1
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Muñoz KA, Ulrich RJ, Vasan AK, Sinclair M, Wen PC, Holmes JR, Lee HY, Hung CC, Fields CJ, Tajkhorshid E, Lau GW, Hergenrother PJ. A Gram-negative-selective antibiotic that spares the gut microbiome. Nature 2024; 630:429-436. [PMID: 38811738 DOI: 10.1038/s41586-024-07502-0] [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: 04/07/2023] [Accepted: 05/01/2024] [Indexed: 05/31/2024]
Abstract
Infections caused by Gram-negative pathogens are increasingly prevalent and are typically treated with broad-spectrum antibiotics, resulting in disruption of the gut microbiome and susceptibility to secondary infections1-3. There is a critical need for antibiotics that are selective both for Gram-negative bacteria over Gram-positive bacteria, as well as for pathogenic bacteria over commensal bacteria. Here we report the design and discovery of lolamicin, a Gram-negative-specific antibiotic targeting the lipoprotein transport system. Lolamicin has activity against a panel of more than 130 multidrug-resistant clinical isolates, shows efficacy in multiple mouse models of acute pneumonia and septicaemia infection, and spares the gut microbiome in mice, preventing secondary infection with Clostridioides difficile. The selective killing of pathogenic Gram-negative bacteria by lolamicin is a consequence of low sequence homology for the target in pathogenic bacteria versus commensals; this doubly selective strategy can be a blueprint for the development of other microbiome-sparing antibiotics.
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Affiliation(s)
- Kristen A Muñoz
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Rebecca J Ulrich
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Archit K Vasan
- Theoretical and Computational Biophysics Group, NIH Center for Macromolecular Modeling and Visualization, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Matt Sinclair
- Theoretical and Computational Biophysics Group, NIH Center for Macromolecular Modeling and Visualization, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Po-Chao Wen
- Theoretical and Computational Biophysics Group, NIH Center for Macromolecular Modeling and Visualization, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Jessica R Holmes
- High-Performance Computing in Biology, Roy J. Carver Biotechnology Center, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Hyang Yeon Lee
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Chien-Che Hung
- Veterinary Diagnostic Laboratory, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Department of Veterinary Clinical Medicine, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Christopher J Fields
- High-Performance Computing in Biology, Roy J. Carver Biotechnology Center, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Emad Tajkhorshid
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Theoretical and Computational Biophysics Group, NIH Center for Macromolecular Modeling and Visualization, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Gee W Lau
- Department of Pathobiology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Paul J Hergenrother
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
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2
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Gose T, Rasouli A, Dehghani-Ghahnaviyeh S, Wen PC, Wang Y, Lynch J, Fukuda Y, Shafi T, Ford RC, Tajkhorshid E, Schuetz JD. Tumor-acquired somatic mutation affects conformation to abolish ABCG2-mediated drug resistance. Drug Resist Updat 2024; 73:101066. [PMID: 38387283 PMCID: PMC11137617 DOI: 10.1016/j.drup.2024.101066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 01/31/2024] [Accepted: 02/03/2024] [Indexed: 02/24/2024]
Abstract
ABCG2 is an important ATP-binding cassette transporter impacting the absorption and distribution of over 200 chemical toxins and drugs. ABCG2 also reduces the cellular accumulation of diverse chemotherapeutic agents. Acquired somatic mutations in the phylogenetically conserved amino acids of ABCG2 might provide unique insights into its molecular mechanisms of transport. Here, we identify a tumor-derived somatic mutation (Q393K) that occurs in a highly conserved amino acid across mammalian species. This ABCG2 mutant seems incapable of providing ABCG2-mediated drug resistance. This was perplexing because it is localized properly and retained interaction with substrates and nucleotides. Using a conformationally sensitive antibody, we show that this mutant appears "locked" in a non-functional conformation. Structural modeling and molecular dynamics simulations based on ABCG2 cryo-EM structures suggested that the Q393K interacts with the E446 to create a strong salt bridge. The salt bridge is proposed to stabilize the inward-facing conformation, resulting in an impaired transporter that lacks the flexibility to readily change conformation, thereby disrupting the necessary communication between substrate binding and transport.
