Biomedical subjects

R Needleman

Publications and source records attributed to R Needleman.

At least 19 recordsLinked to original sources

PubMed1998

Partitioning of free energy gain between the photoisomerized retinal and the protein in bacteriorhodopsin.

Photoisomerization of the all-trans-retinal of bacteriorhodopsin to 13-cis,15-anti initiates a sequence of thermal reactions in which relaxation of the polyene chain back to all-trans is coupled to various changes in the protein and the translocation of a proton across the membrane. We investigated the nature of this high-energy state in a genetically modified bacteriorhodopsin. When the electric charges of residues 85 and 96, the two aspartic acids critical for proton transport, are both changed to what they become after photoexcitation of the wild-type protein, i.e., neutral and anionic, respectively, the retinal assumes a thermally stable 13-cis,15-anti configuration. Thus, we have reversed cause and effect in the photocycle. It follows that when the 13-cis,15-anti isomeric state is produced by illumination, in the wild type it is unstable initially only because of conflicts with the retinal binding pocket. Later in the photocycle, the free energy gain is transferred from the chromophore to the protein. Before recovery of the initial state, it will come to be represented entirely by the free energy of the changed protonation states of aspartic acids 85 and 96.

Amino Acid Substitution↗

PubMed1998

Local-access model for proton transfer in bacteriorhodopsin.

The accessibility of the retinal Schiff base in bacteriorhodopsin was studied in the D85N/D96N mutant where the proton acceptor and donor are absent. Protonation and deprotonation of the Schiff base after pH jump without illumination and in the photocycle of the unprotonated Schiff base were measured in the visible and the infrared. Whether access is extracellular (EC) or cytoplasmic (CP) was decided from the effect of millimolar concentrations of azide on the rates of proton transfers. The results, together with earlier work on the wild-type protein, suggest a new hypothesis for the proton-transfer switch: (i) In the metastable 13-cis, 15-anti and all-trans, 15-syn photoproducts, but not in the stable isomeric states, access flickers between the EC and CP directions. (ii) The direction of proton transfer is decided both by this local access and by the presence of a suitable donor or acceptor group (in the wild type), or the proton conductivity in the EC and CP half-channels (in D85N/D96N). (iii) Thermal reisomerization of the retinal can occur only when the Schiff base is protonated, as is well-known. In the wild-type transport cycle, the concurrent local EC and CP access during the lifetime of the metastable 13-cis, 15-anti state enables the changing pKa's of the proton acceptor and donor to determine the direction of proton transfer. Proton transfer from the Schiff base to Asp-85 in the EC direction is followed by reprotonation by Asp-96 from the CP direction because proton release to the EC surface raises the pKa of Asp-85 and a large-scale protein conformation change lowers the pKa of Asp-96. The unexpected finding we report here for D85N/D96N, that when the retinal is in the stable all-trans, 15-anti and 13-cis, 15-syn isomeric forms access of the Schiff base is locked (in the EC and CP directions, respectively), suggests that in this protein reisomerization, rather than changes in the proton conductivities of the EC and CP half-channels, provides the switch function. With this mechanism, the various modes of transport reported for Asp-85 mutants (CP to EC direction with blue light, and EC to CP direction with blue plus green light) are understood also in terms of rules i-iii.

Amino Acid Substitution↗

PubMed1998

Existence of a proton transfer chain in bacteriorhodopsin: participation of Glu-194 in the release of protons to the extracellular surface.

