Literature DB >> 16852179

Collective oscillations and the linear and two-dimensional infrared spectra of inhomogeneous beta-sheets.

Arend G Dijkstra1, Jasper Knoester.   

Abstract

We numerically calculate the collective amide I oscillations and the associated linear and two-dimensional infrared (2DIR) spectra for model antiparallel beta-sheets and study the effect of inhomogeneity. To visualize the collective vibrational exciton states, a new method is introduced, which proves very useful in classifying the optically dominant states with respect to their symmetry properties and phase relations, even in the absence of exact symmetries. We find that energy (diagonal) and interaction (off-diagonal) disorder may have profoundly different effects on the main peaks in the linear spectrum. We also show that in the 2DIR spectra energy disorder leads to diagonal stretching of the diagonal peaks, while the cross-peaks are typically stretched more horizontally. This offers an explanation for the recently observed overall Z-shape in experimental spectra. Finally, we find that the anharmonic splitting between associated positive and negative features in the 2DIR spectra scales inversely proportionally with the exciton delocalization size imposed by the disorder, thus offering a spectroscopic ruler for this size.

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Year:  2005        PMID: 16852179     DOI: 10.1021/jp044141p

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


  9 in total

1.  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

2.  Two-dimensional infrared spectroscopy displays signatures of structural ordering in peptide aggregates.

Authors:  Casey H Londergan; Jianping Wang; Paul H Axelsen; Robin M Hochstrasser
Journal:  Biophys J       Date:  2006-03-24       Impact factor: 4.033

3.  Spectral signatures of heterogeneous protein ensembles revealed by MD Simulations of 2DIR spectra.

Authors:  Ziad Ganim; Andrei Tokmakoff
Journal:  Biophys J       Date:  2006-07-14       Impact factor: 4.033

4.  Two-dimensional infrared population transfer spectroscopy for enhancing structural markers of proteins.

Authors:  Thomas la Cour Jansen; Jasper Knoester
Journal:  Biophys J       Date:  2007-11-02       Impact factor: 4.033

5.  Distinguishing gramicidin D conformers through two-dimensional infrared spectroscopy of vibrational excitons.

Authors:  Paul Stevenson; Andrei Tokmakoff
Journal:  J Chem Phys       Date:  2015-06-07       Impact factor: 3.488

6.  Development and validation of transferable amide I vibrational frequency maps for peptides.

Authors:  L Wang; C T Middleton; M T Zanni; J L Skinner
Journal:  J Phys Chem B       Date:  2011-03-15       Impact factor: 2.991

7.  Probing the folding transition state of ubiquitin mutants by temperature-jump-induced downhill unfolding.

Authors:  Hoi Sung Chung; Ali Shandiz; Tobin R Sosnick; Andrei Tokmakoff
Journal:  Biochemistry       Date:  2008-12-30       Impact factor: 3.162

8.  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

9.  Interplay between Hydrogen Bonding and Vibrational Coupling in Liquid N-Methylacetamide.

Authors:  Ana V Cunha; Evgeniia Salamatova; Robbert Bloem; Steven J Roeters; Sander Woutersen; Maxim S Pshenichnikov; Thomas L C Jansen
Journal:  J Phys Chem Lett       Date:  2017-05-19       Impact factor: 6.475

  9 in total

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