1
|
Bertalan É, Konno M, Del Carmen Marín M, Bagherzadeh R, Nagata T, Brown L, Inoue K, Bondar AN. Hydrogen-Bonding and Hydrophobic Interaction Networks as Structural Determinants of Microbial Rhodopsin Function. J Phys Chem B 2024; 128:7407-7426. [PMID: 39024507 DOI: 10.1021/acs.jpcb.4c02946] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/20/2024]
Abstract
Microbial pump rhodopsins are highly versatile light-driven membrane proteins that couple protein conformational dynamics with ion translocation across the cell membranes. Understanding how microbial pump rhodopsins use specific amino acid residues at key functional sites to control ion selectivity and ion pumping direction is of general interest for membrane transporters, and could guide site-directed mutagenesis for optogenetics applications. To enable direct comparisons between proteins with different sequences we implement, for the first time, a unique numbering scheme for the microbial pump rhodopsin residues, NS-mrho. We use NS-mrho to show that distinct microbial pump rhodopsins typically have hydrogen-bond networks that are less conserved than anticipated from the amino acid residue conservation, whereas their hydrophobic interaction networks are largely conserved. To illustrate the role of the hydrogen-bond networks as structural elements that determine the functionality of microbial pump rhodopsins, we performed experiments, atomic-level simulations, and hydrogen bond network analyses on GR, the outward proton pump from Gloeobacter violaceus, and KR2, the outward sodium pump from Krokinobacter eikastus. The experiments indicate that multiple mutations that recover KR2 amino acid residues in GR not only fail to convert it into a sodium pump, but completely inactivate GR by abolishing photoisomerization of the retinal chromophore. This observation could be attributed to the drastically altered hydrogen-bond interaction network identified with simulations and network analyses. Taken together, our findings suggest that functional specificity could be encoded in the collective hydrogen-bond network of microbial pump rhodopsins.
Collapse
Affiliation(s)
- Éva Bertalan
- Department of Mathematics and Natural Sciences, RWTH Aachen University, Templergraben 59, 52062 Aachen, Germany
| | - Masae Konno
- The Institute for Solid State Physics, The University of Tokyo, 5-1-5 Kashiwano-ha, Kashiwa 277-8581, Chiba, Japan
| | - María Del Carmen Marín
- The Institute for Solid State Physics, The University of Tokyo, 5-1-5 Kashiwano-ha, Kashiwa 277-8581, Chiba, Japan
| | - Reza Bagherzadeh
- The Institute for Solid State Physics, The University of Tokyo, 5-1-5 Kashiwano-ha, Kashiwa 277-8581, Chiba, Japan
| | - Takashi Nagata
- The Institute for Solid State Physics, The University of Tokyo, 5-1-5 Kashiwano-ha, Kashiwa 277-8581, Chiba, Japan
| | - Leonid Brown
- Department of Physics, University of Guelph, 488 Gordon Street, Guelph, Ontario N1G 2W1, Canada
| | - Keiichi Inoue
- The Institute for Solid State Physics, The University of Tokyo, 5-1-5 Kashiwano-ha, Kashiwa 277-8581, Chiba, Japan
| | - Ana-Nicoleta Bondar
- Institute of Computational Biomedicine, Forschungszentrum Jülich, IAS-5/INM-9, Wilhelm-Johnen Straße, 5428 Jülich, Germany
- Faculty of Physics, University of Bucharest, Atomiştilor 405, 077125 Măgurele, Romania
| |
Collapse
|
2
|
Kariev AM, Green ME. Water, Protons, and the Gating of Voltage-Gated Potassium Channels. MEMBRANES 2024; 14:37. [PMID: 38392664 PMCID: PMC10890431 DOI: 10.3390/membranes14020037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 01/17/2024] [Accepted: 01/23/2024] [Indexed: 02/24/2024]
Abstract
Ion channels are ubiquitous throughout all forms of life. Potassium channels are even found in viruses. Every cell must communicate with its surroundings, so all cells have them, and excitable cells, in particular, especially nerve cells, depend on the behavior of these channels. Every channel must be open at the appropriate time, and only then, so that each channel opens in response to the stimulus that tells that channel to open. One set of channels, including those in nerve cells, responds to voltage. There is a standard model for the gating of these channels that has a section of the protein moving in response to the voltage. However, there is evidence that protons are moving, rather than protein. Water is critical as part of the gating process, although it is hard to see how this works in the standard model. Here, we review the extensive evidence of the importance of the role of water and protons in gating these channels. Our principal example, but by no means the only example, will be the Kv1.2 channel. Evidence comes from the effects of D2O, from mutations in the voltage sensing domain, as well as in the linker between that domain and the gate, and at the gate itself. There is additional evidence from computations, especially quantum calculations. Structural evidence comes from X-ray studies. The hydration of ions is critical in the transfer of ions in constricted spaces, such as the gate region and the pore of a channel; we will see how the structure of the hydrated ion fits with the structure of the channel. In addition, there is macroscopic evidence from osmotic experiments and streaming current measurements. The combined evidence is discussed in the context of a model that emphasizes the role of protons and water in gating these channels.