Glu-194 near the extracellular surface of bacteriorhodopsin is indispensable for proton release to the medium upon protonation of Asp-85 during light-driven transport. As for Glu-204, its replacement with glutamine (but not aspartate) abolishes both proton release and the anomalous titration of Asp-85 that originates from coupling between the pKa of this buried aspartate and those of the other acidic groups. Unlike the case of Glu-204, however, replacement of Glu-194 with aspartate raises the pKa for proton release. In Fourier transform infrared spectra of the E194D mutant a prominent positive band is observed at 1720 cm-1. It can be assigned from [4-13C]aspartate and D2O isotope shifts to the C&dbd;O stretch of protonated Asp-194. Its rise correlates with proton transfer from the retinal Schiff base to Asp-85. Its decay coincides with the appearance of a proton at the surface, detected under similar conditions with fluorescein covalently bound to Lys-129 and with pyranine. Its amplitude decreases with increasing pH, with a pKa of about 9. We show that this pKa is likely to be that of the internal proton donor to Asp-194, the Glu-204 site, before photoexcitation, while 13C NMR titration indicates that Asp-194 has an initial pKa of about 3. We propose that there is a chain of interacting residues between the retinal Schiff base and the extracellular surface. After photoisomerization of the retinal the pKa's change so as to allow (i) Asp-85 to become protonated by the Schiff base, (ii) the Glu-204 site to transfer its proton to Asp-194 in E194D, and therefore to Glu-194 in the wild type, and (iii) residue 194 to release the proton to the medium.

Bacteriorhodopsins↗

PubMed1998

Interaction of the protonated Schiff base with the peptide backbone of valine 49 and the intervening water molecule in the N photointermediate of bacteriorhodopsin.

The effects of replacing Val49, Thr46, Asp96, and Phe219 in the cytoplasmic domain of bacteriorhodopsin on water O-H stretching vibrational bands and the amide I and imide II bands of the peptide backbone were examined in the M, N, and MN intermediates. This study is an extension of previous work on the L photointermediate [Yamazaki, Y., Tuzi, S., Saitô, H., Kandori, H., Needleman, R., Lanyi, J. K., and Maeda, A. (1996) Biochemistry 35, 4063-4068]. The O-H stretching bands at 3671 cm-1 in the M intermediate and at 3654 cm-1 in the N intermediate are shown to originate from the same water molecule. It is located in the region surrounded by the Schiff base, Val49, Thr46, and Phe219 in the M intermediate, and moves closer to Val49 in the M to N reaction. The peptide C-N bond between Val49 and Pro50 and the C=O bond of Val49 undergo perturbations upon formation of the N intermediate but not the M and N-like MN states in which the Schiff base is unprotonated. The carbonyl oxygen of Val49 is proposed to be the acceptor in H-bonding with the protonated Schiff base in the N intermediate. The results suggest that water molecules may be involved in this interaction in the cytoplasmic region, and may play a role in the accessibility change of the Schiff base in the L to M to N photocycle steps.

Bacteriorhodopsins↗

PubMed1998

Stability of the C-terminal alpha-helical domain of bacteriorhodopsin that protrudes from the membrane surface, as studied by high-resolution solid-state 13C NMR.

We have recorded 13C NMR spectra of [1-(13)C]Ala- and [3-(13)C]Ala-bacteriorhodopsin (bR), [1-(13)C]Ala- and [3-(13)C]Ala-papain-cleaved bR, and [3-(13)C]Ala-labeled R227Q bR mutant by cross polarization-magic angle spinning (CP-MAS) and dipolar decoupled-magic angle spinning (DD-MAS) methods. The pH and temperature were varied, and Arg 227 was replaced with Gln (R227Q), in order to clarify their effects on the stability of the alpha-helical domain of the C-terminus that protrudes from the membrane surface. The comparative 13C CP- and DD-MAS NMR study of [3-(13)C]Ala-bR, rather than [1-(13)C]Ala-bR, turned out to be the best means to distinguish the 13C NMR signals of the C-terminus from those of the rest of the transmembrane helices or loops. The inner segment of the C-terminus, from Ala 228 to Ala 235, forms an alpha-helical domain (resonated at 15.9 ppm) either at neutral pH and/or at 10 to -10 degrees C. The alpha-helical peak was not seen, however, after either cleavage of the C-terminus with papain or lowering the pH to 4.25. This alpha-helical structure, and a part of the random coil which was produced from the helix at pH 4.25, were further converted to a low-temperature-type alpha-helix, as indicated by an upfield displacement of the 13C NMR signal, when the temperature was lowered to 10- -10 degrees C. Surprisingly, the corresponding helical structure in R227Q is more stable than in the wild type at the acidic pH. This alpha-helical peak was classified as an alphaII-helix from the 13C chemical shifts of Cbeta carbon, although it was ascribed to an alphaI-helix on the basis of the carbonyl shifts. This is in contrast to Ala 53 which adopts the alphaII-helix as judged from the 13C chemical shifts of Cbeta and the carbonyl carbons. Therefore, this discrepancy might be caused by differential sensitivity of the two types of carbon signals to conformation and to modes of hydrogen bonding when motional fluctuation is involved. It is likely that the alphaII-helix form present at the C-terminus is not always the type originally proposed but should be considered as a form undergoing large-amplitude conformational fluctuation around alpha-helix.