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Affiliation(s)
- Tomoka Gose
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Ali Rasouli
- Theoretical and Computational Biophysics Group, NIH Center for Macromolecular Modeling and Visualization, Beckman Institute for Advanced Science and Technology, Department of Biochemistry, and Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Sepehr Dehghani-Ghahnaviyeh
- Theoretical and Computational Biophysics Group, NIH Center for Macromolecular Modeling and Visualization, Beckman Institute for Advanced Science and Technology, Department of Biochemistry, and Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Po-Chao Wen
- Theoretical and Computational Biophysics Group, NIH Center for Macromolecular Modeling and Visualization, Beckman Institute for Advanced Science and Technology, Department of Biochemistry, and Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Yao Wang
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - John Lynch
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Yu Fukuda
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Talha Shafi
- School of Biological Sciences, The University of Manchester, Oxford Road, Manchester M13 9PL, UK
| | - Robert C Ford
- School of Biological Sciences, The University of Manchester, Oxford Road, Manchester M13 9PL, UK
| | - Emad Tajkhorshid
- Theoretical and Computational Biophysics Group, NIH Center for Macromolecular Modeling and Visualization, Beckman Institute for Advanced Science and Technology, Department of Biochemistry, and Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - John D Schuetz
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA.
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3
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Nguyen ATP, Weigle AT, Shukla D. Functional regulation of aquaporin dynamics by lipid bilayer composition. Nat Commun 2024; 15:1848. [PMID: 38418487 PMCID: PMC10901782 DOI: 10.1038/s41467-024-46027-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Accepted: 02/12/2024] [Indexed: 03/01/2024] Open
Abstract
With the diversity of lipid-protein interactions, any observed membrane protein dynamics or functions directly depend on the lipid bilayer selection. However, the implications of lipid bilayer choice are seldom considered unless characteristic lipid-protein interactions have been previously reported. Using molecular dynamics simulation, we characterize the effects of membrane embedding on plant aquaporin SoPIP2;1, which has no reported high-affinity lipid interactions. The regulatory impacts of a realistic lipid bilayer, and nine different homogeneous bilayers, on varying SoPIP2;1 dynamics are examined. We demonstrate that SoPIP2;1's structure, thermodynamics, kinetics, and water transport are altered as a function of each membrane construct's ensemble properties. Notably, the realistic bilayer provides stabilization of non-functional SoPIP2;1 metastable states. Hydrophobic mismatch and lipid order parameter calculations further explain how lipid ensemble properties manipulate SoPIP2;1 behavior. Our results illustrate the importance of careful bilayer selection when studying membrane proteins. To this end, we advise cautionary measures when performing membrane protein molecular dynamics simulations.
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Affiliation(s)
- Anh T P Nguyen
- Department of Chemical and Biomolecular Engineering, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA
| | - Austin T Weigle
- Department of Chemistry, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA
| | - Diwakar Shukla
- Department of Chemical and Biomolecular Engineering, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA.
- Center for Biophysics and Quantitative Biology, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA.
- Department of Bioengineering, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA.
- Department of Plant Biology, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA.
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4
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Sinclair M, Stein RA, Sheehan JH, Hawes EM, O’Brien RM, Tajkhorshid E, Claxton DP. Integrative analysis of pathogenic variants in glucose-6-phosphatase based on an AlphaFold2 model. PNAS NEXUS 2024; 3:pgae036. [PMID: 38328777 PMCID: PMC10849595 DOI: 10.1093/pnasnexus/pgae036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Accepted: 01/09/2024] [Indexed: 02/09/2024]
Abstract
Mediating the terminal reaction of gluconeogenesis and glycogenolysis, the integral membrane protein glucose-6-phosphate catalytic subunit 1 (G6PC1) regulates hepatic glucose production by catalyzing hydrolysis of glucose-6-phosphate (G6P) within the lumen of the endoplasmic reticulum. Consistent with its vital contribution to glucose homeostasis, inactivating mutations in G6PC1 causes glycogen storage disease (GSD) type 1a characterized by hepatomegaly and severe hypoglycemia. Despite its physiological importance, the structural basis of G6P binding to G6PC1 and the molecular disruptions induced by missense mutations within the active site that give rise to GSD type 1a are unknown. In this study, we determine the atomic interactions governing G6P binding as well as explore the perturbations imposed by disease-linked missense variants by subjecting an AlphaFold2 G6PC1 structural model to molecular dynamics simulations and in silico predictions of thermodynamic stability validated with robust in vitro and in situ biochemical assays. We identify a collection of side chains, including conserved residues from the signature phosphatidic acid phosphatase motif, that contribute to a hydrogen bonding and van der Waals network stabilizing G6P in the active site. The introduction of GSD type 1a mutations modified the thermodynamic landscape, altered side chain packing and substrate-binding interactions, and induced trapping of catalytic intermediates. Our results, which corroborate the high quality of the AF2 model as a guide for experimental design and to interpret outcomes, not only confirm the active-site structural organization but also identify previously unobserved mechanistic contributions of catalytic and noncatalytic side chains.
