1
|
Oldemeyer S, La Greca M, Langner P, Lê Công KL, Schlesinger R, Heberle J. Nanosecond Transient IR Spectroscopy of Halorhodopsin in Living Cells. J Am Chem Soc 2024; 146:19118-19127. [PMID: 38950551 PMCID: PMC11258790 DOI: 10.1021/jacs.4c03891] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Revised: 06/23/2024] [Accepted: 06/25/2024] [Indexed: 07/03/2024]
Abstract
The ability to track minute changes of a single amino acid residue in a cellular environment is causing a paradigm shift in the attempt to fully understand the responses of biomolecules that are highly sensitive to their environment. Detecting early protein dynamics in living cells is crucial to understanding their mechanisms, such as those of photosynthetic proteins. Here, we elucidate the light response of the microbial chloride pump NmHR from the marine bacterium Nonlabens marinus, located in the membrane of living Escherichia coli cells, using nanosecond time-resolved UV/vis and IR absorption spectroscopy over the time range from nanoseconds to seconds. Transient structural changes of the retinal cofactor and the surrounding apoprotein are recorded using light-induced time-resolved UV/vis and IR difference spectroscopy. Of particular note, we have resolved the kinetics of the transient deprotonation of a single cysteine residue during the photocycle of NmHR out of the manifold of molecular vibrations of the cells. These findings are of high general relevance, given the successful development of optogenetic tools from photoreceptors to interfere with enzymatic and neuronal pathways in living organisms using light pulses as a noninvasive trigger.
Collapse
Affiliation(s)
- Sabine Oldemeyer
- Experimental
Molecular Biophysics, Department of Physics, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany
| | - Mariafrancesca La Greca
- Genetic
Biophysics, Department of Physics, Freie
Universität Berlin, Arnimallee 14, 14195 Berlin, Germany
| | - Pit Langner
- Experimental
Molecular Biophysics, Department of Physics, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany
| | - Karoline-Luisa Lê Công
- Experimental
Molecular Biophysics, Department of Physics, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany
| | - Ramona Schlesinger
- Genetic
Biophysics, Department of Physics, Freie
Universität Berlin, Arnimallee 14, 14195 Berlin, Germany
| | - Joachim Heberle
- Experimental
Molecular Biophysics, Department of Physics, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany
| |
Collapse
|
2
|
Meng X, Ganapathy S, van Roemburg L, Post M, Brinks D. Voltage Imaging with Engineered Proton-Pumping Rhodopsins: Insights from the Proton Transfer Pathway. ACS PHYSICAL CHEMISTRY AU 2023; 3:320-333. [PMID: 37520318 PMCID: PMC10375888 DOI: 10.1021/acsphyschemau.3c00003] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 04/13/2023] [Accepted: 04/13/2023] [Indexed: 08/01/2023]
Abstract
Voltage imaging using genetically encoded voltage indicators (GEVIs) has taken the field of neuroscience by storm in the past decade. Its ability to create subcellular and network level readouts of electrical dynamics depends critically on the kinetics of the response to voltage of the indicator used. Engineered microbial rhodopsins form a GEVI subclass known for their high voltage sensitivity and fast response kinetics. Here we review the essential aspects of microbial rhodopsin photocycles that are critical to understanding the mechanisms of voltage sensitivity in these proteins and link them to insights from efforts to create faster, brighter and more sensitive microbial rhodopsin-based GEVIs.
Collapse
Affiliation(s)
- Xin Meng
- Department
of Imaging Physics, Delft University of
Technology, 2628 CJ Delft, The
Netherlands
| | - Srividya Ganapathy
- Department
of Imaging Physics, Delft University of
Technology, 2628 CJ Delft, The
Netherlands
- Department
of Pediatrics & Cellular and Molecular Medicine, UCSD School of Medicine, La Jolla, California 92093, United States
| | - Lars van Roemburg
- Department
of Imaging Physics, Delft University of
Technology, 2628 CJ Delft, The
Netherlands
| | - Marco Post
- Department
of Imaging Physics, Delft University of
Technology, 2628 CJ Delft, The
Netherlands
| | - Daan Brinks
- Department
of Imaging Physics, Delft University of
Technology, 2628 CJ Delft, The
Netherlands
- Department
of Molecular Genetics, Erasmus University
Medical Center, 3015 GD Rotterdam, The Netherlands
| |
Collapse
|
3
|
Helbing J, Hamm P. Versatile Femtosecond Laser Synchronization for Multiple-Timescale Transient Infrared Spectroscopy. J Phys Chem A 2023. [PMID: 37478282 DOI: 10.1021/acs.jpca.3c03526] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/23/2023]
Abstract
Several ways to electronically synchronize different types of amplified femtosecond laser systems are presented based on a single freely programmable electronics hardware: arbitrary-detuning asynchronous optical sampling (ADASOPS), as well as actively locking two femtosecond laser oscillators, albeit not necessarily to the same round-trip frequency. They allow us to rapidly probe a very wide range of timescales, from picoseconds to potentially seconds, in a single transient absorption experiment without the need to move any delay stage. Experiments become possible that address a largely unexplored aspect of many photochemical reactions, in particular in the context of photo-catalysis as well as photoactive proteins, where an initial femtosecond trigger very often initiates a long-lasting cascade of follow-up processes. The approach is very versatile and allows us to synchronize very different lasers, such as a Ti:Sa amplifier and a 100 kHz Yb-laser system. The jitter of the synchronization, and therewith the time-resolution in the transient experiment, lies in the range from 1 to 3 ps, depending on the method. For illustration, transient IR measurements of the excited state solvation and decay of a metal carbonyl complex as well as the full reaction cycle of bacteriorhodopsin are shown. The pros and cons of the various methods are discussed, with regard to the scientific question one might want to address, and also with regard to the laser systems that might be already existent in a laser lab.
Collapse
Affiliation(s)
- Jan Helbing
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | - Peter Hamm
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| |
Collapse
|
4
|
Kouyama T, Ihara K. Existence of two substates in the O intermediate of the bacteriorhodopsin photocycle. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2022; 1864:183998. [PMID: 35753392 DOI: 10.1016/j.bbamem.2022.183998] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 04/12/2022] [Accepted: 06/18/2022] [Indexed: 06/15/2023]
Abstract
The proton pumping cycle of bacteriorhodopsin (bR) is initiated when the retinal chromophore with the 13-trans configuration is photo-isomerized into the 13-cis configuration. To understand the recovery processes of the initial retinal configuration that occur in the late stage of the photocycle, we have performed a comprehensive analysis of absorption kinetics data collected at various pH levels and at different salt concentrations. The result of analysis revealed the following features of the late stages of the trans photocycle. i) Two substates occur in the O intermediate. ii) The visible absorption band of the first substate (O1) appears at a much shorter wavelength than that of the late substate (O2). iii) O1 is in rapid equilibrium with the preceding state (N), but O1 becomes less stable than N when an ionizable residue (X1) with a pKa value of 6.5 (in 2 M KCl) is deprotonated. iv) At a low pH and at a low salt concentration, the decay time constant of O2 is longer than those of the preceding states, but the relationship between these time constants is altered when the medium pH or the salt concentration is increased. On the basis of the present observations and previous studies on the structure of the chromophore in O, we suspect that the retinal chromophore in O1 takes on a distorted 13-cis configuration and the O1-to-O2 transition is accompanied by cis-to-trans isomerization about C13C14 bond.
Collapse
Affiliation(s)
- Tsutomu Kouyama
- Graduate School of Science, Nagoya University, Nagoya 464-8602, Japan.
| | - Kunio Ihara
- Center for Gene Research, Nagoya University, Nagoya 464-8602, Japan
| |
Collapse
|
5
|
La Greca M, Chen JL, Schubert L, Kozuch J, Berneiser T, Terpitz U, Heberle J, Schlesinger R. The Photoreaction of the Proton-Pumping Rhodopsin 1 From the Maize Pathogenic Basidiomycete Ustilago maydis. Front Mol Biosci 2022; 9:826990. [PMID: 35281268 PMCID: PMC8913941 DOI: 10.3389/fmolb.2022.826990] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 01/25/2022] [Indexed: 01/25/2023] Open
Abstract
Microbial rhodopsins have recently been discovered in pathogenic fungi and have been postulated to be involved in signaling during the course of an infection. Here, we report on the spectroscopic characterization of a light-driven proton pump rhodopsin (UmRh1) from the smut pathogen Ustilago maydis, the causative agent of tumors in maize plants. Electrophysiology, time-resolved UV/Vis and vibrational spectroscopy indicate a pH-dependent photocycle. We also characterized the impact of the auxin hormone indole-3-acetic acid that was shown to influence the pump activity of UmRh1 on individual photocycle intermediates. A facile pumping activity test was established of UmRh1 expressed in Pichia pastoris cells, for probing proton pumping out of the living yeast cells during illumination. We show similarities and distinct differences to the well-known bacteriorhodopsin from archaea and discuss the putative role of UmRh1 in pathogenesis.
Collapse
Affiliation(s)
- Mariafrancesca La Greca
- Institute of Experimental Physics, Genetic Biophysics, Freie Universität Berlin, Berlin, Germany
| | - Jheng-Liang Chen
- Institute of Experimental Physics, Genetic Biophysics, Freie Universität Berlin, Berlin, Germany
| | - Luiz Schubert
- Institute of Experimental Physics, Experimental Molecular Biophysics, Freie Universität Berlin, Berlin, Germany
| | - Jacek Kozuch
- Institute of Experimental Physics, Experimental Molecular Biophysics, Freie Universität Berlin, Berlin, Germany
| | - Tim Berneiser
- Institute of Experimental Physics, Genetic Biophysics, Freie Universität Berlin, Berlin, Germany
| | - Ulrich Terpitz
- Department of Biotechnology and Biophysics, Biocenter, Julius Maximilian University of Würzburg, Würzburg, Germany
| | - Joachim Heberle
- Institute of Experimental Physics, Experimental Molecular Biophysics, Freie Universität Berlin, Berlin, Germany
| | - Ramona Schlesinger
- Institute of Experimental Physics, Genetic Biophysics, Freie Universität Berlin, Berlin, Germany
- *Correspondence: Ramona Schlesinger,
| |
Collapse
|
6
|
Mous S, Gotthard G, Ehrenberg D, Sen S, Weinert T, Johnson PJM, James D, Nass K, Furrer A, Kekilli D, Ma P, Brünle S, Casadei CM, Martiel I, Dworkowski F, Gashi D, Skopintsev P, Wranik M, Knopp G, Panepucci E, Panneels V, Cirelli C, Ozerov D, Schertler GFX, Wang M, Milne C, Standfuss J, Schapiro I, Heberle J, Nogly P. Dynamics and mechanism of a light-driven chloride pump. Science 2022; 375:845-851. [PMID: 35113649 DOI: 10.1126/science.abj6663] [Citation(s) in RCA: 38] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Chloride transport by microbial rhodopsins is an essential process for which molecular details such as the mechanisms that convert light energy to drive ion pumping and ensure the unidirectionality of the transport have remained elusive. We combined time-resolved serial crystallography with time-resolved spectroscopy and multiscale simulations to elucidate the molecular mechanism of a chloride-pumping rhodopsin and the structural dynamics throughout the transport cycle. We traced transient anion-binding sites, obtained evidence for how light energy is used in the pumping mechanism, and identified steric and electrostatic molecular gates ensuring unidirectional transport. An interaction with the π-electron system of the retinal supports transient chloride ion binding across a major bottleneck in the transport pathway. These results allow us to propose key mechanistic features enabling finely controlled chloride transport across the cell membrane in this light-powered chloride ion pump.