Amino Acid Sequence↗

PubMed1997

Transient channel-opening in bacteriorhodopsin: an EPR study.

Active translocation of ions across membranes requires alternating access of the ion binding site inside the pump to the two membrane surfaces. Proton translocation by bacteriorhodopsin (bR), the light-driven proton pump in Halobacterium salinarium, involves this kind of a change in the accessibility of the centrally located retinal Schiff base. This key event in bR's photocycle ensures that proton release occurs to the extracellular side and proton uptake from the cytoplasmic side. To study the role of protein conformational changes in this reprotonation switch, spin labels were attached to pairs of engineered cysteine residues in the cytoplasmic interhelical loops of bR. Light-induced changes in the distance between a spin label on the EF interhelical loop and a label on either the AB or the CD interhelical loop were observed, and the changes were monitored following photoactivation with time-resolved electron paramagnetic resonance (EPR) spectroscopy. Both distances increase transiently by about 5 A during the photocycle. This opening occurs between proton release and uptake, and may be the conformational switch that changes the accessibility of the retinal Schiff base to the cytoplasmic surface after proton release to the extracellular side.

Bacteriorhodopsins↗

PubMed1997

Ultraviolet resonance Raman spectra of Trp-182 and Trp-189 in bacteriorhodopsin: novel information on the structure of Trp-182 and its steric interaction with retinal.

Ultraviolet (244 nm) resonance Raman spectra of Trp-182 and Trp-189 in bacteriorhodopsin were obtained by subtracting the spectrum of the mutants, Trp-182-->Phe or Trp-189-->Phe, from that of the wild-type. Analysis of the spectra shows that the chi2,1 torsion angle about the Cbeta-C3 bond is +/-93 degrees for Trp-182 and +/-100 degrees for Trp-189. Both Trp residues are moderately hydrogen bonded to proton acceptors at their indolyl nitrogens in hydrophobic environments. The environmental hydrophobicity is particularly strong for Trp-182, as judged from the splitting of the W7 Raman band to a triplet. The Raman information on the structure and environment of Trp-189 is consistent with the molecular model from electron diffraction [Grigorieff et al. (1996) J. Mol. Biol. 259, 393-421]. On the other hand, the chi2,1 angle and the hydrogen-bonding state of Trp-182 found here differ from those in the model structure. Revision of the model to correspond to the Raman findings would require a 60 degrees rotation of the Trp-182 indole ring about the Cbeta-C3 bond toward the chromophore retinal and the presence of a water molecule that is hydrogen bonded to the indolyl nitrogen. The triplet feature of the W7 band of Trp-182 is attributable to unusually strong steric repulsion between the indole ring and the 9- and 13-methyl groups of the retinal. Resonance Raman spectra in the visible suggest that this steric conflict destabilizes the 13-cis isomeric state of the retinal.

Bacteriorhodopsins↗

PubMed1997

Trp86 --> Phe replacement in bacteriorhodopsin affects a water molecule near Asp85 and light adaptation.

