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Drago VN, Devos JM, Blakeley MP, Forsyth VT, Parks JM, Kovalevsky A, Mueser TC. Neutron diffraction from a microgravity-grown crystal reveals the active site hydrogens of the internal aldimine form of tryptophan synthase. Cell Rep Phys Sci 2024; 5:101827. [PMID: 38645802 PMCID: PMC11027755 DOI: 10.1016/j.xcrp.2024.101827] [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: 04/23/2024]
Abstract
Pyridoxal 5'-phosphate (PLP), the biologically active form of vitamin B6, is an essential cofactor in many biosynthetic pathways. The emergence of PLP-dependent enzymes as drug targets and biocatalysts, such as tryptophan synthase (TS), has underlined the demand to understand PLP-dependent catalysis and reaction specificity. The ability of neutron diffraction to resolve the positions of hydrogen atoms makes it an ideal technique to understand how the electrostatic environment and selective protonation of PLP regulates PLP-dependent activities. Facilitated by microgravity crystallization of TS with the Toledo Crystallization Box, we report the 2.1 Å joint X-ray/neutron (XN) structure of TS with PLP in the internal aldimine form. Positions of hydrogens were directly determined in both the α- and β-active sites, including PLP cofactor. The joint XN structure thus provides insight into the selective protonation of the internal aldimine and the electrostatic environment of TS necessary to understand the overall catalytic mechanism.
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Affiliation(s)
- Victoria N. Drago
- Department of Chemistry and Biochemistry, University of Toledo, Toledo, OH 43606, USA
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Juliette M. Devos
- Life Sciences Group, Institut Laue–Langevin, 71 Avenue des Martyrs, 38000 Grenoble, France
- Partnership for Structural Biology (PSB), 38000 Grenoble, France
| | - Matthew P. Blakeley
- Large Scale Structures Group, Institut Laue–Langevin, 71 Avenue des Martyrs, 38000 Grenoble, France
| | - V. Trevor Forsyth
- Faculty of Medicine, Lund University, and LINXS Institute for Advanced Neutron and X-ray Science, Lund, Sweden
| | - Jerry M. Parks
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Andrey Kovalevsky
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Timothy C. Mueser
- Department of Chemistry and Biochemistry, University of Toledo, Toledo, OH 43606, USA
- Lead contact
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2
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Davidson RB, Coletti M, Gao M, Piatkowski B, Sreedasyam A, Quadir F, Weston DJ, Schmutz J, Cheng J, Skolnick J, Parks JM, Sedova A. Predicted structural proteome of Sphagnum divinum and proteome-scale annotation. Bioinformatics 2023; 39:btad511. [PMID: 37589594 PMCID: PMC10463551 DOI: 10.1093/bioinformatics/btad511] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Revised: 08/01/2023] [Accepted: 08/16/2023] [Indexed: 08/18/2023] Open
Abstract
MOTIVATION Sphagnum-dominated peatlands store a substantial amount of terrestrial carbon. The genus is undersampled and under-studied. No experimental crystal structure from any Sphagnum species exists in the Protein Data Bank and fewer than 200 Sphagnum-related genes have structural models available in the AlphaFold Protein Structure Database. Tools and resources are needed to help bridge these gaps, and to enable the analysis of other structural proteomes now made possible by accurate structure prediction. RESULTS We present the predicted structural proteome (25 134 primary transcripts) of Sphagnum divinum computed using AlphaFold, structural alignment results of all high-confidence models against an annotated nonredundant crystallographic database of over 90,000 structures, a structure-based classification of putative Enzyme Commission (EC) numbers across this proteome, and the computational method to perform this proteome-scale structure-based annotation. AVAILABILITY AND IMPLEMENTATION All data and code are available in public repositories, detailed at https://github.com/BSDExabio/SAFA. The structural models of the S. divinum proteome have been deposited in the ModelArchive repository at https://modelarchive.org/doi/10.5452/ma-ornl-sphdiv.
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Affiliation(s)
- Russell B Davidson
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37830, United States
| | - Mark Coletti
- Computer Science and Mathematics Division, Oak Ridge National Laboratory, Oak Ridge, TN 37830, United States
| | - Mu Gao
- Center for the Study of Systems Biology, School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, United States
| | - Bryan Piatkowski
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37830, United States
| | - Avinash Sreedasyam
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, United States
| | - Farhan Quadir
- Electrical Engineering and Computer Science, University of Missouri, Columbia, MS 65211, United States
| | - David J Weston
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37830, United States
| | - Jeremy Schmutz
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, United States
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
| | - Jianlin Cheng
- Electrical Engineering and Computer Science, University of Missouri, Columbia, MS 65211, United States
| | - Jeffrey Skolnick
- Center for the Study of Systems Biology, School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, United States
| | - Jerry M Parks
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37830, United States
| | - Ada Sedova
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37830, United States
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3
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Russell Lewis B, Uddin MR, Moniruzzaman M, Kuo KM, Higgins AJ, Shah LMN, Sobott F, Parks JM, Hammerschmid D, Gumbart JC, Zgurskaya HI, Reading E. Conformational restriction shapes the inhibition of a multidrug efflux adaptor protein. Nat Commun 2023; 14:3900. [PMID: 37463890 PMCID: PMC10354078 DOI: 10.1038/s41467-023-39615-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [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: 12/20/2022] [Accepted: 06/15/2023] [Indexed: 07/20/2023] Open
Abstract
Membrane efflux pumps play a major role in bacterial multidrug resistance. The tripartite multidrug efflux pump system from Escherichia coli, AcrAB-TolC, is a target for inhibition to lessen resistance development and restore antibiotic efficacy, with homologs in other ESKAPE pathogens. Here, we rationalize a mechanism of inhibition against the periplasmic adaptor protein, AcrA, using a combination of hydrogen/deuterium exchange mass spectrometry, cellular efflux assays, and molecular dynamics simulations. We define the structural dynamics of AcrA and find that an inhibitor can inflict long-range stabilisation across all four of its domains, whereas an interacting efflux substrate has minimal effect. Our results support a model where an inhibitor forms a molecular wedge within a cleft between the lipoyl and αβ barrel domains of AcrA, diminishing its conformational transmission of drug-evoked signals from AcrB to TolC. This work provides molecular insights into multidrug adaptor protein function which could be valuable for developing antimicrobial therapeutics.
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Affiliation(s)
- Benjamin Russell Lewis
- Department of Chemistry, King's College London, Britannia House, 7 Trinity Street, London, SE1 1DB, UK
| | - Muhammad R Uddin
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Norman, OK, 73019, USA
| | - Mohammad Moniruzzaman
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Norman, OK, 73019, USA
| | - Katie M Kuo
- School of Chemistry and Biochemistry, Georgia Institute of Technology, 837 State Street NW, Atlanta, GA, 30332, USA
| | - Anna J Higgins
- School of Molecular and Cellular Biology & Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, UK
| | - Laila M N Shah
- Department of Chemistry, King's College London, Britannia House, 7 Trinity Street, London, SE1 1DB, UK
| | - Frank Sobott
- School of Molecular and Cellular Biology & Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, UK
| | - Jerry M Parks
- Bioscience Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN, 37831, USA
| | - Dietmar Hammerschmid
- Department of Chemistry, King's College London, Britannia House, 7 Trinity Street, London, SE1 1DB, UK
| | - James C Gumbart
- School of Chemistry and Biochemistry, Georgia Institute of Technology, 837 State Street NW, Atlanta, GA, 30332, USA.
