pH dependence of light‐induced proton release by bacteriorhodopsin

Kono, Masahiro; Misra, Saurav; Ebrey, Thomas G.

doi:10.1016/0014-5793(93)80291-2

Cited by 60 publications

(47 citation statements)

References 24 publications

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“…This decrease is also coupled to the acceleration of the microsecond electrogenic phase, coinciding with the acceleration of M intermediate formation. A similar increase in rate of the microsecond phase and decrease in the sum of their amplitudes were detected in photocurrent measurements in oriented PM suspension by Kono et al [30]and Liu [29]. All these observation are in line with the conclusion on the electrogenic nature of the E204 deprotonation.…”

Section: Resultssupporting

confidence: 84%

“…Assay medium: 0.5 M Na P SO R , 5 mM HEPES, 5 mM Tris, 5 mM CHES, 5 mM CHAPS. crease in rate of the microsecond phase and decrease in the sum of their amplitudes were detected in photocurrent measurements in oriented PM suspension by Kono et al [30] and Liu [29]. All these observation are in line with the conclusion on the electrogenic nature of the E204 deprotonation.…”

Section: Resultssupporting

confidence: 73%

“…4A,B), the rate of M formation is greatly accelerated in the wild-type bR but not in the E204Q mutant [14]. The acceleration of M intermediate formation in the wild-type bR is possibly due to E204 deprotonation in the bR ground state [12,14,30]. In the wild-type bR, the acceleration of M intermediate formation is accompanied by a twofold decrease in amplitude of the microsecond electrogenic phase (Fig.…”

Section: Resultsmentioning

confidence: 99%

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Photovoltage evidence that Glu‐204 is the intermediate proton donor rather than the terminal proton release group in bacteriorhodopsin

Kalaidzidis¹,

Belevich²,

Kaulen³

1998

FEBS Letters

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Electrogenic events in the E204Q bacteriorhodopsin mutant have been studied. A two-fold decrease in the magnitude of microsecond photovoltage generation coupled to M intermediate formation in the E204Q mutant is shown. This means that deprotonation of E204 is an electrogenic process and its electrogenicity is comparable to that of the proton transfer from the Schiff base to D85. pH dependence of the electrogenicity of M intermediate formation in the wild-type bacteriorhodopsin reveals only one component corresponding to the protonation of D85 in the bacteriorhodopsin ground state and transition of the purple neutral form into the blue acid form. Thus, the pK of E204 in the M state is close to the pK of D85 in the bacteriorhodopsin ground state ( 6 6 3) and far below the pK of the terminal proton release group (V6). It is concluded that E204 functions as the intermediate proton donor rather than the terminal proton release group in the bacteriorhodopsin proton pump.z 1998 Federation of European Biochemical Societies.

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Section: Resultssupporting

confidence: 84%

Section: Resultssupporting

confidence: 73%

Section: Resultsmentioning

confidence: 99%

See 1 more Smart Citation

Photovoltage evidence that Glu‐204 is the intermediate proton donor rather than the terminal proton release group in bacteriorhodopsin

Kalaidzidis¹,

Belevich²,

Kaulen³

1998

FEBS Letters

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“…The calculated cluster p K a is 12 whereas the experimental value is 9.5 105,106. Thus, the calculations overstabilize the binding of this proton.…”

Section: Resultsmentioning

confidence: 81%

MCCE2: Improving protein pK_a calculations with extensive side chain rotamer sampling

2009

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Multiconformation continuum electrostatics (MCCE) explores different conformational degrees of freedom in Monte Carlo calculations of protein residue and ligand pKas. Explicit changes in side chain conformations throughout a titration create a position dependent, heterogeneous dielectric response giving a more accurate picture of coupled ionization and position changes. The MCCE2 methods for choosing a group of input heavy atom and proton positions are described. The pKas calculated with different isosteric conformers, heavy atom rotamers and proton positions, with different degrees of optimization are tested against a curated group of 305 experimental pKas in 33 proteins. QUICK calculations, with rotation around Asn and Gln termini, sampling His tautomers and torsion minimum hydroxyls yield an RMSD of 1.34 with 84% of the errors being <1.5 pH units. FULL calculations adding heavy atom rotamers and side chain optimization yield an RMSD of 0.90 with 90% of the errors <1.5 pH unit. Good results are also found for pKas in the membrane protein bacteriorhodopsin. The inclusion of extra side chain positions distorts the dielectric boundary and also biases the calculated pKas by creating more neutral than ionized conformers. Methods for correcting these errors are introduced. Calculations are compared with multiple X-ray and NMR derived structures in 36 soluble proteins. Calculations with X-ray structures give significantly better pKas. Results with the default protein dielectric constant of 4 are as good as those using a value of 8.

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“…The L state decays by transferring a proton to a cluster identified with the residues of D85, D212 and R82. This cluster, upon protonation, interacts with a surface group identified by Lanyi and co-workers [22] as E204, shifting it from a high pK state (BH, pK= 9.3) [23] to a low one (BH, pK--5.8) placing VI30. The theoretical curve was calculated using the rate constants given in Table 1.…”

Section: Intraprotein Dynamicsmentioning

confidence: 95%

Quantitative evaluation of the dynamics of proton transfer from photoactivated bacteriorhodopsin to the bulk

Nachliel

Gutman

1996

FEBS Letters

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It has been reported by many research groups that protons released during the photocycle of bacteriorhodopsin are detected by surface bound indicators much faster than by indicators in the bulk. In this study we used numerical simulation of chemical reaction's dynamics for analyzing the delayed appearance of protons in the bulk. The results indicate that the low pK surface groups of the membrane, which form an undilutable concentrated matrix of proton binding sites, retain the protons in this space according to the mass action law. The main sites for proton accumulation are the cluster of carboxylates on the cytoplasmic side of the membrane. The protonation of an indicator in the bulk does not proceed by its reaction with free proton, but rather through self-diffusion of the indicator to the membrane and abstraction of proton from the protonated surface group. The detailed mechanisms which correspond with these reactions are reported.

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pH dependence of light‐induced proton release by bacteriorhodopsin

Cited by 60 publications

References 24 publications

Photovoltage evidence that Glu‐204 is the intermediate proton donor rather than the terminal proton release group in bacteriorhodopsin

Photovoltage evidence that Glu‐204 is the intermediate proton donor rather than the terminal proton release group in bacteriorhodopsin

MCCE2: Improving protein pK_a calculations with extensive side chain rotamer sampling

Quantitative evaluation of the dynamics of proton transfer from photoactivated bacteriorhodopsin to the bulk

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pH dependence of light‐induced proton release by bacteriorhodopsin

Cited by 60 publications

References 24 publications

Photovoltage evidence that Glu‐204 is the intermediate proton donor rather than the terminal proton release group in bacteriorhodopsin

Photovoltage evidence that Glu‐204 is the intermediate proton donor rather than the terminal proton release group in bacteriorhodopsin

MCCE2: Improving protein pKa calculations with extensive side chain rotamer sampling

Quantitative evaluation of the dynamics of proton transfer from photoactivated bacteriorhodopsin to the bulk

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MCCE2: Improving protein pK_a calculations with extensive side chain rotamer sampling