Illumination of the Trp86 --> Phe mutant of bacteriorhodopsin causes anomalous light adaptation, i.e., isomerization of the retinal from all-trans to 13-cis, 15-syn. FTIR spectral analysis shows that illumination at 250 K yields two 13-cis photoproducts, the conventional 13-cis, 15-syn state, BR(C), and another termed BR(X). BR(X) is different from BR(C) because it has a lower N-H in-plane bending frequency and a higher C14-C15 stretching frequency, as well as an absence of coupling between these modes. BR(X), which is stable at 275 K, is more abundant in the photosteady state produced by longer wavelength light and detected as the only photoproduct at 170 K. Its different structural features result from distortion of the C14-C15 bond of the chromophore. In the W86F mutant protein, the small structural changes of a water molecule in the conversion between the all-trans and 13-cis, 15-syn forms and in the formation of the K photointermediate are absent, but the larger changes of water molecule(s) that normally occur in the L and M intermediates are present. We propose that Trp86, together with Asp85, is involved in binding the water molecule and in preventing the formation of the 13-cis, 15-syn photoproducts, BR(C) and BR(X), when the wild type protein is illuminated.

Aspartic Acid↗

PubMed1997

Time-resolved fourier transform infrared study of structural changes in the last steps of the photocycles of Glu-204 and Leu-93 mutants of bacteriorhodopsin.

The last intermediate in the photocycle of the light-driven proton pump bacteriorhodopsin is the red-shifted O state. The structure and dynamics of the last step in the photocycle were characterized with time-resolved Fourier transform infrared spectroscopy of the mutants of Glu-204 and Leu-93, which accumulate this intermediate in much larger amounts than the wild type. The results show that E204Q and E204D give distorted all-trans-retinal chromophore like the O intermediate of the wild type. This is simply due to the perturbation of the proton acceptor function of Glu-204 in the O-to-BR transition in the Glu-204 mutants. The corresponding red-shifted intermediates of L93M, L93T, and L93S have a 13-cis chromophore like the N intermediate of the wild type, as reported from analysis of extracted retinal [Delaney, J. K., Schweiger, U., & Subramaniam, S. (1995) Proc. Natl. Acad. Sci. U.S.A. 92, 11120-11124]. In spite of their different chromophore structures from the O intermediate, the red-shifted intermediates are similar to the O intermediate but not to the N intermediate of the wild type with respect to structural changes in the peptide carbonyls. The structural changes around Asp-96 in the N intermediate are completely restored also in the red-shifted intermediates of the Leu-93 mutants like in the O intermediate. These results imply that the protein structural changes in the last step proceed regardless of thermal isomerization of the chromophore. Time-resolved Fourier transform infrared spectroscopy with the Glu-204 mutants suggests that the response of Asp-204 (Glu-204 in the wild type) to the protonation of Asp-85 during formation of the M intermediate, which results in proton release, is slow and may occur through structural changes.

Bacteriorhodopsins↗

PubMed1997

Genomic footprinting of Mig1p in the MAL62 promoter. Binding is dependent upon carbon source and competitive with the Mal63p activator.

Mig1p inhibits gene expression in glucose by binding the Cyc8p (Ssn6p)-Tup1p repressor to the promoter of glucose-repressible genes. While the binding properties of Mig1p have been studied in vitro and the ability of Mig1p-Cyc8p (Ssn6p)-Tup1p to repress has been studied in vivo, no experiments have measured the effect of a carbon source on the in vivo binding of Mig1p or the effect of bound MIg1p on activator occupancy of the upstream activation sequence (UAS). To obtain this information, we used genomic footprinting to investigate glucose repression of MAL62, a gene that is also regulated by the Mal63p activator. These experiments show that two interrelated mechanisms are involved in the glucose repression of MAL62: 1) competition between the Mal63p activator and Mig1p for DNA binding and 2) modulation of Mig1p binding by the carbon source. Mig1p affects basal MAL62 expression in the absence of Mal63p by binding to a site in the MAL62 promoter and affects Mal63p-dependent synthesis by also inhibiting the access of Mal63p to site 1 in the UASMAL. The binding of Mig1p is increased in glucose and decreased in nonrepressing sugars, but the increased binding in glucose is not due to an increase in the levels of Mig1p.

