Proton release pathway in bacteriorhodopsin: Molecular dynamics and electrostatic calculations

Scharnagl, Christina; Hettenkofer, Johannes; Fischer, Sighart F.

doi:10.1002/qua.560520705

Cited by 23 publications

(32 citation statements)

References 62 publications

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“…The importance of Arg82 for the proton release mechanism was noted in earlier computational and experimental studies. 39,44 A proton transfer from the SB to Asp85 (p.t. 1), and the release of a proton (p.t.…”

Section: Key Proton Transfer Stepsmentioning

confidence: 99%

Proton Affinity Changes Driving Unidirectional Proton Transport in the Bacteriorhodopsin Photocycle

Onufriev

Smondyrev

Bashford

2003

Journal of Molecular Biology

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Bacteriorhodopsin is the smallest autonomous light-driven proton pump. Proposals as to how it achieves the directionality of its trans-membrane proton transport fall into two categories: accessibility-switch models in which proton transfer pathways in different parts of the molecule are opened and closed during the photocycle, and affinity-switch models, which focus on changes in proton affinity of groups along the transport chain during the photocycle. Using newly available structural data, and adapting current methods of protein protonation-state prediction to the non-equilibrium case, we have calculated the relative free energies of protonation microstates of groups on the transport chain during key conformational states of the photocycle. Proton flow is modeled using accessibility limitations that do not change during the photocycle. The results show that changes in affinity (microstate energy) calculable from the structural models are sufficient to drive unidirectional proton transport without invoking an accessibility switch. Modeling studies for the N state relative to late M suggest that small structural re-arrangements in the cytoplasmic side may be enough to produce the crucial affinity change of Asp96 during N that allows it to participate in the reprotonation of the Schiff base from the cytoplasmic side. Methodologically, the work represents a conceptual advance compared to the usual calculations of pK a using macroscopic electrostatic models. We operate with collective states of protonation involving all key groups, rather than the individualgroup pK a values traditionally used. When combined with state-to-state transition rules based on accessibility considerations, a model for nonequilibrium proton flow is obtained. Such methods should also be applicable to other active proton-transport systems.

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Section: Key Proton Transfer Stepsmentioning

confidence: 99%

Proton Affinity Changes Driving Unidirectional Proton Transport in the Bacteriorhodopsin Photocycle

Onufriev

Smondyrev

Bashford

2003

Journal of Molecular Biology

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“…XH therefore must be a group close to the surface whose pK a is drastically reduced during the cycle so that under normal conditions the ejection of a proton becomes possible. From calculations of pK changes on the time scale of the L-M transition, it was predicted that the residue E204 might be a candidate for XH (18)(19)(20). Indeed, it could be confirmed that this residue must be involved in the release process since in the mutant E204Q the normal release process is abolished (21).…”

mentioning

confidence: 99%

Time and pH Dependence of the L-to-M Transition in the Photocycle of Bacteriorhodopsin and Its Correlation with Proton Release

Althaus

Stockburger

1998

Biochemistry

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The pH dependence of the L-to-M transition in the photocycle of bacteriorhodopsin was studied in pump-probe resonance Raman (RR) flow experiments in the range pH 3.5-7.8 on a time scale of 0-700 micros. For pH < 5, following the initial decay of L to M, the two intermediates approach nearly constant levels. From a specially designed perturbation-relaxation experiment at pH 4.6, in which the composition of L and M is perturbed by photoreversal of M, it could be concluded that the incomplete decay of L is due to an intermediate equilibration between L and M. It was found, by both RR and optical transient spectroscopy, that the maximum level of M (approximately 500 micros) increases with pH according to a pKa of 5. 6 (150 mM Na+). Since the proton release from an internal group XH to the extracellular surface is determined by nearly the same pKa of 5.7 [Zimanyi, L., Varo, G., Chang, M., Ni, B., Needleman, R., and Lanyi, J. K. (1992) Biochemistry 31, 8535-8543], it is concluded that this increase is controlled by the dissociation of XH. From the analysis of the perturbation-relaxation experiments and the multiexponential rise of M, a kinetic scheme with two sequential L-M equilibria is proposed for the L-M transition. By comparison with the time behavior of proton release [Heberle, J., and Dencher, N. A. (1992) Proc. Natl. Acad. Sci. U.S.A. 89, 5996-6000], it is suggested that it is the second equilibrium which is further shifted toward the M state by the dissociation of XH. From the magnitude of this shift, it is concluded that the L-M transition and proton release are not as strongly coupled as is generally assumed. Instead, it is proposed that structural changes during the photocycle are the dominating factors which reduce the pKa of XH to approximately 5.7 so that proton release becomes possible under normal conditions.