Collapse
Affiliation(s)
- Sandra Mous
- Institute of Molecular Biology and Biophysics, Department of Biology, ETH Zürich, Zürich, Switzerland
| | - Guillaume Gotthard
- Institute of Molecular Biology and Biophysics, Department of Biology, ETH Zürich, Zürich, Switzerland.,Laboratory of Biomolecular Research, Biology and Chemistry Division, Paul Scherrer Institute, Villigen PSI, Switzerland
| | - David Ehrenberg
- Experimental Molecular Biophysics, Department of Physics, Freie Universität Berlin, Berlin, Germany
| | - Saumik Sen
- Fritz Haber Center for Molecular Dynamics, Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Tobias Weinert
- Laboratory of Biomolecular Research, Biology and Chemistry Division, Paul Scherrer Institute, Villigen PSI, Switzerland
| | - Philip J M Johnson
- Laboratory of Nonlinear Optics, Photon Science Division, Paul Scherrer Institute, Villigen PSI, Switzerland
| | - Daniel James
- Laboratory of Biomolecular Research, Biology and Chemistry Division, Paul Scherrer Institute, Villigen PSI, Switzerland
| | - Karol Nass
- Laboratory of Femtochemistry, Photon Science Division, Paul Scherrer Institute, Villigen PSI, Switzerland
| | - Antonia Furrer
- Laboratory of Biomolecular Research, Biology and Chemistry Division, Paul Scherrer Institute, Villigen PSI, Switzerland
| | - Demet Kekilli
- Laboratory of Biomolecular Research, Biology and Chemistry Division, Paul Scherrer Institute, Villigen PSI, Switzerland
| | - Pikyee Ma
- Laboratory of Biomolecular Research, Biology and Chemistry Division, Paul Scherrer Institute, Villigen PSI, Switzerland
| | - Steffen Brünle
- Laboratory of Biomolecular Research, Biology and Chemistry Division, Paul Scherrer Institute, Villigen PSI, Switzerland
| | - Cecilia Maria Casadei
- Institute of Molecular Biology and Biophysics, Department of Biology, ETH Zürich, Zürich, Switzerland.,Laboratory of Biomolecular Research, Biology and Chemistry Division, Paul Scherrer Institute, Villigen PSI, Switzerland
| | - Isabelle Martiel
- Laboratory for Macromolecules and Bioimaging, Photon Science Division, Paul Scherrer Institute, Villigen PSI, Switzerland
| | - Florian Dworkowski
- Laboratory for Macromolecules and Bioimaging, Photon Science Division, Paul Scherrer Institute, Villigen PSI, Switzerland
| | - Dardan Gashi
- Laboratory of Biomolecular Research, Biology and Chemistry Division, Paul Scherrer Institute, Villigen PSI, Switzerland.,Laboratory of Femtochemistry, Photon Science Division, Paul Scherrer Institute, Villigen PSI, Switzerland
| | - Petr Skopintsev
- Laboratory of Biomolecular Research, Biology and Chemistry Division, Paul Scherrer Institute, Villigen PSI, Switzerland
| | - Maximilian Wranik
- Laboratory of Biomolecular Research, Biology and Chemistry Division, Paul Scherrer Institute, Villigen PSI, Switzerland
| | - Gregor Knopp
- Laboratory of Femtochemistry, Photon Science Division, Paul Scherrer Institute, Villigen PSI, Switzerland
| | - Ezequiel Panepucci
- Laboratory for Macromolecules and Bioimaging, Photon Science Division, Paul Scherrer Institute, Villigen PSI, Switzerland
| | - Valerie Panneels
- Laboratory of Biomolecular Research, Biology and Chemistry Division, Paul Scherrer Institute, Villigen PSI, Switzerland
| | - Claudio Cirelli
- Laboratory of Femtochemistry, Photon Science Division, Paul Scherrer Institute, Villigen PSI, Switzerland
| | - Dmitry Ozerov
- Science IT, Paul Scherrer Institute, Villigen PSI, Switzerland
| | - Gebhard F X Schertler
- Institute of Molecular Biology and Biophysics, Department of Biology, ETH Zürich, Zürich, Switzerland.,Laboratory of Biomolecular Research, Biology and Chemistry Division, Paul Scherrer Institute, Villigen PSI, Switzerland
| | - Meitian Wang
- Laboratory for Macromolecules and Bioimaging, Photon Science Division, Paul Scherrer Institute, Villigen PSI, Switzerland
| | - Chris Milne
- Laboratory of Femtochemistry, Photon Science Division, Paul Scherrer Institute, Villigen PSI, Switzerland
| | - Joerg Standfuss
- Laboratory of Biomolecular Research, Biology and Chemistry Division, Paul Scherrer Institute, Villigen PSI, Switzerland
| | - Igor Schapiro
- Fritz Haber Center for Molecular Dynamics, Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Joachim Heberle
- Experimental Molecular Biophysics, Department of Physics, Freie Universität Berlin, Berlin, Germany
| | - Przemyslaw Nogly
- Institute of Molecular Biology and Biophysics, Department of Biology, ETH Zürich, Zürich, Switzerland
| |
Collapse
|
7
|
Nakai H, Takemura T, Ono J, Nishimura Y. Quantum-Mechanical Molecular Dynamics Simulations on Secondary Proton Transfer in Bacteriorhodopsin Using Realistic Models. J Phys Chem B 2021; 125:10947-10963. [PMID: 34582194 DOI: 10.1021/acs.jpcb.1c06231] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Bacteriorhodopsin (BR) transports a proton from intracellular to extracellular (EC) sites through five proton transfers. The second proton transfer is the release of an excess proton stored in BR into the EC medium, and an atomistic understanding of this whole process has remained unexplored due to its ubiquitous environment. Here, fully quantum mechanical (QM) molecular dynamics (MD) and metadynamics (MTD) simulations for this process were performed at the divide-and-conquer density-functional tight-binding level using realistic models (∼50000 and ∼20000 atoms) based on the time-resolved photointermediate structures from an X-ray free electron laser. Regarding the proton storage process, the QM-MD/MTD simulations confirmed the Glu-shared mechanism, in which an excess proton is stored between Glu194 and Glu204, and clarified that the activation occurs by localizing the proton at Glu204 in the photocycle. Furthermore, the QM-MD/MTD simulations elucidated a release pathway from Glu204 through Ser193 to the EC water molecules and clarified that the proton release starts at ∼250 μs. In the ubiquitous proton diffusion in the EC medium, the transient proton receptors predicted experimentally were assigned to carboxylates in Glu9 and Glu74. Large-scale QM-MD/MTD simulations beyond the conventional sizes, which provided the above findings and confirmations, were possible by adopting our Dcdftbmd program.
Collapse
Affiliation(s)
- Hiromi Nakai
- Department of Chemistry and Biochemistry, School of Advanced Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku, Tokyo 169-8555, Japan.,Waseda Research Institute for Science and Engineering (WISE), Waseda University, 3-4-1 Okubo, Shinjuku, Tokyo 169-8555, Japan.,Elements Strategy Initiative for Catalysts & Batteries (ESICB), Kyoto University, 1-30 Goryo-Ohara, Nishikyo-ku, Kyoto 615-8245, Japan
| | - Toshiaki Takemura
- Department of Chemistry and Biochemistry, School of Advanced Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku, Tokyo 169-8555, Japan
| | - Junichi Ono
- Waseda Research Institute for Science and Engineering (WISE), Waseda University, 3-4-1 Okubo, Shinjuku, Tokyo 169-8555, Japan.,Elements Strategy Initiative for Catalysts & Batteries (ESICB), Kyoto University, 1-30 Goryo-Ohara, Nishikyo-ku, Kyoto 615-8245, Japan
| | - Yoshifumi Nishimura
- Waseda Research Institute for Science and Engineering (WISE), Waseda University, 3-4-1 Okubo, Shinjuku, Tokyo 169-8555, Japan
| |
Collapse
|
8
|
Maag D, Mast T, Elstner M, Cui Q, Kubař T. O to bR transition in bacteriorhodopsin occurs through a proton hole mechanism. Proc Natl Acad Sci U S A 2021; 118:e2024803118. [PMID: 34561302 PMCID: PMC8488608 DOI: 10.1073/pnas.2024803118] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/04/2021] [Indexed: 12/27/2022] Open
Abstract
Extensive classical and quantum mechanical/molecular mechanical (QM/MM) molecular dynamics simulations are used to establish the structural features of the O state in bacteriorhodopsin (bR) and its conversion back to the bR ground state. The computed free energy surface is consistent with available experimental data for the kinetics and thermodynamics of the O to bR transition. The simulation results highlight the importance of the proton release group (PRG, consisting of Glu194/204) and the conserved arginine 82 in modulating the hydration level of the protein cavity. In particular, in the O state, deprotonation of the PRG and downward rotation of Arg82 lead to elevated hydration level and a continuous water network that connects the PRG to the protonated Asp85. Proton exchange through this water network is shown by ∼0.1-μs semiempirical QM/MM free energy simulations to occur through the generation and propagation of a proton hole, which is relayed by Asp212 and stabilized by Arg82. This mechanism provides an explanation for the observation that the D85S mutant of bacteriorhodopsin pumps chloride ions. The electrostatics-hydration coupling mechanism and the involvement of all titration states of water are likely applicable to many biomolecules involved in bioenergetic transduction.
Collapse
Affiliation(s)
- Denis Maag
- Institute of Physical Chemistry, Karlsruhe Institute of Technology, 76131 Karlsruhe, Germany
| | - Thilo Mast
- Institute of Physical Chemistry, Karlsruhe Institute of Technology, 76131 Karlsruhe, Germany
| | - Marcus Elstner
- Institute of Physical Chemistry, Karlsruhe Institute of Technology, 76131 Karlsruhe, Germany
- Institute for Biological Interfaces, Karlsruhe Institute of Technology, 76131 Karlsruhe, Germany
| | - Qiang Cui
- Department of Chemistry, Boston University, Boston, MA 02215
- Department of Physics, Boston University, Boston, MA 02215
- Department of Biomedical Engineering, Boston University, Boston, MA 02215
| | - Tomáš Kubař
- Institute of Physical Chemistry, Karlsruhe Institute of Technology, 76131 Karlsruhe, Germany;
| |
Collapse
|
9
|
Affiliation(s)
- Peter Hamm
- Department of Chemistry, University of Zurich, Winterthurerstr. 190, CH-8057 Zürich, Switzerland
| |
Collapse
|
10
|
Ye M, Crozier KB. Metasurface with metallic nanoantennas and graphene nanoslits for sensing of protein monolayers and sub-monolayers. OPTICS EXPRESS 2020; 28:18479-18492. [PMID: 32680046 DOI: 10.1364/oe.394564] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Accepted: 05/28/2020] [Indexed: 06/11/2023]
Abstract
Biomolecule sensing plays an important role in both fundamental biological studies and medical diagnostic applications. Infrared (IR) spectroscopy presents opportunities for sensing biomolecules as it allows their fingerprints to be determined by directly measuring their absorption spectra. However, the detection of biomolecules at low concentrations is difficult with conventional IR spectroscopy due to signal-to-noise considerations. This has led to recent interest on the use of nanostructured surfaces to boost the signals from biomolecules in a method termed surface enhanced infrared spectroscopy. So far, efforts have largely involved the use of metallic nanoantennas (which produce large field enhancement) or graphene nanostructures (which produce strong field confinement and provide electrical tunability). Here, we propose a nanostructured surface that combines the large field enhancement of metallic nanoantennas with the strong field confinement and electrical tunability of graphene plasmons. Our device consists of an array of plasmonic nanoantennas and graphene nanoslits on a resonant substrate. We perform systematic electromagnetic simulations to quantify the sensing performance of the proposed device and show that it outperforms designs in which only plasmons from metallic nanoantennas or plasmons from graphene are utilized. These investigations consider the model system of a representative protein-goat anti-mouse immunoglobulin G (IgG) - in monolayer or sub-monolayer form. Our findings provide guidance for future biosensors for the sensitive quantification and identification of biomolecules.
