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Affiliation(s)
- J. Krüger
- Institute of Biophotonics, School of Medical Science and Engineering, National Yang-Ming University, 155, Section 2, Li-Nong Street, Taipei 112, Taiwan
| | - W. B. Fischer
- Institute of Biophotonics, School of Medical Science and Engineering, National Yang-Ming University, 155, Section 2, Li-Nong Street, Taipei 112, Taiwan
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2
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Mehnert T, Routh A, Judge PJ, Lam YH, Fischer D, Watts A, Fischer WB. Biophysical characterization of Vpu from HIV-1 suggests a channel-pore dualism. Proteins 2008; 70:1488-97. [PMID: 17910056 PMCID: PMC7167847 DOI: 10.1002/prot.21642] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Vpu from HIV‐1 is an 81 amino acid type I integral membrane protein which consists of a cytoplasmic and a transmembrane (TM) domain. The TM domain is known to alter membrane permeability for ions and substrates when inserted into artificial membranes. Peptides corresponding to the TM domain of Vpu (Vpu1‐32) and mutant peptides (Vpu1‐32‐W23L, Vpu1‐32‐R31V, Vpu1‐32‐S24L) have been synthesized and reconstituted into artificial lipid bilayers. All peptides show channel activity with a main conductance level of around 20 pS. Vpu1‐32‐W23L has a considerable flickering pattern in the recordings and longer open times than Vpu1‐32. Whilst recordings for Vpu1‐32‐R31V are almost indistinguishable from those of the WT peptide, recordings for Vpu1‐32‐S24L do not exhibit any noticeable channel activity. Recordings of WT peptide and Vpu1‐32‐W23L indicate Michaelis–Menten behavior when the salt concentration is increased. Both peptide channels follow the Eisenman series I, indicative for a weak ion channel with almost pore like characteristics. Proteins 2008. © 2007 Wiley‐Liss, Inc.
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Affiliation(s)
- T. Mehnert
- Biomembrane Structure Unit, Department of Biochemistry, Oxford University, Oxford OX1 3QU, United Kingdom
| | - A. Routh
- Biomembrane Structure Unit, Department of Biochemistry, Oxford University, Oxford OX1 3QU, United Kingdom
| | - P. J. Judge
- Biomembrane Structure Unit, Department of Biochemistry, Oxford University, Oxford OX1 3QU, United Kingdom
| | - Y. H. Lam
- Biomembrane Structure Unit, Department of Biochemistry, Oxford University, Oxford OX1 3QU, United Kingdom
| | - D. Fischer
- Biomembrane Structure Unit, Department of Biochemistry, Oxford University, Oxford OX1 3QU, United Kingdom
| | - A. Watts
- Biomembrane Structure Unit, Department of Biochemistry, Oxford University, Oxford OX1 3QU, United Kingdom
| | - W. B. Fischer
- Biomembrane Structure Unit, Department of Biochemistry, Oxford University, Oxford OX1 3QU, United Kingdom
- Bionanotechnology Interdisciplinary Research Collaboration, Clarendon Laboratory, Department of Physics, Oxford University, Oxford OX1 3PU, United Kingdom
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3
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Abstract
Vpu, an integral membrane protein encoded in HIV-1, is implicated in the release of new virus particles from infected cells, presumably mediated by ion channel activity of homo-oligomeric Vpu bundles. Reconstitution of both full length Vpu(1-81) and a short, the transmembrane (TM) domain comprising peptide Vpu(1-32) into bilayers under a constant electric field results in an asymmetric orientation of those channels. For both cases, channel activity with similar kinetics is observed. Channels can open and remain open within a broad series of conductance states even if a small or no electric potential is applied. The mean open time for Vpu peptide channels is voltage-independent. The rate of channel opening shows a biphasic voltage activation, implicating that the gating is influenced by the interaction of the dipole moments of the TM helices with an electric field.