- School of Physics, Georgia Institute of Technology, 837 State Street NW, Atlanta, GA, 30332, USA.
| | - Helen I Zgurskaya
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Norman, OK, 73019, USA.
| | - Eamonn Reading
- Department of Chemistry, King's College London, Britannia House, 7 Trinity Street, London, SE1 1DB, UK.
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Leus IV, Weeks JW, Bonifay V, Shen Y, Yang L, Cooper CJ, Nath D, Duerfeldt AS, Smith JC, Parks JM, Rybenkov VV, Zgurskaya HI. Author Correction: Property space mapping of Pseudomonas aeruginosa permeability to small molecules. Sci Rep 2023; 13:8918. [PMID: 37264107 DOI: 10.1038/s41598-023-35960-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/03/2023] Open
Affiliation(s)
- Inga V Leus
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Norman, OK, 73019, USA
| | - Jon W Weeks
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Norman, OK, 73019, USA
| | - Vincent Bonifay
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Norman, OK, 73019, USA
| | - Yue Shen
- Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, TN, 37996, USA
| | - Liang Yang
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Norman, OK, 73019, USA
| | - Connor J Cooper
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Dinesh Nath
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Norman, OK, 73019, USA
| | - Adam S Duerfeldt
- Department of Medicinal Chemistry, University of Minnesota, 717 Delaware St. SE, Minneapolis, MN, 55414, USA
| | - Jeremy C Smith
- Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, TN, 37996, USA
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, TN, 37996, USA
| | - Jerry M Parks
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Valentin V Rybenkov
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Norman, OK, 73019, USA.
| | - Helen I Zgurskaya
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Norman, OK, 73019, USA.
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5
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Shen Y, Parks JM, Smith JC. HLA-Clus: HLA class I clustering based on 3D structure. BMC Bioinformatics 2023; 24:189. [PMID: 37161375 PMCID: PMC10169335 DOI: 10.1186/s12859-023-05297-x] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Accepted: 04/18/2023] [Indexed: 05/11/2023] Open
Abstract
BACKGROUND In a previous paper, we classified populated HLA class I alleles into supertypes and subtypes based on the similarity of 3D landscape of peptide binding grooves, using newly defined structure distance metric and hierarchical clustering approach. Compared to other approaches, our method achieves higher correlation with peptide binding specificity, intra-cluster similarity (cohesion), and robustness. Here we introduce HLA-Clus, a Python package for clustering HLA Class I alleles using the method we developed recently and describe additional features including a new nearest neighbor clustering method that facilitates clustering based on user-defined criteria. RESULTS The HLA-Clus pipeline includes three stages: First, HLA Class I structural models are coarse grained and transformed into clouds of labeled points. Second, similarities between alleles are determined using a newly defined structure distance metric that accounts for spatial and physicochemical similarities. Finally, alleles are clustered via hierarchical or nearest-neighbor approaches. We also interfaced HLA-Clus with the peptide:HLA affinity predictor MHCnuggets. By using the nearest neighbor clustering method to select optimal allele-specific deep learning models in MHCnuggets, the average accuracy of peptide binding prediction of rare alleles was improved. CONCLUSIONS The HLA-Clus package offers a solution for characterizing the peptide binding specificities of a large number of HLA alleles. This method can be applied in HLA functional studies, such as the development of peptide affinity predictors, disease association studies, and HLA matching for grafting. HLA-Clus is freely available at our GitHub repository ( https://github.com/yshen25/HLA-Clus ).
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Affiliation(s)
- Yue Shen
- Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, TN, 37996, USA
| | - Jerry M Parks
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Jeremy C Smith
- Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, TN, 37996, USA.
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA.
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, TN, 37996, USA.
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Sanders BC, Pokhrel S, Labbe AD, Mathews II, Cooper CJ, Davidson RB, Phillips G, Weiss KL, Zhang Q, O'Neill H, Kaur M, Schmidt JG, Reichard W, Surendranathan S, Parvathareddy J, Phillips L, Rainville C, Sterner DE, Kumaran D, Andi B, Babnigg G, Moriarty NW, Adams PD, Joachimiak A, Hurst BL, Kumar S, Butt TR, Jonsson CB, Ferrins L, Wakatsuki S, Galanie S, Head MS, Parks JM. Potent and selective covalent inhibition of the papain-like protease from SARS-CoV-2. Nat Commun 2023; 14:1733. [PMID: 36977673 PMCID: PMC10044120 DOI: 10.1038/s41467-023-37254-w] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [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: 07/08/2022] [Accepted: 03/08/2023] [Indexed: 03/30/2023] Open
Abstract
Direct-acting antivirals are needed to combat coronavirus disease 2019 (COVID-19), which is caused by severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2). The papain-like protease (PLpro) domain of Nsp3 from SARS-CoV-2 is essential for viral replication. In addition, PLpro dysregulates the host immune response by cleaving ubiquitin and interferon-stimulated gene 15 protein from host proteins. As a result, PLpro is a promising target for inhibition by small-molecule therapeutics. Here we design a series of covalent inhibitors by introducing a peptidomimetic linker and reactive electrophile onto analogs of the noncovalent PLpro inhibitor GRL0617. The most potent compound inhibits PLpro with kinact/KI = 9,600 M-1 s-1, achieves sub-μM EC50 values against three SARS-CoV-2 variants in mammalian cell lines, and does not inhibit a panel of human deubiquitinases (DUBs) at >30 μM concentrations of inhibitor. An X-ray co-crystal structure of the compound bound to PLpro validates our design strategy and establishes the molecular basis for covalent inhibition and selectivity against structurally similar human DUBs. These findings present an opportunity for further development of covalent PLpro inhibitors.
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Affiliation(s)
- Brian C Sanders
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA.
| | - Suman Pokhrel
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA, USA
- Biological Sciences Division, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Audrey D Labbe
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | | | - Connor J Cooper
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | | | - Gwyndalyn Phillips
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Kevin L Weiss
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Qiu Zhang
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Hugh O'Neill
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Manat Kaur
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Jurgen G Schmidt
- B-11 Bioenergy and Biome Sciences, Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, USA
| | - Walter Reichard
- Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Surekha Surendranathan
- Regional Biocontainment Laboratory, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Jyothi Parvathareddy
- Regional Biocontainment Laboratory, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Lexi Phillips
- Institute for Antiviral Research, Department of Animal, Dairy, and Veterinary Sciences, Utah State University, Logan, UT, USA
| | | | | | - Desigan Kumaran
- Biology Department, Brookhaven National Laboratory, Upton, NY, USA
| | - Babak Andi
- Center for BioMolecular Structure, National Synchrotron Light Source II, Brookhaven National Laboratory, Upton, NY, USA
| | - Gyorgy Babnigg
- Center for Structural Genomics of Infectious Diseases, Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL, USA
- Biosciences Division, Argonne National Laboratory, Argonne, IL, USA
| | - Nigel W Moriarty
- Molecular Biosciences and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Paul D Adams
- Molecular Biosciences and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Department of Bioengineering, University of California, Berkeley, CA, USA
| | - Andrzej Joachimiak
- Center for Structural Genomics of Infectious Diseases, Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL, USA
- Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Argonne, IL, USA
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, USA
| | - Brett L Hurst
- Institute for Antiviral Research, Department of Animal, Dairy, and Veterinary Sciences, Utah State University, Logan, UT, USA
| | | | | | - Colleen B Jonsson
- Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Lori Ferrins
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA, USA
| | - Soichi Wakatsuki
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA, USA.
- Stanford Synchrotron Radiation Lightsource, Menlo Park, CA, USA.
