ArticleThe journal of physical chemistry. B2010
Nitrile bonds as infrared probes of electrostatics in ribonuclease S.
Article in The journal of physical chemistry. B, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 45 papers.
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Who cites it
45 citing papers in PubMed, 108 citations in OpenAlex.
- Electrostatic atlas of non-covalent interactions built into metal-organic frameworks.Nature chemistry · 2025Article
- Transmissive hybrid metal-dielectric metasurface bandpass filters for mid-infrared applications.Nanophotonics (Berlin, Germany) · 2025Article
- Unraveling Hydration Shell Dynamics and Viscosity Effects Around Cyanamide Probes via 2D IR Spectroscopy.Journal of the American Chemical Society · 2025Article
- Facile Generation of Cyanoselenocysteine as a Vibrational Label for Measuring Protein Dynamics on Longer Time Scales by 2D IR Spectroscopy.Analytical chemistry · 2025Article
- Noncanonical Amino Acids in Biocatalysis.Chemical reviews · 2024Review
- Nitrile Vibrational Lifetimes as Probes of Local Electric Fields.The journal of physical chemistry letters · 2024Article
- Critical Evaluation of Polarizable and Nonpolarizable Force Fields for Proteins Using Experimentally Derived Nitrile Electric Fields.Journal of the American Chemical Society · 2024Article
- AMOEBA Force Field Predicts Accurate Hydrogen Bond Counts of Nitriles in SNase by Revealing Water-Protein Interaction in Vibrational Absorption Frequencies.The journal of physical chemistry. B · 2023Article
- Unraveling Complex Local Protein Environments with 4-Cyano-l-phenylalanine.The journal of physical chemistry. B · 2022Article
- TUPÃ: Electric field analyses for molecular simulations.Journal of computational chemistry · 2022Article
- Vibrational Stark shift spectroscopy of catalysts under the influence of electric fields at electrode-solution interfaces.Chemical science · 2021Review
- Inhomogeneity of Interfacial Electric Fields at Vibrational Probes on Electrode Surfaces.ACS central science · 2020Article
- 2D-IR studies of cyanamides (NCN) as spectroscopic reporters of dynamics in biomolecules: Uncovering the origin of mysterious peaks.The Journal of chemical physics · 2020Article
- Split Green Fluorescent Proteins: Scope, Limitations, and Outlook.Annual review of biophysics · 2019Review
- Vibrational Approach to the Dynamics and Structure of Protein Amyloids.Molecules (Basel, Switzerland) · 2019Review
- Cyanylated Cysteine Reports Site-Specific Changes at Protein-Protein-Binding Interfaces Without Perturbation.Biochemistry · 2018Article
- Conformational Ensembles of Calmodulin Revealed by Nonperturbing Site-Specific Vibrational Probe Groups.The journal of physical chemistry. A · 2018Article
- Electric Fields and Enzyme Catalysis.Annual review of biochemistry · 2017Review
- Extended timescale 2D IR probes of proteins: p-cyanoselenophenylalanine.Physical chemistry chemical physics : PCCP · 2017Article
- Simple method to introduce an ester infrared probe into proteins.Protein science : a publication of the Protein Society · 2017Article
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
Abstract
Three different nitrile-containing amino acids, p-cyanophenylalanine, m-cyanophenylalanine, and S-cyanohomocysteine, have been introduced near the active site of the semisynthetic enzyme ribonuclease S (RNase S) to serve as probes of electrostatic fields. Vibrational Stark spectra, measured directly on the probe-modified proteins, confirm the predominance of the linear Stark tuning rate in describing the sensitivity of the nitrile stretch to external electric fields, a necessary property for interpreting observed frequency shifts as a quantitative measure of local electric fields that can be compared with simulations. The X-ray structures of these nitrile-modified RNase variants and enzymatic assays demonstrate minimal perturbation to the structure and function, respectively, by the probes and provide a context for understanding the influence of the environment on the nitrile stretching frequency. We examine the ability of simulation techniques to recapitulate the spectroscopic properties of these nitriles as a means to directly test a computational electrostatic model for proteins, specifically that in the ubiquitous Amber-99 force field. Although qualitative agreement between theory and experiment is observed for the largest shifts, substantial discrepancies are observed in some cases, highlighting the ongoing need for experimental metrics to inform the development of theoretical models of electrostatic fields in proteins.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.