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Affiliation(s)
- T Mehnert
- Biomembrane Structure Unit, Department of Biochemistry, Oxford University, South Parks Road, Oxford, UK
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4
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Kim CG, Lemaitre V, Watts A, Fischer WB. Drug–protein interaction with Vpu from HIV-1: proposing binding sites for amiloride and one of its derivatives. Anal Bioanal Chem 2006; 386:2213-7. [PMID: 17082882 DOI: 10.1007/s00216-006-0832-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2006] [Revised: 09/01/2006] [Accepted: 09/05/2006] [Indexed: 10/24/2022]
Abstract
Vpu is an 81-amino-acid auxiliary protein of the genome of HIV-1. It is proposed that one of its roles is to enhance particle release by self-assembling to form water-filled channels enabling the flux of ions at the site of the plasma membrane of the infected cell. Hexamethylene amiloride has been shown to block Vpu channel activity when the protein is reconstituted into lipid bilayers. In a docking approach with monomeric, pentameric and hexameric bundle models of Vpu corresponding to the transmembrane part of the protein, a putative binding site of hexamethylene amiloride is proposed and is compared with the site for the nonpotent amiloride. The binding mode for both ligands is achieved by optimizing hydrogen bond interactions with serines. Binding energies and binding constants are the lowest for protonated hexamethylene amiloride in the pentameric bundle.
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Affiliation(s)
- C G Kim
- Biomembrane Structure Unit, Department of Biochemistry, Oxford University, South Parks Road, Oxford, OX1 3QU, UK
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5
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Abstract
Based on structures made available by solution NMR, molecular models of the protein Vpu from HIV-1 were built and refined by 6 ns MD simulations in a fully hydrated lipid bilayer. Vpu is an 81 amino acid type I integral membrane protein encoded by the human immunodeficiency virus type-1 (HIV-1) and closely related simian immunodeficiency viruses (SIVs). Its role is to amplify viral release. Upon phosphorylation, the cytoplasmic domain adopts a more compact shape with helices 2 and 3 becoming almost parallel to each other. A loss of helicity for several residues belonging to the helices adjacent to both ends of the loop region containing serines 53 and 57 is observed. A fourth helix, present in one of the NMR-based structures of the cytoplasmic domain and located near the C-terminus, is lost upon phosphorylation.
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Affiliation(s)
- V Lemaitre
- Biomembrane Structure Unit, Department of Biochemistry, Oxford University, South Parks Road, Oxford OX1 3QU, UK
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Lemaitre V, Ali R, Kim CG, Watts A, Fischer WB. Interaction of amiloride and one of its derivatives with Vpu from HIV-1: a molecular dynamics simulation. FEBS Lett 2004; 563:75-81. [PMID: 15063726 DOI: 10.1016/s0014-5793(04)00251-0] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2004] [Revised: 02/26/2004] [Accepted: 03/02/2004] [Indexed: 11/24/2022]
Abstract
Vpu is an 81-residue membrane protein, with a single transmembrane segment that is encoded by HIV-1 and is involved in the enhancement of virion release via formation of an ion channel. Cyclohexamethylene amiloride (Hma) has been shown to inhibit ion channel activity. In the present 12-ns simulation study a putative binding site of Hma blockers in a pentameric model bundle built of parallel aligned helices of the first 32 residues of Vpu was found near Ser-23. Hma orientates along the channel axis with its alkyl ring pointing inside the pore, which leads to a blockage of the pore.
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Affiliation(s)
- V Lemaitre
- Biomembrane Structure Unit, Department of Biochemistry, Oxford University, South Parks Road, Oxford OX1 3QU, UK
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7
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Abstract
Vpu is an 81 amino acid protein encoded by HIV-1. Its role is to amplify viral release by two mechanisms: (i) docking to CD4 with the consequence of targeting CD4 for ubiquitine-mediated degradation, and (ii) formation of ion channels to enhance particle release. The intensive research on its in vivo function, combined with structural investigations, makes this viral membrane protein one of the better characterised membrane proteins. The wealth of structural information enables the use of computational methods to elucidate the mechanisms of function on an atomic scale. The discovery of Vpu and the development of structural models in a chronological order is summarised and first efforts on investigating the mechanics are outlined.
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Affiliation(s)
- W B Fischer
- Biomembrane Structure Unit, Department of Biochemistry, Oxford University, South Parks Road, Oxford OX1 3QU, UK.
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8
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Abstract
Vpu is an 81 amino acid protein of HIV-1 with two phosphorylation sites. It consists of a short N-terminal end traversing the bilayer and a longer cytoplasmic part. The dual functional role of Vpu is attributed to these topological distinct regions of the protein. The first 52 amino acids of Vpu (HV1H2) have been simulated, which are thought to be embedded in a fully hydrated lipid bilayer and to consist of a transmembrane helix (helix-1) connected via a flexible linker region, including a Glu-Tyr-Arg (EYR) motif, with a second helix (helix-2) residing with its helix long axis on the bilayer surface. Repeated molecular dynamics simulations show that Glu-28 is involved in salt bridge formation with Lys-31 and Arg-34 establishing a kink between the two helices. Helix-2 remains in a helical conformation indicating its stability and function as a "peptide float," separating helix-1 from the rest of the protein. This leads to the conclusion that Vpu consists of three functional modules: helix-1, helix-2, and the remaining residues toward the C-terminal end.
