Literature DB >> 21809829

Phosphate vibrations probe local electric fields and hydration in biomolecules.

Nicholas M Levinson1, Erin E Bolte, Carrie S Miller, Steven A Corcelli, Steven G Boxer.   

Abstract

The role of electric fields in important biological processes such as binding and catalysis has been studied almost exclusively by computational methods. Experimental measurements of the local electric field in macromolecules are possible using suitably calibrated vibrational probes. Here we demonstrate that the vibrational transitions of phosphate groups are highly sensitive to an electric field and show how that sensitivity can be quantified, allowing electric field measurements to be made in phosphate-containing biological systems without chemical modification.

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Year:  2011        PMID: 21809829      PMCID: PMC3161143          DOI: 10.1021/ja2042589

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


  12 in total

1.  Conformational changes generated in GroEL during ATP hydrolysis as seen by time-resolved infrared spectroscopy.

Authors:  F von Germar; A Galán; O Llorca; J L Carrascosa; J M Valpuesta; W Mäntele; A Muga
Journal:  J Biol Chem       Date:  1999-02-26       Impact factor: 5.157

2.  Monitoring the GAP catalyzed H-Ras GTPase reaction at atomic resolution in real time.

Authors:  C Allin; M R Ahmadian; A Wittinghofer; K Gerwert
Journal:  Proc Natl Acad Sci U S A       Date:  2001-07-03       Impact factor: 11.205

3.  The GAP arginine finger movement into the catalytic site of Ras increases the activation entropy.

Authors:  Carsten Kötting; Angela Kallenbach; Yan Suveyzdis; Alfred Wittinghofer; Klaus Gerwert
Journal:  Proc Natl Acad Sci U S A       Date:  2008-04-23       Impact factor: 11.205

4.  Development of the Colle-Salvetti correlation-energy formula into a functional of the electron density.

Authors: 
Journal:  Phys Rev B Condens Matter       Date:  1988-01-15

5.  A phosphoryl transfer intermediate in the GTPase reaction of Ras in complex with its GTPase-activating protein.

Authors:  Carsten Kötting; Marco Blessenohl; Yan Suveyzdis; Roger S Goody; Alfred Wittinghofer; Klaus Gerwert
Journal:  Proc Natl Acad Sci U S A       Date:  2006-09-12       Impact factor: 11.205

6.  Interactions of phosphate groups of ATP and Aspartyl phosphate with the sarcoplasmic reticulum Ca2+-ATPase: an FTIR study.

Authors:  Man Liu; Maria Krasteva; Andreas Barth
Journal:  Biophys J       Date:  2005-09-16       Impact factor: 4.033

7.  The mechanism of GTP hydrolysis by Ras probed by Fourier transform infrared spectroscopy.

Authors:  X Du; H Frei; S H Kim
Journal:  J Biol Chem       Date:  2000-03-24       Impact factor: 5.157

8.  Vibrational Stark effects calibrate the sensitivity of vibrational probes for electric fields in proteins.

Authors:  Ian T Suydam; Steven G Boxer
Journal:  Biochemistry       Date:  2003-10-21       Impact factor: 3.162

9.  Infrared spectroscopy of phosphatidylcholines in aqueous suspension. A study of the phosphate group vibrations.

Authors:  J L Arrondo; F M Goñi; J M Macarulla
Journal:  Biochim Biophys Acta       Date:  1984-06-06

10.  Nitrile and thiocyanate IR probes: quantum chemistry calculation studies and multivariate least-square fitting analysis.

Authors:  Jun-Ho Choi; Kwang-Im Oh; Hochan Lee; Chewook Lee; Minhaeng Cho
Journal:  J Chem Phys       Date:  2008-04-07       Impact factor: 3.488

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  13 in total

Review 1.  Vibrational Spectroscopic Map, Vibrational Spectroscopy, and Intermolecular Interaction.

Authors:  Carlos R Baiz; Bartosz Błasiak; Jens Bredenbeck; Minhaeng Cho; Jun-Ho Choi; Steven A Corcelli; Arend G Dijkstra; Chi-Jui Feng; Sean Garrett-Roe; Nien-Hui Ge; Magnus W D Hanson-Heine; Jonathan D Hirst; Thomas L C Jansen; Kijeong Kwac; Kevin J Kubarych; Casey H Londergan; Hiroaki Maekawa; Mike Reppert; Shinji Saito; Santanu Roy; James L Skinner; Gerhard Stock; John E Straub; Megan C Thielges; Keisuke Tominaga; Andrei Tokmakoff; Hajime Torii; Lu Wang; Lauren J Webb; Martin T Zanni
Journal:  Chem Rev       Date:  2020-06-29       Impact factor: 60.622

Review 2.  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

3.  Site-Specific Interrogation of Protein Structure and Stability.

Authors:  Debopreeti Mukherjee; Ismail A Ahmed; Feng Gai
Journal:  Methods Mol Biol       Date:  2022

4.  Contact pairs of RNA with magnesium ions-electrostatics beyond the Poisson-Boltzmann equation.

Authors:  Benjamin Philipp Fingerhut; Jakob Schauss; Achintya Kundu; Thomas Elsaesser
Journal:  Biophys J       Date:  2021-10-27       Impact factor: 4.033

5.  Calculation of vibrational shifts of nitrile probes in the active site of ketosteroid isomerase upon ligand binding.

Authors:  Joshua P Layfield; Sharon Hammes-Schiffer
Journal:  J Am Chem Soc       Date:  2012-12-31       Impact factor: 15.419

Review 6.  Water Dynamics in the Hydration Shells of Biomolecules.

Authors:  Damien Laage; Thomas Elsaesser; James T Hynes
Journal:  Chem Rev       Date:  2017-03-01       Impact factor: 60.622

7.  Correlations between the structure and the vibrational spectrum of the phosphate group. Implications for the analysis of an important functional group in phosphoproteins.

Authors:  Pontus Pettersson; Andreas Barth
Journal:  RSC Adv       Date:  2020-01-29       Impact factor: 3.361

8.  Perspective: Structure and ultrafast dynamics of biomolecular hydration shells.

Authors:  Damien Laage; Thomas Elsaesser; James T Hynes
Journal:  Struct Dyn       Date:  2017-04-20       Impact factor: 2.920

9.  Molecular couplings and energy exchange between DNA and water mapped by femtosecond infrared spectroscopy of backbone vibrations.

Authors:  Yingliang Liu; Biswajit Guchhait; Torsten Siebert; Benjamin P Fingerhut; Thomas Elsaesser
Journal:  Struct Dyn       Date:  2017-04-07       Impact factor: 2.920

10.  Ultrafast vibrational dynamics of the DNA backbone at different hydration levels mapped by two-dimensional infrared spectroscopy.

Authors:  Biswajit Guchhait; Yingliang Liu; Torsten Siebert; Thomas Elsaesser
Journal:  Struct Dyn       Date:  2015-12-08       Impact factor: 2.920

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