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Affiliation(s)
- Matt Sinclair
- Theoretical and Computational Biophysics Group, NIH Center for Macromolecular Modeling and Visualization, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Richard A Stein
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN 37232, USA
- Center for Applied Artificial Intelligence in Protein Dynamics, Vanderbilt University, Nashville, TN 37240, USA
| | - Jonathan H Sheehan
- Center for Structural Biology, Vanderbilt University, Nashville, TN 37240, USA
- Division of Infectious Diseases, Department of Internal Medicine, Washington University School of Medicine, St Louis, MO 63110, USA
| | - Emily M Hawes
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN 37232, USA
| | - Richard M O’Brien
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN 37232, USA
| | - Emad Tajkhorshid
- Theoretical and Computational Biophysics Group, NIH Center for Macromolecular Modeling and Visualization, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Derek P Claxton
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN 37232, USA
- Center for Applied Artificial Intelligence in Protein Dynamics, Vanderbilt University, Nashville, TN 37240, USA
- Center for Structural Biology, Vanderbilt University, Nashville, TN 37240, USA
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5
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Tang Q, Sinclair M, Hasdemir HS, Stein RA, Karakas E, Tajkhorshid E, Mchaourab HS. Asymmetric conformations and lipid interactions shape the ATP-coupled cycle of a heterodimeric ABC transporter. Nat Commun 2023; 14:7184. [PMID: 37938578 PMCID: PMC10632425 DOI: 10.1038/s41467-023-42937-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Accepted: 10/26/2023] [Indexed: 11/09/2023] Open
Abstract
Here we used cryo-electron microscopy (cryo-EM), double electron-electron resonance spectroscopy (DEER), and molecular dynamics (MD) simulations, to capture and characterize ATP- and substrate-bound inward-facing (IF) and occluded (OC) conformational states of the heterodimeric ATP binding cassette (ABC) multidrug exporter BmrCD in lipid nanodiscs. Supported by DEER analysis, the structures reveal that ATP-powered isomerization entails changes in the relative symmetry of the BmrC and BmrD subunits that propagates from the transmembrane domain to the nucleotide binding domain. The structures uncover asymmetric substrate and Mg2+ binding which we hypothesize are required for triggering ATP hydrolysis preferentially in one of the nucleotide-binding sites. MD simulations demonstrate that multiple lipid molecules differentially bind the IF versus the OC conformation thus establishing that lipid interactions modulate BmrCD energy landscape. Our findings are framed in a model that highlights the role of asymmetric conformations in the ATP-coupled transport with general implications to the mechanism of ABC transporters.
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Affiliation(s)
- Qingyu Tang
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN, 37232, USA
| | - Matt Sinclair
- Theoretical and Computational Biophysics Group, NIH Resource for Macromolecular Modeling and Visualization, Beckman Institute for Advanced Science and Technology, Department of Biochemistry, and Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Hale S Hasdemir
- Theoretical and Computational Biophysics Group, NIH Resource for Macromolecular Modeling and Visualization, Beckman Institute for Advanced Science and Technology, Department of Biochemistry, and Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Richard A Stein
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN, 37232, USA
| | - Erkan Karakas
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN, 37232, USA
| | - Emad Tajkhorshid
- Theoretical and Computational Biophysics Group, NIH Resource for Macromolecular Modeling and Visualization, Beckman Institute for Advanced Science and Technology, Department of Biochemistry, and Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Hassane S Mchaourab
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN, 37232, USA.
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6
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Cowgill J, Fan C, Haloi N, Tobiasson V, Zhuang Y, Howard RJ, Lindahl E. Structure and dynamics of differential ligand binding in the human ρ-type GABA A receptor. Neuron 2023; 111:3450-3464.e5. [PMID: 37659407 DOI: 10.1016/j.neuron.2023.08.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Revised: 08/01/2023] [Accepted: 08/07/2023] [Indexed: 09/04/2023]
Abstract
The neurotransmitter γ-aminobutyric acid (GABA) drives critical inhibitory processes in and beyond the nervous system, partly via ionotropic type-A receptors (GABAARs). Pharmacological properties of ρ-type GABAARs are particularly distinctive, yet the structural basis for their specialization remains unclear. Here, we present cryo-EM structures of a lipid-embedded human ρ1 GABAAR, including a partial intracellular domain, under apo, inhibited, and desensitized conditions. An apparent resting state, determined first in the absence of modulators, was recapitulated with the specific inhibitor (1,2,5,6-tetrahydropyridin-4-yl)methylphosphinic acid and blocker picrotoxin and provided a rationale for bicuculline insensitivity. Comparative structures, mutant recordings, and molecular simulations with and without GABA further explained the sensitized but slower activation of ρ1 relative to canonical subtypes. Combining GABA with picrotoxin also captured an apparent uncoupled intermediate state. This work reveals structural mechanisms of gating and modulation with applications to ρ-specific pharmaceutical design and to our biophysical understanding of ligand-gated ion channels.