Binding, Competitive↗

PubMed1997

Intramembrane signaling mediated by hydrogen-bonding of water and carboxyl groups in bacteriorhodopsin and rhodopsin.

The light-induced mechanism for proton pumping of bacteriorhodopsin was studied by Fourier transform infrared spectroscopy of the discrete sequential intermediate states, L, M, and N. Attention is focused on L in the early microsecond time range, as a transition state in which the Schiff base forms strong H-bonding with a water molecule coordinated with Asp85. This structure leads to transfer of the Schiff base proton to Asp85 in the L-to-M process, which then triggers proton release from Glu204 to the extracellular surface. H-bonding of Arg82 and water molecules are involved in this process. Chloride can replace Asp85 in the D85T mutant, and this anion will be then transported instead of a proton. In L, structural perturbations are induced also around Asp96, through a string of H-bonding mediated by internal water molecules and peptide carbonyls in helices B and C, and Trp182 in helix F. These may cause the structural changes that occur later in the M-to-N process. Similar interactions, through internal water molecules and the peptide bonds in helices B and C, take place in bovine rhodopsin. They transduce changes across the membrane from the Schiff base to the cytoplasmic surface, where the activation of the transducin occurs.

Animals↗

PubMed1997

X-ray diffraction studies of bacteriorhodopsin. Determination of the positions of mercury label at several engineered cysteine residues.

The single cysteine-containing bacteriorhodopsin mutants F27C, L100C, T170C, F171C and I222C were labeled with p-chloromercuribenzoic acid, which specifically reacts with sulfhydryl groups. These cysteines should be located at the cytoplasmic ends of the transmembrane helices A, C, F or G. We determined the positions of the bound mercury atoms by X-ray diffraction of purple membrane films, with better than 1 A accuracy. The determined mercury positions were compared with the structural model from cryoelectron microscopy (N. Grigorieff, T. A. Ceska, K. H. Downing, J. M. Baldwin and R. Henderson, J. Mol. Biol. 259, 393-421, 1996). Given that the distance between the mercury and the C alpha atom of the cysteine in the xy plane must be shorter than 4.5 A and that the mercury atom is located at the delta position, the positions obtained for the mercury labels agree with their expected positions from the structural model. The present results give a rationale for detecting structural changes upon illumination as shifts occur in the mercury label position.

Amino Acid Sequence↗

PubMed1996

Interaction of proton and chloride transfer pathways in recombinant bacteriorhodopsin with chloride transport activity: implications for the chloride translocation mechanism.

When the protonated retinal Schiff base dissociates in the photocycle of the proton pump bacteriorhodopsin, asp-85 is the proton acceptor. Replacing this residue with threonine confers halorhodopsin-like properties on the protein, including chloride transport [Sasaki, J., Brown, L.S., Chon, Y.-S., Kandori, H., Maeda, A., Needleman, R., & Lanyi, J.K. (1995) Science 269, 73-75]. However, the electrostatic interaction between the vicinity of residue 85 and glu-204, a residue located about 10 A away near the extracellular surface, that is a part of the proton transport mechanism, should still exist. We find that in the D85T mutant glu-204 becomes protonated when chloride is added. This indicates that the binding of chloride at thr-85 must be equivalent to deprotonation of asp-85. The protonation state of glu-204 reports therefore on the presence or absence of chloride bound at thr-85. During the chloride-transport cycle of D85T, but not D85T/E204Q, fluorescein and pyranine detect the transient release of protons from the protein to the surface and the bulk. The release and the subsequent uptake of the protons occur during the rise and decay of a red-shifted photointermediate, respectively, and confirm the earlier suggestion that this state has the same role in the chloride transport as the M intermediate in the proton transport. Consistent with the red-shift of the absorption maximum, the chloride bound near the Schiff base had already moved away, presumably to be released at the cytoplasmic surface, but another chloride ion has not yet been taken up from the extracellular surface. The switch of the connectivity of the chloride binding site from the cytoplasmic to the extracellular membrane surface must occur therefore during the lifetime of this photointermediate.