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Affiliation(s)
- I Sramala
- Biomembrane Structure Unit, Department of Biochemistry, Oxford University, Oxford OX1 3QU, UK
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Cordes FS, Tustian AD, Sansom MSP, Watts A, Fischer WB. Bundles consisting of extended transmembrane segments of Vpu from HIV-1: computer simulations and conductance measurements. Biochemistry 2002; 41:7359-65. [PMID: 12044168 DOI: 10.1021/bi025518p] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Part of the genome of the human immunodeficiency virus type 1 (HIV-1) encodes for a short membrane protein Vpu, which has a length of 81 amino acids. It has two functional roles: (i) to downregulate CD4 and (ii) to support particle release. These roles are attributed to two distinct domains of the peptide, the cytoplasmic and transmembrane (TM) domains, respectively. It has been suggested that the enhanced particle release function is linked to the ion channel activity of Vpu, with a slight preference for cations over anions. To allow ion flux across the membrane Vpu would be required to assemble in homooligomers to form functional water-filled pores. In this study molecular dynamics simulations are used to address the role of particular amino acids in 4, 5, and 6 TM helix bundle structures. The helices (Vpu(6-33)) are extended to include hydrophilic residues such as Glu, Tyr, and Arg (EYR motif). Our simulations indicate that this motif destabilizes the bundles at their C-terminal ends. The arginines point into the pore to form a positive charged ring that could act as a putative selectivity filter. The helices of the bundles adopt slightly higher average tilt angles with decreasing number of helices. We also suggest that the helices are kinked. Conductance measurements on a peptide (Vpu(1-32)) reconstituted into lipid membranes show that the peptide forms ion channels with several conductance levels.
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Affiliation(s)
- F S Cordes
- Biomembrane Structure Unit, Laboratory of Molecular Biophysics, Department of Biochemistry, Oxford University, South Parks Road, Oxford OX1 3QU, U.K
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Fischer WB, Pitkeathly M, Sansom MS. Amantadine blocks channel activity of the transmembrane segment of the NB protein from influenza B. Eur Biophys J 2001; 30:416-20. [PMID: 11718294 DOI: 10.1007/s002490100157] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
NB is short auxiliary protein with ca. 100 amino acids, encoded in the viral genome of influenza B. It is believed to be similar to M2 from influenza A and Vpu from HIV-1 in that it demonstrates ion channel activity. Channels formed by the protein can be blocked by amantadine. We have synthesized the putative transmembrane segment of NB (IRG S20 IIITICVSL I30 VILIVFGCI A40 KIFI (NB, Lee)). Reconstituted in a lipid bilayer, the peptide shows channel activity. The addition of amantadine leads to dose-dependent loss of channel activity. Channel blocking is reversible. Channel behaviour of the peptide in the presence of amantadine is in accordance with findings for the intact channel. Thus, the synthetic transmembrane peptide captures the ion channel activity of the intact NB protein.
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Affiliation(s)
- W B Fischer
- Department of Biochemistry, University of Oxford, UK.
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Abstract
A series of novel resorcin-[4]arenes with extended pi systems have been synthesised and developed as potassium-selective transporters. Resorcin[4]arenes that feature crown ether moieties function as efficient carriers of K+ across bulk liquid membranes showing enhanced selectivity over the other alkali metal ions relative to a model system (benzo[15]crown-5). Incorporation of functionalities suitable for pore formation, in addition to an extra annulus of aromatic residues, gives molecules which have remarkable ion-channel-mimicking behaviour in a biological lipid bilayer with outstanding K+/Na+ selectivity.
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Affiliation(s)
- A J Wright
- Department of Chemistry, University of Oxford, UK
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12
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Cordes FS, Kukol A, Forrest LR, Arkin IT, Sansom MS, Fischer WB. The structure of the HIV-1 Vpu ion channel: modelling and simulation studies. Biochim Biophys Acta 2001; 1512:291-8. [PMID: 11406106 DOI: 10.1016/s0005-2736(01)00332-7] [Citation(s) in RCA: 42] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Vpu is an 81 amino acid auxiliary protein in HIV-1 which exhibits channel activity. We used two homo-pentameric bundles with the helical transmembrane segments derived from FTIR spectroscopy in combination with a global molecular dynamics search protocol: (i) tryptophans (W) pointing into the pore, and (ii) W facing the lipids. Two equivalent bundles have been generated using a simulated annealing via a restrained molecular dynamics simulations (SA/MD) protocol. A fifth model was generated via SA/MD with all serines facing the pore. The latter model adopts a very stable structure during the 2 ns of simulation. The stability of the models with W facing the pore depends on the starting structure. A possible gating mechanism is outlined.