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Affiliation(s)
- John Cowgill
- Department of Biochemistry and Biophysics, SciLifeLab, Stockholm University, 17121 Solna, Sweden
| | - Chen Fan
- Department of Biochemistry and Biophysics, SciLifeLab, Stockholm University, 17121 Solna, Sweden
| | - Nandan Haloi
- Department of Applied Physics, SciLifeLab, KTH Royal Institute of Technology, 17121 Solna, Sweden
| | - Victor Tobiasson
- Department of Biochemistry and Biophysics, SciLifeLab, Stockholm University, 17121 Solna, Sweden
| | - Yuxuan Zhuang
- Department of Biochemistry and Biophysics, SciLifeLab, Stockholm University, 17121 Solna, Sweden
| | - Rebecca J Howard
- Department of Biochemistry and Biophysics, SciLifeLab, Stockholm University, 17121 Solna, Sweden.
| | - Erik Lindahl
- Department of Biochemistry and Biophysics, SciLifeLab, Stockholm University, 17121 Solna, Sweden; Department of Applied Physics, SciLifeLab, KTH Royal Institute of Technology, 17121 Solna, Sweden.
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7
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Dehghani-Ghahnaviyeh S, Smith M, Xia Y, Dousis A, Grossfield A, Sur S. Ionizable Amino Lipids Distribution and Effects on DSPC/Cholesterol Membranes: Implications for Lipid Nanoparticle Structure. J Phys Chem B 2023; 127:6928-6939. [PMID: 37498794 PMCID: PMC10424244 DOI: 10.1021/acs.jpcb.3c01296] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2023] [Revised: 06/05/2023] [Indexed: 07/29/2023]
Abstract
Lipid nanoparticles (LNPs) containing ionizable aminolipids are among the leading platforms for the successful delivery of nucleic-acid-based therapeutics, including messenger RNA (mRNA). The two recently FDA-approved COVID-19 vaccines developed by Moderna and Pfizer/BioNTech belong to this category. Ionizable aminolipids, cholesterol, and DSPC lipids are among the key components of such formulations, crucially modulating physicochemical properties of these formulations and, consequently, the potency of these therapeutics. Despite the importance of these components, the distribution of these molecules in LNPs containing mRNA is not clear. In this study, we used all-atom molecular dynamics (MD) simulations to investigate the distribution and effects of the Lipid-5 (apparent pKa of the lipid nanoparticle = 6.56), a rationally designed and previously reported ionizable aminolipid by Moderna, on lipid bilayers [Mol. Ther. 2018, 26, 1509-1519]. The simulations were conducted with half of the aminolipids charged and half neutral approximately to the expected ionization in the microenvironment of the LNP surface. In all five simulated systems in this work, the cholesterol content was kept constant, whereas the DSPC and Lipid-5 concentrations were changed systematically. We found that at higher concentrations of the ionizable aminolipids, the neutral aminolipids form a disordered aggregate in the membrane interior that preferentially includes cholesterol. The rules underlying the lipid redistribution could be used to rationally choose lipids to optimize the LNP function.
