The DOI matches its Crossref record; 32 of the 32 references it cites were found in a registry or an index.
Revised AMBER Parameters for Bioorganic Phosphates
Open accessAbstract
We report AMBER force field parameters for biological simulations involving phosphorylation of serine, threonine or tyrosine. The initial parameters used RESP fitting for the atomic partial charges and standard values for all other parameters such as Lennard-Jones coefficients. These were refined with the aid of a thermodynamic cycle consisting of experimentally determined pKa values, solvation energies from molecular dynamics free energy simulations, and gas phase basicities from QM calculations. A polarization energy term was included to account for the charge density change between the gas-phase and solution, and solvation free energies were determined using thermodynamic integration. Parameter adjustment is required to obtain consistent thermodynamic results with better balanced electrostatic interactions between water and the phosphate oxygens. To achieve this we modified the phosphate oxygen radii. A thermodynamically consistent parameter set can be derived for monoanions and requires an increase of the van der Waals phosphate oxygen radii of approximately 0.09 Å. Larger, residue-specific radii appear to be needed for dianions. The revised parameters developed here should be of particular interest for environments where simulations of multiple protonation states may be of interest.
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Cites
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Cited by
Li, A., & Gilson, M. K. (2018) · The Journal of Chemical Physics · doi:10.1063/1.5027439 · Cited by 24
“The ff12SB force field[34] was used for the protein, GAFF[35] forcefield parameters were used for HEPES, and forcefield parameters for the phosphotyrosine (PTY) residue were taken from the set determined by Steinbrecher et al[36, 37], as available in the AMBER frcmod.”
MethodShort RNA chaperones promote aggregation-resistant TDP-43 conformers to mitigate neurodegeneration
Copley, K. E., Mauna, J. C., Danielson, H. L., Chen, Q., Ozguney, B., Ngo, M., Xie, L., Smirnov, A., Davis, M., Mayne, L., et al. (2026) · Science · doi:10.1126/science.adv3301 · Cited by 16
Akulov, V., Jiménez Panizo, A., Estébanez-Perpiñá, E., van Noort, J., & Mashaghi, A. (2025) · The Journal of Physical Chemistry B · doi:10.1021/acs.jpcb.5c03257 · Cited by 7
Metadata
- Authors
- Steinbrecher, T., Latzer, J., & Case, D. A.
- Venue
- Journal of Chemical Theory and Computation
- Publisher
- American Chemical Society (ACS)
- Published
- 2012-10-03
- Volume
- 8
- Issue
- 11
- Pages
- 4405-4412
- ISSN
- 1549-9618 (ISSN-L)
- 1549-9626
- OpenAlex
- W2077873773
- Cited by
- 263
- References
- 32
- FWCI
- 3.66
- Type
- journal article
- Language
- en
- Open access
- green
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