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Affiliation(s)
- F S Cordes
- Laboratory of Molecular Biophysics, Department of Biochemistry, Oxford University, UK
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Fischer WB, Pitkeathly M, Wallace BA, Forrest LR, Smith GR, Sansom MS. Transmembrane peptide NB of influenza B: a simulation, structure, and conductance study. Biochemistry 2000; 39:12708-16. [PMID: 11027151 DOI: 10.1021/bi001000e] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The putative transmembrane segment of the ion channel forming peptide NB from influenza B was synthesized by standard solid-phase peptide synthesis. Insertion into the planar lipid bilayer revealed ion channel activity with conductance levels of 20, 61, 107, and 142 pS in a 0.5 M KCl buffer solution. In addition, levels at -100 mV show conductances of 251 and 413 pS. A linear current-voltage relation reveals a voltage-independent channel formation. In methanol and in vesicles the peptide appears to adopt an alpha-helical-like structure. Computational models of alpha-helix bundles using N = 4, 5, and 6 NB peptides per bundle revealed water-filled pores after 1 ns of MD simulation in a solvated lipid bilayer. Calculated conductance values [using HOLE (Smart et al. (1997) Biophys. J. 72, 1109-1126)] of ca. 20, 60, and 90 pS, respectively, suggested that the multiple conductance levels seen experimentally must correspond to different degrees of oligomerization of the peptide to form channels.
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Affiliation(s)
- W B Fischer
- Laboratory of Molecular Biophysics, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, U.K.
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14
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Abstract
Nanosecond molecular dynamics simulations in a fully solvated phospholipid bilayer have been performed on single transmembrane alpha-helices from three putative ion channel proteins encoded by viruses: NB (from influenza B), CM2 (from influenza C), and Vpu (from HIV-1). alpha-Helix stability is maintained within a core region of ca. 28 residues for each protein. Helix perturbations are due either to unfavorable interactions of hydrophobic residues with the lipid headgroups or to the need of the termini of short helices to extend into the surrounding interfacial environment in order to form H-bonds. The requirement of both ends of a helix to form favorable interactions with lipid headgroups and/or water may also lead to tilting and/or kinking of a transmembrane alpha-helix. Residues that are generally viewed as poor helix formers in aqueous solution (e.g., Gly, Ile, Val) do not destabilize helices, if located within a helix that spans a lipid bilayer. However, helix/bilayer mismatch such that a helix ends abruptly within the bilayer core destabilizes the end of the helix, especially in the presence of Gly and Ala residues. Hydrogen bonding of polar side-chains with the peptide backbone and with one another occurs when such residues are present within the bilayer core, thus minimizing the energetic cost of burying such side-chains.
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Affiliation(s)
- W B Fischer
- Laboratory of Molecular Biophysics, Department of Biochemistry, University of Oxford, Rex Richards Building, South Parks Road, Oxford, OX1 3QU, UK.
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Liu X, Lee MJ, Coleman M, Rath P, Nilsson A, Fischer WB, Bizounok M, Herzfeld J, Karstens WF, Raap J, Lugtenburg J, Rothschild KJ. Detection of threonine structural changes upon formation of the M-intermediate of bacteriorhodopsin: evidence for assignment to Thr-89. Biochim Biophys Acta 1998; 1365:363-72. [PMID: 9711293 DOI: 10.1016/s0005-2728(98)00088-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
Abstract
The behavior of threonine residues in the bacteriorhodopsin (bR) photocycle has been investigated by Fourier transform infrared difference spectroscopy. L-Threonine labeled at the hydroxyl group with 18O (L-[3-(18)O]threonine) was incorporated into bR and the bR-->M FTIR difference spectra measured. Bands are assigned to threonine vibrational modes on the basis of 18O induced isotope frequency shifts and normal mode calculations. In the 3500 cm-1 region, a negative band is assigned to the OH stretch of threonine. In the 1125 cm-1 region, a negative band is assigned to a mixed CH3 rock/CO stretch mode. The frequency of both these bands indicates the presence of at least one hydrogen bonded threonine hydroxyl group in light adapted bR which undergoes a change in structure by formation of the M intermediate. Spectral changes induced by the substitution Thr-89-->Asn but not Thr-46-->Asn or Asp-96-->Asn are consistent with the assignment of these bands to Thr-89. These results along with another related study on the mutant Thr-89-->Asn indicate that the active site of bR includes Thr-89 and that its interaction with the retinylidene Schiff base and Asp-85 may play an important role in regulating the color of bacteriorhodopsin and the transfer of a proton to the Schiff base.
