1
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Yu X, Matico RE, Miller R, Chauhan D, Van Schoubroeck B, Grauwen K, Suarez J, Pietrak B, Haloi N, Yin Y, Tresadern GJ, Perez-Benito L, Lindahl E, Bottelbergs A, Oehlrich D, Van Opdenbosch N, Sharma S. Structural basis for the oligomerization-facilitated NLRP3 activation. Nat Commun 2024; 15:1164. [PMID: 38326375 PMCID: PMC10850481 DOI: 10.1038/s41467-024-45396-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Accepted: 01/19/2024] [Indexed: 02/09/2024] Open
Abstract
The NACHT-, leucine-rich-repeat-, and pyrin domain-containing protein 3 (NLRP3) is a critical intracellular inflammasome sensor and an important clinical target against inflammation-driven human diseases. Recent studies have elucidated its transition from a closed cage to an activated disk-like inflammasome, but the intermediate activation mechanism remains elusive. Here we report the cryo-electron microscopy structure of NLRP3, which forms an open octamer and undergoes a ~ 90° hinge rotation at the NACHT domain. Mutations on open octamer's interfaces reduce IL-1β signaling, highlighting its essential role in NLRP3 activation/inflammasome assembly. The centrosomal NIMA-related kinase 7 (NEK7) disrupts large NLRP3 oligomers and forms NEK7/NLRP3 monomers/dimers which is a critical step preceding the assembly of the disk-like inflammasome. These data demonstrate an oligomeric cooperative activation of NLRP3 and provide insight into its inflammasome assembly mechanism.
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Affiliation(s)
- Xiaodi Yu
- Johnson & Johnson Innovation Medicine, Spring House, PA, 19044, USA.
| | - Rosalie E Matico
- Johnson & Johnson Innovation Medicine, Spring House, PA, 19044, USA
| | - Robyn Miller
- Johnson & Johnson Innovation Medicine, Spring House, PA, 19044, USA
| | - Dhruv Chauhan
- Johnson & Johnson Innovation Medicine, J&J Interventional Oncology, Beerse, Belgium
| | | | - Karolien Grauwen
- Johnson & Johnson Innovation Medicine, J&J Interventional Oncology, Beerse, Belgium
| | - Javier Suarez
- Johnson & Johnson Innovation Medicine, Spring House, PA, 19044, USA
| | - Beth Pietrak
- Johnson & Johnson Innovation Medicine, Spring House, PA, 19044, USA
| | - Nandan Haloi
- Department of Applied Physics, Swedish e-Science Research Center, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Yanting Yin
- Johnson & Johnson Innovation Medicine, Spring House, PA, 19044, USA
| | | | - Laura Perez-Benito
- Johnson & Johnson Innovation Medicine, Discovery Sciences, Beerse, Belgium
| | - Erik Lindahl
- Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, Stockholm, Sweden
| | - Astrid Bottelbergs
- Johnson & Johnson Innovation Medicine, Discovery Sciences, Beerse, Belgium
| | - Daniel Oehlrich
- Johnson & Johnson Innovation Medicine, Discovery Sciences, Beerse, Belgium
| | - Nina Van Opdenbosch
- Johnson & Johnson Innovation Medicine, J&J Interventional Oncology, Beerse, Belgium
| | - Sujata Sharma
- Johnson & Johnson Innovation Medicine, Spring House, PA, 19044, USA
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2
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Haloi N, Huang S, Nichols AL, Fine EJ, Friesenhahn NJ, Marotta CB, Dougherty DA, Lindahl E, Howard RJ, Mayo SL, Lester HA. Interactive computational and experimental approaches improve the sensitivity of periplasmic binding protein-based nicotine biosensors for measurements in biofluids. Protein Eng Des Sel 2024; 37:gzae003. [PMID: 38302088 PMCID: PMC10896302 DOI: 10.1093/protein/gzae003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2023] [Revised: 01/17/2024] [Accepted: 01/29/2024] [Indexed: 02/03/2024] Open
Abstract
We developed fluorescent protein sensors for nicotine with improved sensitivity. For iNicSnFR12 at pH 7.4, the proportionality constant for ∆F/F0vs [nicotine] (δ-slope, 2.7 μM-1) is 6.1-fold higher than the previously reported iNicSnFR3a. The activated state of iNicSnFR12 has a fluorescence quantum yield of at least 0.6. We measured similar dose-response relations for the nicotine-induced absorbance increase and fluorescence increase, suggesting that the absorbance increase leads to the fluorescence increase via the previously described nicotine-induced conformational change, the 'candle snuffer' mechanism. Molecular dynamics (MD) simulations identified a binding pose for nicotine, previously indeterminate from experimental data. MD simulations also showed that Helix 4 of the periplasmic binding protein (PBP) domain appears tilted in iNicSnFR12 relative to iNicSnFR3a, likely altering allosteric network(s) that link the ligand binding site to the fluorophore. In thermal melt experiments, nicotine stabilized the PBP of the tested iNicSnFR variants. iNicSnFR12 resolved nicotine in diluted mouse and human serum at 100 nM, the peak [nicotine] that occurs during smoking or vaping, and possibly at the decreasing levels during intervals between sessions. NicSnFR12 was also partially activated by unidentified endogenous ligand(s) in biofluids. Improved iNicSnFR12 variants could become the molecular sensors in continuous nicotine monitors for animal and human biofluids.
