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Journal article
Nearest-Neighbor Effects in Short Unfolded Peptides: An Assessment of Molecular Dynamics Force Fields
Journal of chemical information and modeling, v 66(12), pp 7190-7206
04 Jun 2026
PMID: 42240685
Featured in Collection : Research Supported by Drexel Libraries' OA Programs
Abstract
Molecular dynamics (MD) is a unique tool for the investigation of intrinsically disordered proteins (IDPs); however, the reliability of MD predictions depends on the accuracy of the underlying force field. Here, we evaluate CHARMM36m, Amber ff14SB, and Amber ff24EXP-GA with respect to their capacity to capture experimentally observed nearest-neighbor (NN) effects on the conformational dynamics of amino acid residues in short unfolded peptides in water. Amber ff24EXP-GA, developed from the parent Amber ff14SB, which is more amino acid-specific than the other two force fields and reproduces intrinsic conformational ensembles of amino acid residues significantly better than the parent force field, captures the NN effects better than Amber ff14SB. Despite a lack of residue specificity in intrinsic conformational ensembles, CHARMM36m, calibrated on global properties of IDPs, reproduces the NN effects on par with Amber ff24EXP-GA. These findings are important for the development of next-generation force fields that reproduce both the residue-specific conformational dynamics and global properties of IDPs.
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Details
- Title
- Nearest-Neighbor Effects in Short Unfolded Peptides: An Assessment of Molecular Dynamics Force Fields
- Creators
- Athul Suresh - Drexel UniversityReinhard Schweitzer-Stenner - Drexel UniversityBrigita Urbanc (Corresponding Author) - Drexel University
- Publication Details
- Journal of chemical information and modeling, v 66(12), pp 7190-7206
- Publisher
- ACS Publications
- Number of pages
- 17
- Grant note
This work has been supported by the National Science Foundation through the grant number MCB-1817650. The MD simulations were performed on hardware supported by Drexel's University Research Computing Facility and Pittsburgh Supercomputing Center (PSC) through allocation BIO240326 from the Advanced Cyberinfrastructure Coordination Ecosystem: Services & Support (ACCESS) program, which is supported by U.S. National Science Foundation grants #2138259, #2138286, #2138307, #2137603, and #2138296.
- Resource Type
- Journal article
- Language
- English
- Academic Unit
- Physics; Chemistry
- Web of Science ID
- WOS:001784659300001
- Other Identifier
- 991022189605704721
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- Web of Science research areas
- Chemistry, Medicinal
- Chemistry, Multidisciplinary
- Computer Science, Information Systems
- Computer Science, Interdisciplinary Applications