Collapse
Affiliation(s)
- Alisher M Kariev
- Department of Chemistry and Biochemistry, The City College of New York, New York, NY 10031, USA
| | - Michael E Green
- Department of Chemistry and Biochemistry, The City College of New York, New York, NY 10031, USA
| |
Collapse
|
3
|
Kapur B, Baldessari F, Lazaratos M, Nar H, Schnapp G, Giorgetti A, Bondar AN. Protons taken hostage: Dynamic H-bond networks of the pH-sensing GPR68. Comput Struct Biotechnol J 2023; 21:4370-4384. [PMID: 37711190 PMCID: PMC10498176 DOI: 10.1016/j.csbj.2023.08.034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 08/30/2023] [Accepted: 08/30/2023] [Indexed: 09/16/2023] Open
Abstract
Proton-sensing G Protein Coupled Receptors (GPCRs) sense changes in the extracellular pH to effect cell signaling for cellular homeostasis. They tend to be overexpressed in solid tumors associated with acidic extracellular pH, and are of direct interest as drug targets. How proton-sensing GPCRs sense extracellular acidification and activate upon protonation change is important to understand, because it may guide the design of therapeutics. Lack of publicly available experimental structures make it challenging to discriminate between conflicting mechanisms proposed for proton-binding, as main roles have been assigned to either an extracellular histidine cluster or to an internal carboxylic triad. Here we present a protocol to derive and evaluate structural models of the proton-sensing GPR68. This approach integrates state-of-the-art homology modeling with microsecond-timescale atomistic simulations, and with a detailed assessment of the compatibility of the structural models with known structural features of class A GPCRs. To decipher structural elements of potential interest for protonation-coupled conformational changes of GPR68, we used the best-compatible model as a starting point for independent atomistic simulations of GPR68 with different protonation states, and graph computations to characterize the response of GPR68 to changes in protonation. We found that GPR68 hosts an extended hydrogen-bond network that inter-connects the extracellular histidine cluster to the internal carboxylic triad, and which can even reach groups at the cytoplasmic G-protein binding site. Taken together, results suggest that GPR68 relies on dynamic, hydrogen-bond networks to inter-connect extracellular and internal proton-binding sites, and to elicit conformational changes at the cytoplasmic G-protein binding site.
Collapse
Affiliation(s)
- Bhav Kapur
- Boehringer-Ingelheim Pharma GmbH & Co. KG, Birkendorfer Straße 65, 88397 Biberach an der Riß, Germany
- Christian-Albrechts-University of Kiel, 24118 Kiel, Germany
| | | | - Michalis Lazaratos
- Department of Physics, Theoretical Molecular Biophysics Group, Freie Universität Berlin, Arnimallee 14, D-14195 Berlin, Germany
| | - Herbert Nar
- Boehringer-Ingelheim Pharma GmbH & Co. KG, Birkendorfer Straße 65, 88397 Biberach an der Riß, Germany
| | - Gisela Schnapp
- Boehringer-Ingelheim Pharma GmbH & Co. KG, Birkendorfer Straße 65, 88397 Biberach an der Riß, Germany
| | - Alejandro Giorgetti
- University of Verona, Department of Biotechnology, 37134 Verona, Italy
- Forschungszentrum Jülich, Institute for Neuroscience and Medicine and Institute for Advanced Simulations (IAS-5/INM-9), Computational Biomedicine, Wilhelm-Johnen Straße, 52525 Jülich, Germany
| | - Ana-Nicoleta Bondar
- Forschungszentrum Jülich, Institute for Neuroscience and Medicine and Institute for Advanced Simulations (IAS-5/INM-9), Computational Biomedicine, Wilhelm-Johnen Straße, 52525 Jülich, Germany
- University of Bucharest, Faculty of Physics, Str. Atomiştilor 405, 077125 Bucharest-Măgurele, Romania
| |
Collapse
|
4
|
Wei RJ, Khaniya U, Mao J, Liu J, Batista VS, Gunner MR. Tools for analyzing protonation states and for tracing proton transfer pathways with examples from the Rb. sphaeroides photosynthetic reaction centers. PHOTOSYNTHESIS RESEARCH 2023; 156:101-112. [PMID: 36307598 DOI: 10.1007/s11120-022-00973-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2022] [Accepted: 10/03/2022] [Indexed: 06/16/2023]