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Affiliation(s)
- X Liu
- Physics Department, Boston University, MA 02215, USA
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Fischer WB, Sonar S, Marti T, Khorana HG, Rothschild KJ. Detection of a water molecule in the active-site of bacteriorhodopsin: hydrogen bonding changes during the primary photoreaction. Biochemistry 1994; 33:12757-62. [PMID: 7947680 DOI: 10.1021/bi00209a005] [Citation(s) in RCA: 74] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
FTIR-difference spectroscopy in combination with site-directed mutagenesis has been used to investigate the role of water during the photocycle of bacteriorhodopsin. At least one water molecule is detected which undergoes an increase in H-bonding during the primary bR-->K phototransition. Bands due to water appear in the OH stretch region of the bR-->K FTIR-difference spectrum which downshift by approximately 12 cm-1 when the sample is hydrated with H2(18)O. In contrast to 2H2O, the H2(18)O-induced shift is not complete, even after 24 h of hydration. This indicates that even though water is still able to exchange protons with the outside medium, it is partially trapped in the interior of the protein. In the mutant Y57D, these bands are absent while a new set of bands appear at much lower frequencies which undergo H2(18)O-induced shifts. It is concluded that the water molecule we detect is located inside the bR active-site and may interact with Tyr-57. The change in its hydrogen-bonding strength is most likely due to the photoinduced all-trans-->13-cis isomerization of the retinal chromophore and the associated movement of the positively charged Schiff base during the bR-->K transition. In contrast, a second water molecule, whose infrared difference bands are not affected by the Y57D mutation, appears to undergo a decrease in hydrogen bonding during the K-->L and L-->M transitions.
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Affiliation(s)
- W B Fischer
- Physics Department, Boston University, Massachusetts 02215
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He Y, Krebs MP, Fischer WB, Khorana HG, Rothschild KJ. FTIR difference spectroscopy of the bacteriorhodopsin mutant Tyr-185-->Phe: detection of a stable O-like species and characterization of its photocycle at low temperature. Biochemistry 1993; 32:2282-90. [PMID: 8443171 DOI: 10.1021/bi00060a021] [Citation(s) in RCA: 26] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Fourier transform infrared difference spectroscopy has been used to study the photocycle of the mutant Tyr-185-->Phe expressed in native Halobacterium halobium and isolated as intact purple membrane fragments. We find several changes in the low-temperature bR-->K, bR-->L, and bR-->M FTIR difference spectra of Y185F relative to wild-type bR which are not directly related to the absorption bands associated with Tyr-185. We show that these features arise from the photoreaction of a stable red-shifted species (OY185F) with a vibrational spectrum similar to the O intermediate. By using photoselection and FTIR spectroscopy, we have been able to characterize the photoproducts of this OY185F species. A K-like photoproduct is formed at 80 K which has a 13-cis structure. However, it differs from K630, exhibiting an intense band at 990 cm-1 most likely due to a hydrogen-out-of-plane vibrational mode of the chromophore. At 170 and 250 K, photoexcitation of OY185F produces an intermediate with vibrational features similar to the N intermediate in the wild-type bR photocycle. However, no evidence for an M-like intermediate is found. Although Asp-96 undergoes a change in its environment/protonation state during the OY185F photocycle, no protonation changes involving Asp-85 and Asp-212 were detected. These results provide strong evidence that light adaptation of Y185F produces two species similar to bR570 and the O intermediate. Differences in their respective photocycles can be explained on the basis of differences in the protonation states of the residues Asp-85 and Asp-212 which are ionized in bR570 and undergo net protonation upon OY185F formation.
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Affiliation(s)
- Y He
- Physics Department, Boston University, Massachusetts 02215
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Fischer WB. Acetabular anatomy and the transacetabular fixation of screws in total hip arthroplasty. J Bone Joint Surg Am 1991; 73:1272. [PMID: 1890133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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