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Journal article
Amber ff24EXP-GA, Based on Empirical Ramachandran Distributions of Glycine and Alanine Residues in Water
Journal of chemical theory and computation : JCTC, v 21(5), pp 2515-2534
20 Feb 2025
PMID: 39979079
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Abstract
Molecular dynamics (MD) offers important insights into intrinsically disordered peptides and proteins (IDPs) at a level of detail that often surpasses that available through experiments. Recent studies indicate that MD force fields do not reproduce intrinsic conformational ensembles of amino acid residues in water well, which limits their applicability to IDPs. We report a new MD force field, Amber ff24EXP-GA, derived from Amber ff14SB by optimizing the backbone dihedral potentials for guest glycine and alanine residues in cationic GGG and GAG peptides, respectively, to best match the guest residue-specific spectroscopic data. Amber ff24EXP-GA outperforms Amber ff14SB with respect to conformational ensembles of all 14 guest residues x (G, A, L, V, I, F, Y, Dp, Ep, R, C, N, S, T) in GxG peptides in water, for which complete sets of spectroscopic data are available. Amber ff24EXP-GA captures the spectroscopic data for at least 7 guest residues (G, A, V, F, C, T, Ep) better than CHARMM36m and exhibits more amino acid specificity than both the parent Amber ff14SB and CHARMM36m. Amber ff24EXP-GA reproduces the experimental data on three folded proteins and three longer IDPs well, while outperforming Amber ff14SB on short unfolded peptides.
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Details
- Title
- Amber ff24EXP-GA, Based on Empirical Ramachandran Distributions of Glycine and Alanine Residues in Water
- Creators
- Athul Suresh - Drexel University, PhysicsReinhard Schweitzer-Stenner - Drexel University, ChemistryBrigita Urbanc (Corresponding Author) - Drexel University, Physics
- Publication Details
- Journal of chemical theory and computation : JCTC, v 21(5), pp 2515-2534
- Publisher
- ACS Publications
- Number of pages
- 20
- Grant note
- National Science Foundation: MCB-1817650, OAC-1919691 National Science FoundationDrexel's University Research Computing Facility
This work has been supported by the National Science Foundation through the grant numbers MCB-1817650 (A.S., R.S.S., B.U.) and OAC-1919691 (B.U.). MD simulations were performed on hardware supported by Drexel's University Research Computing Facility.
- Resource Type
- Journal article
- Language
- English
- Academic Unit
- Physics; Chemistry
- Web of Science ID
- WOS:001431467000001
- Scopus ID
- 2-s2.0-86000435488
- Other Identifier
- 991022028737104721
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- Web of Science research areas
- Chemistry, Physical
- Physics, Atomic, Molecular & Chemical