Collapse
|
11
|
Abstract
Infrared difference spectroscopy probes vibrational changes of proteins upon their perturbation. Compared with other spectroscopic methods, it stands out by its sensitivity to the protonation state, H-bonding, and the conformation of different groups in proteins, including the peptide backbone, amino acid side chains, internal water molecules, or cofactors. In particular, the detection of protonation and H-bonding changes in a time-resolved manner, not easily obtained by other techniques, is one of the most successful applications of IR difference spectroscopy. The present review deals with the use of perturbations designed to specifically change the protein between two (or more) functionally relevant states, a strategy often referred to as reaction-induced IR difference spectroscopy. In the first half of this contribution, I review the technique of reaction-induced IR difference spectroscopy of proteins, with special emphasis given to the preparation of suitable samples and their characterization, strategies for the perturbation of proteins, and methodologies for time-resolved measurements (from nanoseconds to minutes). The second half of this contribution focuses on the spectral interpretation. It starts by reviewing how changes in H-bonding, medium polarity, and vibrational coupling affect vibrational frequencies, intensities, and bandwidths. It is followed by band assignments, a crucial aspect mostly performed with the help of isotopic labeling and site-directed mutagenesis, and complemented by integration and interpretation of the results in the context of the studied protein, an aspect increasingly supported by spectral calculations. Selected examples from the literature, predominately but not exclusively from retinal proteins, are used to illustrate the topics covered in this review.
Collapse
|
12
|
Giliberti V, Polito R, Ritter E, Broser M, Hegemann P, Puskar L, Schade U, Zanetti-Polzi L, Daidone I, Corni S, Rusconi F, Biagioni P, Baldassarre L, Ortolani M. Tip-Enhanced Infrared Difference-Nanospectroscopy of the Proton Pump Activity of Bacteriorhodopsin in Single Purple Membrane Patches. NANO LETTERS 2019; 19:3104-3114. [PMID: 30950626 PMCID: PMC6745627 DOI: 10.1021/acs.nanolett.9b00512] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Revised: 04/02/2019] [Indexed: 05/21/2023]
Abstract
Photosensitive proteins embedded in the cell membrane (about 5 nm thickness) act as photoactivated proton pumps, ion gates, enzymes, or more generally, as initiators of stimuli for the cell activity. They are composed of a protein backbone and a covalently bound cofactor (e.g. the retinal chromophore in bacteriorhodopsin (BR), channelrhodopsin, and other opsins). The light-induced conformational changes of both the cofactor and the protein are at the basis of the physiological functions of photosensitive proteins. Despite the dramatic development of microscopy techniques, investigating conformational changes of proteins at the membrane monolayer level is still a big challenge. Techniques based on atomic force microscopy (AFM) can detect electric currents through protein monolayers and even molecular binding forces in single-protein molecules but not the conformational changes. For the latter, Fourier-transform infrared spectroscopy (FTIR) using difference-spectroscopy mode is typically employed, but it is performed on macroscopic liquid suspensions or thick films containing large amounts of purified photosensitive proteins. In this work, we develop AFM-assisted, tip-enhanced infrared difference-nanospectroscopy to investigate light-induced conformational changes of the bacteriorhodopsin mutant D96N in single submicrometric native purple membrane patches. We obtain a significant improvement compared with the signal-to-noise ratio of standard IR nanospectroscopy techniques by exploiting the field enhancement in the plasmonic nanogap that forms between a gold-coated AFM probe tip and an ultraflat gold surface, as further supported by electromagnetic and thermal simulations. IR difference-spectra in the 1450-1800 cm-1 range are recorded from individual patches as thin as 10 nm, with a diameter of less than 500 nm, well beyond the diffraction limit for FTIR microspectroscopy. We find clear spectroscopic evidence of a branching of the photocycle for BR molecules in direct contact with the gold surfaces, with equal amounts of proteins either following the standard proton-pump photocycle or being trapped in an intermediate state not directly contributing to light-induced proton transport. Our results are particularly relevant for BR-based optoelectronic and energy-harvesting devices, where BR molecular monolayers are put in contact with metal surfaces, and, more generally, for AFM-based IR spectroscopy studies of conformational changes of proteins embedded in intrinsically heterogeneous native cell membranes.
Collapse
Affiliation(s)
- Valeria Giliberti
- Istituto
Italiano di Tecnologia, Center for Life NanoScience, Viale Regina Elena 291, I-00161 Roma, Italy
- E-mail:
| | - Raffaella Polito
- Department
of Physics, Sapienza University of Rome, Piazzale Aldo Moro 2, I-00185 Roma, Italy
| | - Eglof Ritter
- Humboldt-Universität
zu Berlin, Institut für
Biologie, Invalidenstraße
42, D-10115 Berlin, Germany
| | - Matthias Broser
- Humboldt-Universität
zu Berlin, Institut für
Biologie, Invalidenstraße
42, D-10115 Berlin, Germany
| | - Peter Hegemann
- Humboldt-Universität
zu Berlin, Institut für
Biologie, Invalidenstraße
42, D-10115 Berlin, Germany
| | - Ljiljana Puskar
- Helmholtz-Zentrum
Berlin für Materialien und Energie GmbH, Albert-Einstein-Str. 15, 12489 Berlin, Germany
| | - Ulrich Schade
- Helmholtz-Zentrum
Berlin für Materialien und Energie GmbH, Albert-Einstein-Str. 15, 12489 Berlin, Germany
| | - Laura Zanetti-Polzi
- Department
of Physical and Chemical Sciences, University
of L’Aquila, Via Vetoio, I-67010 L’Aquila, Italy
| | - Isabella Daidone
- Department
of Physical and Chemical Sciences, University
of L’Aquila, Via Vetoio, I-67010 L’Aquila, Italy
| | - Stefano Corni
- Department
of Chemical Sciences, University of Padova, Via Marzolo 1, I-35131 Padova, Italy
- CNR
Institute
of Nanoscience, Via Campi
213/A, I-41125 Modena, Italy
| | - Francesco Rusconi
- Dipartimento
di Fisica, Politecnico di Milano, Piazza Leonardo da Vinci 32, I-20133 Milano, Italy
| | - Paolo Biagioni
- Dipartimento
di Fisica, Politecnico di Milano, Piazza Leonardo da Vinci 32, I-20133 Milano, Italy
| | - Leonetta Baldassarre
- Department
of Physics, Sapienza University of Rome, Piazzale Aldo Moro 2, I-00185 Roma, Italy
| | - Michele Ortolani
- Istituto
Italiano di Tecnologia, Center for Life NanoScience, Viale Regina Elena 291, I-00161 Roma, Italy
- Department
of Physics, Sapienza University of Rome, Piazzale Aldo Moro 2, I-00185 Roma, Italy
- E-mail:
| |
Collapse
|
13
|
Klocke JL, Mangold M, Allmendinger P, Hugi A, Geiser M, Jouy P, Faist J, Kottke T. Single-Shot Sub-microsecond Mid-infrared Spectroscopy on Protein Reactions with Quantum Cascade Laser Frequency Combs. Anal Chem 2018; 90:10494-10500. [DOI: 10.1021/acs.analchem.8b02531] [Citation(s) in RCA: 94] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
- Jessica L. Klocke
- Physical and Biophysical Chemistry, Department of Chemistry, Bielefeld University, Universitätsstr. 25, 33615 Bielefeld, Germany
| | - Markus Mangold
- IRsweep AG, Laubisruetistrasse 44, 8712 Staefa, Switzerland
| | | | - Andreas Hugi
- IRsweep AG, Laubisruetistrasse 44, 8712 Staefa, Switzerland
| | - Markus Geiser
- IRsweep AG, Laubisruetistrasse 44, 8712 Staefa, Switzerland
| | - Pierre Jouy
- Institute for Quantum Electronics, ETH Zurich, 8093 Zurich, Switzerland
| | - Jérôme Faist
- Institute for Quantum Electronics, ETH Zurich, 8093 Zurich, Switzerland
| | - Tilman Kottke
- Physical and Biophysical Chemistry, Department of Chemistry, Bielefeld University, Universitätsstr. 25, 33615 Bielefeld, Germany
| |
Collapse
|
14
|
Jawurek M, Dröden J, Peter B, Glaubitz C, Hauser K. Lipid-induced dynamics of photoreceptors monitored by time-resolved step-scan FTIR spectroscopy. Chem Phys 2018. [DOI: 10.1016/j.chemphys.2018.04.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
|
15
|
Elghobashi-Meinhardt N, Phatak P, Bondar AN, Elstner M, Smith JC. Catalysis of Ground State cis[Formula: see text] trans Isomerization of Bacteriorhodopsin's Retinal Chromophore by a Hydrogen-Bond Network. J Membr Biol 2018. [PMID: 29516110 DOI: 10.1007/s00232-018-0027-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
For the photocycle of the membrane protein bacteriorhodopsin to proceed efficiently, the thermal 13-cis to all-trans back-isomerization of the retinal chromophore must return the protein to its resting state on a time-scale of milliseconds. Here, we report on quantum mechanical/molecular mechanical energy calculations examining the structural and energetic determinants of the retinal cis-trans isomerization in the protein environment. The results suggest that a hydrogen-bonded network consisting of the retinal Schiff base, active site amino acid residues, and water molecules can stabilize the twisted retinal, thus reducing the intrinsic energy cost of the cis-trans thermal isomerization barrier.
Collapse
Affiliation(s)
- Nadia Elghobashi-Meinhardt
- Department of Physical and Theoretical Chemistry, Theoretical Molecular Biophysics, Institute for Chemistry und Biochemistry, Freie Universität Berlin, Fabeckstr. 36a, Berlin, 14169, Germany.
| | - Prasad Phatak
- Institute of Physical and Theoretical Chemistry, TU Braunschweig, 38106, Braunschweig, Germany.,BASF SE, Carl-Bosch Strasse 38, 67056, Ludwigshafen am Rhein, Germany
| | - Ana-Nicoleta Bondar
- Department of Physics, Theoretical Molecular Biophysics, Freie Universität Berlin, Arnimallee 14, 14195, Berlin, Germany
| | - Marcus Elstner
- Department of Theoretical Chemical Biology, Institute for Physical Chemistry, Karlsruhe Institut of Technology, Kaiserstrasse 12, 76131, Karlsruhe, Germany
| | - Jeremy C Smith
- Oak Ridge National Laboratory, Center for Molecular Biophysics, P.O. Box 2008 MS6309, Oak Ridge, TN, 37831-6309, USA.,Department of Biochemistry and Molecular and Cellular Biology, University of Tennessee, Knoxville, USA
| |
Collapse
|
16
|
Harris A, Saita M, Resler T, Hughes-Visentin A, Maia R, Pranga-Sellnau F, Bondar AN, Heberle J, Brown LS. Molecular details of the unique mechanism of chloride transport by a cyanobacterial rhodopsin. Phys Chem Chem Phys 2018; 20:3184-3199. [PMID: 29057415 DOI: 10.1039/c7cp06068h] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Microbial rhodopsins are well known as versatile and ubiquitous light-driven ion transporters and photosensors. While the proton transport mechanism has been studied in great detail, much less is known about various modes of anion transport. Until recently, only two main groups of light-driven anion pumps were known, archaeal halorhodopsins (HRs) and bacterial chloride pumps (known as ClRs or NTQs). Last year, another group of cyanobacterial anion pumps with a very distinct primary structure was reported. Here, we studied the chloride-transporting photocycle of a representative of this new group, Mastigocladopsis repens rhodopsin (MastR), using time-resolved spectroscopy in the infrared and visible ranges and site-directed mutagenesis. We found that, in accordance with its unique amino acid sequence containing many polar residues in the transmembrane region of the protein, its photocycle features a number of unusual molecular events not known for other anion-pumping rhodopsins. It appears that light-driven chloride ion transfers by MastR are coupled with translocation of protons and water molecules as well as perturbation of several polar sidechains. Of particular interest is transient deprotonation of Asp-85, homologous to the cytoplasmic proton donor of light-driven proton pumps (such as Asp-96 of bacteriorhodopsin), which may serve as a regulatory mechanism.