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA.
| | - Stephanie Galanie
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
- Department of Process Research and Development, Merck & Co., Inc., Rahway, NJ, USA
| | - Martha S Head
- Joint Institute for Biological Sciences, Oak Ridge National Laboratory, Oak Ridge, TN, USA
- Computing and Computational Sciences Directorate, Oak Ridge National Laboratory, Oak Ridge, TN, USA
- Computational and Data Sciences, Center for Research Acceleration by Digital Innovation, Amgen, Inc., Thosand Oaks, CA, USA
| | - Jerry M Parks
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA.
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Gionfriddo CM, Soren AB, Wymore AM, Hartnett DS, Podar M, Parks JM, Elias DA, Gilmour CC. Transcriptional Control of hgcAB by an ArsR-Like Regulator in Pseudodesulfovibrio mercurii ND132. Appl Environ Microbiol 2023; 89:e0176822. [PMID: 36951561 PMCID: PMC10132117 DOI: 10.1128/aem.01768-22] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/24/2023] Open
Abstract
The hgcAB gene pair encodes mercury (Hg) methylation capability in a diverse group of microorganisms, but its evolution and transcriptional regulation remain unknown. Working from the possibility that the evolutionary function of HgcAB may not be Hg methylation, we test a possible link to arsenic resistance. Using model Hg methylator Pseudodesulfovibrio mercurii ND132, we evaluated transcriptional control of hgcAB by a putative ArsR encoded upstream and cotranscribed with hgcAB. This regulator shares homology with ArsR repressors of arsenic resistance and S-adenosylhomocysteine (SAH)-responsive regulators of methionine biosynthesis but is distinct from other ArsR/SahR proteins in P. mercurii. Using quantitative PCR (qPCR) and RNA sequencing (RNA-seq) transcriptome analyses, we confirmed this ArsR regulates hgcAB transcription and is responsive to arsenic and SAH. Additionally, RNA-seq indicated a possible link between hgcAB activity and arsenic transformations, with significant upregulation of other ArsR-regulated arsenic resistance operons alongside hgcAB. Interestingly, wild-type ND132 was less sensitive to As(V) (but not As(III)) than an hgcAB knockout strain, supporting the idea that hgcAB may be linked to arsenic resistance. Arsenic significantly impacted rates of Hg methylation by ND132; however, responses varied with culture conditions. Differences in growth and metabolic activity did not account for arsenic impacts on methylation. While arsenic significantly increased hgcAB expression, hgcAB gene and transcript abundance was not a good predictor of Hg methylation rates. Taken together, these results support the idea that Hg and As cycling are linked in P. mercurii ND132. Our results may hold clues to the evolution of hgcAB and the controls on Hg methylation in nature. IMPORTANCE This work reveals a link between microbial mercury methylation and arsenic resistance and may hold clues to the evolution of mercury methylation genes (hgcAB). Microbes with hgcAB produce methylmercury, a strong neurotoxin that readily accumulates in the food web. This study addresses a critical gap in our understanding about the environmental factors that control hgcAB expression. We show that hgcAB expression is controlled by an ArsR-like regulator responsive to both arsenic and S-adenosylhomocysteine in our model organism, Pseudodesulfovibrio mercurii ND132. Exposure to arsenic also significantly impacted Pseudodesulfovibrio mercurii ND132 mercury methylation rates. However, expression of hgcAB was not always a good predictor of Hg methylation rates, highlighting the roles of Hg bioavailability and other biochemical mechanisms in methylmercury production. This study improves our understanding of the controls on hgcAB expression, which is needed to better predict environmental methylmercury production.
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Affiliation(s)
| | | | - Ann M Wymore
- Biosciences Division, Oak Ridge National Lab, Oak Ridge, Tennessee, USA
| | - D Sean Hartnett
- Smithsonian Environmental Research Center, Edgewater, Maryland, USA
| | - Mircea Podar
- Biosciences Division, Oak Ridge National Lab, Oak Ridge, Tennessee, USA
| | - Jerry M Parks
- Biosciences Division, Oak Ridge National Lab, Oak Ridge, Tennessee, USA
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8
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Shen Y, Parks JM, Smith JC. HLA Class I Supertype Classification Based on Structural Similarity. J Immunol 2023; 210:103-114. [PMID: 36453976 DOI: 10.4049/jimmunol.2200685] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Accepted: 10/31/2022] [Indexed: 12/24/2022]
Abstract
HLA class I proteins, a critical component in adaptive immunity, bind and present intracellular Ags to CD8+ T cells. The extreme polymorphism of HLA genes and associated peptide binding specificities leads to challenges in various endeavors, including neoantigen vaccine development, disease association studies, and HLA typing. Supertype classification, defined by clustering functionally similar HLA alleles, has proven helpful in reducing the complexity of distinguishing alleles. However, determining supertypes via experiments is impractical, and current in silico classification methods exhibit limitations in stability and functional relevance. In this study, by incorporating three-dimensional structures we present a method for classifying HLA class I molecules with improved breadth, accuracy, stability, and flexibility. Critical for these advances is our finding that structural similarity highly correlates with peptide binding specificity. The new classification should be broadly useful in peptide-based vaccine development and HLA-disease association studies.
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Affiliation(s)
- Yue Shen
- UT-ORNL Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, TN
| | - Jerry M Parks
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN; and
| | - Jeremy C Smith
- UT-ORNL Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, TN.,Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN; and.,Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, TN
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9
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Moniruzzaman M, Cooper CJ, Uddin MR, Walker JK, Parks JM, Zgurskaya HI. Analysis of Orthogonal Efflux and Permeation Properties of Compounds Leads to the Discovery of New Efflux Pump Inhibitors. ACS Infect Dis 2022; 8:2149-2160. [PMID: 36070489 PMCID: PMC9942517 DOI: 10.1021/acsinfecdis.2c00263] [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] [Indexed: 02/06/2023]
Abstract
Optimization of compound permeation into Gram-negative bacteria is one of the most challenging tasks in the development of antibacterial agents. Two permeability barriers─the passive diffusion barrier of the outer membrane (OM) and active drug efflux─act synergistically to protect cells from the antibacterial action of compounds. In Escherichia coli (E. coli) and relatives, these two barriers sieve compounds based on different physicochemical properties that are defined by their interactions with OM porins and efflux pumps, respectively. In this study, we critically tested the hypothesis that the best substrates and inhibitors of efflux pumps are compounds that can effectively permeate the OM and are available at relatively high concentrations in the periplasm. For this purpose, we filtered a large subset of the ZINC15 database of commercially available compounds for compounds containing a primary amine, a chemical feature known to facilitate the uptake through E. coli general porins. The assembled library was screened by ensemble docking to AcrA, the periplasmic component of the AcrAB-TolC efflux pump, followed by experimental testing of the top predicted binders for antibacterial activities, efflux recognition, and inhibition. We found that the filtered primary amine library is a rich source of compounds with efflux-inhibiting activities and identified efflux pump inhibitors with novel chemical scaffolds effective against E. coli AcrAB-TolC and efflux pumps of multidrug-resistant clinical isolates of Acinetobacter baumannii. However, primary amines are not required for the recognition of compounds by efflux pumps and their efflux-inhibitory activities.
