Literature DB >> 18078331

Two-dimensional infrared spectroscopy as a probe of the solvent electrostatic field for a twelve residue peptide.

Jianping Wang1, Wei Zhuang, Shaul Mukamel, Robin Hochstrasser.   

Abstract

The linear IR and two-dimensional (2D) IR spectra of the amide-I modes of the 12-residue beta-hairpin peptide tryptophan zipper-2 (SWTWENGKWTWK) and its two 13C isotopomers were simulated, with local mode frequencies evaluated by two solution-phase peptide amide-I frequency maps proposed recently: an electrostatic potential map and an electrostatic field map. Both maps predict a set of nondegenerate local amide-I mode transition energies for the hairpin. Spectral simulations using both maps predict the main spectral features of the linear IR and 2D IR experimental results of the (13)C-labeled and -unlabeled hairpin. The radial distribution functions obtained using trajectories from classical molecular dynamics simulations demonstrate different water distributions at different sites of the hairpin. Our results suggest that the observed difference of the (13)C-shifted band, including its peak position and frequency distributions for different isotopomers, in both linear IR and 2D IR spectra, is likely to be due to the difference in the local environment of the solvated peptide. Ab initio density functional theory calculations show a residue-independent (13)C shift of the amide-I mode, further supporting the result. The variations of these shifts are attributed to the residue level heterogeneity of the electrostatic environment of the peptide. Our results show that 2D IR of peptide with single (13)C isotopic labeling can be used to probe the electrostatic environment of the peptide local structure.

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Year:  2007        PMID: 18078331      PMCID: PMC2888599          DOI: 10.1021/jp075683k

Source DB:  PubMed          Journal:  J Phys Chem B        ISSN: 1520-5207            Impact factor:   2.991


  33 in total

1.  The Protein Data Bank.

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2.  Signatures of beta-peptide unfolding in two-dimensional vibrational echo spectroscopy: a simulation study.

Authors:  C Scheurer; A Piryatinski; S Mukamel
Journal:  J Am Chem Soc       Date:  2001-04-04       Impact factor: 15.419

3.  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

4.  Watching hydrogen-bond dynamics in a beta-turn by transient two-dimensional infrared spectroscopy.

Authors:  Christoph Kolano; Jan Helbing; Mariusz Kozinski; Wolfram Sander; Peter Hamm
Journal:  Nature       Date:  2006-11-23       Impact factor: 49.962

5.  Vibrational spectral diffusion of azide in water.

Authors:  Shuzhou Li; J R Schmidt; A Piryatinski; C P Lawrence; J L Skinner
Journal:  J Phys Chem B       Date:  2006-09-28       Impact factor: 2.991

6.  A transferable electrostatic map for solvation effects on amide I vibrations and its application to linear and two-dimensional spectroscopy.

Authors:  Thomas la Cour Jansen; Jasper Knoester
Journal:  J Chem Phys       Date:  2006-01-28       Impact factor: 3.488

7.  Simulation protocols for coherent femtosecond vibrational spectra of peptides.

Authors:  Wei Zhuang; Darius Abramavicius; Tomoyuki Hayashi; Shaul Mukamel
Journal:  J Phys Chem B       Date:  2006-02-23       Impact factor: 2.991

8.  Hydrogen bond lifetimes and energetics for solute/solvent complexes studied with 2D-IR vibrational echo spectroscopy.

Authors:  Junrong Zheng; Michael D Fayer
Journal:  J Am Chem Soc       Date:  2007-03-21       Impact factor: 15.419

9.  Conformational preferences and vibrational frequency distributions of short peptides in relation to multidimensional infrared spectroscopy.

Authors:  S Gnanakaran; R M Hochstrasser
Journal:  J Am Chem Soc       Date:  2001-12-26       Impact factor: 15.419

10.  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

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  14 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

2.  Discriminating early stage A{beta}42 monomer structures using chirality-induced 2DIR spectroscopy in a simulation study.

Authors:  Wei Zhuang; Nikolaos G Sgourakis; Zhenyu Li; Angel E Garcia; Shaul Mukamel
Journal:  Proc Natl Acad Sci U S A       Date:  2010-08-23       Impact factor: 11.205

3.  Two-dimensional infrared spectra of isotopically diluted amyloid fibrils from Abeta40.

Authors:  Yung Sam Kim; Liu Liu; Paul H Axelsen; Robin M Hochstrasser
Journal:  Proc Natl Acad Sci U S A       Date:  2008-05-22       Impact factor: 11.205

4.  2D IR provides evidence for mobile water molecules in beta-amyloid fibrils.

Authors:  Yung Sam Kim; Liu Liu; Paul H Axelsen; Robin M Hochstrasser
Journal:  Proc Natl Acad Sci U S A       Date:  2009-10-08       Impact factor: 11.205

Review 5.  Empirical amide I vibrational frequency map: application to 2D-IR line shapes for isotope-edited membrane peptide bundles.

Authors:  Y-S Lin; J M Shorb; P Mukherjee; M T Zanni; J L Skinner
Journal:  J Phys Chem B       Date:  2009-01-22       Impact factor: 2.991

6.  Sensitivity of 2D IR spectra to peptide helicity: a concerted experimental and simulation study of an octapeptide.

Authors:  Neelanjana Sengupta; Hiroaki Maekawa; Wei Zhuang; Claudio Toniolo; Shaul Mukamel; Douglas J Tobias; Nien-Hui Ge
Journal:  J Phys Chem B       Date:  2009-09-03       Impact factor: 2.991

7.  Applications of 2D IR spectroscopy to peptides, proteins, and hydrogen-bond dynamics.

Authors:  Yung Sam Kim; Robin M Hochstrasser
Journal:  J Phys Chem B       Date:  2009-06-18       Impact factor: 2.991

8.  2D-IR experiments and simulations of the coupling between amide-I and ionizable side chains in proteins: application to the Villin headpiece.

Authors:  Sayan Bagchi; Cyril Falvo; Shaul Mukamel; Robin M Hochstrasser
Journal:  J Phys Chem B       Date:  2009-08-13       Impact factor: 2.991

9.  Equilibrium exchange processes of the aqueous tryptophan dipeptide.

Authors:  Sayan Bagchi; Adam K Charnley; Amos B Smith Iii; Robin M Hochstrasser
Journal:  J Phys Chem B       Date:  2009-06-18       Impact factor: 2.991

Review 10.  Folding mechanism of β-hairpin trpzip2: heterogeneity, transition state and folding pathways.

Authors:  Yi Xiao; Changjun Chen; Yi He
Journal:  Int J Mol Sci       Date:  2009-06-22       Impact factor: 6.208

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