Collapse
Affiliation(s)
- Andrew Harris
- Department of Physics and Biophysics Interdepartmental Group, University of Guelph, 50 Stone Road East, Guelph, Ontario N1G 2W1, Canada.
| | | | | | | | | | | | | | | | | |
Collapse
|
17
|
Schultz BJ, Mohrmann H, Lorenz-Fonfria VA, Heberle J. Protein dynamics observed by tunable mid-IR quantum cascade lasers across the time range from 10ns to 1s. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2018; 188:666-674. [PMID: 28110813 DOI: 10.1016/j.saa.2017.01.010] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2016] [Revised: 12/29/2016] [Accepted: 01/04/2017] [Indexed: 06/06/2023]
Abstract
We have developed a spectrometer based on tunable quantum cascade lasers (QCLs) for recording time-resolved absorption spectra of proteins in the mid-infrared range. We illustrate its performance by recording time-resolved difference spectra of bacteriorhodopsin in the carboxylic range (1800-1700cm-1) and on the CO rebinding reaction of myoglobin (1960-1840cm-1), at a spectral resolution of 1cm-1. The spectrometric setup covers the time range from 4ns to nearly a second with a response time of 10-15ns. Absorption changes as low as 1×10-4 are detected in single-shot experiments at t>1μs, and of 5×10-6 in kinetics obtained after averaging 100 shots. While previous time-resolved IR experiments have mostly been conducted on hydrated films of proteins, we demonstrate here that the brilliance of tunable quantum cascade lasers is superior to perform ns time-resolved experiments even in aqueous solution (H2O).
Collapse
Affiliation(s)
- Bernd-Joachim Schultz
- Experimental Molecular Biophysics, Department of Physics, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany
| | - Hendrik Mohrmann
- Experimental Molecular Biophysics, Department of Physics, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany
| | - Victor A Lorenz-Fonfria
- Experimental Molecular Biophysics, Department of Physics, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany; Department of Biochemistry and Molecular Biology, Universitat de València, Dr. Moliner 50, 46100 Burjassot, Spain; Interdisciplinary Research Structure for Biotechnology and Biomedicine (ERI BIOTECMED), Universitat de València, Dr. Moliner 50, 46100 Burjassot, Spain
| | - Joachim Heberle
- Experimental Molecular Biophysics, Department of Physics, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany.
| |
Collapse
|
18
|
pH-sensitive vibrational probe reveals a cytoplasmic protonated cluster in bacteriorhodopsin. Proc Natl Acad Sci U S A 2017; 114:E10909-E10918. [PMID: 29203649 DOI: 10.1073/pnas.1707993114] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Infrared spectroscopy has been used in the past to probe the dynamics of internal proton transfer reactions taking place during the functional mechanism of proteins but has remained mostly silent to protonation changes in the aqueous medium. Here, by selectively monitoring vibrational changes of buffer molecules with a temporal resolution of 6 µs, we have traced proton release and uptake events in the light-driven proton-pump bacteriorhodopsin and correlate these to other molecular processes within the protein. We demonstrate that two distinct chemical entities contribute to the temporal evolution and spectral shape of the continuum band, an unusually broad band extending from 2,300 to well below 1,700 cm-1 The first contribution corresponds to deprotonation of the proton release complex (PRC), a complex in the extracellular domain of bacteriorhodopsin where an excess proton is shared by a cluster of internal water molecules and/or ionic E194/E204 carboxylic groups. We assign the second component of the continuum band to the proton uptake complex, a cluster with an excess proton reminiscent to the PRC but located in the cytoplasmic domain and possibly stabilized by D38. Our findings refine the current interpretation of the continuum band and call for a reevaluation of the last proton transfer steps in bacteriorhodopsin.
Collapse
|
19
|
Zimmer M, Dietrich F, Volz D, Bräse S, Gerhards M. Solid-State Step-Scan FTIR Spectroscopy of Binuclear Copper(I) Complexes. Chemphyschem 2017; 18:3023-3029. [DOI: 10.1002/cphc.201700753] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Revised: 08/11/2017] [Indexed: 11/06/2022]
Affiliation(s)
- Manuel Zimmer
- Chemistry Department and Research Center Optimas; TU Kaiserslautern; Erwin-Schrödinger-Strasse 52 67663 Kaiserslautern Germany
| | - Fabian Dietrich
- Chemistry Department and Research Center Optimas; TU Kaiserslautern; Erwin-Schrödinger-Strasse 52 67663 Kaiserslautern Germany
| | - Daniel Volz
- CYNORA GmbH; Werner-von-Siemens-Strasse 2-6, Building 5110 76646 Bruchsal Germany
| | - Stefan Bräse
- Institute of Organic Chemistry; Karlsruhe Institute of Technology; Fritz-Haber-Weg 6 76131 Karlsruhe Germany
- Institute of Toxicology and Genetics; Karlsruhe Institute of Technology; Hermann-von-Helmholtz-Platz 1 76344 Eggenstein-Leopoldshafen Germany
| | - Markus Gerhards
- Chemistry Department and Research Center Optimas; TU Kaiserslautern; Erwin-Schrödinger-Strasse 52 67663 Kaiserslautern Germany
| |
Collapse
|
20
|
Süss B, Ringleb F, Heberle J. New ultrarapid-scanning interferometer for FT-IR spectroscopy with microsecond time-resolution. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2016; 87:063113. [PMID: 27370432 DOI: 10.1063/1.4953658] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
A novel Fourier-transform infrared (FT-IR) rapid-scan spectrometer has been developed (patent pending EP14194520.4) which yields 1000 times higher time resolution as compared to conventional rapid-scanning spectrometers. The central element to achieve faster scanning rates is based on a sonotrode whose front face represents the movable mirror of the interferometer. A prototype spectrometer with a time resolution of 13 μs was realized, capable of fully automated long-term measurements with a flow cell for liquid samples, here a photosynthetic membrane protein in solution. The performance of this novel spectrometer is demonstrated by recording the photoreaction of bacteriorhodopsin initiated by a short laser pulse that is synchronized to the data recording. The resulting data are critically compared to those obtained by step-scan spectroscopy and demonstrate the relevance of performing experiments on proteins in solution. The spectrometer allows for future investigations of fast, non-repetitive processes, whose investigation is challenging to step-scan FT-IR spectroscopy.
Collapse
Affiliation(s)
- B Süss
- Department of Physics, Experimental Molecular Biophysics, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany
| | - F Ringleb
- Institute for Crystal Growth, Max-Born Straße 2, 12489 Berlin, Germany
| | - J Heberle
- Department of Physics, Experimental Molecular Biophysics, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany
| |
Collapse
|
21
|
Lórenz-Fonfría VA, Schultz BJ, Resler T, Schlesinger R, Bamann C, Bamberg E, Heberle J. Pre-gating conformational changes in the ChETA variant of channelrhodopsin-2 monitored by nanosecond IR spectroscopy. J Am Chem Soc 2015; 137:1850-61. [PMID: 25584873 DOI: 10.1021/ja5108595] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Light-gated ion permeation by channelrhodopsin-2 (ChR2) relies on the photoisomerization of the retinal chromophore and the subsequent photocycle, leading to the formation (on-gating) and decay (off-gating) of the conductive state. Here, we have analyzed the photocycle of a fast-cycling ChR2 variant (E123T mutation, also known as ChETA), by time-resolved UV/vis, step-scan FT-IR, and tunable quantum cascade laser IR spectroscopies with nanosecond resolution. Pre-gating conformational changes rise with a half-life of 200 ns, silent to UV/vis but detected by IR spectroscopy. They involve changes in the peptide backbone and in the H-bond of the side chain of the critical residue D156. Thus, the P1(500) intermediate must be separated into early and late states. Light-adapted ChR2 contains a mixture of all-trans and 13-cis retinal in a 70:30 ratio which are both photoactive. Analysis of ethylenic and fingerprint vibrations of retinal provides evidence that the 13-cis photocycle recovers in 1 ms. This recovery is faster than channel off-gating and most of the proton transfer reactions, implying that the 13-cis photocycle is of minor functional relevance for ChR2.
Collapse
Affiliation(s)
- Víctor A Lórenz-Fonfría
- Experimental Molecular Biophysics, Department of Physics, Freie Universität Berlin , Arnimallee 14, 14195 Berlin, Germany
| | | | | | | | | | | | | |
Collapse
|
22
|
Balashov SP, Imasheva ES, Dioumaev A, Wang JM, Jung KH, Lanyi JK. Light-driven Na(+) pump from Gillisia limnaea: a high-affinity Na(+) binding site is formed transiently in the photocycle. Biochemistry 2014; 53:7549-61. [PMID: 25375769 PMCID: PMC4263435 DOI: 10.1021/bi501064n] [Citation(s) in RCA: 72] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2014] [Revised: 10/17/2014] [Indexed: 02/06/2023]
Abstract
A group of microbial retinal proteins most closely related to the proton pump xanthorhodopsin has a novel sequence motif and a novel function. Instead of, or in addition to, proton transport, they perform light-driven sodium ion transport, as reported for one representative of this group (KR2) from Krokinobacter. In this paper, we examine a similar protein, GLR from Gillisia limnaea, expressed in Escherichia coli, which shares some properties with KR2 but transports only Na(+). The absorption spectrum of GLR is insensitive to Na(+) at concentrations of ≤3 M. However, very low concentrations of Na(+) cause profound differences in the decay and rise time of photocycle intermediates, consistent with a switch from a "Na(+)-independent" to a "Na(+)-dependent" photocycle (or photocycle branch) at ∼60 μM Na(+). The rates of photocycle steps in the latter, but not the former, are linearly dependent on Na(+) concentration. This suggests that a high-affinity Na(+) binding site is created transiently after photoexcitation, and entry of Na(+) from the bulk to this site redirects the course of events in the remainder of the cycle. A greater concentration of Na(+) is needed for switching the reaction path at lower pH. The data suggest therefore competition between H(+) and Na(+) to determine the two alternative pathways. The idea that a Na(+) binding site can be created at the Schiff base counterion is supported by the finding that upon perturbation of this region in the D251E mutant, Na(+) binds without photoexcitation. Binding of Na(+) to the mutant shifts the chromophore maximum to the red like that of H(+), which occurs in the photocycle of the wild type.
