ArticleThe journal of physical chemistry. B2012
Ribonuclease S dynamics measured using a nitrile label with 2D IR vibrational echo spectroscopy.
Article in The journal of physical chemistry. B, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 36 papers.
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Who cites it
36 citing papers in PubMed, 111 citations in OpenAlex.
- Hydrogen Bond Blueshifts in Nitrile Vibrational Spectra Are Dictated by Hydrogen Bond Geometry and Dynamics.JACS Au · 2024Article
- Noncanonical Amino Acids in Biocatalysis.Chemical reviews · 2024Review
- Critical Evaluation of Polarizable and Nonpolarizable Force Fields for Proteins Using Experimentally Derived Nitrile Electric Fields.Journal of the American Chemical Society · 2024Article
- Nitrile Substituents at the Conjugated Dipyridophenazine Moiety as Infrared Redox Markers in Electrochemically Reduced Heteroleptic Ru(II) Polypyridyl Complexes.Inorganic chemistry · 2024Article
- Unraveling Complex Local Protein Environments with 4-Cyano-l-phenylalanine.The journal of physical chemistry. B · 2022Article
- Structure and diffusive dynamics of aspartate α-decarboxylase (ADC) liganded with D-serine in aqueous solution.Physical chemistry chemical physics : PCCP · 2022Article
- Cross-Correlated Motions in Azidolysozyme.Molecules (Basel, Switzerland) · 2022Article
- Probing Ligand Effects on the Ultrafast Dynamics of Copper Complexes via Midinfrared Pump-Probe and 2DIR Spectroscopies.The journal of physical chemistry. B · 2021Article
- Coupling chemical biology and vibrational spectroscopy for studies of amyloids in vitro and in cells.Current opinion in chemical biology · 2021Review
- Vibrational Stark shift spectroscopy of catalysts under the influence of electric fields at electrode-solution interfaces.Chemical science · 2021Review
- Protein Dynamics by Two-Dimensional Infrared Spectroscopy.Annual review of analytical chemistry (Palo Alto, Calif.) · 2021Article
- Shot-to-shot 2D IR spectroscopy at 100 kHz using a Yb laser and custom-designed electronics.Optics express · 2020Article
- Exploring local solvation environments of a heme protein using the spectroscopic reporter 4-cyano-l-phenylalanine.RSC advances · 2018Article
- Ultrafast dynamics induced by the interaction of molecules with electromagnetic fields: Several quantum, semiclassical, and classical approaches.Structural dynamics (Melville, N.Y.) · 2017Review
- Sensitivity of core-level spectroscopy to electrostatic environments of nitrile groups: AnStructural dynamics (Melville, N.Y.) · 2017Article
- Watching Proteins Wiggle: Mapping Structures with Two-Dimensional Infrared Spectroscopy.Chemical reviews · 2017Review
- Minimalist IR and fluorescence probes of protein function.Current opinion in chemical biology · 2016Review
- Two-Dimensional Infrared Study of Vibrational Coupling between Azide and Nitrile Reporters in a RNA Nucleoside.The journal of physical chemistry. B · 2016Article
- Unraveling the dynamics and structure of functionalized self-assembled monolayers on gold using 2D IR spectroscopy and MD simulations.Proceedings of the National Academy of Sciences of the United States of America · 2016Article
- Probing the effectiveness of spectroscopic reporter unnatural amino acids: a structural study.Acta crystallographica. Section D, Structural biology · 2016Article
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3 authors at 1 institution in 1 country.
Funding
Abstract
A nitrile-labeled amino acid, p-cyanophenylalanine, is introduced near the active site of the semisynthetic enzyme ribonuclease S to serve as a probe of protein dynamics and fluctuations. Ribonuclease S is the limited proteolysis product of subtilisin acting on ribonuclease A, and consists of a small fragment including amino acids 1-20, the S-peptide, and a larger fragment including residues 21-124, the S-protein. A series of two-dimensional vibrational echo experiments performed on the nitrile-labeled S-peptide and the RNase S are described. The time-dependent changes in the two-dimensional infrared vibrational echo line shapes are analyzed using the center line slope method to obtain the frequency-frequency correlation function (FFCF). The observations show that the nitrile probe in the S-peptide has dynamics that are similar to, but faster than, those of the single amino acid p-cyanophenylalanine in water. In contrast, the dynamics of the nitrile label when the peptide is bound to form ribonuclease S are dominated by homogeneous dephasing (motionally narrowed) contributions with only a small contribution from very fast inhomogeneous structural dynamics. The results provide insights into the nature of the structural dynamics of the ribonuclease S complex. The equilibrium dynamics of the nitrile labeled S-peptide and the ribonuclease S complex are also investigated by molecular dynamics simulations. The experimentally determined FFCFs are compared to the FFCFs obtained from the molecular dynamics simulations, thereby testing the capacity of simulations to determine the amplitudes and time scales of protein structural fluctuations on fast time scales under thermal equilibrium conditions.
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