ArticleJournal of the American Chemical Society2013
Calculation of vibrational shifts of nitrile probes in the active site of ketosteroid isomerase upon ligand binding.
Article in Journal of the American Chemical Society, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed, 63 citations in OpenAlex.
- Hydrogen Bond Blueshifts in Nitrile Vibrational Spectra Are Dictated by Hydrogen Bond Geometry and Dynamics.JACS Au · 2024Article
- From random to rational: improving enzyme design through electric fields, second coordination sphere interactions, and conformational dynamics.Chemical science · 2023Review
- Biomacromolecule-Assisted Screening for Reaction Discovery and Catalyst Optimization.Chemical reviews · 2022Review
- Vibrational Stark shift spectroscopy of catalysts under the influence of electric fields at electrode-solution interfaces.Chemical science · 2021Review
- Local Electric Fields as a Natural Switch of Heme-Iron Protein Reactivity.ACS catalysis · 2021Article
- Vibrational Spectroscopic Map, Vibrational Spectroscopy, and Intermolecular Interaction.Chemical reviews · 2020Review
- Electric Field Measurements Reveal the Pivotal Role of Cofactor-Substrate Interaction in Dihydrofolate Reductase Catalysis.ACS catalysis · 2020Article
- Inhomogeneity of Interfacial Electric Fields at Vibrational Probes on Electrode Surfaces.ACS central science · 2020Article
- A Biophysical Perspective on Enzyme Catalysis.Biochemistry · 2019Article
- Cyanylated Cysteine Reports Site-Specific Changes at Protein-Protein-Binding Interfaces Without Perturbation.Biochemistry · 2018Article
- Parametrization of Combined Quantum Mechanical and Molecular Mechanical Methods: Bond-Tuned Link Atoms.Molecules (Basel, Switzerland) · 2018Article
- A thiocyanopalladation/carbocyclization transformation identified through enzymatic screening: stereocontrolled tandem C-SCN and C-C bond formation.Chemical science · 2017Article
- Ultrafast dynamics induced by the interaction of molecules with electromagnetic fields: Several quantum, semiclassical, and classical approaches.Structural dynamics (Melville, N.Y.) · 2017Review
- Site-specific infrared probes of proteins.Annual review of physical chemistry · 2015Review
- Perspectives on electrostatics and conformational motions in enzyme catalysis.Accounts of chemical research · 2015Review
- Probing the phosphopantetheine arm conformations of acyl carrier proteins using vibrational spectroscopy.Journal of the American Chemical Society · 2014Article
- Probing the electrostatics of active site microenvironments along the catalytic cycle for Escherichia coli dihydrofolate reductase.Journal of the American Chemical Society · 2014Article
- Solvatochromism and the solvation structure of benzophenone.The Journal of chemical physics · 2013Article
- Catalytic efficiency of enzymes: a theoretical analysis.Biochemistry · 2013Review
Corrections and comments
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
Abstract
The vibrational Stark effect provides insight into the roles of hydrogen bonding, electrostatics, and conformational motions in enzyme catalysis. In a recent application of this approach to the enzyme ketosteroid isomerase (KSI), thiocyanate probes were introduced in site-specific positions throughout the active site. This paper implements a quantum mechanical/molecular mechanical (QM/MM) approach for calculating the vibrational shifts of nitrile (CN) probes in proteins. This methodology is shown to reproduce the experimentally measured vibrational shifts upon binding of the intermediate analogue equilinen to KSI for two different nitrile probe positions. Analysis of the molecular dynamics simulations provides atomistic insight into the roles that key residues play in determining the electrostatic environment and hydrogen-bonding interactions experienced by the nitrile probe. For the M116C-CN probe, equilinen binding reorients an active-site water molecule that is directly hydrogen-bonded to the nitrile probe, resulting in a more linear C≡N--H angle and increasing the CN frequency upon binding. For the F86C-CN probe, equilinen binding orients the Asp103 residue, decreasing the hydrogen-bonding distance between the Asp103 backbone and the nitrile probe and slightly increasing the CN frequency. This QM/MM methodology is applicable to a wide range of biological systems and has the potential to assist in the elucidation of the fundamental principles underlying enzyme catalysis.
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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.