Collapse
Affiliation(s)
- Sergei P. Balashov
- Department
of Physiology and Biophysics, University
of California, Irvine, California 92697, United States
| | - Eleonora S. Imasheva
- Department
of Physiology and Biophysics, University
of California, Irvine, California 92697, United States
| | - Andrei
K. Dioumaev
- Department
of Physiology and Biophysics, University
of California, Irvine, California 92697, United States
| | - Jennifer M. Wang
- Department
of Physiology and Biophysics, University
of California, Irvine, California 92697, United States
| | - Kwang-Hwan Jung
- Department
of Life Science and Interdisciplinary Program of Integrated Biotechnology, Sogang University, Shinsu-Dong 1, Mapo-Gu, Seoul 121-742, Korea
| | - Janos K. Lanyi
- Department
of Physiology and Biophysics, University
of California, Irvine, California 92697, United States
| |
Collapse
|
23
|
Adato R, Altug H. In-situ ultra-sensitive infrared absorption spectroscopy of biomolecule interactions in real time with plasmonic nanoantennas. Nat Commun 2014; 4:2154. [PMID: 23877168 PMCID: PMC3759039 DOI: 10.1038/ncomms3154] [Citation(s) in RCA: 170] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2012] [Accepted: 06/17/2013] [Indexed: 01/28/2023] Open
Abstract
Infrared absorption spectroscopy is a powerful biochemical analysis tool as it extracts detailed molecular structural information in a label-free fashion. Its molecular specificity renders the technique sensitive to the subtle conformational changes exhibited by proteins in response to a variety of stimuli. Yet, sensitivity limitations and the extremely strong absorption bands of liquid water severely limit infrared spectroscopy in performing kinetic measurements in biomolecules’ native, aqueous environments. Here we demonstrate a plasmonic chip-based technology that overcomes these challenges, enabling the in-situ monitoring of protein and nanoparticle interactions at high sensitivity in real time, even allowing the observation of minute volumes of water displacement during binding events. Our approach leverages the plasmonic enhancement of absorption bands in conjunction with a non-classical form of internal reflection. These features not only expand the reach of infrared spectroscopy to a new class of biological interactions but also additionally enable a unique chip-based technology. Infrared absorption spectroscopy provides important information about molecules, but is hampered by the absorption of water. Adato and Altug exploit the plasmonic enhancement from nanoantennas to overcome this, enabling chip-based monitoring of biological samples in aqueous environments.
Collapse
Affiliation(s)
- Ronen Adato
- Insititute of Bioengineering, Ecole Polytechnique Federale De Lausanne, Lausanne 1015, Switzerland
| | | |
Collapse
|
24
|
Ernst OP, Lodowski DT, Elstner M, Hegemann P, Brown L, Kandori H. Microbial and animal rhodopsins: structures, functions, and molecular mechanisms. Chem Rev 2014; 114:126-63. [PMID: 24364740 PMCID: PMC3979449 DOI: 10.1021/cr4003769] [Citation(s) in RCA: 771] [Impact Index Per Article: 77.1] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2013] [Indexed: 12/31/2022]
Affiliation(s)
- Oliver P. Ernst
- Departments
of Biochemistry and Molecular Genetics, University of Toronto, 1 King’s College Circle, Medical Sciences Building, Toronto, Ontario M5S 1A8, Canada
| | - David T. Lodowski
- Center
for Proteomics and Bioinformatics, Case
Western Reserve University School of Medicine, 10900 Euclid Avenue, Cleveland, Ohio 44106, United States
| | - Marcus Elstner
- Institute
for Physical Chemistry, Karlsruhe Institute
of Technology, Kaiserstrasse
12, 76131 Karlsruhe, Germany
| | - Peter Hegemann
- Institute
of Biology, Experimental Biophysics, Humboldt-Universität
zu Berlin, Invalidenstrasse
42, 10115 Berlin, Germany
| | - Leonid
S. Brown
- Department
of Physics and Biophysics Interdepartmental Group, University of Guelph, 50 Stone Road East, Guelph, Ontario N1G 2W1, Canada
| | - Hideki Kandori
- Department
of Frontier Materials, Nagoya Institute
of Technology, Showa-ku, Nagoya 466-8555, Japan
| |
Collapse
|
25
|
Lórenz-Fonfría VA, Heberle J. Channelrhodopsin unchained: structure and mechanism of a light-gated cation channel. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2013; 1837:626-42. [PMID: 24212055 DOI: 10.1016/j.bbabio.2013.10.014] [Citation(s) in RCA: 95] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2013] [Revised: 10/21/2013] [Accepted: 10/30/2013] [Indexed: 12/25/2022]
Abstract
The new and vibrant field of optogenetics was founded by the seminal discovery of channelrhodopsin, the first light-gated cation channel. Despite the numerous applications that have revolutionised neurophysiology, the functional mechanism is far from understood on the molecular level. An arsenal of biophysical techniques has been established in the last decades of research on microbial rhodopsins. However, application of these techniques is hampered by the duration and the complexity of the photoreaction of channelrhodopsin compared with other microbial rhodopsins. A particular interest in resolving the molecular mechanism lies in the structural changes that lead to channel opening and closure. Here, we review the current structural and mechanistic knowledge that has been accomplished by integrating the static structure provided by X-ray crystallography and electron microscopy with time-resolved spectroscopic and electrophysiological techniques. The dynamical reactions of the chromophore are effectively coupled to structural changes of the protein, as shown by ultrafast spectroscopy. The hierarchical sequence of structural changes in the protein backbone that spans the time range from 10(-12)s to 10(-3)s prepares the channel to open and, consequently, cations can pass. Proton transfer reactions that are associated with channel gating have been resolved. In particular, glutamate 253 and aspartic acid 156 were identified as proton acceptor and donor to the retinal Schiff base. The reprotonation of the latter is the critical determinant for channel closure. The proton pathway that eventually leads to proton pumping is also discussed. This article is part of a Special Issue entitled: Retinal Proteins - You can teach an old dog new tricks.
Collapse
Affiliation(s)
- Víctor A Lórenz-Fonfría
- Freie Universität Berlin, Experimental Molecular Biophysics, Arnimallee 14, 14195 Berlin, Germany
| | - Joachim Heberle
- Freie Universität Berlin, Experimental Molecular Biophysics, Arnimallee 14, 14195 Berlin, Germany.
| |
Collapse
|
26
|
Gerwert K, Freier E, Wolf S. The role of protein-bound water molecules in microbial rhodopsins. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2013; 1837:606-13. [PMID: 24055285 DOI: 10.1016/j.bbabio.2013.09.006] [Citation(s) in RCA: 105] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2013] [Revised: 09/08/2013] [Accepted: 09/10/2013] [Indexed: 02/06/2023]
Abstract
Protein-bound internal water molecules are essential features of the structure and function of microbial rhodopsins. Besides structural stabilization, they act as proton conductors and even proton storage sites. Currently, the most understood model system exhibiting such features is bacteriorhodopsin (bR). During the last 20 years, the importance of water molecules for proton transport has been revealed through this protein. It has been shown that water molecules are as essential as amino acids for proton transport and biological function. In this review, we present an overview of the historical development of this research on bR. We furthermore summarize the recently discovered protein-bound water features associated with proton transport. Specifically, we discuss a pentameric water/amino acid arrangement close to the protonated Schiff base as central proton-binding site, a protonated water cluster as proton storage site at the proton-release site, and a transient linear water chain at the proton uptake site. We highlight how protein conformational changes reposition or reorient internal water molecules, thereby guiding proton transport. Last, we compare the water positions in bR with those in other microbial rhodopsins to elucidate how protein-bound water molecules guide the function of microbial rhodopsins. This article is part of a Special Issue entitled: Retinal Proteins - You can teach an old dog new tricks.
Collapse
Affiliation(s)
- Klaus Gerwert
- Department of Biophysics, University of Bochum, ND 04 North, 44780 Bochum, Germany; Department of Biophysics, Chinese Academy of Sciences-Max-Planck Partner Institute for Computational Biology (PICB), Shanghai Institutes for Biological Sciences (SIBS), 320 Yue Yang Lu, 200031 Shanghai, PR China.
| | - Erik Freier
- Department of Biophysics, University of Bochum, ND 04 North, 44780 Bochum, Germany
| | - Steffen Wolf
- Department of Biophysics, Chinese Academy of Sciences-Max-Planck Partner Institute for Computational Biology (PICB), Shanghai Institutes for Biological Sciences (SIBS), 320 Yue Yang Lu, 200031 Shanghai, PR China
| |
Collapse
|
27
|
Dioumaev AK, Petrovskaya LE, Wang JM, Balashov SP, Dolgikh DA, Kirpichnikov MP, Lanyi JK. Photocycle of Exiguobacterium sibiricum rhodopsin characterized by low-temperature trapping in the IR and time-resolved studies in the visible. J Phys Chem B 2013; 117:7235-53. [PMID: 23718558 DOI: 10.1021/jp402430w] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The photocycle of the retinal protein from Exiguobacterium sibiricum, which differs from bacteriorhodopsin in both its primary donor and acceptor, is characterized by visible and infrared spectroscopy. At pH above pKa ~6.5, we find a bacteriorhodopsin-like photocycle, which originates from excitation of the all-trans retinal chromophore with K-, L-, M-, and N-like intermediates. At pH below pKa ~6.5, the M state, which reflects Schiff base deprotonation during proton pumping, is not accumulated. However, using the infrared band at ~1760 cm(-1) as a marker for transient protonation of the primary acceptor, we find that Schiff base deprotonation must have occurred at pH not only above but also below the pKa ~6.5. Thus, the M state is formed but not accumulated for kinetic reasons. Further, chromophore reisomerization from the 13-cis to the all-trans conformation occurs very late in the photocycle. The strongly red-shifted states that dominate the second half of the cycle are produced before the reisomerization step, and by this criterion, they are not O-like but rather N-like states. The assignment of photocycle intermediates enables reevaluation of the photocycle; its specific features are discussed in relation to the general mechanism of proton transport in retinal proteins.
Collapse
Affiliation(s)
- Andrei K Dioumaev
- Department of Physiology and Biophysics, University of California, Irvine, California 92697, USA.
| | | | | | | | | | | | | |
Collapse
|
28
|
Morgan JE, Vakkasoglu AS, Lanyi JK, Lugtenburg J, Gennis RB, Maeda A. Structure changes upon deprotonation of the proton release group in the bacteriorhodopsin photocycle. Biophys J 2013; 103:444-452. [PMID: 22947860 DOI: 10.1016/j.bpj.2012.06.022] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2012] [Revised: 05/19/2012] [Accepted: 06/04/2012] [Indexed: 11/18/2022] Open
Abstract
In the photocycle of bacteriorhodopsin at pH 7, a proton is ejected to the extracellular medium during the protonation of Asp-85 upon formation of the M intermediate. The group that releases the ejected proton does not become reprotonated until the prephotolysis state is restored from the N and O intermediates. In contrast, at acidic pH, this proton release group remains protonated to the end of the cycle. Time-resolved Fourier transform infrared measurements obtained at pH 5 and 7 were fitted to obtain spectra of kinetic intermediates, from which the spectra of M and N/O versus unphotolyzed state were calculated. Vibrational features that appear in both M and N/O spectra at pH 7, but not at pH 5, are attributable to deprotonation from the proton release group and resulting structural alterations. Our results agree with the earlier conclusion that this group is a protonated internal water cluster, and provide a stronger experimental basis for this assignment. A decrease in local polarity at the N-C bond of the side chain of Lys-216 resulting from deprotonation of this water cluster may be responsible for the increase in the proton affinity of Asp-85 through M and N/O, which is crucial for maintaining the directionality of proton pumping.