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Affiliation(s)
- Sepehr Dehghani-Ghahnaviyeh
- Moderna,
Inc., Cambridge, Massachusetts 02139, United States
- Theoretical
and Computational Biophysics Group, NIH Center for Macromolecular
Modeling and Bioinformatics, Beckman Institute for Advanced Science
and Technology, Department of Biochemistry, and Center for Biophysics
and Quantitative Biology, University of
Illinois at Urbana−Champaign, Urbana, Illinois 61820, United States
| | - Michael Smith
- Moderna,
Inc., Cambridge, Massachusetts 02139, United States
| | - Yan Xia
- Moderna,
Inc., Cambridge, Massachusetts 02139, United States
| | | | - Alan Grossfield
- Department
of Biochemistry and Biophysics, University
of Rochester Medical Center, Rochester, New York 14642, United States
| | - Sreyoshi Sur
- Moderna,
Inc., Cambridge, Massachusetts 02139, United States
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8
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Tang Q, Sinclair M, Hasdemir HS, Stein R, Karakas E, Tajkhorshid E, Mchaourab H. Asymmetric conformations and lipid interactions shape the ATP-coupled cycle of a heterodimeric ABC transporter. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.29.541986. [PMID: 37398337 PMCID: PMC10312460 DOI: 10.1101/2023.05.29.541986] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
To illuminate the structural origin of catalytic asymmetry of heterodimeric ABC transporters and how it shapes the energetics of their conformational cycles, we used cryo-electron microscopy (cryo-EM), double electron-electron resonance spectroscopy (DEER), and molecular dynamics (MD) simulations, to capture and characterize conformational states of the heterodimeric ABC multidrug exporter BmrCD in lipid nanodiscs. In addition to multiple ATP- and substrate-bound inward-facing (IF) conformations, we obtained the structure of an occluded (OC) conformation wherein the unique extracellular domain (ECD) twists to partially open the extracellular gate. In conjunction with DEER analysis of the populations of these conformations, the structures reveal that ATP-powered isomerization entails changes in the relative symmetry of the BmrC and BmrD subunits that propagates from the transmembrane domain (TMD) to the nucleotide binding domain (NBD). The structures uncover asymmetric substrate and Mg 2+ binding which we hypothesize are required for triggering ATP hydrolysis preferentially in one of the nucleotide-binding sites. MD simulations demonstrated that multiple lipid molecules, identified from the cryo-EM density maps, differentially bind the IF versus the OC conformation thus modulating their relative stability. In addition to establishing how lipid interactions with BmrCD modulate the energy landscape, our findings are framed in a distinct transport model that highlights the role of asymmetric conformations in the ATP-coupled cycle with implications to the mechanism of ABC transporters in general.
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9
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Nguyen ATP, Weigle AT, Shukla D. Functional Regulation of Aquaporin Dynamics by Lipid Bilayer Composition. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.20.549977. [PMID: 37502896 PMCID: PMC10370204 DOI: 10.1101/2023.07.20.549977] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
With the diversity of lipid-protein interactions, any observed membrane protein dynamics or functions directly depend on the lipid bilayer selection. However, the implications of lipid bilayer choice are seldom considered unless characteristic lipid-protein interactions have been previously reported. Using molecular dynamics simulation, we characterize the effects of membrane embedding on plant aquaporin SoPIP2;1, which has no reported high-affinity lipid interactions. The regulatory impacts of a realistic lipid bilayer, and nine different homogeneous bilayers, on varying SoPIP2;1 dynamics were examined. We demonstrate that SoPIP2;1s structure, thermodynamics, kinetics, and water transport are altered as a function of each membrane construct's ensemble properties. Notably, the realistic bilayer provides stabilization of non-functional SoPIP2;1 metastable states. Hydrophobic mismatch and lipid order parameter calculations further explain how lipid ensemble properties manipulate SoPIP2;1 behavior. Our results illustrate the importance of careful bilayer selection when studying membrane proteins. To this end, we advise cautionary measures when performing membrane protein molecular dynamics simulations.
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Affiliation(s)
- Anh T P Nguyen
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, IL 61801
| | - Austin T Weigle
- Department of Chemistry, University of Illinois at Urbana-Champaign, IL 61801
| | - Diwakar Shukla
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, IL 61801
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, IL 61801
- Department of Bioengineering, University of Illinois at Urbana-Champaign, IL 61801
- Department of Plant Biology, University of Illinois at Urbana-Champaign, IL 61801
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10
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Yang D, Zhao Z, Tajkhorshid E, Gouaux E. Structures and membrane interactions of native serotonin transporter in complexes with psychostimulants. Proc Natl Acad Sci U S A 2023; 120:e2304602120. [PMID: 37436958 PMCID: PMC10629533 DOI: 10.1073/pnas.2304602120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Accepted: 05/03/2023] [Indexed: 07/14/2023] Open
Abstract
The serotonin transporter (SERT) is a member of the SLC6 neurotransmitter transporter family that mediates serotonin reuptake at presynaptic nerve terminals. SERT is the target of both therapeutic antidepressant drugs and psychostimulant substances such as cocaine and methamphetamines, which are small molecules that perturb normal serotonergic transmission by interfering with serotonin transport. Despite decades of studies, important functional aspects of SERT such as the oligomerization state of native SERT and its interactions with potential proteins remain unresolved. Here, we develop methods to isolate SERT from porcine brain (pSERT) using a mild, nonionic detergent, utilize fluorescence-detection size-exclusion chromatography to investigate its oligomerization state and interactions with other proteins, and employ single-particle cryo-electron microscopy to elucidate the structures of pSERT in complexes with methamphetamine or cocaine, providing structural insights into psychostimulant recognition and accompanying pSERT conformations. Methamphetamine and cocaine both bind to the central site, stabilizing the transporter in an outward open conformation. We also identify densities attributable to multiple cholesterol or cholesteryl hemisuccinate (CHS) molecules, as well as to a detergent molecule bound to the pSERT allosteric site. Under our conditions of isolation, we find that pSERT is best described as a monomeric entity, isolated without interacting proteins, and is ensconced by multiple cholesterol or CHS molecules.