Abstract
Protons participate in many reactions. In proteins, protons need paths to move in and out of buried active sites. The vectorial movement of protons coupled to electron transfer reactions establishes the transmembrane electrochemical gradient used for many reactions, including ATP synthesis. Protons move through hydrogen bonded chains of waters and hydroxy side chains via the Grotthuss mechanism and by proton binding and release from acidic and basic residues. MCCE analysis shows that proteins exist in a large number of protonation states. Knowledge of the equilibrium ensemble can provide a rational basis for setting protonation states in simulations that fix them, such as molecular dynamics (MD). The proton path into the QB site in the bacterial reaction centers (RCs) of Rb. sphaeroides is analyzed by MD to provide an example of the benefits of using protonation states found by the MCCE program. A tangled web of side chains and waters link the cytoplasm to QB. MCCE analysis of snapshots from multiple trajectories shows that changing the input protonation state of a residue in MD biases the trajectory shifting the proton affinity of that residue. However, the proton affinity of some residues is more sensitive to the input structure. The proton transfer networks derived from different trajectories are quite robust. There are some changes in connectivity that are largely restricted to the specific residues whose protonation state is changed. Trajectories with QB•- are compared with earlier results obtained with QB [Wei et. al Photosynthesis Research volume 152, pages153-165 (2022)] showing only modest changes. While introducing new methods the study highlights the difficulty of establishing the connections between protein conformation.
Collapse
Affiliation(s)
- Rongmei Judy Wei
- Ph.D. Program in Chemistry, The Graduate Center, City University of New York, New York, NY, 10016, USA
- Department of Physics, City College of New York, New York, NY, 10031, USA
| | - Umesh Khaniya
- Department of Physics, City College of New York, New York, NY, 10031, USA
- Ph.D. Program in Physics, The Graduate Center of the City University of New York, New York, NY, 10016, USA
| | - Junjun Mao
- Department of Physics, City College of New York, New York, NY, 10031, USA
| | - Jinchan Liu
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA
| | - Victor S Batista
- Department of Chemistry, Yale University, New Haven, CT, 06520, USA
| | - M R Gunner
- Ph.D. Program in Chemistry, The Graduate Center, City University of New York, New York, NY, 10016, USA.
- Department of Physics, City College of New York, New York, NY, 10031, USA.
- Ph.D. Program in Physics, The Graduate Center of the City University of New York, New York, NY, 10016, USA.
| |
Collapse
|
5
|
Bertalan É, Bondar AN. Graphs of protein-water hydrogen bond networks to dissect structural movies of ion-transfer microbial rhodopsins. Front Chem 2023; 10:1075648. [PMID: 36712989 PMCID: PMC9880326 DOI: 10.3389/fchem.2022.1075648] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Accepted: 12/31/2022] [Indexed: 01/15/2023] Open
Abstract
Microbial rhodopsins are membrane proteins that use the energy absorbed by the covalently bound retinal chromophore to initiate reaction cycles resulting in ion transport or signal transduction. Thousands of distinct microbial rhodopsins are known and, for many rhodopsins, three-dimensional structures have been solved with structural biology, including as entire sets of structures solved with serial femtosecond crystallography. This sets the stage for comprehensive studies of large datasets of static protein structures to dissect structural elements that provide functional specificity to the various microbial rhodopsins. A challenge, however, is how to analyze efficiently intra-molecular interactions based on large datasets of static protein structures. Our perspective discusses the usefulness of graph-based approaches to dissect structural movies of microbial rhodopsins solved with time-resolved crystallography.