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Affiliation(s)
- Mohammad Moniruzzaman
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73072, United States
| | - Connor J Cooper
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Muhammad R Uddin
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73072, United States
| | - John K Walker
- Department of Pharmacology and Physiology, Saint Louis University School of Medicine, St. Louis, Missouri 63110, United States
| | - Jerry M Parks
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Helen I Zgurskaya
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73072, United States
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10
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Pal D, De K, Shanks CM, Feng K, Yates TB, Morrell-Falvey J, Davidson RB, Parks JM, Muchero W. Core cysteine residues in the Plasminogen-Apple-Nematode (PAN) domain are critical for HGF/c-MET signaling. Commun Biol 2022; 5:646. [PMID: 35778602 PMCID: PMC9249922 DOI: 10.1038/s42003-022-03582-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [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: 10/05/2021] [Accepted: 06/10/2022] [Indexed: 11/09/2022] Open
Abstract
The Plasminogen-Apple-Nematode (PAN) domain, with a core of four to six cysteine residues, is found in > 28,000 proteins across 959 genera. Still, its role in protein function is not fully understood. The PAN domain was initially characterized in numerous proteins, including HGF. Dysregulation of HGF-mediated signaling results in multiple deadly cancers. The binding of HGF to its cell surface receptor, c-MET, triggers all biological impacts. Here, we show that mutating four core cysteine residues in the HGF PAN domain reduces c-MET interaction, subsequent c-MET autophosphorylation, and phosphorylation of its downstream targets, perinuclear localization, cellular internalization of HGF, and its receptor, c-MET, and c-MET ubiquitination. Furthermore, transcriptional activation of HGF/c-MET signaling-related genes involved in cancer progression, invasion, metastasis, and cell survival were impaired. Thus, targeting the PAN domain of HGF may represent a mechanism for selectively regulating the binding and activation of the c-MET pathway.
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Affiliation(s)
- Debjani Pal
- Bioscience Division, Oak Ridge National Laboratory, 1 Bethel Valley Rd, Oak Ridge, TN, 37831, USA
| | - Kuntal De
- Bioscience Division, Oak Ridge National Laboratory, 1 Bethel Valley Rd, Oak Ridge, TN, 37831, USA
| | - Carly M Shanks
- Bioscience Division, Oak Ridge National Laboratory, 1 Bethel Valley Rd, Oak Ridge, TN, 37831, USA
| | - Kai Feng
- Bioscience Division, Oak Ridge National Laboratory, 1 Bethel Valley Rd, Oak Ridge, TN, 37831, USA
| | - Timothy B Yates
- Bioscience Division, Oak Ridge National Laboratory, 1 Bethel Valley Rd, Oak Ridge, TN, 37831, USA.,Bredesen Center for Interdisciplinary Research, University of Tennessee, Knoxville, TN, 37996, USA
| | - Jennifer Morrell-Falvey
- Bioscience Division, Oak Ridge National Laboratory, 1 Bethel Valley Rd, Oak Ridge, TN, 37831, USA
| | - Russell B Davidson
- Bioscience Division, Oak Ridge National Laboratory, 1 Bethel Valley Rd, Oak Ridge, TN, 37831, USA
| | - Jerry M Parks
- Bioscience Division, Oak Ridge National Laboratory, 1 Bethel Valley Rd, Oak Ridge, TN, 37831, USA
| | - Wellington Muchero
- Bioscience Division, Oak Ridge National Laboratory, 1 Bethel Valley Rd, Oak Ridge, TN, 37831, USA. .,Bredesen Center for Interdisciplinary Research, University of Tennessee, Knoxville, TN, 37996, USA.
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11
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Leus IV, Weeks JW, Bonifay V, Shen Y, Yang L, Cooper CJ, Nash D, Duerfeldt AS, Smith JC, Parks JM, Rybenkov VV, Zgurskaya HI. Property space mapping of Pseudomonas aeruginosa permeability to small molecules. Sci Rep 2022; 12:8220. [PMID: 35581346 PMCID: PMC9114115 DOI: 10.1038/s41598-022-12376-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Accepted: 05/10/2022] [Indexed: 02/03/2023] Open
Abstract
Two membrane cell envelopes act as selective permeability barriers in Gram-negative bacteria, protecting cells against antibiotics and other small molecules. Significant efforts are being directed toward understanding how small molecules permeate these barriers. In this study, we developed an approach to analyze the permeation of compounds into Gram-negative bacteria and applied it to Pseudomonas aeruginosa, an important human pathogen notorious for resistance to multiple antibiotics. The approach uses mass spectrometric measurements of accumulation of a library of structurally diverse compounds in four isogenic strains of P. aeruginosa with varied permeability barriers. We further developed a machine learning algorithm that generates a deterministic classification model with minimal synonymity between the descriptors. This model predicted good permeators into P. aeruginosa with an accuracy of 89% and precision above 58%. The good permeators are broadly distributed in the property space and can be mapped to six distinct regions representing diverse chemical scaffolds. We posit that this approach can be used for more detailed mapping of the property space and for rational design of compounds with high Gram-negative permeability.
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Affiliation(s)
- Inga V Leus
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Norman, OK, 73019, USA
| | - Jon W Weeks
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Norman, OK, 73019, USA
| | - Vincent Bonifay
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Norman, OK, 73019, USA
| | - Yue Shen
- Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, TN, 37996, USA
| | - Liang Yang
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Norman, OK, 73019, USA
| | - Connor J Cooper
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Dinesh Nash
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Norman, OK, 73019, USA
| | - Adam S Duerfeldt
- Department of Medicinal Chemistry, University of Minnesota, 717 Delaware St. SE, Minneapolis, MN, 55414, USA
| | - Jeremy C Smith
- Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, TN, 37996, USA
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, TN, 37996, USA
| | - Jerry M Parks
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Valentin V Rybenkov
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Norman, OK, 73019, USA.
| | - Helen I Zgurskaya
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Norman, OK, 73019, USA.
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12
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Glaser J, Sedova A, Galanie S, Kneller DW, Davidson RB, Maradzike E, Del Galdo S, Labbé A, Hsu DJ, Agarwal R, Bykov D, Tharrington A, Parks JM, Smith DMA, Daidone I, Coates L, Kovalevsky A, Smith JC. Hit Expansion of a Noncovalent SARS-CoV-2 Main Protease Inhibitor. ACS Pharmacol Transl Sci 2022; 5:255-265. [PMID: 35434531 PMCID: PMC9003389 DOI: 10.1021/acsptsci.2c00026] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [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: 02/17/2022] [Indexed: 11/29/2022]
Abstract
![]()
Inhibition of the SARS-CoV-2 main
protease (Mpro) is
a major focus of drug discovery efforts against COVID-19. Here we
report a hit expansion of non-covalent inhibitors of Mpro. Starting from a recently discovered scaffold (The COVID Moonshot
Consortium. Open Science Discovery of Oral Non-Covalent SARS-CoV-2
Main Protease Inhibitor Therapeutics. bioRxiv 2020.10.29.339317) represented by an isoquinoline
series, we searched a database of over a billion compounds using a
cheminformatics molecular fingerprinting approach. We identified and
tested 48 compounds in enzyme inhibition assays, of which 21 exhibited
inhibitory activity above 50% at 20 μM. Among these,
four compounds with IC50 values around 1 μM
were found. Interestingly, despite the large search space, the isoquinolone
motif was conserved in each of these four strongest binders. Room-temperature
X-ray structures of co-crystallized protein–inhibitor complexes
were determined up to 1.9 Å resolution for two of these
compounds as well as one of the stronger inhibitors in the original
isoquinoline series, revealing essential interactions with the binding
site and water molecules. Molecular dynamics simulations and quantum
chemical calculations further elucidate the binding interactions as
well as electrostatic effects on ligand binding. The results help
explain the strength of this new non-covalent scaffold for Mpro inhibition and inform lead optimization efforts for this series,
while demonstrating the effectiveness of a high-throughput computational
approach to expanding a pharmacophore library.
