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Journal article
Intrinsic Conformational Dynamics of Glycine and Alanine in Polarizable Molecular Dynamics Force Fields: Comparison to Spectroscopic Data
The journal of physical chemistry. B, v 128(25), pp 6217-6231
15 Jun 2024
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Abstract
Molecular dynamics (MD) is a great tool for elucidating conformational dynamics of proteins and peptides in water at the atomistic level that often surpasses the level of detail available experimentally. Structure predictions, however, are limited by the accuracy of the underlying MD force field. This limitation is particularly stark in the case of intrinsically disordered peptides and proteins, which are characterized by solvent-accessible and disordered peptide regions and domains. Recent studies show that most additive MD force fields, including CHARMM36m, do not reproduce the intrinsic conformational distributions of guest amino acid residues x in cationic GxG peptides in water in line with experimental data. Positing that a lack of polarizability in additive MD force fields may be the culprit for the reported discrepancies, we here examine the conformational dynamics of guest glycine and alanine residues in cationic GxG peptides in water using two polarizable MD force fields, CHARMM Drude and AMOEBA. Our results indicate that while AMOEBA captures the experimental data better than CHARMM Drude, neither of the two polarizable force fields offers an improvement of the Ramachandran distributions of glycine and alanine residues in cationic GGG and GAG peptides, respectively, over CHARMM36m.Molecular dynamics (MD) is a great tool for elucidating conformational dynamics of proteins and peptides in water at the atomistic level that often surpasses the level of detail available experimentally. Structure predictions, however, are limited by the accuracy of the underlying MD force field. This limitation is particularly stark in the case of intrinsically disordered peptides and proteins, which are characterized by solvent-accessible and disordered peptide regions and domains. Recent studies show that most additive MD force fields, including CHARMM36m, do not reproduce the intrinsic conformational distributions of guest amino acid residues x in cationic GxG peptides in water in line with experimental data. Positing that a lack of polarizability in additive MD force fields may be the culprit for the reported discrepancies, we here examine the conformational dynamics of guest glycine and alanine residues in cationic GxG peptides in water using two polarizable MD force fields, CHARMM Drude and AMOEBA. Our results indicate that while AMOEBA captures the experimental data better than CHARMM Drude, neither of the two polarizable force fields offers an improvement of the Ramachandran distributions of glycine and alanine residues in cationic GGG and GAG peptides, respectively, over CHARMM36m.
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Details
- Title
- Intrinsic Conformational Dynamics of Glycine and Alanine in Polarizable Molecular Dynamics Force Fields: Comparison to Spectroscopic Data
- Creators
- Brian Andrews - Drexel UniversityReinhard Schweitzer-StennerBrigita Urbanc (Corresponding Author) - Drexel University
- Publication Details
- The journal of physical chemistry. B, v 128(25), pp 6217-6231
- Publisher
- ACS Publications
- Resource Type
- Journal article
- Language
- English
- Academic Unit
- Physics; Chemistry
- Web of Science ID
- WOS:001248668700001
- Scopus ID
- 2-s2.0-85196421065
- Other Identifier
- 991021888114904721
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- Web of Science research areas
- Chemistry, Physical