Literature DB >> 23808481

Measuring electrostatic fields in both hydrogen-bonding and non-hydrogen-bonding environments using carbonyl vibrational probes.

Stephen D Fried1, Sayan Bagchi, Steven G Boxer.   

Abstract

Vibrational probes can provide a direct readout of the local electrostatic field in complex molecular environments, such as protein binding sites and enzyme active sites. This information provides an experimental method to explore the underlying physical causes of important biomolecular processes such as binding and catalysis. However, specific chemical interactions such as hydrogen bonds can have complicated effects on vibrational probes and confound simple electrostatic interpretations of their frequency shifts. We employ vibrational Stark spectroscopy along with infrared spectroscopy of carbonyl probes in different solvent environments and in ribonuclease S to understand the sensitivity of carbonyl frequencies to electrostatic fields, including those due to hydrogen bonds. Additionally, we carried out molecular dynamics simulations to calculate ensemble-averaged electric fields in solvents and in ribonuclease S and found excellent correlation between calculated fields and vibrational frequencies. These data enabled the construction of a robust field-frequency calibration curve for the C═O vibration. The present results suggest that carbonyl probes are capable of quantitatively assessing the electrostatics of hydrogen bonding, making them promising for future study of protein function.

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Year:  2013        PMID: 23808481      PMCID: PMC3762491          DOI: 10.1021/ja403917z

Source DB:  PubMed          Journal:  J Am Chem Soc        ISSN: 0002-7863            Impact factor:   15.419


  40 in total

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2.  Myoglobin-CO substate structures and dynamics: multidimensional vibrational echoes and molecular dynamics simulations.

Authors:  Kusai A Merchant; W G Noid; Ryo Akiyama; Ilya J Finkelstein; Alexei Goun; Brian L McClain; Roger F Loring; M D Fayer
Journal:  J Am Chem Soc       Date:  2003-11-12       Impact factor: 15.419

3.  Development and testing of a general amber force field.

Authors:  Junmei Wang; Romain M Wolf; James W Caldwell; Peter A Kollman; David A Case
Journal:  J Comput Chem       Date:  2004-07-15       Impact factor: 3.376

4.  Cyano groups as probes of protein microenvironments and dynamics.

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Journal:  Angew Chem Int Ed Engl       Date:  2011-07-20       Impact factor: 15.336

Review 5.  Stark spectroscopy: applications in chemistry, biology, and materials science.

Authors:  G U Bublitz; S G Boxer
Journal:  Annu Rev Phys Chem       Date:  1997       Impact factor: 12.703

6.  Studies on the conformation of ribonuclease S-peptide.

Authors:  W A Klee
Journal:  Biochemistry       Date:  1968-08       Impact factor: 3.162

7.  The Two Dimensional Vibrational Echo of a Nitrile Probe of the Villin HP35 Protein.

Authors:  Diana C Urbanek; Dmitriy Yu Vorobyev; Arnaldo L Serrano; Feng Gai; Robin M Hochstrasser
Journal:  J Phys Chem Lett       Date:  2010       Impact factor: 6.475

8.  5-Cyanotryptophan as an Infrared Probe of Local Hydration Status of Proteins.

Authors:  Matthias M Waegele; Matthew J Tucker; Feng Gai
Journal:  Chem Phys Lett       Date:  2009-09-01       Impact factor: 2.328

9.  Refinement of the crystal structure of ribonuclease S. Comparison with and between the various ribonuclease A structures.

Authors:  E E Kim; R Varadarajan; H W Wyckoff; F M Richards
Journal:  Biochemistry       Date:  1992-12-15       Impact factor: 3.162

10.  Improved side-chain torsion potentials for the Amber ff99SB protein force field.

Authors:  Kresten Lindorff-Larsen; Stefano Piana; Kim Palmo; Paul Maragakis; John L Klepeis; Ron O Dror; David E Shaw
Journal:  Proteins       Date:  2010-06
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  43 in total

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Journal:  J Phys Chem B       Date:  2019-06-10       Impact factor: 2.991

2.  Calcium-Lipid Interactions Observed with Isotope-Edited Infrared Spectroscopy.

Authors:  Mason L Valentine; Alfredo E Cardenas; Ron Elber; Carlos R Baiz
Journal:  Biophys J       Date:  2020-04-21       Impact factor: 4.033

3.  Solvent-induced infrared frequency shifts in aromatic nitriles are quantitatively described by the vibrational Stark effect.

Authors:  Nicholas M Levinson; Stephen D Fried; Steven G Boxer
Journal:  J Phys Chem B       Date:  2012-04-05       Impact factor: 2.991

4.  Physiological Calcium Concentrations Slow Dynamics at the Lipid-Water Interface.

Authors:  Mason L Valentine; Alfredo E Cardenas; Ron Elber; Carlos R Baiz
Journal:  Biophys J       Date:  2018-09-06       Impact factor: 4.033

Review 5.  Site-specific infrared probes of proteins.

Authors:  Jianqiang Ma; Ileana M Pazos; Wenkai Zhang; Robert M Culik; Feng Gai
Journal:  Annu Rev Phys Chem       Date:  2015-01-12       Impact factor: 12.703

6.  Site-Specific 1D and 2D IR Spectroscopy to Characterize the Conformations and Dynamics of Protein Molecular Recognition.

Authors:  Sashary Ramos; Megan C Thielges
Journal:  J Phys Chem B       Date:  2019-03-21       Impact factor: 2.991

7.  Instantaneous ion configurations in the K+ ion channel selectivity filter revealed by 2D IR spectroscopy.

Authors:  Huong T Kratochvil; Joshua K Carr; Kimberly Matulef; Alvin W Annen; Hui Li; Michał Maj; Jared Ostmeyer; Arnaldo L Serrano; H Raghuraman; Sean D Moran; J L Skinner; Eduardo Perozo; Benoît Roux; Francis I Valiyaveetil; Martin T Zanni
Journal:  Science       Date:  2016-09-02       Impact factor: 47.728

8.  Ester carbonyl vibration as a sensitive probe of protein local electric field.

Authors:  Ileana M Pazos; Ayanjeet Ghosh; Matthew J Tucker; Feng Gai
Journal:  Angew Chem Int Ed Engl       Date:  2014-04-30       Impact factor: 15.336

9.  Live-cell vibrational imaging of choline metabolites by stimulated Raman scattering coupled with isotope-based metabolic labeling.

Authors:  Fanghao Hu; Lu Wei; Chaogu Zheng; Yihui Shen; Wei Min
Journal:  Analyst       Date:  2014-05-21       Impact factor: 4.616

10.  Conformational Heterogeneity in the Michaelis Complex of Lactate Dehydrogenase: An Analysis of Vibrational Spectroscopy Using Markov and Hidden Markov Models.

Authors:  Xiaoliang Pan; Steven D Schwartz
Journal:  J Phys Chem B       Date:  2016-07-05       Impact factor: 2.991

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