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Affiliation(s)
- Jens Glaser
- Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, Tennessee 37830, United States
| | - Ada Sedova
- Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, Tennessee 37830, United States
| | - Stephanie Galanie
- Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, Tennessee 37830, United States.,Protein Engineering, Merck, 126 East Lincoln Avenue, RY800-C303, Rahway, New Jersey 07065, United States
| | - Daniel W Kneller
- Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, Tennessee 37830, United States.,New England Biolabs, 240 County Road, Ipswich, Massachusetts 01938, United States
| | - Russell B Davidson
- Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, Tennessee 37830, United States
| | - Elvis Maradzike
- Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, Tennessee 37830, United States
| | - Sara Del Galdo
- Department of Physical and Chemical Sciences, University of L'Aquila, I-67010 L'Aquila, Italy
| | - Audrey Labbé
- Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, Tennessee 37830, United States
| | - Darren J Hsu
- Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, Tennessee 37830, United States
| | - Rupesh Agarwal
- Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, Tennessee 37830, United States
| | - Dmytro Bykov
- Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, Tennessee 37830, United States
| | - Arnold Tharrington
- Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, Tennessee 37830, United States
| | - Jerry M Parks
- Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, Tennessee 37830, United States
| | - Dayle M A Smith
- Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, Tennessee 37830, United States
| | - Isabella Daidone
- Department of Physical and Chemical Sciences, University of L'Aquila, I-67010 L'Aquila, Italy
| | - Leighton Coates
- Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, Tennessee 37830, United States
| | - Andrey Kovalevsky
- Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, Tennessee 37830, United States
| | - Jeremy C Smith
- Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, Tennessee 37830, United States
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13
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Gao M, Nakajima An D, Parks JM, Skolnick J. AF2Complex predicts direct physical interactions in multimeric proteins with deep learning. Nat Commun 2022; 13:1744. [PMID: 35365655 PMCID: PMC8975832 DOI: 10.1038/s41467-022-29394-2] [Citation(s) in RCA: 89] [Impact Index Per Article: 44.5] [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: 11/08/2021] [Accepted: 03/15/2022] [Indexed: 12/20/2022] Open
Abstract
Accurate descriptions of protein-protein interactions are essential for understanding biological systems. Remarkably accurate atomic structures have been recently computed for individual proteins by AlphaFold2 (AF2). Here, we demonstrate that the same neural network models from AF2 developed for single protein sequences can be adapted to predict the structures of multimeric protein complexes without retraining. In contrast to common approaches, our method, AF2Complex, does not require paired multiple sequence alignments. It achieves higher accuracy than some complex protein-protein docking strategies and provides a significant improvement over AF-Multimer, a development of AlphaFold for multimeric proteins. Moreover, we introduce metrics for predicting direct protein-protein interactions between arbitrary protein pairs and validate AF2Complex on some challenging benchmark sets and the E. coli proteome. Lastly, using the cytochrome c biogenesis system I as an example, we present high-confidence models of three sought-after assemblies formed by eight members of this system. Accurate descriptions of protein-protein interactions are essential for understanding biological systems. Here the authors present AF2Complex and show that application to the E. coli cytochrome biogenesis system I yields confident computational models for three sought-after assemblies.
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Affiliation(s)
- Mu Gao
- Center for the Study of Systems Biology, School of Biological Sciences, Atlanta, GA, USA.
| | - Davi Nakajima An
- School of Computer Science, Georgia Institute of Technology, Atlanta, GA, USA
| | - Jerry M Parks
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Jeffrey Skolnick
- Center for the Study of Systems Biology, School of Biological Sciences, Atlanta, GA, USA.
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14
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Drago VN, Dajnowicz S, Parks JM, Blakeley MP, Keen DA, Coquelle N, Weiss KL, Gerlits O, Kovalevsky A, Mueser TC. An N⋯H⋯N low-barrier hydrogen bond preorganizes the catalytic site of aspartate aminotransferase to facilitate the second half-reaction. Chem Sci 2022; 13:10057-10065. [PMID: 36128223 PMCID: PMC9430417 DOI: 10.1039/d2sc02285k] [Citation(s) in RCA: 0] [Impact Index Per Article: 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: 04/22/2022] [Accepted: 07/20/2022] [Indexed: 11/21/2022] Open
Abstract
Pyridoxal 5′-phosphate (PLP)-dependent enzymes have been extensively studied for their ability to fine-tune PLP cofactor electronics to promote a wide array of chemistries. Neutron crystallography offers a straightforward approach to studying the electronic states of PLP and the electrostatics of enzyme active sites, responsible for the reaction specificities, by enabling direct visualization of hydrogen atom positions. Here we report a room-temperature joint X-ray/neutron structure of aspartate aminotransferase (AAT) with pyridoxamine 5′-phosphate (PMP), the cofactor product of the first half reaction catalyzed by the enzyme. Between PMP NSB and catalytic Lys258 Nζ amino groups an equally shared deuterium is observed in an apparent low-barrier hydrogen bond (LBHB). Density functional theory calculations were performed to provide further evidence of this LBHB interaction. The structural arrangement and the juxtaposition of PMP and Lys258, facilitated by the LBHB, suggests active site preorganization for the incoming ketoacid substrate that initiates the second half-reaction. The neutron structure of pyridoxal 5′-phosphate-dependent enzyme aspartate aminotransferase with pyridoxamine 5′-phosphate (PMP) reveals a low-barrier hydrogen bond between the amino groups of PMP and catalytic Lys258, preorganizing the active site for catalysis![]()
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Affiliation(s)
- Victoria N. Drago
- Department of Chemistry and Biochemistry, University of Toledo, Toledo, OH 43606, USA
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Steven Dajnowicz
- Department of Chemistry and Biochemistry, University of Toledo, Toledo, OH 43606, USA
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Jerry M. Parks
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Matthew P. Blakeley
- Large Scale Structures Group, Institut Laue–Langevin, 71 Avenue des Martyrs, 38000 Grenoble, France
| | - David A. Keen
- ISIS Facility, Rutherford Appleton Laboratory, Harwell Campus, Didcot, OX11 0QX, UK
| | - Nicolas Coquelle
- Large Scale Structures Group, Institut Laue–Langevin, 71 Avenue des Martyrs, 38000 Grenoble, France
| | - Kevin L. Weiss
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Oksana Gerlits
- Department of Natural Sciences, Tennessee Wesleyan University, Athens, TN 37303, USA
| | - Andrey Kovalevsky
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Timothy C. Mueser
- Department of Chemistry and Biochemistry, University of Toledo, Toledo, OH 43606, USA
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15
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Gumbart JC, Ferreira JL, Hwang H, Hazel AJ, Cooper CJ, Parks JM, Smith JC, Zgurskaya HI, Beeby M. Lpp positions peptidoglycan at the AcrA-TolC interface in the AcrAB-TolC multidrug efflux pump. Biophys J 2021; 120:3973-3982. [PMID: 34411576 DOI: 10.1016/j.bpj.2021.08.016] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Revised: 07/02/2021] [Accepted: 08/11/2021] [Indexed: 01/07/2023] Open
Abstract
The multidrug efflux pumps of Gram-negative bacteria are a class of complexes that span the periplasm, coupling both the inner and outer membranes to expel toxic molecules. The best-characterized example of these tripartite pumps is the AcrAB-TolC complex of Escherichia coli. However, how the complex interacts with the peptidoglycan (PG) cell wall, which is anchored to the outer membrane (OM) by Braun's lipoprotein (Lpp), is still largely unknown. In this work, we present molecular dynamics simulations of a complete, atomistic model of the AcrAB-TolC complex with the inner membrane, OM, and PG layers all present. We find that the PG localizes to the junction of AcrA and TolC, in agreement with recent cryo-tomography data. Free-energy calculations reveal that the positioning of PG is determined by the length and conformation of multiple Lpp copies anchoring it to the OM. The distance between the PG and OM measured in cryo-electron microscopy images of wild-type E. coli also agrees with the simulation-derived spacing. Sequence analysis of AcrA suggests a conserved role for interactions with PG in the assembly and stabilization of efflux pumps, one that may extend to other trans-envelope complexes as well.
