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Bick T, Dominiak PM, Wendler P. Exploiting the full potential of cryo-EM maps. BBA ADVANCES 2024; 5:100113. [PMID: 38292063 PMCID: PMC10825613 DOI: 10.1016/j.bbadva.2024.100113] [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: 01/04/2024] [Accepted: 01/05/2024] [Indexed: 02/01/2024] Open
Abstract
The Coulomb potential maps generated by electron microscopy (EM) experiments contain not only information about the position but also about the charge state of the atom. This feature of EM maps allows the identification of specific ions and the protonation state of amino acid side chains in the sample. Here, we summarize qualitative observations of charges in EM maps, discuss the difficulties in interpreting the charge in Coulomb potential maps with respect to distinguishing it from radiation damage, and outline considerations to implement the correct charge in fitting algorithms.
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Affiliation(s)
- Thomas Bick
- Institute of Biochemistry and Biology, Department of Biochemistry, University of Potsdam, Karl-Liebknecht Strasse 24-25, 14476 Potsdam Golm, Germany
| | - Paulina M. Dominiak
- Biological and Chemical Research Centre, Faculty of Chemistry, University of Warsaw, ul. Żwirki i Wigury 101, 02-089 Warsaw, Poland
| | - Petra Wendler
- Institute of Biochemistry and Biology, Department of Biochemistry, University of Potsdam, Karl-Liebknecht Strasse 24-25, 14476 Potsdam Golm, Germany
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2
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Braun HP, Klusch N. Promotion of oxidative phosphorylation by complex I-anchored carbonic anhydrases? TRENDS IN PLANT SCIENCE 2024; 29:64-71. [PMID: 37599162 DOI: 10.1016/j.tplants.2023.07.007] [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: 05/17/2023] [Revised: 07/12/2023] [Accepted: 07/19/2023] [Indexed: 08/22/2023]
Abstract
The mitochondrial NADH-dehydrogenase complex of the respiratory chain, known as complex I, includes a carbonic anhydrase (CA) module attached to its membrane arm on the matrix side in protozoans, algae, and plants. Its physiological role is so far unclear. Recent electron cryo-microscopy (cryo-EM) structures show that the CA module may directly provide protons for translocation across the inner mitochondrial membrane at complex I. CAs can have a central role in adjusting the proton concentration in the mitochondrial matrix. We suggest that CA anchoring in complex I represents the original configuration to secure oxidative phosphorylation (OXPHOS) in the context of early endosymbiosis. After development of 'modern mitochondria' with pronounced cristae structures, this anchoring became dispensable, but has been retained in protozoans, algae, and plants.
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Affiliation(s)
- Hans-Peter Braun
- Institute of Plant Genetics, Leibniz Universität Hannover, Herrenhäuser Str. 2, 30419 Hannover, Germany.
| | - Niklas Klusch
- Department of Structural Biology, Max-Planck-Institute of Biophysics, Max-von-Laue-Straße 3, 60438 Frankfurt, Germany.
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3
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Phan LX, Owji AP, Yang T, Crain J, Sansom MSP, Tucker SJ. Electronic Polarizability Tunes the Function of the Human Bestrophin 1 Cl - Channel. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.14.567055. [PMID: 38014257 PMCID: PMC10680768 DOI: 10.1101/2023.11.14.567055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
Mechanisms of anion permeation within ion channels and nanopores remain poorly understood. Recent cryo-electron microscopy structures of the human bestrophin 1 chloride channel (hBest1) provide an opportunity to evaluate ion interactions predicted by molecular dynamics (MD) simulations against experimental observations. We implement the fully polarizable forcefield AMOEBA in MD simulations of open and partially-open states of the hBest1. The AMOEBA forcefield models multipole moments up to the quadrupole; therefore, it captures induced dipole and anion- π interactions. By including polarization we demonstrate the key role that aromatic residues play in ion permeation and the functional advantages of pore asymmetry within the highly conserved hydrophobic neck of the pore. We establish that these only arise when electronic polarization is included in the molecular models. We also show that Cl - permeation in this region can be achieved through hydrophobic solvation concomitant with partial ion dehydration, which is compensated for by the formation of contacts with the edge of the phenylalanine ring. Furthermore, we demonstrate how polarizable simulations can help determine the identity of ion-like densities within high-resolution cryo-EM structures. Crucially, neglecting polarization in simulation of these systems results in the localization of Cl - at positions that do not correspond with their experimentally resolved location. Overall, our results demonstrate the importance of including electronic polarization in realistic and physically accurate models of biological systems. Statement of Significance Ion channels are nanoscale protein pores that enable the selective passage of charged ions across cell membranes. Understanding the underlying mechanisms for selective anion permeation through such pores remains a challenge. To simulate their behavior efficiently in silico , fixed charge models are typically employed. However, this approach is insufficient for the study of anions. Here, we use simulations with explicit treatment of electrostatics to investigate the interactions of chloride ions in the human bestrophin 1 channel. We find that electronic polarization tunes the state of the channel and affects the interactions of chloride ions thereby revealing a mechanism for permeation. Furthermore, these simulations can be used to resolve experimental ambiguity in ion-like densities from cryo-EM structures.