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Affiliation(s)
- Dongxue Yang
- Vollum Institute, Oregon Health and Science University, Portland, OR97239
| | - Zhiyu Zhao
- Department of Biochemistry, NIH Center for Macromolecular Modeling and Visualization, Beckman Institute for Advanced Science and Technology, and Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL61801
| | - Emad Tajkhorshid
- Department of Biochemistry, NIH Center for Macromolecular Modeling and Visualization, Beckman Institute for Advanced Science and Technology, and Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL61801
| | - Eric Gouaux
- Vollum Institute, Oregon Health and Science University, Portland, OR97239
- HHMI, Oregon Health and Science University, Portland, OR97239
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11
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Bondarenko V, Chen Q, Singewald K, Haloi N, Tillman TS, Howard RJ, Lindahl E, Xu Y, Tang P. Structural Elucidation of Ivermectin Binding to α7nAChR and the Induced Channel Desensitization. ACS Chem Neurosci 2023; 14:1156-1165. [PMID: 36821490 PMCID: PMC10020961 DOI: 10.1021/acschemneuro.2c00783] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/24/2023] Open
Abstract
The α7 nicotinic acetylcholine receptor (α7nAChR) mediates signaling in the central nervous system and cholinergic anti-inflammatory pathways. Ivermectin is a positive allosteric modulator of a full-length α7nAChR and an agonist of the α7nAChR construct containing transmembrane (TMD) and intracellular (ICD) domains, but structural insights of the binding have not previously been determined. Here, combining nuclear magnetic resonance as a primary experimental tool with Rosetta comparative modeling and molecular dynamics simulations, we have revealed details of ivermectin binding to the α7nAChR TMD + ICD and corresponding structural changes in an ivermectin-induced desensitized state. Ivermectin binding was stabilized predominantly by hydrophobic interactions from interfacial residues between adjacent subunits near the extracellular end of the TMD, where the inter-subunit gap was substantially expanded in comparison to the apo structure. The ion-permeation pathway showed a profile distinctly different from the resting-state profile but similar to profiles of desensitized α7nAChR. The ICD also exhibited structural changes, including reorientation of the MX and h3 helices relative to the channel axis. The resulting structures of the α7nAChR TMD + ICD in complex with ivermectin provide opportunities for discovering new modulators of therapeutic potential and exploring the structural basis of cytoplasmic signaling under different α7nAChR functional states.
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Affiliation(s)
- Vasyl Bondarenko
- Department
of Anesthesiology and Perioperative Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Qiang Chen
- Department
of Anesthesiology and Perioperative Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Kevin Singewald
- Department
of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Nandan Haloi
- Department
of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, PO Box 1031, SE-17121 Solna, Sweden
- Department
of Applied Physics, Swedish e-Science Research Center, KTH Royal Institute of Technology, PO Box 1031, SE-17121 Solna, Sweden
| | - Tommy S. Tillman
- Department
of Anesthesiology and Perioperative Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Rebecca J. Howard
- Department
of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, PO Box 1031, SE-17121 Solna, Sweden
- Department
of Applied Physics, Swedish e-Science Research Center, KTH Royal Institute of Technology, PO Box 1031, SE-17121 Solna, Sweden
| | - Erik Lindahl
- Department
of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, PO Box 1031, SE-17121 Solna, Sweden
- Department
of Applied Physics, Swedish e-Science Research Center, KTH Royal Institute of Technology, PO Box 1031, SE-17121 Solna, Sweden
| | - Yan Xu
- Department
of Anesthesiology and Perioperative Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
- Department
of Pharmacology and Chemical Biology, University
of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
- Department
of Structural Biology, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
- Department
of Physics and Astronomy, University of
Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Pei Tang
- Department
of Anesthesiology and Perioperative Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
- Department
of Pharmacology and Chemical Biology, University
of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
- Department
of Computational and Systems Biology, University
of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
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12
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Sousa CF, Becker RA, Lehr CM, Kalinina OV, Hub JS. Simulated Tempering-Enhanced Umbrella Sampling Improves Convergence of Free Energy Calculations of Drug Membrane Permeation. J Chem Theory Comput 2023; 19:1898-1907. [PMID: 36853966 DOI: 10.1021/acs.jctc.2c01162] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/02/2023]
Abstract