Aspartic Acid↗

PubMed1996

Relationship of retinal configuration and internal proton transfer at the end of the bacteriorhodopsin photocycle.

In the last step of the bacteriorhodopsin photocycle the initial state is regenerated from the O intermediate in an essentially unidirectional reaction. Comparison of the rate of this photocycle step and the rate of deprotonation of Asp-85 in pH jump experiments with various site-specific mutants indicates that recovery of the initial state is influenced by (1) residues such as Glu-204 that affect deprotonation of Asp-85 and (2) residues such as Leu-93 that contact the retinal and therefore must affect its thermal reisomerization from 13-cis to all-trans as suggested by Delaney, Schweiger, and Subramaniam (Proc. Natl. Acad. Sci. U.S.A. 92, 11120-11124, 1995). These results, together with FTIR spectra (Kandori, Hatanaka, Yamazaki, Needleman, Brown, Richter, Lanyi, & Maeda, manuscript in preparation) of the last intermediate in the photocycles of representatives of the two kinds of mutants, E204Q and L93M, suggest the following sequence of events: reisomerization of the retinal from 13-cis to an all-trans configuration that contains a twisted chain (with high amplitude hydrogen out-of-plane vibrational bands) triggers proton transfer from Asp-85 to Glu-204 or directly to the extracellular surface, and the proton transfer in turn triggers relaxation of the twist in the retinal. The involvement of the proton transfer in the kinetics of this sequence suggests the reason for the unidirectionality of the overall reaction: upon reisomerization of the retinal the very low pKa of Asp-85 in the unphotolyzed protein is reestablished and this residue thereby becomes a good proton donor.

Aspartic Acid↗

PubMed1996

Hydration of the counterion of the Schiff base in the chloride-transporting mutant of bacteriorhodopsin: FTIR and FT-raman studies of the effects of anion binding when Asp85 is replaced with a neutral residue.

The chromophores of the D85T and D85N mutants of bacteriorhodopsin are blue but become purple like the wild type when chloride or bromide binds near the Schiff base. In D85T this occurs near neutral pH, but in D85N only at pH < 4. The structures of the L and the unphotolyzed states of these proteins were examined with Fourier transform infrared spectroscopy. The difference spectra of the purple forms, but not the blue forms in the absence of these anions, resembled the spectrum of the wild-type protein. Shift of the ethylenic band toward lower frequency upon replacing chloride by bromide confirmed the contribution of the negative charge of the anions to the Schiff base counterion. These anions restored the change of water, which is bound near the protonated Schiff base but is absent in the blue form of the D85N mutant, though with stronger H-bonding than in the wild type. The C = N stretching vibration of the Schiff base in H2O and 2H2O was detected by Fourier transform Raman spectroscopy. The H-bonding strength of the Schiff base in the unphotolyzed state was weaker when chloride or bromide was bound to the mutants than with Asp85 as the counterion in the wild type. Thus, although the geometry of the environment is different, there is at least one water molecule coordinated to the bound halide in these mutants, in a way similar to water bound to Asp85 in the wild type.

Anions↗

PubMed1996

Conformation and dynamics of [3-13C]Ala- labeled bacteriorhodopsin and bacterioopsin, induced by interaction with retinal and its analogs, as studied by 13C nuclear magnetic resonance.

