ArticleThe journal of physical chemistry. B2014
Empirical maps for the calculation of amide I vibrational spectra of proteins from classical molecular dynamics simulations.
Article in The journal of physical chemistry. B, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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Who cites it
10 citing papers in PubMed, 50 citations in OpenAlex.
- IR Spectroscopy: From Experimental Spectra to High-Resolution Structural Analysis by Integrating Simulations and Machine Learning.The journal of physical chemistry. B · 2025Article
- Estimation of vibrational spectra of Trp-cage protein from nonequilibrium metadynamics simulations.Biophysical journal · 2024Article
- Origin of thiocyanate spectral shifts in water and organic solvents.The Journal of chemical physics · 2022Article
- Vibrational Spectroscopic Map, Vibrational Spectroscopy, and Intermolecular Interaction.Chemical reviews · 2020Review
- Vibrational exciton nanoimaging of phases and domains in porphyrin nanocrystals.Proceedings of the National Academy of Sciences of the United States of America · 2020Article
- Interplay between Hydrogen Bonding and Vibrational Coupling in Liquid N-Methylacetamide.The journal of physical chemistry letters · 2017Article
- Solvent-Independent Anharmonicity for Carbonyl Oscillators.The journal of physical chemistry. B · 2017Article
- Role of Charge and Solvation in the Structure and Dynamics of Alanine-Rich Peptide AKA2 in AOT Reverse Micelles.The journal of physical chemistry. B · 2015Article
- Exploring the role of hydration and confinement in the aggregation of amyloidogenic peptides Aβ(16-22) and Sup35(7-13) in AOT reverse micelles.The Journal of chemical physics · 2014Article
- Assessment of amide I spectroscopic maps for a gas-phase peptide using IR-UV double-resonance spectroscopy and density functional theory calculations.The Journal of chemical physics · 2014Article
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
Abstract
New sets of parameters (maps) for calculating amide I vibrational spectra for proteins through a vibrational exciton model are proposed. The maps are calculated as a function of electric field and van der Waals forces on the atoms of peptide bonds, taking into account the full interaction between peptide bonds and the surrounding environment. The maps are designed to be employed using data obtained from standard all-atom molecular simulations without any additional constraints on the system. Six proteins representing a wide range of sizes and secondary structure complexity were chosen as a test set. Spectra calculated for these proteins reproduce experimental data both qualitatively and quantitatively. The proposed maps lead to spectra that capture the weak second peak observed in proteins containing β-sheets, allowing for clear distinction between α-helical and β-sheet proteins. While the parametrization is specific to the CHARMM force field, the methodology presented can be readily applied to any empirical force field.
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