Journal ArticleDOI
Protein dynamics modulated electron transfer kinetics in early stage photosynthesis.
Prasanta Kundu,Arti Dua +1 more
TLDR
This work presents a model where the electron transfer kinetics of the donor-acceptor pair is described along the reaction coordinate associated with the distance fluctuations in a protein backbone and explains the microscopic origins of the non-exponential decay of the transient absorption curve at 280 nm in terms of multiple time scales of relaxation of the protein normal modes.Abstract:
A recent experiment has probed the electron transfer kinetics in the early stage of photosynthesis in Rhodobacter sphaeroides for the reaction center of wild type and different mutants [Science 316, 747 (2007)]. By monitoring the changes in the transient absorption of the donor-acceptor pair at 280 and 930 nm, both of which show non-exponential temporal decay, the experiment has provided a strong evidence that the initial electron transfer kinetics is modulated by the dynamics of protein backbone. In this work, we present a model where the electron transfer kinetics of the donor-acceptor pair is described along the reaction coordinate associated with the distance fluctuations in a protein backbone. The stochastic evolution of the reaction coordinate is described in terms of a non-Markovian generalized Langevin equation with a memory kernel and Gaussian colored noise, both of which are completely described in terms of the microscopics of the protein normal modes. This model provides excellent fits to the transient absorption signals at 280 and 930 nm associated with protein distance fluctuations and protein dynamics modulated electron transfer reaction, respectively. In contrast to previous models, the present work explains the microscopic origins of the non-exponential decay of the transient absorption curve at 280 nm in terms of multiple time scales of relaxation of the protein normal modes. Dynamic disorder in the reaction pathway due to protein conformational fluctuations which occur on time scales slower than or comparable to the electron transfer kinetics explains the microscopic origin of the non-exponential nature of the transient absorption decay at 930 nm. The theoretical estimates for the relative driving force for five different mutants are in close agreement with the experimental estimates obtained using electrochemical measurements.read more
Citations
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Journal ArticleDOI
The role of protein dynamics and thermal fluctuations in regulating cytochrome c/cytochrome c oxidase electron transfer.
TL;DR: How protein dynamics and thermal fluctuations may impact on protein ET reactions, and how a regulatory mechanism that may operate in the Cyt/CcO electron transfer reaction in vivo are discussed are discussed.
Journal ArticleDOI
Understanding chain looping kinetics in polymer solutions: crowding effects of microviscosity and collapse
TL;DR: A theoretical framework based on a generalized Langevin equation with fractional Gaussian noise is presented to describe the looping kinetics of chains in polymer solutions, revealing that non-trivial behaviors can be attributed to the competition between the two opposing factors of viscosity-associated inhibition and collapse-induced facilitation of loop formation.
Journal ArticleDOI
Redox state dependence of axial ligand dynamics in Nitrosomonas europaea cytochrome c552.
Ravinder Kaur,Kara L. Bren +1 more
TL;DR: Analysis of NMR spectra reveals that the heme axial Met ligand orientation and dynamics in Nitrosomonas europaea cytochrome c552 (Ne cyt c) are dependent on the he me redox state, and analysis of nuclear Overhauser effects and existing structural data provides further support.
Journal ArticleDOI
Solvent-quality dependent contact formation dynamics in proteins
Prasanta Kundu,Arti Dua +1 more
TL;DR: In this paper, the mean time of contact formation between two ends of a protein chain shows power law dependence with respect to the number of residues, and a comparison of these two time scales yields reaction-controlled and diffusion-controlled kinetic regimes with different values of the scaling exponents.
Journal ArticleDOI
Unusual crowding-induced chain looping kinetics in hard-sphere fluids: a contrastive study with polymer solutions
TL;DR: It is concluded that the looping kinetics in specific systems actually should be governed by the critical competition between the two crowding factors, and reasonable measurements of effective viscosity and collapse can provide a unified strategy to analyze crowding effects on thelooping rate in a systematic manner.
References
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Book
The theory of polymer dynamics
Masao Doi,Sam F. Edwards +1 more
TL;DR: In this article, the viscoelasticity of polymeric liquids was studied in the context of rigid rod-like polymers and concentrated solutions of rigid rods like polymers.
Book
Stochastic processes in physics and chemistry
TL;DR: In this article, the authors introduce the Fokker-planck equation, the Langevin approach, and the diffusion type of the master equation, as well as the statistics of jump events.
Stochastic Processes in Physics and Chemistry
Abstract: Preface to the first edition. Preface to the second edition. Abbreviated references. I. Stochastic variables. II. Random events. III. Stochastic processes. IV. Markov processes. V. The master equation. VI. One-step processes. VII. Chemical reactions. VIII. The Fokker-Planck equation. IX. The Langevin approach. X. The expansion of the master equation. XI. The diffusion type. XII. First-passage problems. XIII. Unstable systems. XIV. Fluctuations in continuous systems. XV. The statistics of jump events. XVI. Stochastic differential equations. XVII. Stochastic behavior of quantum systems.
Journal ArticleDOI
Generalized Langevin equation with fractional Gaussian noise: subdiffusion within a single protein molecule.
Samuel C. Kou,X. Sunney Xie +1 more
TL;DR: By introducing fractional Gaussian noise into the generalized Langevin equation, the subdiffusion of a particle can be described as a stationary Gaussian process with analytical tractability.