Literature DB >> 17146054

Two-dimensional vibrational optical probes for peptide fast folding investigation.

Wei Zhuang1, Darius Abramavicius, Shaul Mukamel.   

Abstract

A simulation study shows that early protein folding events may be investigated by using a recently developed family of nonlinear infrared techniques that combine the high temporal and spatial resolution of multidimensional spectroscopy with the chirality-specific sensitivity of amide vibrations to structure. We demonstrate how the structural sensitivity of cross-peaks in two-dimensional correlation plots of chiral signals of an alpha helix and a beta hairpin may be used to clearly resolve structural and dynamical details undetectable by one-dimensional techniques (e.g. circular dichroism) and identify structures indistinguishable by NMR.

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Year:  2006        PMID: 17146054      PMCID: PMC1748155          DOI: 10.1073/pnas.0606912103

Source DB:  PubMed          Journal:  Proc Natl Acad Sci U S A        ISSN: 0027-8424            Impact factor:   11.205


  17 in total

1.  Two-dimensional IR spectroscopy can be designed to eliminate the diagonal peaks and expose only the crosspeaks needed for structure determination.

Authors:  M T Zanni; N H Ge; Y S Kim; R M Hochstrasser
Journal:  Proc Natl Acad Sci U S A       Date:  2001-09-18       Impact factor: 11.205

2.  Understanding the key factors that control the rate of beta-hairpin folding.

Authors:  Deguo Du; Yongjin Zhu; Cheng-Yen Huang; Feng Gai
Journal:  Proc Natl Acad Sci U S A       Date:  2004-11-01       Impact factor: 11.205

3.  Two-dimensional spectroscopy of electronic couplings in photosynthesis.

Authors:  Tobias Brixner; Jens Stenger; Harsha M Vaswani; Minhaeng Cho; Robert E Blankenship; Graham R Fleming
Journal:  Nature       Date:  2005-03-31       Impact factor: 49.962

Review 4.  Long-timescale simulation methods.

Authors:  Ron Elber
Journal:  Curr Opin Struct Biol       Date:  2005-04       Impact factor: 6.809

5.  Probing the structure of a rotaxane with two-dimensional infrared spectroscopy.

Authors:  Olaf F A Larsen; Pavol Bodis; Wybren Jan Buma; Jeffrey S Hannam; David A Leigh; Sander Woutersen
Journal:  Proc Natl Acad Sci U S A       Date:  2005-09-06       Impact factor: 11.205

6.  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

7.  Chirality-induced signals in coherent multidimensional spectroscopy of excitons.

Authors:  Darius Abramavicius; Shaul Mukamel
Journal:  J Chem Phys       Date:  2006-01-21       Impact factor: 3.488

8.  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

Review 9.  Infrared and Raman vibrational optical activity: theoretical and experimental aspects.

Authors:  L A Nafie
Journal:  Annu Rev Phys Chem       Date:  1997       Impact factor: 12.703

10.  Tryptophan zippers: stable, monomeric beta -hairpins.

Authors:  A G Cochran; N J Skelton; M A Starovasnik
Journal:  Proc Natl Acad Sci U S A       Date:  2001-05-01       Impact factor: 11.205

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  12 in total

1.  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

2.  Simulation of two-dimensional infrared spectroscopy of amyloid fibrils.

Authors:  Wei Zhuang; Darius Abramavicius; Dimitrii V Voronine; Shaul Mukamel
Journal:  Proc Natl Acad Sci U S A       Date:  2007-08-03       Impact factor: 11.205

3.  Two-dimensional infrared spectra reveal relaxation of the nonnucleoside inhibitor TMC278 complexed with HIV-1 reverse transcriptase.

Authors:  Chong Fang; Joseph D Bauman; Kalyan Das; Amanda Remorino; Eddy Arnold; Robin M Hochstrasser
Journal:  Proc Natl Acad Sci U S A       Date:  2007-11-26       Impact factor: 11.205

4.  Transient 2D IR spectroscopy of ubiquitin unfolding dynamics.

Authors:  Hoi Sung Chung; Ziad Ganim; Kevin C Jones; Andrei Tokmakoff
Journal:  Proc Natl Acad Sci U S A       Date:  2007-06-05       Impact factor: 11.205

Review 5.  Coherent multidimensional optical spectroscopy of excitons in molecular aggregates; quasiparticle versus supermolecule perspectives.

Authors:  Darius Abramavicius; Benoit Palmieri; Dmitri V Voronine; Frantisek Sanda; Shaul Mukamel
Journal:  Chem Rev       Date:  2009-06       Impact factor: 60.622

6.  Vibrational coherence and energy transfer in two-dimensional spectra with the optimized mean-trajectory approximation.

Authors:  Mallory Alemi; Roger F Loring
Journal:  J Chem Phys       Date:  2015-06-07       Impact factor: 3.488

7.  An optimized semiclassical approximation for vibrational response functions.

Authors:  Mallory Gerace; Roger F Loring
Journal:  J Chem Phys       Date:  2013-03-28       Impact factor: 3.488

8.  Two-Dimensional Infrared (2DIR) Spectroscopy of the Peptide Beta3s Folding.

Authors:  Zaizhi Lai; Nicholas K Preketes; Jun Jiang; Shaul Mukamel; Jin Wang
Journal:  J Phys Chem Lett       Date:  2013-06-06       Impact factor: 6.475

9.  Monitoring the folding of Trp-cage peptide by two-dimensional infrared (2DIR) spectroscopy.

Authors:  Zaizhi Lai; Nicholas K Preketes; Shaul Mukamel; Jin Wang
Journal:  J Phys Chem B       Date:  2013-04-05       Impact factor: 2.991

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

Authors:  Jianping Wang; Wei Zhuang; Shaul Mukamel; Robin Hochstrasser
Journal:  J Phys Chem B       Date:  2007-12-14       Impact factor: 2.991

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