<?xml version="1.0" encoding="UTF-8"?><xml><records><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Volkov, V. V.</style></author><author><style face="normal" font="default" size="100%">Svirko, Y P</style></author><author><style face="normal" font="default" size="100%">Kamalov, Valey F.</style></author><author><style face="normal" font="default" size="100%">Song, Li</style></author><author><style face="normal" font="default" size="100%">El-Sayed, Mostafa A</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Optical rotation of the second harmonic radiation from retinal in bacteriorhodopsin monomers in Langmuir-Blodgett film: evidence for nonplanar retinal structure.</style></title><secondary-title><style face="normal" font="default" size="100%">Biophysical journal</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Biophys. J.</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Bacteriorhodopsins</style></keyword><keyword><style  face="normal" font="default" size="100%">Biophysical Phenomena</style></keyword><keyword><style  face="normal" font="default" size="100%">Biophysics</style></keyword><keyword><style  face="normal" font="default" size="100%">Circular Dichroism</style></keyword><keyword><style  face="normal" font="default" size="100%">Molecular Structure</style></keyword><keyword><style  face="normal" font="default" size="100%">Optics and Photonics</style></keyword><keyword><style  face="normal" font="default" size="100%">Retinaldehyde</style></keyword><keyword><style  face="normal" font="default" size="100%">Spectrophotometry</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">1997</style></year><pub-dates><date><style  face="normal" font="default" size="100%">1997 Dec</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">73</style></volume><pages><style face="normal" font="default" size="100%">3164-70</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">We observed optical rotation of the plane of polarization of the second harmonic (SH) radiation at 532 nm (in resonance with the retinal absorption) generated in reflection geometry in Langmuir-Blodgett film of bacteriorhodopsin (bR). The analysis of the experimental data showed that this effect arises from the nonvanishing contribution of the antisymmetrical part of the hyperpolarizability tensor. This requires that the dipole moment of the resonant electronic transition, the change of the dipole moment upon electronic excitation, and the long axis of the retinal not be coplanar. Such conditions are satisfied only if the retinal has a nonplanar geometry, a conclusion that could lend support to the heterogeneity model of the origin of the biphasic band shape of the linear CD spectrum of the retinal in bR. On the basis of our theoretical analysis, we were able to estimate the angle between the induced dipole moment and the plan that contains the long axis of the chromophore and the transition dipole moment of the retinal absorption.</style></abstract><issue><style face="normal" font="default" size="100%">6</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/9414228?dopt=Abstract</style></custom1><electronic-resource-num><style face="normal" font="default" size="100%">10.1016/S0006-3495(97)78342-5</style></electronic-resource-num></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Zhang, K</style></author><author><style face="normal" font="default" size="100%">Song, Li</style></author><author><style face="normal" font="default" size="100%">Dong, J</style></author><author><style face="normal" font="default" size="100%">El-Sayed, Mostafa A</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Studies of cation binding in ZnCl2-regenerated bacteriorhodopsin by x-ray absorption fine structures: effects of removing water molecules and adding Cl- ions.</style></title><secondary-title><style face="normal" font="default" size="100%">Biophysical journal</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Biophys. J.</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Bacteriorhodopsins</style></keyword><keyword><style  face="normal" font="default" size="100%">Binding Sites</style></keyword><keyword><style  face="normal" font="default" size="100%">Biophysical Phenomena</style></keyword><keyword><style  face="normal" font="default" size="100%">Biophysics</style></keyword><keyword><style  face="normal" font="default" size="100%">Cations</style></keyword><keyword><style  face="normal" font="default" size="100%">Chlorides</style></keyword><keyword><style  face="normal" font="default" size="100%">Kinetics</style></keyword><keyword><style  face="normal" font="default" size="100%">Ligands</style></keyword><keyword><style  face="normal" font="default" size="100%">Spectrum Analysis</style></keyword><keyword><style  face="normal" font="default" size="100%">Water</style></keyword><keyword><style  face="normal" font="default" size="100%">X-Rays</style></keyword><keyword><style  face="normal" font="default" size="100%">Zinc</style></keyword><keyword><style  face="normal" font="default" size="100%">Zinc Compounds</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">1997</style></year><pub-dates><date><style  face="normal" font="default" size="100%">1997 Oct</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">73</style></volume><pages><style face="normal" font="default" size="100%">2097-105</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">The binding of Zn2+ in Zn2+-regenerated bacteriorhodopsin (bR) was studied under various conditions by x-ray absorption fine structures (XAFS). The 0.9:1 and 2:1 Zn2+:bR samples gave similar XAFS spectra, suggesting that Zn2+ might have only one strong binding site in bR. It was found that in aqueous bR solution, Zn2+ has an average of six oxygen or nitrogen ligands. Upon drying, two ligands are lost, suggesting the existence of two weakly bound water ligands near the cation-binding site in bacteriorhodopsin. When excess Cl- ions were present before drying in the Zn2+-regenerated bR samples, it was found that two of the ligands were replaced by Cl- ions in the dried film, whereas two remain unchanged. The above observations suggest that Zn2+ has three types of ligands in regenerated bR (referred to as types I, II, and III). Type I ligands are strongly bound. These ligands cannot be removed by drying or by exchanging with Cl- ions. Type II ligands cannot be removed by drying, but can be replaced by Cl- ligands. Type III ligands are weakly bound to the metal cation and are most likely water molecules that can be removed by evaporation under vacuum or by drying with anhydrous CaSO4. The results are discussed in terms of the possible structure of the strongly binding site of Zn2+ in bR.