy model", where the positive charge of the metal ion is transferred toward dummy particles that are bonded to the central metal ion in a predefined coordination geometry. While this approach allows for ligand exchange, and captures the correct electrostatics as demonstrated for different divalent metal ions, current dummy models neglect ion-induced dipole interactions. In the present work, we resolve this weakness by taking advantage of the recently introduced 12-6-4 type Lennard-Jones potential to include ion-induced dipole interactions. We revise our previous dummy model for Mg2+ and demonstrate that the resulting model can simultaneously reproduce the experimental solvation free energy and metal-ligand distances without the need for artificial restraints or bonds. As ion-induced dipole interactions become particularly important for highly charged metal ions, we develop dummy models for the biologically relevant ions Al3+, Fe3+, and Cr3+. Finally, the effectiveness of our new models is demonstrated in MD simulations of several diverse (and highly challenging to simulate) metalloproteins.</p>}},
author = {{Liao, Qinghua and Pabis, Anna and Strodel, Birgit and Kamerlin, Shina Caroline Lynn}},
issn = {{1948-7185}},
language = {{eng}},
month = {{11}},
number = {{21}},
pages = {{5408--5414}},
publisher = {{The American Chemical Society (ACS)}},
series = {{The Journal of Physical Chemistry Letters}},
title = {{Extending the Nonbonded Cationic Dummy Model to Account for Ion-Induced Dipole Interactions}},
url = {{http://dx.doi.org/10.1021/acs.jpclett.7b02358}},
doi = {{10.1021/acs.jpclett.7b02358}},
volume = {{8}},
year = {{2017}},
}