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Affiliation(s)
- James C Gumbart
- School of Physics, Georgia Institute of Technology, Atlanta, Georgia.
| | - Josie L Ferreira
- Department of Life Sciences, Imperial College London, London, United Kingdom
| | - Hyea Hwang
- School of Materials Science and Engineering, Georgia Institute of Technology, Atlanta, Georgia
| | - Anthony J Hazel
- School of Physics, Georgia Institute of Technology, Atlanta, Georgia
| | - Connor J Cooper
- UT/ORNL Center for Molecular Biophysics, Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee
| | - Jerry M Parks
- UT/ORNL Center for Molecular Biophysics, Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee
| | - Jeremy C Smith
- UT/ORNL Center for Molecular Biophysics, Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee; Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee
| | - Helen I Zgurskaya
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma
| | - Morgan Beeby
- Department of Life Sciences, Imperial College London, London, United Kingdom
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16
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D’Cunha N, Moniruzzaman M, Haynes K, Malloci G, Cooper CJ, Margiotta E, Vargiu AV, Uddin MR, Leus IV, Cao F, Parks JM, Rybenkov VV, Ruggerone P, Zgurskaya HI, Walker JK. Mechanistic Duality of Bacterial Efflux Substrates and Inhibitors: Example of Simple Substituted Cinnamoyl and Naphthyl Amides. ACS Infect Dis 2021; 7:2650-2665. [PMID: 34379382 DOI: 10.1021/acsinfecdis.1c00100] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Antibiotic resistance poses an immediate and growing threat to human health. Multidrug efflux pumps are promising targets for overcoming antibiotic resistance with small-molecule therapeutics. Previously, we identified a diaminoquinoline acrylamide, NSC-33353, as a potent inhibitor of the AcrAB-TolC efflux pump in Escherichia coli. This inhibitor potentiates the antibacterial activities of novobiocin and erythromycin upon binding to the membrane fusion protein AcrA. It is also a substrate for efflux and lacks appreciable intrinsic antibacterial activity of its own in wild-type cells. Here, we have modified the substituents of the cinnamoyl group of NSC-33353, giving rise to analogs that retain the ability to inhibit efflux, lost the features of the efflux substrates, and gained antibacterial activity in wild-type cells. The replacement of the cinnamoyl group with naphthyl isosteres generated compounds that lack antibacterial activity but are both excellent efflux pump inhibitors and substrates. Surprisingly, these inhibitors potentiate the antibacterial activity of novobiocin but not erythromycin. Surface plasmon resonance experiments and molecular docking suggest that the replacement of the cinnamoyl group with naphthyl shifts the affinity of the compounds away from AcrA to the AcrB transporter, making them better efflux substrates and changing their mechanism of inhibition. These results provide new insights into the duality of efflux substrate/inhibitor features in chemical scaffolds that will facilitate the development of new efflux pump inhibitors.
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Affiliation(s)
- Napoleon D’Cunha
- Department of Pharmacology and Physiology, Saint Louis University School of Medicine, St. Louis, Missouri 63110, United States
| | - Mohammad Moniruzzaman
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73072, United States
| | - Keith Haynes
- Department of Pharmacology and Physiology, Saint Louis University School of Medicine, St. Louis, Missouri 63110, United States
| | - Giuliano Malloci
- Department of Physics, University of Cagliari, Monserrato, Cagliari 09042, Italy
| | - Connor J. Cooper
- Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, Tennessee 37996, United States
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Enrico Margiotta
- Department of Physics, University of Cagliari, Monserrato, Cagliari 09042, Italy
| | - Attilio V. Vargiu
- Department of Physics, University of Cagliari, Monserrato, Cagliari 09042, Italy
| | - Muhammad R. Uddin
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73072, United States
| | - Inga V. Leus
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73072, United States
| | - Feng Cao
- John Cochran Division, Department of Veteran Affairs Medical Center, St. Louis, Missouri 63106, United States
| | - Jerry M. Parks
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Valentin V. Rybenkov
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73072, United States
| | - Paolo Ruggerone
- Department of Physics, University of Cagliari, Monserrato, Cagliari 09042, Italy
| | - Helen I. Zgurskaya
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73072, United States
| | - John K. Walker
- Department of Pharmacology and Physiology, Saint Louis University School of Medicine, St. Louis, Missouri 63110, United States
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17
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Mishra SK, Cooper CJ, Parks JM, Mitchell JC. Hotspot Coevolution Is a Key Identifier of Near-Native Protein Complexes. J Phys Chem B 2021; 125:6058-6067. [PMID: 34077660 DOI: 10.1021/acs.jpcb.0c11525] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Protein-protein interactions play a key role in mediating numerous biological functions, with more than half the proteins in living organisms existing as either homo- or hetero-oligomeric assemblies. Protein subunits that form oligomers minimize the free energy of the complex, but exhaustive computational search-based docking methods have not comprehensively addressed the challenge of distinguishing a natively bound complex from non-native forms. Current protein docking approaches address this problem by sampling multiple binding modes in proteins and scoring each mode, with the lowest-energy (or highest scoring) binding mode being regarded as a near-native complex. However, high-scoring modes often match poorly with the true bound form, suggesting a need for improvement of the scoring function. In this study, we propose a scoring function, KFC-E, that accounts for both conservation and coevolution of putative binding hotspot residues at protein-protein interfaces. We tested KFC-E on four benchmark sets of unbound examples and two benchmark sets of bound examples, with the results demonstrating a clear improvement over scores that examine conservation and coevolution across the entire interface.
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Affiliation(s)
- Sambit K Mishra
- Biosciences Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, Tennessee 37831-6038, United States
| | - Connor J Cooper
- Biosciences Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, Tennessee 37831-6038, United States
| | - Jerry M Parks
- Biosciences Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, Tennessee 37831-6038, United States
| | - Julie C Mitchell
- Biosciences Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, Tennessee 37831-6038, United States
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18
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Pavlova A, Zhang Z, Acharya A, Lynch DL, Pang YT, Mou Z, Parks JM, Chipot C, Gumbart JC. Machine Learning Reveals the Critical Interactions for SARS-CoV-2 Spike Protein Binding to ACE2. J Phys Chem Lett 2021; 12:5494-5502. [PMID: 34086459 PMCID: PMC8204752 DOI: 10.1021/acs.jpclett.1c01494] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Accepted: 06/02/2021] [Indexed: 05/06/2023]
Abstract
SARS-CoV and SARS-CoV-2 bind to the human ACE2 receptor in practically identical conformations, although several residues of the receptor-binding domain (RBD) differ between them. Herein, we have used molecular dynamics (MD) simulations, machine learning (ML), and free-energy perturbation (FEP) calculations to elucidate the differences in binding by the two viruses. Although only subtle differences were observed from the initial MD simulations of the two RBD-ACE2 complexes, ML identified the individual residues with the most distinctive ACE2 interactions, many of which have been highlighted in previous experimental studies. FEP calculations quantified the corresponding differences in binding free energies to ACE2, and examination of MD trajectories provided structural explanations for these differences. Lastly, the energetics of emerging SARS-CoV-2 mutations were studied, showing that the affinity of the RBD for ACE2 is increased by N501Y and E484K mutations but is slightly decreased by K417N.