</style></abstract><issue><style face="normal" font="default" size="100%">4</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/9336205?dopt=Abstract</style></custom1><electronic-resource-num><style face="normal" font="default" size="100%">10.1016/S0006-3495(97)78240-7</style></electronic-resource-num></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Logunov, Stephan L.</style></author><author><style face="normal" font="default" size="100%">El-Sayed, Mostafa A</style></author><author><style face="normal" font="default" size="100%">Lanyi, Janos K.</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Catalysis of the retinal subpicosecond photoisomerization process in acid purple bacteriorhodopsin and some bacteriorhodopsin mutants by chloride ions.</style></title><secondary-title><style face="normal" font="default" size="100%">Biophysical journal</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Biophys. J.</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Acoustics</style></keyword><keyword><style  face="normal" font="default" size="100%">Anions</style></keyword><keyword><style  face="normal" font="default" size="100%">Bacteriorhodopsins</style></keyword><keyword><style  face="normal" font="default" size="100%">Biophysical Phenomena</style></keyword><keyword><style  face="normal" font="default" size="100%">Biophysics</style></keyword><keyword><style  face="normal" font="default" size="100%">Catalysis</style></keyword><keyword><style  face="normal" font="default" size="100%">Chlorides</style></keyword><keyword><style  face="normal" font="default" size="100%">Halobacterium salinarum</style></keyword><keyword><style  face="normal" font="default" size="100%">Hydrogen-Ion Concentration</style></keyword><keyword><style  face="normal" font="default" size="100%">Kinetics</style></keyword><keyword><style  face="normal" font="default" size="100%">Photochemistry</style></keyword><keyword><style  face="normal" font="default" size="100%">Point Mutation</style></keyword><keyword><style  face="normal" font="default" size="100%">Retinaldehyde</style></keyword><keyword><style  face="normal" font="default" size="100%">Spectrophotometry</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">1996</style></year><pub-dates><date><style  face="normal" font="default" size="100%">1996 Sep</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">71</style></volume><pages><style face="normal" font="default" size="100%">1545-53</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">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.</style></abstract><issue><style face="normal" font="default" size="100%">3</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/8874028?dopt=Abstract</style></custom1><electronic-resource-num><style face="normal" font="default" size="100%">10.1016/S0006-3495(96)79357-8</style></electronic-resource-num></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Logunov, Stephan L.</style></author><author><style face="normal" font="default" size="100%">El-Sayed, Mostafa A</style></author><author><style face="normal" font="default" size="100%">Lanyi, Janos K.</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">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.</style></title><secondary-title><style face="normal" font="default" size="100%">Biophysical journal</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Biophys. J.</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Bacteriorhodopsins</style></keyword><keyword><style  face="normal" font="default" size="100%">Binding Sites</style></keyword><keyword><style  face="normal" font="default" size="100%">Biophysical Phenomena</style></keyword><keyword><style  face="normal" font="default" size="100%">Biophysics</style></keyword><keyword><style  face="normal" font="default" size="100%">Halobacterium salinarum</style></keyword><keyword><style  face="normal" font="default" size="100%">Kinetics</style></keyword><keyword><style  face="normal" font="default" size="100%">Mutagenesis, Site-Directed</style></keyword><keyword><style  face="normal" font="default" size="100%">Photochemistry</style></keyword><keyword><style  face="normal" font="default" size="100%">Quantum Theory</style></keyword><keyword><style  face="normal" font="default" size="100%">Retinaldehyde</style></keyword><keyword><style  face="normal" font="default" size="100%">Schiff Bases</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">1996</style></year><pub-dates><date><style  face="normal" font="default" size="100%">1996 Jun</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">70</style></volume><pages><style face="normal" font="default" size="100%">2875-81</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">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.</style></abstract><issue><style face="normal" font="default" size="100%">6</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/8744325?dopt=Abstract</style></custom1><electronic-resource-num><style face="normal" font="default" size="100%">10.1016/S0006-3495(96)79857-0</style></electronic-resource-num></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Yang, Difei</style></author><author><style face="normal" font="default" size="100%">El-Sayed, Mostafa A</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">The Ca2+ binding to deionized monomerized and to retinal removed bacteriorhodopsin.