@article {863,
	title = {Catalysis of the retinal subpicosecond photoisomerization process in acid purple bacteriorhodopsin and some bacteriorhodopsin mutants by chloride ions.},
	journal = {Biophysical journal},
	volume = {71},
	year = {1996},
	month = {1996 Sep},
	pages = {1545-53},
	abstract = {The dynamics and the spectra of the excited state of the retinal in bacteriorhodopsin (bR) and its K-intermediate at pH 0 was compared with that of bR and halorhodopsin at pH 6.5. The quantum yield of photoisomerization in acid purple bR was estimated to be at least 0.5. The change of pH from 6.5 to 2 causes a shift of the absorption maximum from 568 to 600 nm (acid blue bR) and decreases the rate of photoisomerization. A further decrease in pH from 2 to 0 shifts the absorption maximum back to 575 nm when HCl is used (acid purple bR). We found that the rate of photoisomerization increases when the pH decreases from 2 to 0. The effect of chloride anions on the dynamics of the retinal photoisomerization of acid bR (pH 2 and 0) and some mutants (D85N, D212N, and R82Q) was also studied. The addition of 1 M HCl (to make acid purple bR, pH 0) or 1 M NaCl to acid blue bR (pH 2) was found to catalyze the rate of the retinal photoisomerization process. Similarly, the addition of 1 M NaCl to the solution of some bR mutants that have a reduced rate of retinal photoisomerization (D85N, D212N, and R82Q) was found to catalyze the rate of their retinal photoisomerization process up to the value observed in wild-type bR. These results are explained by proposing that the bound Cl- compensates for the loss of the negative charges of the COO- groups of Asp85 and/or Asp212 either by neutralization at low pH or by residue replacement in D85N and D212N mutants.},
	keywords = {Acoustics, Anions, Bacteriorhodopsins, Biophysical Phenomena, Biophysics, Catalysis, Chlorides, Halobacterium salinarum, Hydrogen-Ion Concentration, Kinetics, Photochemistry, Point Mutation, Retinaldehyde, Spectrophotometry},
	issn = {0006-3495},
	doi = {10.1016/S0006-3495(96)79357-8},
	author = {Logunov, Stephan L. and El-Sayed, Mostafa A and Lanyi, Janos K.}
}
@article {1267,
	title = {Effect of Changing the Position and Orientation of Asp85 Relative to the Protonated Schiff Base within the Retinal Cavity on the Rate of Photoisomerization in Bacteriorhodopsin},
	journal = {The Journal of Physical Chemistry},
	volume = {100},
	year = {1996},
	note = {doi: 10.1021/jp960734r},
	month = {1996},
	pages = {10479 - 10481},
	publisher = {American Chemical Society},
	abstract = {Replacement of either Val49 with Ala or Ala53 with Val by site-specific mutagenesis is known to change the position and orientation of the protonated Schiff base relative to Asp85 within the retinal cavity of bacteriorhodopsin (bR) (Brown, L. S.; Gat, Y.; Sheves, M.; Yamazaki, Y.; Maeda, A.; Needleman, R.; Lanyi, J. K. Biochemistry 1994, 33, 12001). The effect of mutation on the rate of the subpicosecond photoisomerization of retinal in bR is examined by using a pump?probe technique. A decrease in the rate of photoisomerization of retinal in V49A and A53V is observed. This is discussed in terms of the previously proposed mechanism of the protein catalysis to the retinal photoisomerization process in bR.Replacement of either Val49 with Ala or Ala53 with Val by site-specific mutagenesis is known to change the position and orientation of the protonated Schiff base relative to Asp85 within the retinal cavity of bacteriorhodopsin (bR) (Brown, L. S.; Gat, Y.; Sheves, M.; Yamazaki, Y.; Maeda, A.; Needleman, R.; Lanyi, J. K. Biochemistry 1994, 33, 12001). The effect of mutation on the rate of the subpicosecond photoisomerization of retinal in bR is examined by using a pump?probe technique. A decrease in the rate of photoisomerization of retinal in V49A and A53V is observed. This is discussed in terms of the previously proposed mechanism of the protein catalysis to the retinal photoisomerization process in bR.},
	isbn = {0022-3654},
	doi = {doi: 10.1021/jp960734r},
	url = {http://dx.doi.org/10.1021/jp960734r},
	author = {Song, Li and El-Sayed, Mostafa A and Lanyi, Janos K.}
}
@article {872,
	title = {Photoisomerization Quantum Yield and Apparent Energy Content of the K Intermediate in the Photocycles of Bacteriorhodopsin, Its Mutants D85N, R82Q, and D212N, and Deionized Blue Bacteriorhodopsin},
	journal = {The Journal of Physical Chemistry},
	volume = {100},
	year = {1996},
	note = {doi: 10.1021/jp9515242},
	month = {1996},
	pages = {2391 - 2398},
	publisher = {American Chemical Society},
	abstract = {The quantum yield of photoisomerization and the energy content of the K intermediate in the photocycle of bacteriorhodopsin and its mutants D85N, R82Q, and D212N and deionized blue bR were measured. Transient optical absorption and photoacoustic spectroscopy with excitation using 400 fs laser pulse were combined to obtain results. The spectroscopic characteristics of the excited state, the J and K intermediates in the photocycle of the mutants, and deionized blue bR were determined. The presence of both 13-cis and all-trans isomers in the ground state of light-adapted D85N, R82Q, and D212N and deionized blue bR makes extraction of the quantum yield for each isomer difficult. Thus, only average values of the quantum yield for these samples were determined. The replacement of charged groups in