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Affiliation(s)
- Anna Pavlova
- School
of Physics, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Zijian Zhang
- School
of Physics, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Atanu Acharya
- School
of Physics, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Diane L. Lynch
- School
of Physics, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Yui Tik Pang
- School
of Physics, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Zhongyu Mou
- UT/ORNL
Center for Molecular Biophysics, Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Jerry M. Parks
- UT/ORNL
Center for Molecular Biophysics, Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Chris Chipot
- Université
de Lorraine, UMR 7019, Laboratoire International Associé
CNRS and University of Illinois at Urbana−Champaign, Vandoeuvre-lès-Nancy F-54506, France
- Department
of Physics, University of Illinois at Urbana−Champaign, Urbana 61801-3003, Illinois, United States
| | - James C. Gumbart
- School
of Physics, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
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19
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Lian P, Mou Z, Cooper CJ, Johnston RC, Brooks SC, Gu B, Govind N, Jonsson S, Parks JM. Mechanistic Investigation of Dimethylmercury Formation Mediated by a Sulfide Mineral Surface. J Phys Chem A 2021; 125:5397-5405. [PMID: 34114820 DOI: 10.1021/acs.jpca.1c04014] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Mercury (Hg) pollution is a global environmental problem. The abiotic formation of dimethylmercury (DMeHg) from monomethylmercury (MMeHg) may account for a large portion of DMeHg in oceans. Previous experimental work has shown that abiotic formation of DMeHg from MMeHg can be facilitated by reduced sulfur groups on sulfide mineral surfaces. In that work, a mechanism was proposed in which neighboring MMeHg moieties bound to sulfide sites on a mineral surface react through an SN2-type mechanism to form DMeHg and incorporate the remaining Hg atoms into the mineral surface. Here, we perform density functional theory calculations to explore the mechanisms of DMeHg formation on the 110 surface of a CdS(s) (hawleyite) nanoparticle. We show that coordination of MMeHg substituents to adjacent reduced sulfur groups protruding from the surface indeed facilitates DMeHg formation and that the reaction proceeds through direct transmethylation from one MMeHg substituent to another. Coordination of Hg by multiple S atoms provides a transition-state stabilization and activates a C-Hg bond for methyl transfer. In addition, solvation effects play an important role in the surface reconstruction of the nanoparticle and in decreasing the energetic barrier for DMeHg formation relative to the corresponding reaction in vacuo.
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Affiliation(s)
- Peng Lian
- UT/ORNL Center for Molecular Biophysics, Biosciences Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, Tennessee 37831, United States.,Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Zhongyu Mou
- UT/ORNL Center for Molecular Biophysics, Biosciences Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, Tennessee 37831, United States
| | - Connor J Cooper
- UT/ORNL Center for Molecular Biophysics, Biosciences Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, Tennessee 37831, United States
| | - Ryne C Johnston
- UT/ORNL Center for Molecular Biophysics, Biosciences Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, Tennessee 37831, United States
| | - Scott C Brooks
- Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Baohua Gu
- Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Niranjan Govind
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Sofi Jonsson
- Department of Environmental Science, Stockholm University, 106 91 Stockholm, Sweden
| | - Jerry M Parks
- UT/ORNL Center for Molecular Biophysics, Biosciences Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, Tennessee 37831, United States.,Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee 37996, United States
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20
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Baudry J, Bondar AN, Cournia Z, Parks JM, Petridis L, Roux B. Editorial: Advances in computational molecular biophysics. Biochim Biophys Acta Gen Subj 2021; 1865:129888. [PMID: 33662454 DOI: 10.1016/j.bbagen.2021.129888] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Affiliation(s)
- Jerome Baudry
- The University of Alabama in Huntsville, Department of Biological Sciences, 301 Sparkman Drive, Huntsville, AL 35899, USA.
| | - Ana-Nicoleta Bondar
- Freie Universität Berlin, Department of Physics, Theoretical Molecular Biophysics, Arnimallee 14, D-14195 Berlin, Germany.
| | - Zoe Cournia
- Soranou Ephessiou, Biomedical Research Foundation, Academy of Athens, 11527 Athens, Greece.
| | - Jerry M Parks
- Biosciences Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37831-6309, USA.
| | - Loukas Petridis
- Biosciences Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37831-6309, USA.
| | - Benoit Roux
- Department of Biochemistry and Molecular Biology, The University of Chicago, 929 E57th Street, Chicago, IL 60637, USA.
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21
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Abstract
Antibiotics are miracle drugs that can cure infectious bacterial diseases. However, their utility is challenged by antibiotic-resistant bacteria emerging in clinics and straining modern medicine and our ways of life. Certain bacteria such as Gram-negative (Gram(-)) and Mycobacteriales species are intrinsically resistant to most clinical antibiotics and can further gain multidrug resistance through mutations and plasmid acquisition. These species stand out by the presence of an additional external lipidic membrane, the outer membrane (OM), that is composed of unique glycolipids. Although formidable, the OM is a passive permeability barrier that can reduce penetration of antibiotics but cannot affect intracellular steady-state concentrations of drugs. The two-membrane envelopes are further reinforced by active efflux transporters that expel antibiotics from cells against their concentration gradients. The major mechanism of antibiotic resistance in Gram(-) pathogens is the active efflux of drugs, which acts synergistically with the low permeability barrier of the OM and other mutational and plasmid-borne mechanisms of antibiotic resistance.The synergy between active efflux and slow uptake offers Gram(-) bacteria an impressive degree of protection from potentially harmful chemicals, but it is also their Achilles heel. Kinetic studies have revealed that even small changes in the efficiency of either of the two factors can have dramatic effects on drug penetration into the cell. In line with these expectations, two major approaches to overcome this antibiotic resistance mechanism are currently being explored: (1) facilitation of antibiotic penetration across the outer membranes and (2) avoidance and inhibition of clinically relevant multidrug efflux pumps. Herein we summarize the progress in the latter approach with a focus on efflux pumps from the resistance-nodulation-division (RND) superfamily. The ability to export various substrates across the OM at the expense of the proton-motive force acting on the inner membrane and the engagement of accessory proteins for their functions are the major mechanistic advantages of these pumps. Both the RND transporters and their accessory proteins are being targeted in the discovery of efflux pump inhibitors, which in combination with antibiotics can potentiate antibacterial activities. We discuss intriguing relationships between substrates and inhibitors of efflux pumps, as these two types of ligands face similar barriers and binding sites in the transporters and accessory proteins and both types of activities often occur with the same chemical scaffold. Several distinct chemical classes of efflux inhibitors have been discovered that are as structurally diverse as the substrates of efflux pumps. Recent mechanistic insights, both empirical and computational, have led to the identification of features that distinguish OM permeators and efflux pump avoiders as well as efflux inhibitors from substrates. These findings suggest a path forward for optimizing the OM permeation and efflux-inhibitory activities in antibiotics and other chemically diverse compounds.