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Affiliation(s)
- Nandan Haloi
- Department of Applied Physics, Science for Life Laboratory, KTH Royal Institute of Technology, Stockholm 10044, Sweden
| | - Shan Huang
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Aaron L Nichols
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Eve J Fine
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Nicholas J Friesenhahn
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Christopher B Marotta
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Dennis A Dougherty
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Erik Lindahl
- Department of Applied Physics, Science for Life Laboratory, KTH Royal Institute of Technology, Stockholm 10044, Sweden
- Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, Stockholm 10691, Sweden
| | - Rebecca J Howard
- Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, Stockholm 10691, Sweden
| | - Stephen L Mayo
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Henry A Lester
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
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3
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Haloi N, Huang S, Nichols AL, Fine EJ, Friesenhahn NJ, Marotta CB, Dougherty DA, Lindahl E, Howard RJ, Mayo SL, Lester HA. Interactive computational and experimental approaches improve the sensitivity of periplasmic binding protein-based nicotine biosensors for measurements in biofluids. bioRxiv 2024:2023.01.16.524298. [PMID: 36712031 PMCID: PMC9882114 DOI: 10.1101/2023.01.16.524298] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
We developed fluorescent protein sensors for nicotine with improved sensitivity. For iNicSnFR12 at pH 7.4, the proportionality constant for Δ F / F 0 vs [nicotine] (δ-slope, 2.7 μM-1) is 6.1-fold higher than the previously reported iNicSnFR3a. The activated state of iNicSnFR12 has a fluorescence quantum yield of at least 0.6. We measured similar dose-response relations for the nicotine-induced absorbance increase and fluorescence increase, suggesting that the absorbance increase leads to the fluorescence increase via the previously described nicotine-induced conformational change, the "candle snuffer" mechanism. Molecular dynamics (MD) simulations identified a binding pose for nicotine, previously indeterminate from experimental data. MD simulations also showed that Helix 4 of the periplasmic binding protein (PBP) domain appears tilted in iNicSnFR12 relative to iNicSnFR3a, likely altering allosteric network(s) that link the ligand binding site to the fluorophore. In thermal melt experiments, nicotine stabilized the PBP of the tested iNicSnFR variants. iNicSnFR12 resolved nicotine in diluted mouse and human serum at 100 nM, the peak [nicotine] that occurs during smoking or vaping, and possibly at the decreasing levels during intervals between sessions. NicSnFR12 was also partially activated by unidentified endogenous ligand(s) in biofluids. Improved iNicSnFR12 variants could become the molecular sensors in continuous nicotine monitors for animal and human biofluids.
