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Literature DB >> 24126634

Two-dimensional stimulated resonance Raman spectroscopy study of the Trp-cage peptide folding.

Hao Ren¹, Zaizhi Lai, Jason D Biggs, Jin Wang, Shaul Mukamel.

Abstract

We report a combined molecular dynamics (MD) and ab initio simulation study of the ultrafast broadband ultraviolet (UV) stimulated resonance Raman (SRR) spectra of the Trp-cage mini protein. Characteristic two dimensional (2D) SRR features of various folding states are identified. Structural fluctuations erode the cross peaks and the correlation between diagonal peaks is a good indicator of the α-helix formation.

Entities: CellLine Chemical Disease Gene

Mesh：

Substances：
Peptides
Trp-cage peptide

Year: 2013 PMID： 24126634 PMCID： PMC3859311 DOI： 10.1039/c3cp51347e

Source DB: PubMed Journal: Phys Chem Chem Phys ISSN： 1463-9076 Impact factor: 3.676

54 in total

1. Trp-cage: folding free energy landscape in explicit water.

Authors: Ruhong Zhou
Journal: Proc Natl Acad Sci U S A Date: 2003-10-27 Impact factor: 11.205

2. Coherent nonlinear optical studies of elementary processes in biological complexes: diagrammatic techniques based on the wave function versus the density matrix.

Authors: Jason D Biggs; Judith A Voll; Shaul Mukamel
Journal: Philos Trans A Math Phys Eng Sci Date: 2012-08-13 Impact factor: 4.226

3. Structural variations in the cross-beta core of amyloid beta fibrils revealed by deep UV resonance Raman spectroscopy.

Authors: Ludmila A Popova; Ravindra Kodali; Ronald Wetzel; Igor K Lednev
Journal: J Am Chem Soc Date: 2010-05-12 Impact factor: 15.419

4. Two-dimensional ultraviolet (2DUV) spectroscopic tools for identifying fibrillation propensity of protein residue sequences.

Authors: Jun Jiang; Shaul Mukamel
Journal: Angew Chem Int Ed Engl Date: 2010-12-10 Impact factor: 15.336

Review 5. Native state kinetic stabilization as a strategy to ameliorate protein misfolding diseases: a focus on the transthyretin amyloidoses.

Authors: Steven M Johnson; R Luke Wiseman; Yoshiki Sekijima; Nora S Green; Sara L Adamski-Werner; Jeffery W Kelly
Journal: Acc Chem Res Date: 2005-12 Impact factor: 22.384

6. Comparison of multiple Amber force fields and development of improved protein backbone parameters.

Authors: Viktor Hornak; Robert Abel; Asim Okur; Bentley Strockbine; Adrian Roitberg; Carlos Simmerling
Journal: Proteins Date: 2006-11-15

7. Femtosecond time-resolved stimulated Raman reveals the birth of bacteriorhodopsin's J and K intermediates.

Authors: Sangdeok Shim; Jyotishman Dasgupta; Richard A Mathies
Journal: J Am Chem Soc Date: 2009-06-10 Impact factor: 15.419

Review 8. 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

Two-dimensional stimulated resonance Raman spectroscopy study of the Trp-cage peptide folding.

1. Trp-cage: folding free energy landscape in explicit water.

2. Coherent nonlinear optical studies of elementary processes in biological complexes: diagrammatic techniques based on the wave function versus the density matrix.

3. Structural variations in the cross-beta core of amyloid beta fibrils revealed by deep UV resonance Raman spectroscopy.

4. Two-dimensional ultraviolet (2DUV) spectroscopic tools for identifying fibrillation propensity of protein residue sequences.

Review 5. Native state kinetic stabilization as a strategy to ameliorate protein misfolding diseases: a focus on the transthyretin amyloidoses.

6. Comparison of multiple Amber force fields and development of improved protein backbone parameters.

7. Femtosecond time-resolved stimulated Raman reveals the birth of bacteriorhodopsin's J and K intermediates.

Review 8. Coherent multidimensional optical spectroscopy of excitons in molecular aggregates; quasiparticle versus supermolecule perspectives.

9. Conformational dynamics of the trp-cage miniprotein at its folding temperature.

10. Coherent multidimensional optical probes for electron correlations and exciton dynamics: from NMR to X-rays.

1. Machine learning recognition of protein secondary structures based on two-dimensional spectroscopic descriptors.

2. Signatures of the Protein Folding Pathway in Two-Dimensional Ultraviolet Spectroscopy.

3. Enriched Conformational Sampling of DNA and Proteins with a Hybrid Hamiltonian Derived from the Protein Data Bank.