Nuclear Dynamics and Electronic Transition in a Photosynthetic Reaction Center

Souaille, Marc; Marchi, Massimo

doi:10.1021/ja943841c

Cited by 22 publications

(35 citation statements)

References 39 publications

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“…In principle, an alternative pathway which could lead to a more precise assignment of the observed vibrational modes is the use of molecular dynamics simulations. In a recent study (48), spectra were calculated for the wt RC that exhibited similar features to those observed in the experimental spectra. In future work, the inclusion of the chromophore self-energies may enhance the quantitative correspondence between simulation and experiment.…”

Section: Discussionmentioning

confidence: 65%

Low frequency vibrational modes in proteins: Changes induced by point-mutations in the protein-cofactor matrix of bacterial reaction centers

Rischel

Spiedel

Ridge

et al. 1998

Proc. Natl. Acad. Sci. U.S.A.

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As a step toward understanding their functional role, the low frequency vibrational motions (<300 cm ؊1 ) that are coupled to optical excitation of the primary donor bacteriochlorophyll cofactors in the reaction center from Rhodobacter sphaeroides were investigated. The pattern of hydrogen-bonding interaction between these bacteriochlorophylls and the surrounding protein was altered in several ways by mutation of single amino acids. The spectrum of low frequency vibrational modes identified by femtosecond coherence spectroscopy varied strongly between the different reaction center complexes, including between different mutants where the pattern of hydrogen bonds was the same. It is argued that these variations are primarily due to changes in the nature of the individual modes, rather than to changes in the charge distribution in the electronic states involved in the optical excitation. Pronounced effects of point mutations on the low frequency vibrational modes active in a proteincofactor system have not been reported previously. The changes in frequency observed indicate a strong involvement of the protein in these nuclear motions and demonstrate that the protein matrix can increase or decrease the f luctuations of the cofactor along specific directions.Any fundamental description of a biological process must ultimately encompass an account of small and possibly large scale changes in the nuclear geometry of the participating molecules. In particular, a central element in the determination of reaction efficiencies is the structure and accessibility of the transition state, which is the highest point on the free energy barrier that opposes changes in nuclear geometry as the system moves from reactant to product state. For proteins, atoms are most easily displaced along the ''soft'' directionsthe delocalized, low frequency modes-and the study of such motion during a reaction is therefore of particular interest.In recent years, a new aspect of low frequency motion has been revealed by the observation of coherent nuclear motion, persisting on the picosecond (ps) timescale following impulsive optical excitation, and manifested as oscillations in the transient optical properties of the protein cofactors. The discovery of this phenomenon in a variety of protein-cofactor systems, including the bacterial reaction center (RC) (1, 2), bacteriorhodopsin (3), and heme proteins (4), implies that ultrafast biological processes can occur on a timescale that is faster than vibrational relaxation (5). Therefore the possibility of coherent (in addition to thermal) motion along the reaction coordinate must be included in any complete description of a reaction. In addition, the measurement of oscillations by using femtosecond (fs) transient spectroscopy provides a new and convenient method for probing the spectrum of low frequency, nuclear vibrations that are set in motion by a physiological trigger. This study is aimed at assessing the factors that influence the character of such nuclear motions, by exploiting the possibil...

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Section: Discussionmentioning

confidence: 65%

Low frequency vibrational modes in proteins: Changes induced by point-mutations in the protein-cofactor matrix of bacterial reaction centers

Rischel

Spiedel

Ridge

et al. 1998

Proc. Natl. Acad. Sci. U.S.A.

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“…The effective inverse temperature β is 12) and Z(t) = [2 sinh(h Ω β/2)] −1 . The transformed density matrix (2.10) corresponds to the equilibrium density matrix of the harmonic oscillator H considered at fixed time t.…”

Section: Gaussian Density Matricesmentioning

confidence: 99%

“…However, as such an approach relies on perturbation theory in the system-bath coupling, its application to condensed-phase reactions characterized by strong system-bath coupling remains questionable. Other methods are based on classical molecular dynamics (MD) simulations [12] or projection operator techniques [5].…”

Section: Introductionmentioning

confidence: 99%

Coherent nuclear motion in a condensed-phase environment: Wave-packet approach and pump–probe spectroscopy

Mühlbacher

Lücke

Egger

1999

The Journal of Chemical Physics

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A quantum-mechanical Gaussian wave-packet approach to the theoretical description of nuclear motions in a condensedphase environment is developed. General expressions for the time-dependent reduced density matrix are given for a harmonic potential surface, and the exact quantum dynamics is found for a microscopic system-plus-bath model. Particular attention is devoted to the influence of initial correlations between system and bath for the outcome of a pump-probe experiment. We show that the standard factorized preparation, compared to a more realistic correlated preparation, leads to significantly different stimulated emission spectra at high temperatures. Recent experiments for the reaction center are analyzed using this formalism.

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“…In Ref. [10] we have improved on this model by simulating a RC of rhodobacter (rb.) sphaeroides in water.…”

mentioning

confidence: 99%

“…All the simulation runs in Ref. [10] were carried out by using our in-house molecular dynamics program ORAC [ll, 12]. In this earlier work, a spherical cutoff of 9 Â was applied to the non-bonded interactions thus neglecting long range electrostatic effects.…”

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confidence: 99%

Molecular Modeling and Simulation of a Reaction Center Protein

Ceccarelli

Souaille

March

2004

ACS Symposium Series

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In this paper we give an account of our ongoing effort to un -derstand bacterial photosynthesis at the atomic level. First, we de -scribe earlier simulations which investigate the nuclear motion cou -pled to the primary donor excitation in bacterial reaction centers (RC). Then, we discuss the molecular modeling of the chromophores of the RC of rhodobacter sphaeroides. Finally, we report on our latest molecular dynamics simulation results concerning a RC in a deter -gent micelle.The bacterial photosynthetic reaction center (RC)[1, 2] is a membrane protein composed of chromophores (bacteriochlorophylls, bacteriopheophytins and quinones) and three protein subunits named L, M and H. While pro teins L and M form two branches of the RC (almost the mirror images of each other) and provide the necessary scaffolding to hold in place bacteri ochlorophylls and bacteriopheophytins, the H subunit is in contact with the bacterial cytoplasm and binds the quinones in its interior. In the region of the RC near the pery-plasm is located a bacteriochlorophylls dimer, the socalled special pair (P). This chromophore is at the junction point between the L and M branches and is involved directly in the first photosynthetic electron transfer.Photosynthesis in purple bacteria commences with the excitation of P, the energy for such excitation being transferred directly from surrounding light harvesting proteins. The excited state P* then decays in a charge

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Nuclear Dynamics and Electronic Transition in a Photosynthetic Reaction Center

Cited by 22 publications

References 39 publications

Low frequency vibrational modes in proteins: Changes induced by point-mutations in the protein-cofactor matrix of bacterial reaction centers

Low frequency vibrational modes in proteins: Changes induced by point-mutations in the protein-cofactor matrix of bacterial reaction centers

Coherent nuclear motion in a condensed-phase environment: Wave-packet approach and pump–probe spectroscopy

Molecular Modeling and Simulation of a Reaction Center Protein

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