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Affiliation(s)
- Nandan Haloi
- Department of Applied Physics, Science for Life Laboratory, KTH Royal Institute of Technology, 10044 Stockholm, Sweden
| | - Shan Huang
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena CA 91125 USA
| | - Aaron L Nichols
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena CA 91125 USA
| | - Eve J Fine
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena CA 91125 USA
| | - Nicholas J Friesenhahn
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena CA 91125 USA
| | - Christopher B Marotta
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena CA 91125 USA
| | - Dennis A Dougherty
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena CA 91125 USA
| | - Erik Lindahl
- Department of Applied Physics, Science for Life Laboratory, KTH Royal Institute of Technology, 10044 Stockholm, Sweden
- Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, 10691 Stockholm, Sweden
| | - Rebecca J Howard
- Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, 10691 Stockholm, Sweden
| | - Stephen L Mayo
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena CA 91125 USA
| | - Henry A Lester
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena CA 91125 USA
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4
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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5
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Dey S, Patel A, Haloi N, Srimayee S, Paul S, Barik GK, Akhtar N, Shaw D, Hazarika G, Prusty BM, Kumar M, Santra MK, Tajkhorshid E, Bhattacharjee S, Manna D. Quinoline Thiourea-Based Zinc Ionophores with Antibacterial Activity. J Med Chem 2023; 66:11078-11093. [PMID: 37466499 DOI: 10.1021/acs.jmedchem.3c00368] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/20/2023]
Abstract
The increasing resistance of bacteria to commercially available antibiotics threatens patient safety in healthcare settings. Perturbation of ion homeostasis has emerged as a potential therapeutic strategy to fight against antibacterial resistance and other channelopathies. This study reports the development of 8-aminoquinoline (QN) derivatives and their transmembrane Zn2+ transport activities. Our findings showed that a potent QN-based Zn2+ transporter exhibits promising antibacterial properties against Gram-positive bacteria with reduced hemolytic activity and cytotoxicity to mammalian cells. Furthermore, this combination showed excellent in vivo efficacy against Staphylococcus aureus. Interestingly, this combination prevented bacterial resistance and restored susceptibility of gentamicin and methicillin-resistant S. aureus to commercially available β-lactam and other antibiotics that had lost their activity against the drug-resistant bacterial strain. Our findings suggest that the transmembrane transport of Zn2+ by QN derivatives could be a promising strategy to combat bacterial infections and restore the activity of other antibiotics.
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Affiliation(s)
- Subhasis Dey
- Department of Chemistry, Indian Institute of Technology Guwahati, Guwahati, Assam 781039, India
| | - Anjali Patel
- Centre for Environment, Indian Institute of Technology Guwahati, Guwahati, Assam 781039, India
| | - Nandan Haloi
- 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 61801, United States
| | - Soumya Srimayee
- Department of Chemistry, Indian Institute of Technology Guwahati, Guwahati, Assam 781039, India
| | - Suman Paul
- Department of Molecular Biology and Bioinformatics, Tripura University (A Central University), Suryamaninagar, Tripura 799022, India
| | | | - Nasim Akhtar
- Department of Chemistry, Indian Institute of Technology Guwahati, Guwahati, Assam 781039, India
| | - Dipanjan Shaw
- Department of Chemistry, Indian Institute of Technology Guwahati, Guwahati, Assam 781039, India
| | - Gunanka Hazarika
- Centre for Environment, Indian Institute of Technology Guwahati, Guwahati, Assam 781039, India
| | - Biswa Mohan Prusty
- Department of Chemistry, Indian Institute of Technology Guwahati, Guwahati, Assam 781039, India
| | - Mohit Kumar
- Department of Chemistry, Indian Institute of Technology Guwahati, Guwahati, Assam 781039, India
| | | | - 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, Illinois 61801, United States
| | - Surajit Bhattacharjee
- Department of Molecular Biology and Bioinformatics, Tripura University (A Central University), Suryamaninagar, Tripura 799022, India
| | - Debasis Manna
- Department of Chemistry, Indian Institute of Technology Guwahati, Guwahati, Assam 781039, India
- Centre for Environment, Indian Institute of Technology Guwahati, Guwahati, Assam 781039, India
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6
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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7
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Mishra J, Yang M, Cheng Q, Haloi N, Tajkhorshid E, Camara AK, Kwok WM. Site-specific phosphorylation of VDAC1 dictates the susceptibility to cardiac ischemia/reperfusion injury and cell death. Biophys J 2022. [DOI: 10.1016/j.bpj.2021.11.240] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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8
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Vasan AK, Haloi N, Geddes E, Prasanna A, Wen PC, Metcalf WW, Hergenrother P, Tajkhorshid E. Characterizing permeation energetics and mechanisms through membrane transport proteins in high-dimensional conformational space. Biophys J 2022. [DOI: 10.1016/j.bpj.2021.11.2759] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
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9
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Haloi N, Vasan AK, Geddes EJ, Prasanna A, Wen PC, Metcalf WW, Hergenrother PJ, Tajkhorshid E. Rationalizing the generation of broad spectrum antibiotics with the addition of a positive charge. Chem Sci 2021; 12:15028-15044. [PMID: 34909143 PMCID: PMC8612397 DOI: 10.1039/d1sc04445a] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Accepted: 10/13/2021] [Indexed: 11/28/2022] Open