</style></title><secondary-title><style face="normal" font="default" size="100%">Biophysical journal</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Biophys. J.</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Bacteriorhodopsins</style></keyword><keyword><style  face="normal" font="default" size="100%">Binding Sites</style></keyword><keyword><style  face="normal" font="default" size="100%">Biophysical Phenomena</style></keyword><keyword><style  face="normal" font="default" size="100%">Biophysics</style></keyword><keyword><style  face="normal" font="default" size="100%">Calcium</style></keyword><keyword><style  face="normal" font="default" size="100%">Electrochemistry</style></keyword><keyword><style  face="normal" font="default" size="100%">Halobacterium</style></keyword><keyword><style  face="normal" font="default" size="100%">Ions</style></keyword><keyword><style  face="normal" font="default" size="100%">Kinetics</style></keyword><keyword><style  face="normal" font="default" size="100%">Protein Conformation</style></keyword><keyword><style  face="normal" font="default" size="100%">Retinaldehyde</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">1995</style></year><pub-dates><date><style  face="normal" font="default" size="100%">1995 Nov</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">69</style></volume><pages><style face="normal" font="default" size="100%">2056-9</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">In our continuing effort to characterize the metal cation binding in bacteriorhodopsin (bR) using Ca(2+)-specific electrodes, potentiometric titration was carried out on deionized solubilized bR (containing monomeric units) and deionized bacterioopsin (bR with its retinal removed). Scatchard plots were analyzed. The monomer was found to have plots similar to those of the trimer, suggesting that the binding sites in bR are localized within the protein monomer unit and not between the molecules within the trimer structure. This also supports the previous assumption that the curvature in the Scatchard plot of regenerated bR is not due to cooperativity of metal cation within the trimer, but rather due to multiple sites. Recent studies further support the finding that the curved Scatchard plot is not due to the cooperativity between the metal ions in the two high affinity sites, wherever they are. The results of the analysis of the Scatchard plot for deionized bacterioopsin have shown a change in the binding characteristics of the high affinity but not the low affinity sites from that observed in bR. This result supports previous conclusions that metal cations in the high affinity sites are not far from the retinal cavity.</style></abstract><issue><style face="normal" font="default" size="100%">5</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/8580348?dopt=Abstract</style></custom1><electronic-resource-num><style face="normal" font="default" size="100%">10.1016/S0006-3495(95)80075-5</style></electronic-resource-num></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Song, Li</style></author><author><style face="normal" font="default" size="100%">Logunov, Stephan L.</style></author><author><style face="normal" font="default" size="100%">Yang, Difei</style></author><author><style face="normal" font="default" size="100%">El-Sayed, Mostafa A</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">The pH dependence of the subpicosecond retinal photoisomerization process in bacteriorhodopsin: evidence for parallel photocycles.</style></title><secondary-title><style face="normal" font="default" size="100%">Biophysical journal</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Biophys. J.</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Bacteriorhodopsins</style></keyword><keyword><style  face="normal" font="default" size="100%">Biophysical Phenomena</style></keyword><keyword><style  face="normal" font="default" size="100%">Biophysics</style></keyword><keyword><style  face="normal" font="default" size="100%">Hydrogen-Ion Concentration</style></keyword><keyword><style  face="normal" font="default" size="100%">Isomerism</style></keyword><keyword><style  face="normal" font="default" size="100%">Kinetics</style></keyword><keyword><style  face="normal" font="default" size="100%">Molecular Structure</style></keyword><keyword><style  face="normal" font="default" size="100%">Photochemistry</style></keyword><keyword><style  face="normal" font="default" size="100%">Retinaldehyde</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">1994</style></year><pub-dates><date><style  face="normal" font="default" size="100%">1994 Nov</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">67</style></volume><pages><style face="normal" font="default" size="100%">2008-12</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">The pH dependence of the subpicosecond decay of the retinal photoexcited state in bacteriorhodopsin (bR) is determined in the pH range 6.8-11.3. A rapid change in the decay rate of the retinal photoexcited state is observed in the pH range 9-10, the same pH range in which a rapid change in the M412 formation kinetics was observed. This observation supports the previously proposed heterogeneity model in which parallel photocycles contribute to the observed pH dependence of the M412 formation kinetics in bR.</style></abstract><issue><style face="normal" font="default" size="100%">5</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/7858138?dopt=Abstract</style></custom1><electronic-resource-num><style face="normal" font="default" size="100%">10.1016/S0006-3495(94)80684-8</style></electronic-resource-num></record></records></xml>