title: Elastic Vibrations in the Photosynthetic Bacterial Reaction Center Coupled to the Primary Charge Separation: Implications from Molecular Dynamics Simulations and Stochastic Langevin Approach.
abstract: Primary electron transfer reactions in the bacterial reaction center are difficult for theoretical explication: the reaction kinetics, almost unalterable over a wide range of temperature and free energy changes, revealed oscillatory features observed initially by Shuvalov and coauthors (1997, 2002). Here the reaction mechanism was studied by molecular dynamics and analyzed within a phenomenological Langevin approach. The spectral function of polarization around the bacteriochlorophyll special pair PLPM and the dielectric response upon the formation of PL(+)PM(-) dipole within the special pair were calculated. The system response was approximated by Langevin oscillators; the respective frequencies, friction, and energy coupling coefficients were determined. The protein dynamics around PL and PM were distinctly asymmetric. The polarization around PL included slow modes with the frequency 30-80 cm(-1) and the total amplitude of 130 mV. Two main low-frequency modes of protein response around PM had frequencies of 95 and 155 cm(-1) and the total amplitude of 30 mV. In addition, a slowly damping mode with the frequency of 118 cm(-1) and the damping time >1.1 ps was coupled to the formation of PL(+)PM(-) dipole. It was attributed to elastic vibrations of α-helices in the vicinity of PLPM. The proposed trapping of P excitation energy in the form of the elastic vibrations can rationalize the observed properties of the primary electron transfer reactions, namely, the unusual temperature and ΔG dependences, the oscillating phenomena in kinetics, and the asymmetry of the charge separation reactions.
authors.affiliation: A. N. Belozersky Institute of Physical-Chemical Biology, Moscow State University , Leninskiye Gory, 119992 Moscow, Russia.
authors.forename: Georgy E
authors.initials: GE
authors.lastname: Milanovsky
authors.affiliation: A. N. Belozersky Institute of Physical-Chemical Biology, Moscow State University , Leninskiye Gory, 119992 Moscow, Russia.|N. N. Semenov Institute of Chemical Physics, Russian Academy of Sciences , Kosygina st., 4, 117977 Moscow, Russia.
authors.forename: Vladimir A
authors.initials: VA
authors.lastname: Shuvalov
authors.affiliation: A. N. Belozersky Institute of Physical-Chemical Biology, Moscow State University , Leninskiye Gory, 119992 Moscow, Russia.|N. N. Semenov Institute of Chemical Physics, Russian Academy of Sciences , Kosygina st., 4, 117977 Moscow, Russia.
authors.forename: Alexey Yu
authors.initials: AY
authors.lastname: Semenov
authors.affiliation: A. N. Belozersky Institute of Physical-Chemical Biology, Moscow State University , Leninskiye Gory, 119992 Moscow, Russia.|A. N. Frumkin Institute of Physical Chemistry and Electrochemistry, Russian Academy of Sciences , 31, Leninsky Prospect, 119071 Moscow, Russia.
authors.forename: Dmitry A
authors.initials: DA
authors.lastname: Cherepanov
mesh_terms: D004548:Elasticity; D004579:Electron Transport; D056004:Molecular Dynamics Simulation; D045322:Photosynthetic Reaction Center Complex Proteins / Q000737:chemistry / Q000378:metabolism*; D012242:Rhodobacter sphaeroides / Q000737:chemistry / Q000378:metabolism*; D013269:Stochastic Processes; D014732:Vibration
chemical_list: D045322:Photosynthetic Reaction Center Complex Proteins