ArticleThe journal of physical chemistry. B2009
2D-IR experiments and simulations of the coupling between amide-I and ionizable side chains in proteins: application to the Villin headpiece.
Article in The journal of physical chemistry. B, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 31 papers.
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Who cites it
31 citing papers in PubMed.
- Coengineering Vapor-Deposited Polycationic Microenvironments and Immobilization Strategy to Enhance β‑Galactosidase Kinetics at Acidic pH.ACS omega · 2026Article
- Interaction-Dependent Secondary Structure of Peptides in Biomolecular Condensates.Journal of the American Chemical Society · 2024Article
- Suppressing sidechain modes and improving structural resolution for 2D IR spectroscopy via vibrational lifetimes.The Journal of chemical physics · 2024Article
- Ultrafast Spectroscopy Reveals Slow Water Dynamics in Biocondensates.Journal of the American Chemical Society · 2023Article
- Revealing the Relationship between Electric Fields and the Conformation of Oxytocin Using Quasi-Static Amide-I Two-Dimensional Infrared Spectra.ACS omega · 2022Article
- Amino acid side chain contribution to protein FTIR spectra: impact on secondary structure evaluation.European biophysics journal : EBJ · 2021Article
- Interspecies Bombolitins Exhibit Structural Diversity upon Membrane Binding, Leading to Cell Specificity.Biophysical journal · 2019Article
- Physiological Calcium Concentrations Slow Dynamics at the Lipid-Water Interface.Biophysical journal · 2018Article
- Synthesis of 5-Cyano-Tryptophan as a Two-Dimensional Infrared Spectroscopic Reporter of Structure.Angewandte Chemie (International ed. in English) · 2018Article
- Isotope-Labeled Aspartate Sidechain as a Non-Perturbing Infrared Probe: Application to Investigate the Dynamics of a Carboxylate Buried Inside a Protein.Chemical physics letters · 2017Article
- Watching Proteins Wiggle: Mapping Structures with Two-Dimensional Infrared Spectroscopy.Chemical reviews · 2017Review
- How Sensitive is the Amide I Vibration of the Polypeptide Backbone to Electric Fields?Chemphyschem : a European journal of chemical physics and physical chemistry · 2015Article
- Hydration and vibrational dynamics of betaine (N,N,N-trimethylglycine).The Journal of chemical physics · 2015Article
- Site-specific infrared probes of proteins.Annual review of physical chemistry · 2015Review
- Vibrational dynamics of a non-degenerate ultrafast rotor: the (C12,C13)-oxalate ion.The Journal of chemical physics · 2013Article
- Simulations of Two-dimensional Infrared and Stimulated Resonance Raman Spectra of Photoactive Yellow Protein.Chemical physics · 2013Article
- Measuring electrostatic fields in both hydrogen-bonding and non-hydrogen-bonding environments using carbonyl vibrational probes.Journal of the American Chemical Society · 2013Article
- Two-Dimensional Infrared (2DIR) Spectroscopy of the Peptide Beta3s Folding.The journal of physical chemistry letters · 2013Article
- Monitoring the folding of Trp-cage peptide by two-dimensional infrared (2DIR) spectroscopy.The journal of physical chemistry. B · 2013Article
- Parallel β-sheet vibrational couplings revealed by 2D IR spectroscopy of an isotopically labeled macrocycle: quantitative benchmark for the interpretation of amyloid and protein infrared spectra.Journal of the American Chemical Society · 2012Article
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4 authors.
Funding
Abstract
The carboxylate side chains of Asp and Glu have significant coupling with the amide states of the backbone of the Villin headpiece. In two-dimensional spectroscopy, cross peaks are observed between these side chains and the main amide-I band. To model the absorption of the side chains, the electric field variations of vibrational frequencies of a carboxylic acid group (neutral form, CH(3)-COOH) and a carboxylate group (ionized form, CH(3)-COO(-)) are parametrized by means of density functional theory calculations. Simulations indicate that the side chains significantly couple to only one or two amide-I modes out of all of the amino acid residues which makes them useful as spectroscopic markers, providing information about the local structural behavior of the protein. Both experiment and simulations show that the cross peaks between the carboxylate and the amide-I bands are significantly diminished above the melting temperature.
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