the vicinity of the retinal Schiff base was found to decrease the rate of the photoisomerization by up to 30 times, but with no signficant change in either the apparent quantum yield of the photoisomerization or the energy stored in the K intermediate. The results are discussed in terms of the different models for the excited and ground state potential surfaces of the retinal configuration in bacteriorhodopsin.The quantum yield of photoisomerization and the energy content of the K intermediate in the photocycle of bacteriorhodopsin and its mutants D85N, R82Q, and D212N and deionized blue bR were measured. Transient optical absorption and photoacoustic spectroscopy with excitation using 400 fs laser pulse were combined to obtain results. The spectroscopic characteristics of the excited state, the J and K intermediates in the photocycle of the mutants, and deionized blue bR were determined. The presence of both 13-cis and all-trans isomers in the ground state of light-adapted D85N, R82Q, and D212N and deionized blue bR makes extraction of the quantum yield for each isomer difficult. Thus, only average values of the quantum yield for these samples were determined. The replacement of charged groups in the vicinity of the retinal Schiff base was found to decrease the rate of the photoisomerization by up to 30 times, but with no signficant change in either the apparent quantum yield of the photoisomerization or the energy stored in the K intermediate. The results are discussed in terms of the different models for the excited and ground state potential surfaces of the retinal configuration in bacteriorhodopsin.},
	isbn = {0022-3654},
	url = {http://dx.doi.org/10.1021/jp9515242},
	author = {Logunov, Stephan L. and El-Sayed, Mostafa A and Song, Li and Lanyi, Janos K.}
}
@article {861,
	title = {Replacement effects of neutral amino acid residues of different molecular volumes in the retinal binding cavity of bacteriorhodopsin on the dynamics of its primary process.},
	journal = {Biophysical journal},
	volume = {70},
	year = {1996},
	month = {1996 Jun},
	pages = {2875-81},
	abstract = {We have determined the rate and quantum yield of retinal photoisomerization, the spectra of the primary transients, and the energy stored in the K intermediate in the photocycle of some bacteriorhodopsin mutants (V49A, A53G, and W182F) in which residue replacements are found to change the Schiff base deprotonation kinetics (and thus the protein-retinal interaction). Because of their change in the local volume resulting from these individual replacements, these substitutions perturb the proton donor-acceptor relative orientation change and thus the Schiff base deprotonation kinetics. These replacements are thus expected to change the charge distribution around the retinal, which controls its photoisomerization dynamics. Subpicosecond transient spectroscopy as well as photoacoustic technique are used to determine the retinal photoisomerization rate, quantum yield, and the energy stored in the K-intermediate for these mutants. The results are compared with those obtained for wild-type bacteriorhodopsin and other mutants in which charged residues in the cavity are replaced by neutral ones. In some of the mutants the rate of photoisomerization is changed, but in none is the quantum yield or the energy stored in the K intermediate altered from that in the wild type. These results are discussed in terms of the shapes of the potential energy surfaces of the excited and ground states of retinal in the perpendicular configuration within the protein and the stabilization of the positive charge in the ground and the excited state of the electronic system of retinal.},
	keywords = {Bacteriorhodopsins, Binding Sites, Biophysical Phenomena, Biophysics, Halobacterium salinarum, Kinetics, Mutagenesis, Site-Directed, Photochemistry, Quantum Theory, Retinaldehyde, Schiff Bases},
	issn = {0006-3495},
	doi = {10.1016/S0006-3495(96)79857-0},
	author = {Logunov, Stephan L. and El-Sayed, Mostafa A and Lanyi, Janos K.}
}
@article {1287,
	title = {Fourier Transform Infrared Spectroscopic Studies of the Effect of Ca2+ Binding on the States of Aspartic Acid Side Chains in Bacteriorhodopsin},
	journal = {The Journal of Physical Chemistry},
	volume = {99},
	year = {1995},
	note = {doi: 10.1021/j100019a066},
	month = {1995},
	pages = {7776 - 7781},
	publisher = {American Chemical Society},
	abstract = {View http://dx.doi.org/10.1021/j100019a066 for article{\textquoteright}s front page in lieu of an abstract},
	isbn = {0022-3654},
	doi = {doi: 10.1021/j100019a066},
	url = {http://dx.doi.org/10.1021/j100019a066},
	author = {Masuda, Satoshi and Nara, Masayuki and Tasumi, Mitsuo and El-Sayed, Mostafa A and Lanyi, Janos K.}
}
@article {1268,
	title = {Retinal Isomer Composition in Some Bacteriorhodopsin Mutants under Light and Dark Adaptation Conditions},
	journal = {The Journal of Physical Chemistry},
	volume = {99},
	year = {1995},
	note = {doi: 10.1021/j100024a056},
	month = {1995},
	pages = {10052 - 10055},
	publisher = {American Chemical Society},
	abstract = {View http://dx.doi.org/10.1021/j100024a056 for the article{\textquoteright}s first page in lieu of an abstract},
	isbn = {0022-3654},
	doi = {doi: 10.1021/j100024a056},
	url = {http://dx.doi.org/10.1021/j100024a056},
	author = {Song, Li and Yang, Difei and El-Sayed, Mostafa A and Lanyi, Janos K.}
}
