Literature DB >> 22844177

A peptide's perspective of water dynamics.

Ayanjeet Ghosh1, Robin M Hochstrasser.   

Abstract

This Perspective is focused on amide groups of peptides interacting with water. The 2D IR spectroscopy has already enabled structural aspects of the peptide backbone to be determined through its ability to measure the coupling between different amide-I modes. Here we describe why nonlinear IR is emerging as the method of choice to examine the fast components of the water dynamics near peptides and how isotopically edited peptide links can be used to probe the local water at a residue level in proteins. This type of research necessarily involves an intimate mix of theory and experiment. The description of the results is underpinned by relatively well established quantum-statistical theories that describe the important manifestations of peptide vibrational frequency fluctuations.

Entities:  

Year:  2011        PMID: 22844177      PMCID: PMC3404498          DOI: 10.1016/j.chemphys.2011.07.018

Source DB:  PubMed          Journal:  Chem Phys        ISSN: 0301-0104            Impact factor:   2.348


  64 in total

Review 1.  Dynamics of water in biological recognition.

Authors:  Samir Kumar Pal; Ahmed H Zewail
Journal:  Chem Rev       Date:  2004-04       Impact factor: 60.622

2.  Chemical exchange 2D IR of hydrogen-bond making and breaking.

Authors:  Yung Sam Kim; Robin M Hochstrasser
Journal:  Proc Natl Acad Sci U S A       Date:  2005-07-22       Impact factor: 11.205

3.  Pronounced non-Condon effects in the ultrafast infrared spectroscopy of water.

Authors:  J R Schmidt; S A Corcelli; J L Skinner
Journal:  J Chem Phys       Date:  2005-07-22       Impact factor: 3.488

4.  Picosecond dynamics of a membrane protein revealed by 2D IR.

Authors:  Prabuddha Mukherjee; Itamar Kass; Isaiah T Arkin; Isaiah Arkin; Martin T Zanni
Journal:  Proc Natl Acad Sci U S A       Date:  2006-02-27       Impact factor: 11.205

5.  Vibrational dynamics of N-H, C-D, and C=O modes in formamide.

Authors:  Jeong-Hyon Ha; Yung Sam Kim; Robin M Hochstrasser
Journal:  J Chem Phys       Date:  2006-02-14       Impact factor: 3.488

6.  Mapping hydration dynamics around a protein surface.

Authors:  Luyuan Zhang; Lijuan Wang; Ya-Ting Kao; Weihong Qiu; Yi Yang; Oghaghare Okobiah; Dongping Zhong
Journal:  Proc Natl Acad Sci U S A       Date:  2007-11-14       Impact factor: 11.205

7.  Does the dynamic Stokes shift report on slow protein hydration dynamics?

Authors:  Bertil Halle; Lennart Nilsson
Journal:  J Phys Chem B       Date:  2009-06-18       Impact factor: 2.991

8.  Dynamics of amide-I modes of the alanine dipeptide in D2O.

Authors:  Yung Sam Kim; Robin M Hochstrasser
Journal:  J Phys Chem B       Date:  2005-04-14       Impact factor: 2.991

9.  The hydration of amides in helices; a comprehensive picture from molecular dynamics, IR, and NMR.

Authors:  Scott T R Walsh; Richard P Cheng; Wayne W Wright; Darwin O V Alonso; Valerie Daggett; Jane M Vanderkooi; William F DeGrado
Journal:  Protein Sci       Date:  2003-03       Impact factor: 6.725

10.  Ion-water hydrogen-bond switching observed with 2D IR vibrational echo chemical exchange spectroscopy.

Authors:  David E Moilanen; Daryl Wong; Daniel E Rosenfeld; Emily E Fenn; M D Fayer
Journal:  Proc Natl Acad Sci U S A       Date:  2008-12-23       Impact factor: 11.205

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  13 in total

1.  Intrinsic structural heterogeneity and long-term maturation of amyloid β peptide fibrils.

Authors:  Jianqiang Ma; Hiroaki Komatsu; Yung Sam Kim; Liu Liu; Robin M Hochstrasser; Paul H Axelsen
Journal:  ACS Chem Neurosci       Date:  2013-06-12       Impact factor: 4.418

2.  2D IR spectroscopy reveals the role of water in the binding of channel-blocking drugs to the influenza M2 channel.

Authors:  Ayanjeet Ghosh; Jun Wang; Yurii S Moroz; Ivan V Korendovych; Martin Zanni; William F DeGrado; Feng Gai; Robin M Hochstrasser
Journal:  J Chem Phys       Date:  2014-06-21       Impact factor: 3.488

3.  Hydration and vibrational dynamics of betaine (N,N,N-trimethylglycine).

Authors:  Tanping Li; Yaowen Cui; John Mathaga; Revati Kumar; Daniel G Kuroda
Journal:  J Chem Phys       Date:  2015-06-07       Impact factor: 3.488

Review 4.  Applications of two-dimensional infrared spectroscopy.

Authors:  Amanda L Le Sueur; Rachel E Horness; Megan C Thielges
Journal:  Analyst       Date:  2015-07-07       Impact factor: 4.616

Review 5.  Watching Proteins Wiggle: Mapping Structures with Two-Dimensional Infrared Spectroscopy.

Authors:  Ayanjeet Ghosh; Joshua S Ostrander; Martin T Zanni
Journal:  Chem Rev       Date:  2017-01-06       Impact factor: 60.622

6.  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

7.  Three-dimensional structures by two-dimensional vibrational spectroscopy.

Authors:  Amanda Remorino; Robin M Hochstrasser
Journal:  Acc Chem Res       Date:  2012-03-29       Impact factor: 22.384

8.  Microscopic insights into the protein-stabilizing effect of trimethylamine N-oxide (TMAO).

Authors:  Jianqiang Ma; Ileana M Pazos; Feng Gai
Journal:  Proc Natl Acad Sci U S A       Date:  2014-05-27       Impact factor: 11.205

9.  Spatially Resolved Two-Dimensional Infrared Spectroscopy via Wide-Field Microscopy.

Authors:  Joshua S Ostrander; Arnaldo L Serrano; Ayanjeet Ghosh; Martin T Zanni
Journal:  ACS Photonics       Date:  2016-06-10       Impact factor: 7.529

10.  2D IR spectroscopy of histidine: probing side-chain structure and dynamics via backbone amide vibrations.

Authors:  Ayanjeet Ghosh; Matthew J Tucker; Feng Gai
Journal:  J Phys Chem B       Date:  2014-04-18       Impact factor: 2.991

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