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Accepted (AM)Open Access (License Unspecified), Open
Journal article
Nitrile Bonds as Infrared Probes of Electrostatics in Ribonuclease S
The journal of physical chemistry. B, v 114(42), pp 13536-13544
28 Oct 2010
PMID: 20883003
Featured in Collection : UN Sustainable Development Goals @ Drexel
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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Details
- Title
- Nitrile Bonds as Infrared Probes of Electrostatics in Ribonuclease S
- Creators
- Aaron T. Fafarman - Stanford UniversitySteven G. Boxer - Stanford University
- Publication Details
- The journal of physical chemistry. B, v 114(42), pp 13536-13544
- Publisher
- American Chemical Society; Washington, DC
- Number of pages
- 9
- Grant note
- R37GM027738 / NATIONAL INSTITUTE OF GENERAL MEDICAL SCIENCES; United States Department of Health & Human Services; National Institutes of Health (NIH) - USA; NIH National Institute of General Medical Sciences (NIGMS) GM27738 / NIH; United States Department of Health & Human Services; National Institutes of Health (NIH) - USA U.S. Department of Energy, Office of Basic Energy Sciences; United States Department of Energy (DOE) National Institutes of Health, National Center for Research Resources; United States Department of Health & Human Services; National Institutes of Health (NIH) - USA; NIH National Center for Research Resources (NCRR) National Institute of General Medical Sciences; United States Department of Health & Human Services; National Institutes of Health (NIH) - USA; NIH National Institute of General Medical Sciences (NIGMS) Department of Energy, Office of Biological and Environmental Research; United States Department of Energy (DOE)
- Resource Type
- Journal article
- Language
- English
- Academic Unit
- Chemical and Biological Engineering
- Web of Science ID
- WOS:000283110500033
- Scopus ID
- 2-s2.0-77958474269
- Other Identifier
- 991020834713504721
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- Web of Science research areas
- Chemistry, Physical