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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
Particle mesh Ewald: An N ⋅log( N ) method for Ewald sums in large systems
Darden, T., York, D., & Pedersen, L. (1993) · The Journal of Chemical Physics · doi:10.1063/1.464397 · Cited by 30,546
A smooth particle mesh Ewald method
Essmann, U., Perera, L., Berkowitz, M. L., Darden, T., Lee, H., & Pedersen, L. G. (1995) · The Journal of Chemical Physics · doi:10.1063/1.470117 · Cited by 22,514
Ryckaert, J.-P., Ciccotti, G., & Berendsen, H. J. C. (1977) · Journal of Computational Physics · doi:10.1016/0021-9991(77)90098-5 · Cited by 21,239
The missing term in effective pair potentials
Berendsen, H. J. C., Grigera, J. R., & Straatsma, T. P. (1987) · The Journal of Physical Chemistry · doi:10.1021/j100308a038 · Cited by 13,345
Bayly, C. I., Cieplak, P., Cornell, W., & Kollman, P. A. (1993) · The Journal of Physical Chemistry · doi:10.1021/j100142a004 · Cited by 8,081
Cell Signaling by Receptor Tyrosine Kinases
Lemmon, M. A., & Schlessinger, J. (2010) · Cell · doi:10.1016/j.cell.2010.06.011 · Cited by 7,929
Cell Signaling by Receptor Tyrosine Kinases
Schlessinger, J. (2000) · Cell · doi:10.1016/s0092-8674(00)00114-8 · Cited by 3,774
Joung, I. S., & Cheatham, T. E. (2008) · The Journal of Physical Chemistry B · doi:10.1021/jp8001614 · Cited by 3,483
Gaussian-3 (G3) theory for molecules containing first and second-row atoms
Curtiss, L. A., Raghavachari, K., Redfern, P. C., Rassolov, V., & Pople, J. A. (1998) · The Journal of Chemical Physics · doi:10.1063/1.477422 · Cited by 2,865
Thermodynamics of solvation of ions. Part 5.—Gibbs free energy of hydration at 298.15 K
Marcus, Y. (1991) · J. Chem. Soc., Faraday Trans. · doi:10.1039/ft9918702995 · Cited by 2,211
Foloppe, N., & MacKerell, Jr. (2000) · Journal of Computational Chemistry · doi:10.1002/(sici)1096-987x(20000130)21:2<86::aid-jcc2>3.0.co;2-g · Cited by 1,582
The regulation of transcription by phosphorylation
Hunter, T., & Karin, M. (1992) · Cell · doi:10.1016/0092-8674(92)90162-6 · Cited by 1,281
Tissandier, M. D., Cowen, K. A., Feng, W. Y., Gundlach, E., Cohen, M. H., Earhart, A. D., Coe, J. V., & Tuttle, T. R. (1998) · The Journal of Physical Chemistry A · doi:10.1021/jp982638r · Cited by 1,149
Specificity in Signal Transduction
Pawson, T. (2004) · Cell · doi:10.1016/s0092-8674(03)01077-8 · Cited by 816
Karin, M., & Hunter, T. (1995) · Current Biology · doi:10.1016/s0960-9822(95)00151-5 · Cited by 752
MacKerell, A. D., & Banavali, N. K. (2000) · Journal of Computational Chemistry · doi:10.1002/(sici)1096-987x(20000130)21:2<105::aid-jcc3>3.0.co;2-p · Cited by 751
From Form to Function: Signaling by Protein Tyrosine Phosphatases
Tonks, N. K., & Neel, B. G. (1996) · Cell · doi:10.1016/s0092-8674(00)81357-4 · Cited by 531
Ion Solvation Thermodynamics from Simulation with a Polarizable Force Field
Grossfield, A., Ren, P., & Ponder, J. W. (2003) · Journal of the American Chemical Society · doi:10.1021/ja037005r · Cited by 525
Thermodynamics of Ion Hydration as a Measure of Effective Dielectric Properties of Water
Noyes, R. M. (1962) · Journal of the American Chemical Society · doi:10.1021/ja00863a002 · Cited by 456
Ionization potentials and electron affinities in aqueous solution
Pearson, R. G. (1986) · Journal of the American Chemical Society · doi:10.1021/ja00280a002 · Cited by 437
Lamoureux, G., & Roux, B. (2006) · The Journal of Physical Chemistry B · doi:10.1021/jp056043p · Cited by 395
Homeyer, N., Horn, A. H. C., Lanig, H., & Sticht, H. (2006) · Journal of Molecular Modeling · doi:10.1007/s00894-005-0028-4 · Cited by 394
Kumler, W. D., & Eiler, J. J. (1943) · Journal of the American Chemical Society · doi:10.1021/ja01252a028 · Cited by 274
Soft‐core potentials in thermodynamic integration: Comparing one‐ and two‐step transformations
Steinbrecher, T., Joung, I., & Case, D. A. (2011) · Journal of Computational Chemistry · doi:10.1002/jcc.21909 · Cited by 233
Self-citationExtension of the platform of applicability of the SM5.42R universal solvation model
Li, J., Zhu, T., Hawkins, G. D., Winget, P., Liotard, D. A., Cramer, C. J., & Truhlar, D. G. (1999) · Theoretical Chemistry Accounts: Theory, Computation, and Modeling (Theoretica Chimica Acta) · doi:10.1007/s002140050513 · Cited by 195
Steinbrecher, T. B., Case, D. A., & Labahn, A. (2006) · Journal of Medicinal Chemistry · doi:10.1021/jm0505720 · Cited by 84
Self-citationSwope, W. C., Horn, H. W., & Rice, J. E. (2010) · The Journal of Physical Chemistry B · doi:10.1021/jp911699p · Cited by 52
Prediction of Secondary Ionization of the Phosphate Group in Phosphotyrosine Peptides
Wojciechowski, M., Grycuk, T., Antosiewicz, J. M., & Lesyng, B. (2003) · Biophysical Journal · doi:10.1016/s0006-3495(03)74894-2 · Cited by 36
Pantano, S., & Carafoli, E. (2006) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.21239 · Cited by 33
The Mechanism of the Hydrolysis of Organic Phosphates. III. Aromatic Phosphates1
Chanley, J. D., & Feageson, E. (1955) · Journal of the American Chemical Society · doi:10.1021/ja01620a015 · Cited by 31
Gough, C. A., Gojobori, T., & Imanishi, T. (2006) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.21188 · Cited by 25
Zhang, N., Jiang, Y., Zou, J., Zhuang, S., Jin, H., & Yu, Q. (2007) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.21359 · Cited by 24
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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