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“…The later part of the photocycle still lies beyond the time window of traditional molecular dynamics theory. Based on the high-resolution structure of bR determined by diffraction experiments, several attempts have been made by using semiempirical or classical force field calculations and the method of simulated annealing to compute the further progression of the photocycle (18)(19)(20)30). Taking into account some known empirical parameters (pK's, Fourier-transformed IR data, etc.)…”

Section: Discussionmentioning

confidence: 99%

“…The results are discussed and related to predictions from molecular dynamics calculations (18)(19)(20).…”

mentioning

confidence: 89%

Interpretation of the spatial charge displacements in bacteriorhodopsin in terms of structural changes during the photocycle

Dér

Oroszi

Kulcsár

et al. 1999

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

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We have recently introduced a method, made possible by an improved orienting technique using a combination of electric and magnetic fields, that allows the threedimensional detection of the intramolecular charge displacements during the photocycle of bacteriorhodopsin. This method generates electric asymmetry, a prerequisite for the detection of electric signal on the macroscopic sample, in all three spatial dimensions. Purple membrane fragments containing bacteriorhodopsin were oriented so that their permanent electric dipole moment vectors were perpendicular to the membrane plane and pointed in the same direction. The resulting cylindrical symmetry was broken by photoselection, i. e., by f lash excitation with low intensity linearly polarized light. From the measured electric signals, the threedimensional motion of the electric charge center in the bacteriorhodopsin molecules was calculated for the first 400 s. Simultaneous absorption kinetic recording provided the time-dependent concentrations of the intermediates. Combining the two sets of data, we determined the discrete dipole moments of intermediates up to M. When compared with the results of current molecular dynamics calculations, the data provided a decisive experimental test for selecting the optimal theoretical model for the proton transport and should eventually lead to a full description of the mechanism of the bacteriorhodopsin proton pump.Bacteriorhodopsin (bR) is an integral protein in the plasma membrane of Halobacterium salinarum (1). Upon light absorption, bR transports protons across the membrane, converting the photon energy into the energy of a proton electrochemical gradient (for recent reviews, see refs. 2 and 3). bR is a single small protein and is the simplest known active ion pump and biological light energy transducer. Consequently, it is a prototype system for studying the basic steps and rules of biological energy transduction. bR consists of the 23-kDa protein moiety and a retinal chromophore attached to the side chain of Lys-216 via a protonated Schiff base. The retinal is located about halfway through the membrane and sustains an angle of Ϸ70°with the membrane normal. Trimers of bR form twodimensional crystalline patches in the plasma membrane. These purple membrane fragments (pm) can be isolated as sheets of about 0.5-m diameter.

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Proton release pathway in bacteriorhodopsin: Molecular dynamics and electrostatic calculations

Cited by 23 publications

References 62 publications

Proton Affinity Changes Driving Unidirectional Proton Transport in the Bacteriorhodopsin Photocycle

Proton Affinity Changes Driving Unidirectional Proton Transport in the Bacteriorhodopsin Photocycle

Time and pH Dependence of the L-to-M Transition in the Photocycle of Bacteriorhodopsin and Its Correlation with Proton Release

Interpretation of the spatial charge displacements in bacteriorhodopsin in terms of structural changes during the photocycle

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