Collapse
Affiliation(s)
- Joel E Morgan
- Department of Biology, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York
| | - Ahmet S Vakkasoglu
- Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois
| | - Janos K Lanyi
- Department of Physiology and Biophysics, University of California, Irvine, California
| | - Johan Lugtenburg
- Department of Chemistry, University of Leiden, Leiden, The Netherlands
| | - Robert B Gennis
- Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois; Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois
| | - Akio Maeda
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois.
| |
Collapse
|
29
|
Low temperature FTIR spectroscopy provides new insights in the pH-dependent proton pathway of proteorhodopsin. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2011; 1807:1583-90. [DOI: 10.1016/j.bbabio.2011.09.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2011] [Revised: 08/25/2011] [Accepted: 09/05/2011] [Indexed: 11/15/2022]
|
30
|
Fan Y, Solomon P, Oliver RP, Brown LS. Photochemical characterization of a novel fungal rhodopsin from Phaeosphaeria nodorum. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2011; 1807:1457-66. [PMID: 21791197 DOI: 10.1016/j.bbabio.2011.07.005] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2011] [Revised: 07/11/2011] [Accepted: 07/12/2011] [Indexed: 02/09/2023]
Abstract
Eukaryotic microbial rhodopsins are widespread bacteriorhodopsin-like proteins found in many lower eukaryotic groups including fungi. Many fungi contain multiple rhodopsins, some significantly diverged from the original bacteriorhodopsin template. Although few fungal rhodopsins have been studied biophysically, both fast-cycling light-driven proton pumps and slow-cycling photosensors have been found. The purpose of this study was to characterize photochemically a new subgroup of fungal rhodopsins, the so-called auxiliary group. The study used the two known rhodopsin genes from the fungal wheat pathogen, Phaeosphaeria nodorum. One of the genes is a member of the auxiliary group while the other is highly similar to previously characterized proton-pumping Leptosphaeria rhodopsin. Auxiliary rhodopsin genes from a range of species form a distinct group with a unique primary structure and are located in carotenoid biosynthesis gene cluster. Amino acid conservation pattern suggests that auxiliary rhodopsins retain the transmembrane core of bacteriorhodopsins, including all residues important for proton transport, but have unique polar intramembrane residues. Spectroscopic characterization of the two yeast-expressed Phaeosphaeria rhodopsins showed many similarities: absorption spectra, conformation of the retinal chromophore, fast photocycling, and carboxylic acid protonation changes. It is likely that both Phaeosphaeria rhodopsins are proton-pumping, at least in vitro. We suggest that auxiliary rhodopsins have separated from their ancestors fairly recently and have acquired the ability to interact with as yet unidentified transducers, performing a photosensory function without changing their spectral properties and basic photochemistry.
Collapse
Affiliation(s)
- Ying Fan
- Department of Physics and Biophysics Interdepartmental Group, University of Guelph, Ontario, Canada, N1G 2W1
| | | | | | | |
Collapse
|
31
|
Lórenz-Fonfría VA, Kandori H, Padrós E. Probing specific molecular processes and intermediates by time-resolved Fourier transform infrared spectroscopy: application to the bacteriorhodopsin photocycle. J Phys Chem B 2011; 115:7972-85. [PMID: 21615095 DOI: 10.1021/jp201739w] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We present a general approach for probing the kinetics of specific molecular processes in proteins by time-resolved Fourier transform infrared (IR) spectroscopy. Using bacteriorhodopsin (bR) as a model we demonstrate that by appropriately monitoring some selected IR bands it is possible obtaining the kinetics of the most important events occurring in the photocycle, namely changes in the chromophore and the protein backbone conformation, and changes in the protonation state of the key residues implicated in the proton transfers. Besides confirming widely accepted views of the bR photocycle, our analysis also sheds light into some disputed issues: the degree of retinal torsion in the L intermediate to respect the ground state; the possibility of a proton transfer from Asp85 to Asp212; the relationship between the protonation/deprotonation of Asp85 and the proton release complex; and the timing of the protein backbone dynamics. By providing a direct way to estimate the kinetics of photocycle intermediates the present approach opens new prospects for a robust quantitative kinetic analysis of the bR photocycle, which could also benefit the study of other proteins involved in photosynthesis, in phototaxis, or in respiratory chains.
Collapse
Affiliation(s)
- Víctor A Lórenz-Fonfría
- Unitat de Biofísica, Departament de Bioquímica i de Biologia Molecular, and Centre d'Estudis en Biofísica, Universitat Autònoma de Barcelona, Barcelona 08193, Spain.
| | | | | |
Collapse
|
32
|
Radu I, Schleeger M, Nack M, Heberle J. Time-resolved FT-IR Spectroscopy of Membrane Proteins. Aust J Chem 2011. [DOI: 10.1071/ch10286] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Time-resolved Fourier transform infrared spectroscopy (FT-IR) offers distinct advantages concerning restrictions pertinent to biomolecules. In particular, it is possible to monitor the temporal evolution of the reaction mechanism of complex machineries as membrane proteins, where other techniques encounter significant experimental difficulties. Here, we present the classical principles and experimental realizations of time-resolved FT-IR spectroscopy together with recent developments employed in our laboratory. Examples from applications to retinal proteins are reviewed that underline the impact of time-resolved FT-IR spectroscopy on the understanding of protein reactions on the level of single bonds.
Collapse
|
33
|
Jiang X, Engelhard M, Ataka K, Heberle J. Molecular Impact of the Membrane Potential on the Regulatory Mechanism of Proton Transfer in Sensory Rhodopsin II. J Am Chem Soc 2010; 132:10808-15. [DOI: 10.1021/ja102295g] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Xiue Jiang
- Department of Chemistry, Biophysical Chemistry (PC III), Bielefeld University, 33615 Bielefeld, Germany, MaxPlanck Institute of Molecular Physiology, 44221 Dortmund, Germany, Department of Physics, Experimental Molecular Biophysics, Freie Universität Berlin, 14195 Berlin, Germany, and Japan Science and Technology Agency, 102-0075, Tokyo, Japan
| | - Martin Engelhard
- Department of Chemistry, Biophysical Chemistry (PC III), Bielefeld University, 33615 Bielefeld, Germany, MaxPlanck Institute of Molecular Physiology, 44221 Dortmund, Germany, Department of Physics, Experimental Molecular Biophysics, Freie Universität Berlin, 14195 Berlin, Germany, and Japan Science and Technology Agency, 102-0075, Tokyo, Japan
| | - Kenichi Ataka
- Department of Chemistry, Biophysical Chemistry (PC III), Bielefeld University, 33615 Bielefeld, Germany, MaxPlanck Institute of Molecular Physiology, 44221 Dortmund, Germany, Department of Physics, Experimental Molecular Biophysics, Freie Universität Berlin, 14195 Berlin, Germany, and Japan Science and Technology Agency, 102-0075, Tokyo, Japan
| | - Joachim Heberle
- Department of Chemistry, Biophysical Chemistry (PC III), Bielefeld University, 33615 Bielefeld, Germany, MaxPlanck Institute of Molecular Physiology, 44221 Dortmund, Germany, Department of Physics, Experimental Molecular Biophysics, Freie Universität Berlin, 14195 Berlin, Germany, and Japan Science and Technology Agency, 102-0075, Tokyo, Japan
| |
Collapse
|
34
|
Dioumaev AK, Lanyi JK. Two bathointermediates of the bacteriorhodopsin photocycle, from time-resolved nanosecond spectra in the visible. J Phys Chem B 2009; 113:16643-53. [PMID: 19994879 PMCID: PMC3808455 DOI: 10.1021/jp907393m] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Time-resolved measurements were performed on wild-type bacteriorhodopsin with an optical multichannel analyzer in the spectral range 350-735 nm, from 100 ns to the photocycle completion, at four temperatures in the 5-30 degrees C range. The intent was to examine the possibility of two K-like bathochromic intermediates and to obtain their spectra and kinetics in the visible. The existence of a second K-like intermediate, termed KL, had been postulated (Shichida et al., Biochim. Biophys. Acta 1983, 723, 240-246) to reconcile inconsistencies in data in the pico- and microsecond time domains. However, introduction of KL led to a controversy, since neither its visible spectrum nor its kinetics could be confirmed. Infrared data (Dioumaev and Braiman, J. Phys. Chem. B 1997, 101, 1655-1662) revealed a state which might have been considered a homologue to KL, but it had a kinetic pattern different from that of the earlier proposed KL. Here, we characterize two distinct K-like intermediates, K(E) ("early") and K(L) ("late"), by their spectra and kinetics in the visible as revealed by global kinetic analysis. The K(E)-to-K(L) transition has a time constant of approximately 250 ns at 20 degrees C, and describes a shift from K(E) with lambda(max) at approximately 600 nm and extinction of approximately 56,000 M(-1) x cm(-1) to K(L) with lambda(max) at approximately 590 nm and extinction of approximately 50,000 M(-1) x cm(-1). The temperature dependence of this transition is characterized by an enthalpy of activation of DeltaH(++) approximately 40 kJ/mol and a positive entropy of activation of DeltaS(++)/R approximately 4. The consequences of multiple K-like states for interpreting the spectral evolution in the early stages of the photocycle are discussed.
Collapse
Affiliation(s)
- Andrei K Dioumaev
- Department of Physiology and Biophysics, University of California, Irvine, Irvine, California 92697, USA.
| | | |
Collapse
|
35
|
Radu I, Bamann C, Nack M, Nagel G, Bamberg E, Heberle J. Conformational changes of channelrhodopsin-2. J Am Chem Soc 2009; 131:7313-9. [PMID: 19422231 DOI: 10.1021/ja8084274] [Citation(s) in RCA: 93] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Channelrhodopsin-2 (ChR2) is a member of the new class of light-gated ion channels which serve as phototaxis receptors in the green alga Chlamydomonas reinhardtii. The protein is employed in optogenetics where neural circuits are optically stimulated under high spatiotemporal control. Despite its rapidly growing use in physiological experiments, the reaction mechanism of ChR2 is poorly understood. Here, we applied vibrational spectroscopy to trace structural changes of ChR2 after light-excitation of the retinal chromophore. FT-IR difference spectra of the various photocycle intermediates revealed that stages of the photoreaction preceding (P(1) state) and succeeding (P(4)) the conductive state of the channel (P(3)) are associated with large conformational changes of the protein backbone as indicate by strong differences in the amide I bands. Critical hydrogen-bonding changes of protonated carboxylic amino acid side chains (D156, E90) were detected and discussed with regard to the functional mechanism. We used the C128T mutant where the lifetime of P(3) is prolonged and applied FT-IR and resonance Raman spectroscopy to study the conductive P(3) state of ChR2. Finally, a mechanistic model is proposed that links the observed structural changes of ChR2 to the changes in the channel's conductance.