13C nuclear magnetic resonance (NMR) spectra of [3-13C]Ala-labeled bacteriorhodopsin (bR), bacterioopsin (bO), and regenerated bR with retinal or bO complex with retinal analogs were recorded in order to gain insights into how the conformation and dynamics of apoprotein (bO) vary with or without retinal or its analogs. First, we assigned the 13C NMR peak resonating at 16.3 ppm to Ala 53 of both bR and bO, which appears to contact the side chain of Lys 216 at the site of the Schiff base in the former, utilizing the 13C NMR peaks of A53V and A53G proteins in comparison with those of wild-type bR and bO. Characteristic spectral differences between the apoprotein and bR were observed upon removal of the retinal: the changes of the peak intensities at 16.4, 15.9, and 16.9 ppm are notable. We found that the loops (17.4 ppm) and transmembrane alpha II helical region (15.9 ppm) acquired motional freedom with a correlation time of 10(-5)s when the retinal was removed, as detected by proton spin-lattice relaxation times in the rotating frame. A 13C NMR spectrum very similar to that of native bR was recorded when bR was regenerated by addition of retinal to bO. On the other hand, the addition of the retinal analogs retinol or beta-ionone, which are bound in the retinal binding site but are incapable of forming a Schiff base to the apoprotein, caused distinct spectral changes different from those of bR, as manifested from the displacements of 13C chemical shifts. These spectral changes must be ascribed to significant conformational changes of apoprotein at various locations in the protein, including the site of Ala 53 induced by modified interaction between the apoprotein and chromophore.

Alanine↗

PubMed1996

Proton transport by halorhodopsin.

In halorhodopsin from Natronobacterium pharaonis, a light-driven chloride pump, the chloride binding site also binds azide. When azide is bound at this location the retinal Schiff base transiently deprotonates after photoexcitation with light > 530 nm, like in the light-driven proton pump bacteriorhodopsin. As in the photocycle of bacteriorhodopsin, pyranine detects the release of protons to the bulk. The subsequent reprotonation of the Schiff base is also dependent on azide, but with different kinetics that suggest a shuttling of protons from the surface as described earlier for halorhodopsin from Halobacterium salinarium. This azide-dependent, bacteriorhodopsin-like photocycle results in active electrogenic proton transport in the cytoplasmic to extracellular direction, detected in cell envelope vesicle suspensions both with a potential-sensitive electrode and by measuring light-dependent pH change. We conclude that in halorhodopsin an azide bound to the extracellular side of the Schiff base, and another azide shuttling between the Schiff base and the cytoplasmic surface, fulfill the functions of Asp-85 and Asp-96, respectively, in bacteriorhodopsin. Thus, although halorhodopsin is normally a chloride ion pump, it evidently contains all structural requirements, except an internal proton acceptor and a donor, of a proton pump. This observation complements our earlier finding that when a chloride binding site was created in bacteriorhodopsin through replacement of Asp-85 with a threonine, that protein became a chloride ion pump.

Azides↗

PubMed1996

Effects of arginine-82 on the interactions of internal water molecules in bacteriorhodopsin.

Arg82, one of the residues near the protonated Schiff base of bacteriorhodopsin, facilitates proton release to the medium during the L-to-M reaction of the photocycle, but retards the rate of proton transfer from the Schiff base to Asp85. In order to understand the role of Arg82 in these processes, the structural changes upon formation of the M intermediate were studied by Fourier transform infrared spectroscopy of the hydrated films of Arg82 mutants at pH 9.5. The negative band at 1700 cm-1 in the BR --> M spectrum due to the deprotonation of Glu204 was absent when Arg82 was replaced with alanine (R82A), but present with small amplitude when residue 82 was a glutamine (R82Q), or a lysine (R82K), with a shift to 1696 cm-1. The O-H stretch of water at 3643 cm-1 is shifted toward a lower frequency in R82Q, R82K, and R82A in the unphotolyzed state. However, R82Q retains a fraction of the unshifted band. Another O-H stretch is prominent in R82Q around 3625 cm-1 but absent in R82A and probably in R82K. In parallel, R82Q retains a fraction of the slow component of the formation of the M intermediate, which is almost completely absent in R82K and R82A. These results, along with previous data for the mutants of Glu204, suggest that the guanidium group of Arg82 influences the H-bonding of water molecules located close to Asp85 and Arg82-Glu204 regions, and the rate of proton transfer from the Schiff base to Asp85. The amide group of Gln82 can substitute for it but weakly.

Arginine↗