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Li J, Sharma M, Meek R, Alhifthi A, Armstrong Z, Soler NM, Lee M, Goddard-Borger ED, Blaza JN, Davies GJ, Williams SJ. Molecular basis of sulfolactate synthesis by sulfolactaldehyde dehydrogenase from Rhizobium leguminosarum. Chem Sci 2023; 14:11429-11440. [PMID: 37886098 PMCID: PMC10599462 DOI: 10.1039/d3sc01594g] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Accepted: 08/25/2023] [Indexed: 10/28/2023] Open
Abstract
Sulfolactate (SL) is a short-chain organosulfonate that is an important reservoir of sulfur in the biosphere. SL is produced by oxidation of sulfolactaldehyde (SLA), which in turn derives from sulfoglycolysis of the sulfosugar sulfoquinovose, or through oxidation of 2,3-dihydroxypropanesulfonate. Oxidation of SLA is catalyzed by SLA dehydrogenases belonging to the aldehyde dehydrogenase superfamily. We report that SLA dehydrogenase RlGabD from the sulfoglycolytic bacterium Rhizobium leguminsarum SRDI565 can use both NAD+ and NADP+ as cofactor to oxidize SLA, and indicatively operates through a rapid equilibrium ordered mechanism. We report the cryo-EM structure of RlGabD bound to NADH, revealing a tetrameric quaternary structure and supporting proposal of organosulfonate binding residues in the active site, and a catalytic mechanism. Sequence based homology searches identified SLA dehydrogenase homologs in a range of putative sulfoglycolytic gene clusters in bacteria predominantly from the phyla Actinobacteria, Firmicutes, and Proteobacteria. This work provides a structural and biochemical view of SLA dehydrogenases to complement our knowledge of SLA reductases, and provide detailed insights into a critical step in the organosulfur cycle.
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Affiliation(s)
- Jinling Li
- School of Chemistry and Bio21 Molecular Science and Biotechnology Institute, University of Melbourne Parkville Victoria 3010 Australia
| | - Mahima Sharma
- York Structural Biology Laboratory, Department of Chemistry, University of York York YO10 5DD UK
| | - Richard Meek
- York Structural Biology Laboratory, Department of Chemistry, University of York York YO10 5DD UK
| | - Amani Alhifthi
- School of Chemistry and Bio21 Molecular Science and Biotechnology Institute, University of Melbourne Parkville Victoria 3010 Australia
- Chemistry Department, Faculty of Science (Female Section), Jazan University Jazan 82621 Saudi Arabia
| | - Zachary Armstrong
- School of Chemistry and Bio21 Molecular Science and Biotechnology Institute, University of Melbourne Parkville Victoria 3010 Australia
| | - Niccolay Madiedo Soler
- ACRF Chemical Biology Division, The Walter and Eliza Hall Institute of Medical Research Parkville Victoria 3010 Australia
| | - Mihwa Lee
- School of Chemistry and Bio21 Molecular Science and Biotechnology Institute, University of Melbourne Parkville Victoria 3010 Australia
| | - Ethan D Goddard-Borger
- ACRF Chemical Biology Division, The Walter and Eliza Hall Institute of Medical Research Parkville Victoria 3010 Australia
- Department of Medical Biology, University of Melbourne Parkville Victoria 3010 Australia
| | - James N Blaza
- York Structural Biology Laboratory, Department of Chemistry, University of York York YO10 5DD UK
| | - Gideon J Davies
- York Structural Biology Laboratory, Department of Chemistry, University of York York YO10 5DD UK
| | - Spencer J Williams
- School of Chemistry and Bio21 Molecular Science and Biotechnology Institute, University of Melbourne Parkville Victoria 3010 Australia
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Mott TM, Ibarra JS, Kandula N, Senning EN. Mutagenesis studies of TRPV1 subunit interfaces informed by genomic variant analysis. Biophys J 2023; 122:322-332. [PMID: 36518076 PMCID: PMC9892609 DOI: 10.1016/j.bpj.2022.12.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 11/11/2022] [Accepted: 12/08/2022] [Indexed: 12/15/2022] Open
Abstract
Protein structures and mutagenesis studies have been instrumental in elucidating molecular mechanisms of ion channel function, but making informed choices about which residues to target for mutagenesis can be challenging. Therefore, we investigated the potential for using human population genomic data to further refine our selection of mutagenesis sites in TRPV1. Single nucleotide polymorphism data of TRPV1 from gnomAD 2.1.1 revealed a lower number of missense variants within buried residues of the ankyrin repeat domain and an increased number of variants between secondary structure elements of the transmembrane segments. We hypothesized that residues critical to interactions at interfaces between subunits or domains in the channel would exhibit a similar reduction in variants. We identified in the structure of ground squirrel TRPV1 (PDB: 7LQY) a possible electrostatic network between K155 and K160 in the N-terminal ankyrin repeat domain and E761 and D762 in the C-terminus (K-KED). Consistent with our hypothesis for residues at key interface sites, none of the four residues have any variants reported in gnomAD 2.1.1. Ca2+ imaging of TRPV1 K-KED mutants confirmed significant roles for these residues, but we found that the electrostatic interaction is not essential since channel function is still observed in total charge reversals on the C-terminal side of the interface (E761K/D762K). Interestingly, Ca2+ imaging responses for a charge swap experiment with K155D/D762K showed partially restored wild-type responses. Using electrophysiology, we found that charge reversals on either K155 or D762 increased the baseline currents of TRPV1, and the charge swapped double mutant, K155D/D762K, partially restored baseline currents to wild-type levels. We interpret these results to mean that contacts across residues in the K-KED interface shift the equilibria of conformations to closed pore states. Our study demonstrates the utility and applicability of a combined missense variant and structure targeted investigation of residues at TRPV1 subunit interfaces.