Collapse
Affiliation(s)
- Ionela Radu
- Bielefeld University, Biophysical Chemistry, 33615 Bielefeld
| | | | | | | | | | | |
Collapse
|
36
|
Babitzki G, Denschlag R, Tavan P. Polarization Effects Stabilize Bacteriorhodopsin’s Chromophore Binding Pocket: A Molecular Dynamics Study. J Phys Chem B 2009; 113:10483-95. [DOI: 10.1021/jp902428x] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- G. Babitzki
- Theoretische Biophysik, Lehrstuhl für Biomolekulare Optik, Ludwig-Maximilians-Universität, Oettingenstr. 67, 80538 München, Germany
| | - R. Denschlag
- Theoretische Biophysik, Lehrstuhl für Biomolekulare Optik, Ludwig-Maximilians-Universität, Oettingenstr. 67, 80538 München, Germany
| | - P. Tavan
- Theoretische Biophysik, Lehrstuhl für Biomolekulare Optik, Ludwig-Maximilians-Universität, Oettingenstr. 67, 80538 München, Germany
| |
Collapse
|
37
|
Time-resolved flow-flash FT-IR difference spectroscopy: the kinetics of CO photodissociation from myoglobin revisited. Anal Bioanal Chem 2009; 394:1869-77. [PMID: 19521691 PMCID: PMC2709881 DOI: 10.1007/s00216-009-2871-0] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2009] [Revised: 05/19/2009] [Accepted: 05/26/2009] [Indexed: 11/24/2022]
Abstract
Fourier-transform infrared (FT-IR) difference spectroscopy has been proven to be a significant tool in biospectroscopy. In particular, the step-scan technique monitors structural and electronic changes at time resolutions down to a few nanoseconds retaining the multiplex advantage of FT-IR. For the elucidation of the functional mechanisms of proteins, this technique is currently limited to repetitive systems undergoing a rapid photocycle. To overcome this obstacle, we developed a flow-flash experiment in a miniaturised flow channel which was integrated into a step-scan FT-IR spectroscopic setup. As a proof of principle, we studied the rebinding reaction of CO to myoglobin after photodissociation. The use of microfluidics reduced the sample consumption drastically such that a typical step-scan experiment takes only a few 10 ml of a millimolar sample solution, making this method particularly interesting for the investigation of biological samples that are only available in small quantities. Moreover, the flow cell provides the unique opportunity to assess the reaction mechanism of proteins that cycle slowly or react irreversibly. We infer that this novel approach will help in the elucidation of molecular reactions as complex as those of vectorial ion transfer in membrane proteins. The potential application to the oxygen splitting reaction of cytochrome c oxidase is discussed.
Collapse
|
38
|
Phatak P, Frähmcke JS, Wanko M, Hoffmann M, Strodel P, Smith J, Suhai S, Bondar AN, Elstner M. Long-distance proton transfer with a break in the bacteriorhodopsin active site. J Am Chem Soc 2009; 131:7064-78. [PMID: 19405533 PMCID: PMC2746972 DOI: 10.1021/ja809767v] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Bacteriorhodopsin is a proton-pumping membrane protein found in the plasma membrane of the archaeon Halobacterium salinarium. Light-induced isomerization of the retinal chromophore from all-trans to 13-cis leads to a sequence of five conformation-coupled proton transfer steps and the net transport of one proton from the cytoplasmic to the extracellular side of the membrane. The mechanism of the long-distance proton transfer from the primary acceptor Asp85 to the extracellular proton release group during the O --> bR is poorly understood. Experiments suggest that this long-distance transfer could involve a transient state [O] in which the proton resides on the intermediate carrier Asp212. To assess whether the transient protonation of Asp212 participates in the deprotonation of Asp85, we performed hybrid Quantum Mechanics/Molecular Mechanics proton transfer calculations using different protein structures and with different retinal geometries and active site water molecules. The structural models were assessed by computing UV-vis excitation energies and C=O vibrational frequencies. The results indicate that a transient [O] conformer with protonated Asp212 could indeed be sampled during the long-distance proton transfer to the proton release group. Our calculations suggest that, in the starting proton transfer state O, the retinal is strongly twisted and at least three water molecules are present in the active site.
Collapse
Affiliation(s)
- Prasad Phatak
- Institute of Physical and Theoretical Chemistry, TU Braunschweig, D-38106 Braunschweig, Germany
| | - Jan S. Frähmcke
- Institute of Physical and Theoretical Chemistry, TU Braunschweig, D-38106 Braunschweig, Germany
| | - Marius Wanko
- BCCMS, Universität Bremen, D-28334 Bremen, Germany
| | | | - Paul Strodel
- Accelrys Ltd., Cambridge CB4 0WN, United Kingdom
| | - Jeremy Smith
- Computational Molecular Biophysics, IWR, University of Heidelberg, Im Neuenheimer Feld 368, D-69120, Heidelberg, Germany
- Center for Molecular Biophysics, Oak Ridge National Laboratory, PO BOX 2008 MS6164, Oak Ridge, Tennessee 37831, USA
- Department of Biochemistry and Molecular Biology, University of Tennessee, M407 Walters Life Sciences, 1414 Cumberland Ave, Knoxville Tennessee 37996, USA
| | - Sándor Suhai
- Molecular Biophysics Department, German Cancer Research Institute, Im Neuheimer Feld 280, D-69120, Heidelberg, Germany
| | - Ana-Nicoleta Bondar
- Molecular Biophysics Department, German Cancer Research Institute, Im Neuheimer Feld 280, D-69120, Heidelberg, Germany
- Computational Molecular Biophysics, IWR, University of Heidelberg, Im Neuenheimer Feld 368, D-69120, Heidelberg, Germany
- Department of Physiology and Biophysics and the Center for Biomembrane Systems, University of California at Irvine, Med. Sci. I, D-347, Irvine, CA 92697, USA
| | - Marcus Elstner
- Institute of Physical and Theoretical Chemistry, TU Braunschweig, D-38106 Braunschweig, Germany
- Molecular Biophysics Department, German Cancer Research Institute, Im Neuheimer Feld 280, D-69120, Heidelberg, Germany
| |
Collapse
|
39
|
Lórenz-Fonfría VA, Kandori H. Spectroscopic and Kinetic Evidence on How Bacteriorhodopsin Accomplishes Vectorial Proton Transport under Functional Conditions. J Am Chem Soc 2009; 131:5891-901. [DOI: 10.1021/ja900334c] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Víctor A. Lórenz-Fonfría
- Department of Frontier Materials, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan
| | - Hideki Kandori
- Department of Frontier Materials, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan
| |
Collapse
|
40
|
Miranda MRM, Choi AR, Shi L, Bezerra AG, Jung KH, Brown LS. The photocycle and proton translocation pathway in a cyanobacterial ion-pumping rhodopsin. Biophys J 2009; 96:1471-81. [PMID: 19217863 DOI: 10.1016/j.bpj.2008.11.026] [Citation(s) in RCA: 81] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2008] [Accepted: 11/14/2008] [Indexed: 10/21/2022] Open
Abstract
The genome of thylakoidless cyanobacterium Gloeobacter violaceus encodes a fast-cycling rhodopsin capable of light-driven proton transport. We characterize the dark state, the photocycle, and the proton translocation pathway of GR spectroscopically. The dark state of GR contains predominantly all-trans-retinal and, similar to proteorhodopsin, does not show the light/dark adaptation. We found an unusually strong coupling between the conformation of the retinal and the site of Glu132, the homolog of Asp96 of BR. Although the photocycle of GR is similar to that of proteorhodopsin in general, it differs in accumulating two intermediates typical for BR, the L-like and the N-like states. The latter state has a deprotonated cytoplasmic proton donor and is spectrally distinct from the strongly red-shifted N intermediate known for proteorhodopsin. The proton uptake precedes the release and occurs during the transition to the O intermediate. The proton translocation pathway of GR is similar to those of other proton-pumping rhodopsins, involving homologs of BR Schiff base proton acceptor and donor Asp85 and Asp96 (Asp121 and Glu132). We assigned a pair of FTIR bands (positive at 1749 cm(-1) and negative at 1734 cm(-1)) to the protonation and deprotonation, respectively, of these carboxylic acids.
Collapse
Affiliation(s)
- Mylene R M Miranda
- Department of Physics, University of Guelph, Guelph, Ontario N1G 2W1, Canada
| | | | | | | | | | | |
Collapse
|
41
|
Radu I, Schleeger M, Bolwien C, Heberle J. Time-resolved methods in biophysics. 10. Time-resolved FT-IR difference spectroscopy and the application to membrane proteins. Photochem Photobiol Sci 2009; 8:1517-28. [DOI: 10.1039/b9pp00050j] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
|
42
|
Morgan JE, Gennis RB, Maeda A. A role for internal water molecules in proton affinity changes in the Schiff base and Asp85 for one-way proton transfer in bacteriorhodopsin. Photochem Photobiol 2008; 84:1038-45. [PMID: 18557823 DOI: 10.1111/j.1751-1097.2008.00377.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Light-induced proton pumping in bacteriorhodospin is carried out through five proton transfer steps. We propose that the proton transfer to Asp85 from the Schiff base in the L-to-M transition is accompanied by the relocation of a water cluster on the cytoplasmic side of the Schiff base from a site close to the Schiff base in L to the Phe219-Thr46 region in M. The water cluster present in L, formed at 170 K, is more rigid than that at room temperature. This may be responsible for blocking the conversion of L to M at 170 K. In the photocycle at room temperature, this water cluster returns to the site close to the Schiff base in N, with a rigid structure similar to that of L at 170 K. The increase in the proton affinity of Asp85, which is a prerequisite for the one-way proton transfer in the M-to-N transition, is suggested to be facilitated by a structural change which disrupts interactions between Asp212 and the Schiff base, and between Asp212 and Arg82. We propose that this liberation of Asp212 is accompanied by a rearrangement of the structure of water molecules between Asp85 and Asp212, stabilizing the protonated Asp85 in M.
Collapse
Affiliation(s)
- Joel E Morgan
- Department of Biology, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY, USA
| | | | | |
Collapse
|
43
|
Lórenz-Fonfría VA, Furutani Y, Kandori H. Active Internal Waters in the Bacteriorhodopsin Photocycle. A Comparative Study of the L and M Intermediates at Room and Cryogenic Temperatures by Infrared Spectroscopy. Biochemistry 2008; 47:4071-81. [DOI: 10.1021/bi7024063] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Víctor A. Lórenz-Fonfría
- Department of Materials Science and Engineering, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan
| | - Yuji Furutani
- Department of Materials Science and Engineering, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan
| | - Hideki Kandori
- Department of Materials Science and Engineering, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan
| |
Collapse
|
44
|
Sudo Y, Furutani Y, Iwamoto M, Kamo N, Kandori H. Structural changes in the O-decay accelerated mutants of pharaonis phoborhodopsin. Biochemistry 2008; 47:2866-74. [PMID: 18247579 DOI: 10.1021/bi701885k] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
pharaonis phoborhodopsin ( ppR, also called pharaonis sensory rhodopsin II, psRII) is a receptor for negative phototaxis in Natronomonas pharaonis. The X-ray crystallographic structure of ppR is very similar to those of the ion-pumping rhodopsins, bacteriorhodopsin (BR) and halorhodopsin (hR). However, the decay processes of the photocycle intermediates such as M and O are much slower than those of BR and hR, which is advantageous for the sensor function of ppR. Iwamoto et al. previously found that, in a quadruple mutant (P182S/P183E/V194T/T204C; denoted as SETC) of ppR, the decay of the O intermediate was accelerated by approximately 100 times ( t 1/2 approximately 6.6 ms vs 690 ms for the wild type of ppR), being almost equal to that of BR (Iwamoto, M., et al. (2005) Biophys. J. 88, 1215-1223). The mutated residues are located on the extracellular surface (Pro182, Pro183, and Val194) and near the Schiff base (Thr204). The present Fourier-transform infrared (FTIR) spectroscopy of SETC revealed that protein structural changes in the K and M states were similar to those of the wild type. In contrast, the ppR O minus ppR infrared difference spectra of SETC are clearly different from those of the wild type in amide-I (1680-1640 cm (-1)) and S-H stretching (2580-2520 cm (-1)) vibrations. The 1673 (+) and 1656 (-) cm (-1) bands newly appear for SETC in the frequency region typical for the amide-I vibration of the alpha II- and alpha I-helices, respectively. The intensities of the 1673 (+) cm (-1) band of various mutants were well correlated with their O-decay half-times. Since the alpha II-helix possesses a considerably distorted structure, the result implies that distortion of the helix is required for fast O-decay. In addition, the characteristic changes in the S-H stretching vibration of Cys204 were different between SETC and T204C, suggesting that structural change near the Schiff base was induced by mutations of the extracellular surface. We conclude that the lifetime of the O intermediate in ppR is regulated by the distorted alpha-helix and strengthened hydrogen bond of Cys204.