Abstract
Antibiotic resistance of Gram-negative bacteria is largely attributed to the low permeability of their outer membrane (OM). Recently, we disclosed the eNTRy rules, a key lesson of which is that the introduction of a primary amine enhances OM permeation in certain contexts. To understand the molecular basis for this finding, we perform an extensive set of molecular dynamics (MD) simulations and free energy calculations comparing the permeation of aminated and amine-free antibiotic derivatives through the most abundant OM porin of E. coli, OmpF. To improve sampling of conformationally flexible drugs in MD simulations, we developed a novel, Monte Carlo and graph theory based algorithm to probe more efficiently the rotational and translational degrees of freedom visited during the permeation of the antibiotic molecule through OmpF. The resulting pathways were then used for free-energy calculations, revealing a lower barrier against the permeation of the aminated compound, substantiating its greater OM permeability. Further analysis revealed that the amine facilitates permeation by enabling the antibiotic to align its dipole to the luminal electric field of the porin and form favorable electrostatic interactions with specific, highly-conserved charged residues. The importance of these interactions in permeation was further validated with experimental mutagenesis and whole cell accumulation assays. Overall, this study provides insights on the importance of the primary amine for antibiotic permeation into Gram-negative pathogens that could help the design of future antibiotics. We also offer a new computational approach for calculating free-energy of processes where relevant molecular conformations cannot be efficiently captured. A rapid pathway sampling method combining Monte Carlo and graph theory, developed to describe permeation pathways through outer membrane porins, can distinguish between structurally similar analogs with different permeabilities.![]()
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Affiliation(s)
- Nandan Haloi
- Theoretical and Computational Biophysics Group, NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, Department of Biochemistry, Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign Urbana IL 61801 USA
| | - Archit Kumar Vasan
- Theoretical and Computational Biophysics Group, NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, Department of Biochemistry, Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign Urbana IL 61801 USA
| | - Emily J Geddes
- Department of Chemistry, University of Illinois at Urbana-Champaign Urbana IL 61801 USA.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign Urbana IL 61801 USA
| | - Arjun Prasanna
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign Urbana IL 61801 USA.,Department of Microbiology, University of Illinois at Urbana-Champaign Urbana IL 61801 USA
| | - Po-Chao Wen
- Theoretical and Computational Biophysics Group, NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, Department of Biochemistry, Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign Urbana IL 61801 USA
| | - William W Metcalf
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign Urbana IL 61801 USA.,Department of Microbiology, University of Illinois at Urbana-Champaign Urbana IL 61801 USA
| | - Paul J Hergenrother
- Department of Chemistry, University of Illinois at Urbana-Champaign Urbana IL 61801 USA.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign Urbana IL 61801 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, Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign Urbana IL 61801 USA
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10
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Haloi N, Vasan A, Hergenrother P, Tajkhorshid E. Role of the Internal Loops in Gating of Outer Membrane Porins. Biophys J 2021. [DOI: 10.1016/j.bpj.2020.11.1002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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11
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Vasan AK, Haloi N, Wen PC, Tajkhorshid E. Monte Carlo Pathway Search (MCPS) for Exploring Permeation Pathways in High-Dimensional Conformational Space. Biophys J 2021. [DOI: 10.1016/j.bpj.2020.11.721] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
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12
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Petroff JT, Omlid SM, Haloi N, Sith L, Johnson S, McCulla RD. Reactions of sulfenic acids with amines, thiols, and thiolates studied by quantum chemical calculations. COMPUT THEOR CHEM 2020. [DOI: 10.1016/j.comptc.2020.112979] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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13
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Kumar Bharathkar S, Parker BW, Malyutin AG, Haloi N, Huey-Tubman KE, Tajkhorshid E, Stadtmueller BM. The structures of secretory and dimeric immunoglobulin A. eLife 2020; 9:56098. [PMID: 33107820 PMCID: PMC7707832 DOI: 10.7554/elife.56098] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Accepted: 10/26/2020] [Indexed: 12/19/2022] Open
Abstract
Secretory (S) Immunoglobulin (Ig) A is the predominant mucosal antibody, which binds pathogens and commensal microbes. SIgA is a polymeric antibody, typically containing two copies of IgA that assemble with one joining-chain (JC) to form dimeric (d) IgA that is bound by the polymeric Ig-receptor ectodomain, called secretory component (SC). Here, we report the cryo-electron microscopy structures of murine SIgA and dIgA. Structures reveal two IgAs conjoined through four heavy-chain tailpieces and the JC that together form a β-sandwich-like fold. The two IgAs are bent and tilted with respect to each other, forming distinct concave and convex surfaces. In SIgA, SC is bound to one face, asymmetrically contacting both IgAs and JC. The bent and tilted arrangement of complex components limits the possible positions of both sets of antigen-binding fragments (Fabs) and preserves steric accessibility to receptor-binding sites, likely influencing antigen binding and effector functions.