Collapse
Affiliation(s)
- Éva Bertalan
- Physikzentrum, RWTH Aachen University, Aachen, Germany
| | - Ana-Nicoleta Bondar
- Forschungszentrum Jülich, Institute of Computational Biomedicine, Jülich, Germany,Faculty of Physics, University of Bucharest, Măgurele, Romania,*Correspondence: Ana-Nicoleta Bondar, ,
| |
Collapse
|
6
|
de Grip WJ, Ganapathy S. Rhodopsins: An Excitingly Versatile Protein Species for Research, Development and Creative Engineering. Front Chem 2022; 10:879609. [PMID: 35815212 PMCID: PMC9257189 DOI: 10.3389/fchem.2022.879609] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2022] [Accepted: 05/16/2022] [Indexed: 01/17/2023] Open
Abstract
The first member and eponym of the rhodopsin family was identified in the 1930s as the visual pigment of the rod photoreceptor cell in the animal retina. It was found to be a membrane protein, owing its photosensitivity to the presence of a covalently bound chromophoric group. This group, derived from vitamin A, was appropriately dubbed retinal. In the 1970s a microbial counterpart of this species was discovered in an archaeon, being a membrane protein also harbouring retinal as a chromophore, and named bacteriorhodopsin. Since their discovery a photogenic panorama unfolded, where up to date new members and subspecies with a variety of light-driven functionality have been added to this family. The animal branch, meanwhile categorized as type-2 rhodopsins, turned out to form a large subclass in the superfamily of G protein-coupled receptors and are essential to multiple elements of light-dependent animal sensory physiology. The microbial branch, the type-1 rhodopsins, largely function as light-driven ion pumps or channels, but also contain sensory-active and enzyme-sustaining subspecies. In this review we will follow the development of this exciting membrane protein panorama in a representative number of highlights and will present a prospect of their extraordinary future potential.
Collapse
Affiliation(s)
- Willem J. de Grip
- Leiden Institute of Chemistry, Department of Biophysical Organic Chemistry, Leiden University, Leiden, Netherlands
- Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, Netherlands
| | - Srividya Ganapathy
- Department of Imaging Physics, Delft University of Technology, Netherlands
| |
Collapse
|
7
|
Lazaratos M, Siemers M, Brown LS, Bondar AN. Conserved hydrogen-bond motifs of membrane transporters and receptors. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2022; 1864:183896. [PMID: 35217000 DOI: 10.1016/j.bbamem.2022.183896] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 02/04/2022] [Accepted: 02/16/2022] [Indexed: 01/18/2023]
Abstract
Membrane transporters and receptors often rely on conserved hydrogen bonds to assemble transient paths for ion transfer or long-distance conformational couplings. For transporters and receptors that use proton binding and proton transfer for function, inter-helical hydrogen bonds of titratable protein sidechains that could change protonation are of central interest to formulate hypotheses about reaction mechanisms. Knowledge of hydrogen bonds common at sites of potential interest for proton binding could thus inform and guide studies on functional mechanisms of protonation-coupled membrane proteins. Here we apply graph-theory approaches to identify hydrogen-bond motifs of carboxylate and histidine sidechains in a large data set of static membrane protein structures. We find that carboxylate-hydroxyl hydrogen bonds are present in numerous structures of the dataset, and can be part of more extended H-bond clusters that could be relevant to conformational coupling. Carboxylate-carboxyamide and imidazole-imidazole hydrogen bonds are represented in comparably fewer protein structures of the dataset. Atomistic simulations on two membrane transporters in lipid membranes suggest that many of the hydrogen bond motifs present in static protein structures tend to be robust, and can be part of larger hydrogen-bond clusters that recruit additional hydrogen bonds.
Collapse
Affiliation(s)
- Michalis Lazaratos
- Freie Universität Berlin, Department of Physics, Theoretical Molecular Biophysics, Arnimallee 14, D14195 Berlin, Germany
| | - Malte Siemers
- Freie Universität Berlin, Department of Physics, Theoretical Molecular Biophysics, Arnimallee 14, D14195 Berlin, Germany
| | - Leonid S Brown
- University of Guelph, Department of Physics, 50 Stone Road E., Guelph, Ontario N1G 2W1, Canada
| | - Ana-Nicoleta Bondar
- Freie Universität Berlin, Department of Physics, Theoretical Molecular Biophysics, Arnimallee 14, D14195 Berlin, Germany; University of Bucharest, Faculty of Physics, Atomiștilor 405, Măgurele 077125, Romania; Forschungszentrum Jülich, Institute for Neuroscience and Medicine and Institute for Advanced Simulations (IAS-5/INM-9), Computational Biomedicine, Wilhelm-Johnen Straße, 52428 Jülich, Germany.
| |
Collapse
|