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Affiliation(s)
- Taylor M Mott
- Department of Neuroscience, The University of Texas at Austin, Austin, Texas 78712
| | - Jordan S Ibarra
- Department of Neuroscience, The University of Texas at Austin, Austin, Texas 78712
| | - Nivitha Kandula
- School of Medicine, University of Missouri-Kansas City, 5000 Holmes St, Kansas City, Missouri 64110
| | - Eric N Senning
- Department of Neuroscience, The University of Texas at Austin, Austin, Texas 78712.
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Full-Length Model of SaCas9-sgRNA-DNA Complex in Cleavage State. Int J Mol Sci 2023; 24:ijms24021204. [PMID: 36674715 PMCID: PMC9867433 DOI: 10.3390/ijms24021204] [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: 11/23/2022] [Revised: 12/24/2022] [Accepted: 12/27/2022] [Indexed: 01/10/2023] Open
Abstract
Staphylococcus aureus Cas9 (SaCas9) is a widely used genome editing tool. Understanding its molecular mechanisms of DNA cleavage could effectively guide the engineering optimization of this system. Here, we determined the first cryo-electron microscopy structure of the SaCas9-sgRNA-DNA ternary complex. This structure reveals that the HNH nuclease domain is tightly bound to the cleavage site of the target DNA strand, and is in close contact with the WED and REC domains. Moreover, it captures the complete structure of the sgRNA, including the previously unresolved stem-loop 2. Based on this structure, we build a full-length model for the ternary complex in cleavage state. This model enables identification of the residues for the interactions between the HNH domain and the WED and REC domains. Moreover, we found that the stem-loop 2 of the sgRNA tightly binds to the PI and RuvC domains and may also regulate the position shift of the RuvC domain. Further mutagenesis and molecular dynamics simulations supported the idea that the interactions of the HNH domain with the WED and REC domains play an important role in the DNA cleavage. Thus, this study provides new mechanistic insights into the DNA cleavage of SaCas9 and is also useful for guiding the future engineering of SaCas9-mediated gene editing systems.
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Wood DM, Dobson RC, Horne CR. Using cryo-EM to uncover mechanisms of bacterial transcriptional regulation. Biochem Soc Trans 2021; 49:2711-2726. [PMID: 34854920 PMCID: PMC8786299 DOI: 10.1042/bst20210674] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 11/10/2021] [Accepted: 11/15/2021] [Indexed: 11/17/2022]
Abstract
Transcription is the principal control point for bacterial gene expression, and it enables a global cellular response to an intracellular or environmental trigger. Transcriptional regulation is orchestrated by transcription factors, which activate or repress transcription of target genes by modulating the activity of RNA polymerase. Dissecting the nature and precise choreography of these interactions is essential for developing a molecular understanding of transcriptional regulation. While the contribution of X-ray crystallography has been invaluable, the 'resolution revolution' of cryo-electron microscopy has transformed our structural investigations, enabling large, dynamic and often transient transcription complexes to be resolved that in many cases had resisted crystallisation. In this review, we highlight the impact cryo-electron microscopy has had in gaining a deeper understanding of transcriptional regulation in bacteria. We also provide readers working within the field with an overview of the recent innovations available for cryo-electron microscopy sample preparation and image reconstruction of transcription complexes.
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Affiliation(s)
- David M. Wood
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Renwick C.J. Dobson
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
- Bio21 Molecular Science and Biotechnology Institute, Department of Biochemistry and Pharmacology, University of Melbourne, Parkville, VIC, Australia
| | - Christopher R. Horne
- Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC 3052, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC 3052, Australia
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