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Affiliation(s)
- Sonya Kumar Bharathkar
- Department of Biochemistry, University of Illinois Urbana-Champaign, Urbana, United States
| | - Benjamin W Parker
- Department of Biochemistry, University of Illinois Urbana-Champaign, Urbana, United States
| | - Andrey G Malyutin
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, United States.,Beckman Institute, California Institute of Technology, Pasadena, United States
| | - Nandan Haloi
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, United States.,NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, Urbana, United States
| | - Kathryn E Huey-Tubman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, United States
| | - Emad Tajkhorshid
- Department of Biochemistry, University of Illinois Urbana-Champaign, Urbana, United States.,Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, United States.,NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, Urbana, United States
| | - Beth M Stadtmueller
- Department of Biochemistry, University of Illinois Urbana-Champaign, Urbana, United States
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14
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Cheng Q, Natarajan GK, Yang M, Wen PC, Haloi N, Tajkhorshid E, Camara AK, Kwok WM. A Phosphomimetic Mutation S215E in VDAC1 Interferes with Hekokinase Binding. Biophys J 2020. [DOI: 10.1016/j.bpj.2019.11.1124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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15
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Haloi N, Wen PC, Camara AK, Kwok WM, Tajkhorshid E. Modeling the Insertion of Hexokinase in the Mitochondrial Outer Membrane and its Complex Formation with VDAC. Biophys J 2019. [DOI: 10.1016/j.bpj.2018.11.1451] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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16
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Yang M, Grzybowski M, Cheng Q, Stowe DF, Geurts A, Wen PC, Haloi N, Tajkhorshid E, Camara AK, Kwok WM. Phosphorylation of Cardiac Mitochondrial VDAC1 at S215 Facilitates Cell Death. Biophys J 2018. [DOI: 10.1016/j.bpj.2017.11.3563] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
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17
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Gorai S, Paul D, Borah R, Haloi N, Santra MK, Manna D. Role of Cationic Groove and Hydrophobic Residues in Phosphatidylinositol-Dependent Membrane-Binding Properties of Tks5-Phox Homology Domain. ChemistrySelect 2018. [DOI: 10.1002/slct.201702558] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- Sukhamoy Gorai
- Department of Chemistry; Indian Institute of Technology Guwahati; Guwahati - 781039, Assam India
| | - Debasish Paul
- National Centre for Cell Science; Pune 411007, Maharashtra India
| | - Rituparna Borah
- Department of Chemistry; Indian Institute of Technology Guwahati; Guwahati - 781039, Assam India
| | - Nandan Haloi
- Department of Chemistry; Indian Institute of Technology Guwahati; Guwahati - 781039, Assam India
| | | | - Debasis Manna
- Department of Chemistry; Indian Institute of Technology Guwahati; Guwahati - 781039, Assam India
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18
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Gorai S, Paul D, Haloi N, Borah R, Santra MK, Manna D. Mechanistic insights into the phosphatidylinositol binding properties of the pleckstrin homology domain of lamellipodin. Mol BioSyst 2016; 12:747-57. [DOI: 10.1039/c5mb00731c] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Lpd-PH domain strongly interacts with PI(3,4)P2containing liposome without any membrane penetration.
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Affiliation(s)
- Sukhamoy Gorai
- Department of Chemistry
- Indian Institute of Technology Guwahati
- India
| | | | - Nandan Haloi
- Department of Chemistry
- Indian Institute of Technology Guwahati
- India
| | - Rituparna Borah
- Department of Chemistry
- Indian Institute of Technology Guwahati
- India
| | | | - Debasis Manna
- Department of Chemistry
- Indian Institute of Technology Guwahati
- India
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