Molecular dynamics simulations have been widely used to study solute permeation across biological membranes. The potential of mean force (PMF) for solute permeation is typically computed using enhanced sampling techniques such as umbrella sampling (US). For bulky drug-like permeants, however, obtaining converged PMFs remains challenging and often requires long simulation times, resulting in an unacceptable computational cost. Here, we augmented US with simulated tempering (ST), an extended-ensemble technique that consists in varying the temperature of the system along a pre-defined temperature ladder. Simulated tempering-enhanced US (STeUS) was employed to improve the convergence of PMF calculations for the permeation of methanol and three common drug molecules. To obtain sufficient sampling of the umbrella histograms, which were computed only from the ground temperature, we modified the simulation time fraction spent at the ground temperature between 1/K and 50%, where K is the number of ST temperature states. We found that STeUS accelerates convergence, when compared to standard US, and that the benefit of STeUS is system-dependent. For bulky molecules, for which standard US poorly converged, the application of ST was highly successful, leading to a more than fivefold accelerated convergence of the PMFs. For the small methanol solute, for which conventional US converges moderately, the application of ST is only beneficial if 50% of the STeUS simulation time is spent at the ground temperature. This study establishes STeUS as an efficient and simple method for PMF calculations, thereby strongly reducing the computational cost of routine high-throughput studies of drug permeability.
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Affiliation(s)
- Carla F Sousa
- Drug Bioinformatics Group, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), 66123 Saarbrücken, Germany.,Department of Biological Barriers and Drug Delivery, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), 66123 Saarbrücken, Germany
| | - Robert A Becker
- Theoretical Physics and Center for Biophysics (ZBP), Saarland University, 66123 Saarbrücken, Germany
| | - Claus-Michael Lehr
- Department of Biological Barriers and Drug Delivery, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), 66123 Saarbrücken, Germany.,Department of Pharmacy, Saarland University, 66123 Saarbrücken, Germany
| | - Olga V Kalinina
- Drug Bioinformatics Group, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), 66123 Saarbrücken, Germany.,Center for Bioinformatics, Saarland University, 66123 Saarbrücken, Germany.,Medical Faculty, Saarland University, 66421 Homburg, Germany
| | - Jochen S Hub
- Theoretical Physics and Center for Biophysics (ZBP), Saarland University, 66123 Saarbrücken, Germany
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13
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Sarkar D, Kulke M, Vermaas JV. LongBondEliminator: A Molecular Simulation Tool to Remove Ring Penetrations in Biomolecular Simulation Systems. Biomolecules 2023; 13:biom13010107. [PMID: 36671493 PMCID: PMC9856086 DOI: 10.3390/biom13010107] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 12/30/2022] [Accepted: 01/01/2023] [Indexed: 01/07/2023] Open
Abstract
We develop a workflow, implemented as a plugin to the molecular visualization program VMD, that can fix ring penetrations with minimal user input. LongBondEliminator, detects ring piercing artifacts by the long, strained bonds that are the local minimum energy conformation during minimization for some assembled simulation system. The LongBondEliminator tool then automatically treats regions near these long bonds using multiple biases applied through NAMD. By combining biases implemented through the collective variables module, density-based forces, and alchemical techniques in NAMD, LongBondEliminator will iteratively alleviate long bonds found within molecular simulation systems. Through three concrete examples with increasing complexity, a lignin polymer, an viral capsid assembly, and a large, highly glycosylated protein aggrecan, we demonstrate the utility for this method in eliminating ring penetrations from classical MD simulation systems. The tool is available via gitlab as a VMD plugin, and has been developed to be generically useful across a variety of biomolecular simulations.
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14
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Dastvan R, Rasouli A, Dehghani-Ghahnaviyeh S, Gies S, Tajkhorshid E. Proton-driven alternating access in a spinster lipid transporter. Nat Commun 2022; 13:5161. [PMID: 36055994 PMCID: PMC9440201 DOI: 10.1038/s41467-022-32759-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 08/16/2022] [Indexed: 11/16/2022] Open
Abstract
Spinster (Spns) lipid transporters are critical for transporting sphingosine-1-phosphate (S1P) across cellular membranes. In humans, Spns2 functions as the main S1P transporter in endothelial cells, making it a potential drug target for modulating S1P signaling. Here, we employed an integrated approach in lipid membranes to identify unknown conformational states of a bacterial Spns from Hyphomonas neptunium (HnSpns) and to define its proton- and substrate-coupled conformational dynamics. Our systematic study reveals conserved residues critical for protonation steps and their regulation, and how sequential protonation of these proton switches coordinates the conformational transitions in the context of a noncanonical ligand-dependent alternating access. A conserved periplasmic salt bridge (Asp60TM2:Arg289TM7) keeps the transporter in a closed conformation, while proton-dependent conformational dynamics are significantly enhanced on the periplasmic side, providing a pathway for ligand exchange. The Spns lipid transporters use ion gradients to drive substrate transport, including bioactive sphingolipids. Here, Dastvan et al. investigated how binding of protons powers the conformational changes that enable broad transport by a bacterial Spns.
