Journal ArticleDOI
Protein Conformational Dynamics Probed by Single-Molecule Electron Transfer
Haw Yang,Haw Yang,Haw Yang,Guobin Luo,Guobin Luo,Guobin Luo,Pallop Karnchanaphanurach,Pallop Karnchanaphanurach,Pallop Karnchanaphanurach,Tai Man Louie,Tai Man Louie,Tai Man Louie,Ivan Rech,Ivan Rech,Ivan Rech,Sergio Cova,Sergio Cova,Sergio Cova,Luying Xun,Luying Xun,Luying Xun,X. Sunney Xie,X. Sunney Xie,X. Sunney Xie +23 more
TLDR
By probing the fluorescence lifetime of the single flavin on a photon-by-photon basis, the variation of flavin-tyrosine distance over time is observed, suggesting the existence of multiple interconverting conformers related to the fluctuating catalytic reactivity.Abstract:
Electron transfer is used as a probe for angstrom-scale structural changes in single protein molecules. In a flavin reductase, the fluorescence of flavin is quenched by a nearby tyrosine residue by means of photo-induced electron transfer. By probing the fluorescence lifetime of the single flavin on a photon-by-photon basis, we were able to observe the variation of flavin-tyrosine distance over time. We could then determine the potential of mean force between the flavin and the tyrosine, and a correlation analysis revealed conformational fluctuation at multiple time scales spanning from hundreds of microseconds to seconds. This phenomenon suggests the existence of multiple interconverting conformers related to the fluctuating catalytic reactivity.read more
Citations
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Book ChapterDOI
Ergodic Problems for Real Complex Systems in Chemical Physics
Tamiki Komatsuzaki,Akinori Baba,Shinnosuke Kawai,Mikito Toda,John E. Straub,R. Stephen Berry +5 more
TL;DR: In this paper, the authors present a survey of the major departments at Hokkaido University and the University of Chicago, which includes the departments of Chemistry, Biology, and Physics, as well as the Department of Chemistry at MIT.
Journal ArticleDOI
Systematic evaluation of fluorescence correlation spectroscopy data analysis on the nanosecond time scale
TL;DR: A previously unrecognized photophysical process in ATTO655 is identified that introduces fluorescence intermittency on nanosecond time scales that is absent in MR121 and the optimized fitting procedure is used to resolve the viscosity dependence of fluorescence quenching for photoinduced electron transfer probes.
Journal ArticleDOI
Dissecting the Dynamics during Enzyme Catalysis: A Case Study of Pin1 Peptidyl-Prolyl Isomerase.
Toshifumi Mori,Shinji Saito +1 more
TL;DR: The reaction coordinates that describe the transition states of the free energy and transition pathways are investigated by minimizing the cross-entropy function and show that the isomerization transition events can be expressed by the concerted changes in the improper torsion angle $\zeta$ and nearby backbone torsional angles of the ligand.
Journal ArticleDOI
Anomalous pressure effects on the photoreaction of a light-sensor protein from: Synechocystis, PixD (Slr1694), and the compressibility change of its intermediates
Tsubasa Nakajima,Kunisato Kuroi,Yusuke Nakasone,Koji Okajima,Masahiko Ikeuchi,Satoru Tokutomi,Masahide Terazima +6 more
TL;DR: SyPixD is a blue-light receptor that contains a BLUF (blue-light sensor using a flavin chromophore) domain for the function of phototaxis and the key reaction of this protein is a light-induced conformational change and subsequent dissociation reaction from the decamer to the dimer.
Journal ArticleDOI
Simulations of coherent nonlinear optical response of molecular vibronic dimers
Václav Perlík,František Šanda +1 more
TL;DR: A computational model for the spectra of molecular aggregates with signatures of vibronic progression and simulations of the third-order coherent response account for bath reorganization during excitonic transport, which allows for line-shape evolution of cross peaks of 2D spectra.
References
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疟原虫var基因转换速率变化导致抗原变异[英]／Paul H, Robert P, Christodoulou Z, et al//Proc Natl Acad Sci U S A
TL;DR: PfPMP1）与感染红细胞、树突状组胞以及胎盘的单个或多个受体作用，在黏附及免疫逃避中起关键的作�ly.
Journal ArticleDOI
Electron transfers in chemistry and biology
Rudolph A. Marcus,Norman Sutin +1 more
TL;DR: In this paper, the electron transfer reactions between ions and molecules in solution have been the subject of considerable experimental study during the past three decades, including charge transfer, photoelectric emission spectra, chemiluminescent electron transfer, and electron transfer through frozen media.
Journal ArticleDOI
Formation of glasses from liquids and biopolymers.
TL;DR: The onset of a sharp change in ddT( is the Debye-Waller factor and T is temperature) in proteins, which is controversially indentified with the glass transition in liquids, is shown to be general for glass formers and observable in computer simulations of strong and fragile ionic liquids, where it proves to be close to the experimental glass transition temperature.
Journal ArticleDOI
The energy landscapes and motions of proteins.
TL;DR: The concepts that emerge from studies of the conformational substates and the motions between them permit a quantitative discussion of one simple reaction, the binding of small ligands such as carbon monoxide to myoglobin.
Journal ArticleDOI
Fluorescence spectroscopy of single biomolecules.
TL;DR: The progress in applying single-molecule detection and single-Molecule spectroscopy at room temperature by laser-induced fluorescence with the use of fluorophores that are site-specifically attached to macromolecules is reviewed.