Collapse
Affiliation(s)
- Yuki Sudo
- Department of Materials Science and Engineering, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan
| | | | | | | | | |
Collapse
|
45
|
Perálvarez-Marín A, Lórenz-Fonfría VA, Bourdelande JL, Querol E, Kandori H, Padrós E. Inter-helical Hydrogen Bonds Are Essential Elements for Intra-protein Signal Transduction: The Role of Asp115 in Bacteriorhodopsin Transport Function. J Mol Biol 2007; 368:666-76. [PMID: 17367807 DOI: 10.1016/j.jmb.2007.02.021] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2006] [Revised: 01/31/2007] [Accepted: 02/07/2007] [Indexed: 11/25/2022]
Abstract
The behavior of the D115A mutant was analyzed by time-resolved UV-Vis and Fourier transformed infrared (FTIR) spectroscopies, aiming to clarify the role of Asp115 in the intra-protein signal transductions occurring during the bacteriorhodopsin photocycle. UV-Vis data on the D115A mutant show severely desynchronized photocycle kinetics. FTIR data show a poor transmission of the retinal isomerization to the chromoprotein, evidenced by strongly attenuated helical changes (amide I), the remarkable absence of environment alterations and protonation/deprotonation events related to Asp96 and direct Schiff base (SB) protonation form the bulk. This argues for the interactions of Asp115 with Leu87 (via water molecule) and Thr90 as key elements for the effective and vectorial proton path between Asp96 and the SB, in the cytoplasmic half of bacteriorhodopsin. The results strongly suggest the presence of a regulation motif enclosed in helices C and D (Thr90-Pro91/Asp115) which drives properly the dynamics of helix C through a set of interactions. It also supports the idea that intra-helical hydrogen bonding clusters in the buried regions of transmembrane proteins can be potential elements in intra-protein signal transduction.
Collapse
Affiliation(s)
- Alex Perálvarez-Marín
- Unitat de Biofísica, Departament de Bioquímica i de Biologia Molecular, Facultat de Medicina, and Centre d'Estudis en Biofísica, Universitat Autònoma de Barcelona, Bellaterra (Cerdanyola del Vallès), Barcelona 08193, Spain.
| | | | | | | | | | | |
Collapse
|
46
|
Lórenz-Fonfría VA, Kandori H. Bayesian maximum entropy (two-dimensional) lifetime distribution reconstruction from time-resolved spectroscopic data. APPLIED SPECTROSCOPY 2007; 61:428-43. [PMID: 17456263 DOI: 10.1366/000370207780466172] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
Time-resolved spectroscopy is often used to monitor the relaxation processes (or reactions) of physical, chemical, and biochemical systems after some fast physical or chemical perturbation. Time-resolved spectra contain information about the relaxation kinetics, in the form of macroscopic time constants of decay and their decay associated spectra. In the present paper we show how the Bayesian maximum entropy inversion of the Laplace transform (MaxEnt-iLT) can provide a lifetime distribution without sign-restrictions (or two-dimensional (2D)-lifetime distribution), representing the most probable inference given the data. From the reconstructed (2D) lifetime distribution it is possible to obtain the number of exponentials decays, macroscopic rate constants, and exponential amplitudes (or their decay associated spectra) present in the data. More importantly, the obtained (2D) lifetime distribution is obtained free from pre-conditioned ideas about the number of exponential decays present in the data. In contrast to the standard regularized maximum entropy method, the Bayesian MaxEnt approach automatically estimates the regularization parameter, providing an unsupervised and more objective analysis. We also show that the regularization parameter can be automatically determined by the L-curve and generalized cross-validation methods, providing (2D) lifetime reconstructions relatively close to the Bayesian best inference. Finally, we propose the use of MaxEnt-iLT for a more objective discrimination between data-supported and data-unsupported quantitative kinetic models, which takes both the data and the analysis limitations into account. All these aspects are illustrated with realistic time-resolved Fourier transform infrared (FT-IR) synthetic spectra of the bacteriorhodopsin photocycle.
Collapse
Affiliation(s)
- Victor A Lórenz-Fonfría
- Department of Materials Science and Engineering, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan.
| | | |
Collapse
|
47
|
Lórenz-Fonfría VA, Kandori H. Practical aspects of the maximum entropy inversion of the laplace transform for the quantitative analysis of multi-exponential data. APPLIED SPECTROSCOPY 2007; 61:74-84. [PMID: 17311720 DOI: 10.1366/000370207779701460] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
The number, position, area, and width of the bands in a lifetime distribution give the number of exponentials present in time-resolved data and their time constants, amplitudes, and heterogeneities. The maximum entropy inversion of the Laplace transform (MaxEnt-iLT) provides a lifetime distribution from time-resolved data, which is very helpful in the analysis of the relaxation of complex systems. In some applications both positive and negative values for the lifetime distribution amplitudes are physical, but most studies to date have focused on positive-constrained solutions. In this work, we first discuss optimal conditions to obtain a sign-unrestricted maximum entropy lifetime distribution, i.e., the selection of the entropy function and the regularization value. For the selection of the regularization value we compared four methods: the chi2 criterion and Bayesian inference (already used in sign-restricted MaxEnt-iLT), and the L-curve and the generalized cross-validation methods (not yet used in MaxEnt-iLT to our knowledge). Except for the frequently used chi2 criterion, these methods recommended similar regularization values, providing close to optimum solutions. However, even when an optimal entropy function and regularization value are used, a MaxEnt lifetime distribution will contain noise-induced errors, as well as systematic distortions induced by the entropy maximization (regularization-induced errors). We introduce the concept of the apparent resolution function in MaxEnt, which allows both the noise and regularization-induced errors to be estimated. We show the capability of this newly introduced concept in both synthetic and experimental time-resolved Fourier transform infrared (FT-IR) data from the bacteriorhodopsin photocycle.
Collapse
Affiliation(s)
- Víctor A Lórenz-Fonfría
- Department of Materials Science and Engineering, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan.
| | | |
Collapse
|
48
|
Efremov R, Gordeliy VI, Heberle J, Büldt G. Time-resolved microspectroscopy on a single crystal of bacteriorhodopsin reveals lattice-induced differences in the photocycle kinetics. Biophys J 2006; 91:1441-51. [PMID: 16731567 PMCID: PMC1518640 DOI: 10.1529/biophysj.106.083345] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The determination of the intermediate state structures of the bacteriorhodopsin photocycle has lead to an unprecedented level of understanding of the catalytic process exerted by a membrane protein. However, the crystallographic structures of the intermediate states are only relevant if the working cycle is not impaired by the crystal lattice. Therefore, we applied visible and Fourier transform infrared spectroscopy (FTIR) microspectroscopy with microsecond time resolution to compare the photoreaction of a single bacteriorhodopsin crystal to that of bacteriorhodopsin residing in the native purple membrane. The analysis of the FTIR difference spectra of the resolved intermediate states reveals great similarity in structural changes taking place in the crystal and in PM. However, the kinetics of the photocycle are significantly altered in the three-dimensional crystal as compared to PM. Strikingly, the L state decay is accelerated in the crystal, whereas the M decay is delayed. The physical origin of this deviation and the implications for trapping of intermediate states are discussed. As a methodological advance, time-resolved step-scan FTIR spectroscopy on a single protein crystal is demonstrated for the first time which may be used in the future to gauge the functionality of other crystallized proteins with the molecular resolution of vibrational spectroscopy.
Collapse
Affiliation(s)
- R Efremov
- Forschungszentrum Jülich, IBI-2: Structural Biology, 52425 Jülich, Germany
| | | | | | | |
Collapse
|
49
|
Shi L, Yoon SR, Bezerra AG, Jung KH, Brown LS. Cytoplasmic Shuttling of Protons in Anabaena Sensory Rhodopsin: Implications for Signaling Mechanism. J Mol Biol 2006; 358:686-700. [PMID: 16530786 DOI: 10.1016/j.jmb.2006.02.036] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2006] [Revised: 02/08/2006] [Accepted: 02/13/2006] [Indexed: 11/22/2022]
Abstract
It was found recently that Anabaena sensory rhodopsin (ASR), which possibly serves as a photoreceptor for chromatic adaptation, interacts with a soluble cytoplasmic transducer. The X-ray structure of the transducer-free protein revealed an extensive hydrogen-bonded network of amino acid residues and water molecules in the cytoplasmic half of ASR, in high contrast to its haloarchaeal counterparts. Using time-resolved spectroscopy of the wild-type and mutant ASR in the visible and infrared ranges, we tried to determine whether this hydrogen-bonded network is used to translocate protons and whether those proton transfers are important for interaction with the transducer. We found that the retinal Schiff base deprotonation, which occurs in the M intermediate of the photocycle of all-trans-ASR, results in protonation of Asp217 on the cytoplasmic side of the protein. The deprotonation of the Schiff base induces a conformational change of ASR observed through the perturbation of associated lipids. We suggest that the cytoplasmic shuttling of protons in the photocycle of all-trans-ASR and the ensuing conformational changes might activate the transducer. Consequently, the M intermediate may be the signaling state of ASR.
Collapse
Affiliation(s)
- Lichi Shi
- Department of Physics University of Guelph, Ontario, Canada N1G 2W1
| | | | | | | | | |
Collapse
|
50
|
Kaun N, Kulka S, Frank J, Schade U, Vellekoop MJ, Harasek M, Lendl B. Towards biochemical reaction monitoring using FT-IR synchrotron radiation. Analyst 2006; 131:489-94. [PMID: 16568164 DOI: 10.1039/b514102h] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A lab-on-a-chip device made of CaF2 windows and SU-8 polymer was used for fluid lamination to achieve rapid mixing of two streamlines with a cross section of 300 x 5 microm each. Time resolved measurements of the induced chemical reaction was achieved by applying constant feeding low flow rates and by on-chip measurement at defined distances after the mixing point. Synchrotron IR microscopic detection was employed for direct and label-free monitoring of (bio)chemical reactions. Furthermore, using synchrotron IR microscopy the measurement spot could be reduced to the diffraction limit, thus maximizing time resolution in the experimental set-up under study. Based on computational fluid dynamic simulations the principle of the set-up is discussed. Experimental results on the basic hydrolysis of methyl chloroacetate proved the working principle of the experimental set-up. First results on the interaction between the antibiotic vancomycin and a tripeptide (Ac2KAA) involved in the build up of the membrane proteins of gram-positive bacteria are presented.
Collapse
Affiliation(s)
- N Kaun
- Institute of Chemical Technologies and Analytics, Vienna University of Technology, Getreidemarkt 9-164, 1060 Vienna, Austria
| | | | | | | | | | | | | |
Collapse
|