Development and Application of a Nonbonded Cu2+ Model That Includes the Jahn-Teller Effect
Liao, Qinghua ; Kamerlin, Shina Caroline Lynn LU
and Strodel, Birgit
(2015)
In The Journal of Physical Chemistry Letters
6(13).
p.62-2657
- Abstract
Metal ions are both ubiquitous to and crucial in biology. In classical simulations, they are typically described as simple van der Waals spheres, making it difficult to provide reliable force field descriptions for them. An alternative is given by nonbonded dummy models, in which the central metal atom is surrounded by dummy particles that each carry a partial charge. While such dummy models already exist for other metal ions, none is available yet for Cu(2+) because of the challenge to reproduce the Jahn-Teller distortion. This challenge is addressed in the current study, where, for the first time, a dummy model including a Jahn-Teller effect is developed for Cu(2+). We successfully validate its usefulness by studying metal binding in... (More)
Metal ions are both ubiquitous to and crucial in biology. In classical simulations, they are typically described as simple van der Waals spheres, making it difficult to provide reliable force field descriptions for them. An alternative is given by nonbonded dummy models, in which the central metal atom is surrounded by dummy particles that each carry a partial charge. While such dummy models already exist for other metal ions, none is available yet for Cu(2+) because of the challenge to reproduce the Jahn-Teller distortion. This challenge is addressed in the current study, where, for the first time, a dummy model including a Jahn-Teller effect is developed for Cu(2+). We successfully validate its usefulness by studying metal binding in two biological systems: the amyloid-β peptide and the mixed-metal enzyme superoxide dismutase. We believe that our parameters will be of significant value for the computational study of Cu(2+)-dependent biological systems using classical models.
(Less)
- author
- Liao, Qinghua
; Kamerlin, Shina Caroline Lynn
LU
and Strodel, Birgit
- publishing date
- 2015-07-02
- type
- Contribution to journal
- publication status
- published
- keywords
- Copper/chemistry, Models, Chemical
- in
- The Journal of Physical Chemistry Letters
- volume
- 6
- issue
- 13
- pages
- 6 pages
- publisher
- The American Chemical Society (ACS)
- external identifiers
-
- pmid:26167255
- scopus:84947751672
- ISSN
- 1948-7185
- DOI
- 10.1021/acs.jpclett.5b01122
- language
- English
- LU publication?
- no
- id
- 3c44b678-a468-4d3b-a004-40bfc06eb879
- date added to LUP
- 2025-01-11 21:36:07
- date last changed
- 2025-05-18 18:08:34
@article{3c44b678-a468-4d3b-a004-40bfc06eb879,
abstract = {{<p>Metal ions are both ubiquitous to and crucial in biology. In classical simulations, they are typically described as simple van der Waals spheres, making it difficult to provide reliable force field descriptions for them. An alternative is given by nonbonded dummy models, in which the central metal atom is surrounded by dummy particles that each carry a partial charge. While such dummy models already exist for other metal ions, none is available yet for Cu(2+) because of the challenge to reproduce the Jahn-Teller distortion. This challenge is addressed in the current study, where, for the first time, a dummy model including a Jahn-Teller effect is developed for Cu(2+). We successfully validate its usefulness by studying metal binding in two biological systems: the amyloid-β peptide and the mixed-metal enzyme superoxide dismutase. We believe that our parameters will be of significant value for the computational study of Cu(2+)-dependent biological systems using classical models.</p>}},
author = {{Liao, Qinghua and Kamerlin, Shina Caroline Lynn and Strodel, Birgit}},
issn = {{1948-7185}},
keywords = {{Copper/chemistry; Models, Chemical}},
language = {{eng}},
month = {{07}},
number = {{13}},
pages = {{62--2657}},
publisher = {{The American Chemical Society (ACS)}},
series = {{The Journal of Physical Chemistry Letters}},
title = {{Development and Application of a Nonbonded Cu<sup>2+</sup> Model That Includes the Jahn-Teller Effect}},
url = {{http://dx.doi.org/10.1021/acs.jpclett.5b01122}},
doi = {{10.1021/acs.jpclett.5b01122}},
volume = {{6}},
year = {{2015}},
}