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Affiliation(s)
- Reza Dastvan
- Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, MO, 63104, USA.
| | - Ali Rasouli
- Theoretical and Computational Biophysics Group, NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, Department of Biochemistry, and Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Sepehr Dehghani-Ghahnaviyeh
- Theoretical and Computational Biophysics Group, NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, Department of Biochemistry, and Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Samantha Gies
- Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, MO, 63104, USA
| | - Emad Tajkhorshid
- Theoretical and Computational Biophysics Group, NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, Department of Biochemistry, and Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
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15
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Jeong H, Clark S, Goehring A, Dehghani-Ghahnaviyeh S, Rasouli A, Tajkhorshid E, Gouaux E. Structures of the TMC-1 complex illuminate mechanosensory transduction. Nature 2022; 610:796-803. [PMID: 36224384 PMCID: PMC9605866 DOI: 10.1038/s41586-022-05314-8] [Citation(s) in RCA: 47] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Accepted: 08/02/2022] [Indexed: 02/05/2023]
Abstract
The initial step in the sensory transduction pathway underpinning hearing and balance in mammals involves the conversion of force into the gating of a mechanosensory transduction channel1. Despite the profound socioeconomic impacts of hearing disorders and the fundamental biological significance of understanding mechanosensory transduction, the composition, structure and mechanism of the mechanosensory transduction complex have remained poorly characterized. Here we report the single-particle cryo-electron microscopy structure of the native transmembrane channel-like protein 1 (TMC-1) mechanosensory transduction complex isolated from Caenorhabditis elegans. The two-fold symmetric complex is composed of two copies each of the pore-forming TMC-1 subunit, the calcium-binding protein CALM-1 and the transmembrane inner ear protein TMIE. CALM-1 makes extensive contacts with the cytoplasmic face of the TMC-1 subunits, whereas the single-pass TMIE subunits reside on the periphery of the complex, poised like the handles of an accordion. A subset of complexes additionally includes a single arrestin-like protein, arrestin domain protein (ARRD-6), bound to a CALM-1 subunit. Single-particle reconstructions and molecular dynamics simulations show how the mechanosensory transduction complex deforms the membrane bilayer and suggest crucial roles for lipid-protein interactions in the mechanism by which mechanical force is transduced to ion channel gating.
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Affiliation(s)
- Hanbin Jeong
- grid.433851.80000 0004 0608 3919Vollum Institute, Oregon Health and Science University, Portland, OR USA
| | - Sarah Clark
- grid.433851.80000 0004 0608 3919Vollum Institute, Oregon Health and Science University, Portland, OR USA
| | - April Goehring
- grid.433851.80000 0004 0608 3919Vollum Institute, Oregon Health and Science University, Portland, OR USA ,grid.5288.70000 0000 9758 5690Howard Hughes Medical Institute, Oregon Health and Science University, Portland, OR USA
| | - Sepehr Dehghani-Ghahnaviyeh
- grid.35403.310000 0004 1936 9991Theoretical and Computational Biophysics Group, NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL USA ,grid.35403.310000 0004 1936 9991Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL USA ,grid.35403.310000 0004 1936 9991Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL USA
| | - Ali Rasouli
- grid.35403.310000 0004 1936 9991Theoretical and Computational Biophysics Group, NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL USA ,grid.35403.310000 0004 1936 9991Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL USA ,grid.35403.310000 0004 1936 9991Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL USA
| | - Emad Tajkhorshid
- grid.35403.310000 0004 1936 9991Theoretical and Computational Biophysics Group, NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL USA ,grid.35403.310000 0004 1936 9991Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL USA ,grid.35403.310000 0004 1936 9991Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL USA
| | - Eric Gouaux
- grid.433851.80000 0004 0608 3919Vollum Institute, Oregon Health and Science University, Portland, OR USA ,grid.5288.70000 0000 9758 5690Howard Hughes Medical Institute, Oregon Health and Science University, Portland, OR USA
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