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Affiliation(s)
- Helen I Zgurskaya
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Norman, Oklahoma 73019, United States
| | - John K Walker
- Department of Pharmacological and Physiological Science, Saint Louis University School of Medicine, St. Louis, Missouri 63104, United States
| | - Jerry M Parks
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Valentin V Rybenkov
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Norman, Oklahoma 73019, United States
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22
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Ajina R, Malchiodi ZX, Fitzgerald AA, Zuo A, Wang S, Moussa M, Cooper CJ, Shen Y, Johnson QR, Parks JM, Smith JC, Catalfamo M, Fertig EJ, Jablonski SA, Weiner LM. Antitumor T-cell Immunity Contributes to Pancreatic Cancer Immune Resistance. Cancer Immunol Res 2021; 9:386-400. [PMID: 33509790 DOI: 10.1158/2326-6066.cir-20-0272] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 10/27/2020] [Accepted: 01/26/2021] [Indexed: 12/14/2022]
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is the third leading cause of cancer death in the United States. Pancreatic tumors are minimally infiltrated by T cells and are largely refractory to immunotherapy. Accordingly, the role of T-cell immunity in pancreatic cancer has been somewhat overlooked. Here, we hypothesized that immune resistance in pancreatic cancer was induced in response to antitumor T-cell immune responses and that understanding how pancreatic tumors respond to immune attack may facilitate the development of more effective therapeutic strategies. We now provide evidence that T-cell-dependent host immune responses induce a PDAC-derived myeloid mimicry phenomenon and stimulate immune resistance. Three KPC mouse models of pancreatic cancer were used: the mT3-2D (Kras+/LSL-G12D; Trp53+/LSL-R172H; Pdx1-Cre) subcutaneous and orthotopic models, as well as the KP1 (p48-CRE/LSL-Kras/Trp53 flox/flox ) subcutaneous model. KPC cancer cells were grown in immunocompetent and immunodeficient C57BL/6 mice and analyzed to determine the impact of adaptive immunity on malignant epithelial cells, as well as on whole tumors. We found that induced T-cell antitumor immunity, via signal transducer and activator of transcription 1 (STAT1), stimulated malignant epithelial pancreatic cells to induce the expression of genes typically expressed by myeloid cells and altered intratumoral immunosuppressive myeloid cell profiles. Targeting the Janus Kinase (JAK)/STAT signaling pathway using the FDA-approved drug ruxolitinib overcame these tumor-protective responses and improved anti-PD-1 therapeutic efficacy. These findings provide future directions for treatments that specifically disable this mechanism of resistance in PDAC.
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Affiliation(s)
- Reham Ajina
- Department of Oncology and Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, District of Columbia
| | - Zoe X Malchiodi
- Department of Oncology and Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, District of Columbia
| | - Allison A Fitzgerald
- Department of Oncology and Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, District of Columbia
| | - Annie Zuo
- Department of Oncology and Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, District of Columbia
| | - Shangzi Wang
- Department of Oncology and Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, District of Columbia
| | - Maha Moussa
- Department of Microbiology and Immunology, Georgetown University Medical Center, Washington, District of Columbia
| | - Connor J Cooper
- Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, Tennessee
| | - Yue Shen
- Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, Tennessee
| | - Quentin R Johnson
- Department of Chemistry and Biochemistry, Berry College, Mount Berry, Georgia
| | - Jerry M Parks
- Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, Tennessee.,Department of Chemistry and Biochemistry, Berry College, Mount Berry, Georgia
| | - Jeremy C Smith
- Department of Chemistry and Biochemistry, Berry College, Mount Berry, Georgia.,Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee
| | - Marta Catalfamo
- Department of Microbiology and Immunology, Georgetown University Medical Center, Washington, District of Columbia
| | - Elana J Fertig
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland.,Department of Applied Mathematics and Statistics, Johns Hopkins University Whiting School of Engineering, Baltimore, Maryland.,Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Sandra A Jablonski
- Department of Oncology and Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, District of Columbia
| | - Louis M Weiner
- Department of Oncology and Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, District of Columbia.
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23
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Pavlova A, Lynch DL, Daidone I, Zanetti-Polzi L, Smith MD, Chipot C, Kneller DW, Kovalevsky A, Coates L, Golosov AA, Dickson CJ, Velez-Vega C, Duca JS, Vermaas JV, Pang YT, Acharya A, Parks JM, Smith JC, Gumbart JC. Inhibitor binding influences the protonation states of histidines in SARS-CoV-2 main protease. Chem Sci 2021; 12:1513-1527. [PMID: 35356437 PMCID: PMC8899719 DOI: 10.1039/d0sc04942e] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [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: 09/07/2020] [Accepted: 11/25/2020] [Indexed: 12/11/2022] Open
Abstract
The main protease (Mpro) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is an attractive target for antiviral therapeutics. Recently, many high-resolution apo and inhibitor-bound structures of Mpro, a cysteine protease, have been determined, facilitating structure-based drug design. Mpro plays a central role in the viral life cycle by catalyzing the cleavage of SARS-CoV-2 polyproteins. In addition to the catalytic dyad His41–Cys145, Mpro contains multiple histidines including His163, His164, and His172. The protonation states of these histidines and the catalytic nucleophile Cys145 have been debated in previous studies of SARS-CoV Mpro, but have yet to be investigated for SARS-CoV-2. In this work we have used molecular dynamics simulations to determine the structural stability of SARS-CoV-2 Mpro as a function of the protonation assignments for these residues. We simulated both the apo and inhibitor-bound enzyme and found that the conformational stability of the binding site, bound inhibitors, and the hydrogen bond networks of Mpro are highly sensitive to these assignments. Additionally, the two inhibitors studied, the peptidomimetic N3 and an α-ketoamide, display distinct His41/His164 protonation-state-dependent stabilities. While the apo and the N3-bound systems favored Nδ (HD) and Nϵ (HE) protonation of His41 and His164, respectively, the α-ketoamide was not stably bound in this state. Our results illustrate the importance of using appropriate histidine protonation states to accurately model the structure and dynamics of SARS-CoV-2 Mpro in both the apo and inhibitor-bound states, a necessary prerequisite for drug-design efforts. The main protease (Mpro) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is an attractive target for antiviral therapeutics.![]()
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24
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Mou Z, Eakes J, Cooper CJ, Foster CM, Standaert RF, Podar M, Doktycz MJ, Parks JM. Machine learning‐based prediction of enzyme substrate scope: Application to bacterial nitrilases. Proteins 2020; 89:336-347. [DOI: 10.1002/prot.26019] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Revised: 09/02/2020] [Accepted: 10/17/2020] [Indexed: 01/11/2023]
Affiliation(s)
- Zhongyu Mou
- Biosciences Division Oak Ridge National Laboratory Oak Ridge Tennessee USA
| | - Jason Eakes
- Biosciences Division Oak Ridge National Laboratory Oak Ridge Tennessee USA
| | - Connor J. Cooper
- Graduate School of Genome Science and Technology University of TennesseeWalters Life Science Knoxville Tennessee USA
| | - Carmen M. Foster
- Biosciences Division Oak Ridge National Laboratory Oak Ridge Tennessee USA
| | | | - Mircea Podar
- Biosciences Division Oak Ridge National Laboratory Oak Ridge Tennessee USA
| | - Mitchel J. Doktycz
- Biosciences Division Oak Ridge National Laboratory Oak Ridge Tennessee USA
- Graduate School of Genome Science and Technology University of TennesseeWalters Life Science Knoxville Tennessee USA
| | - Jerry M. Parks
- Biosciences Division Oak Ridge National Laboratory Oak Ridge Tennessee USA
- Graduate School of Genome Science and Technology University of TennesseeWalters Life Science Knoxville Tennessee USA
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25
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Devarajan D, Liang L, Gu B, Brooks SC, Parks JM, Smith JC. Molecular Dynamics Simulation of the Structures, Dynamics, and Aggregation of Dissolved Organic Matter. Environ Sci Technol 2020; 54:13527-13537. [PMID: 32985864 DOI: 10.1021/acs.est.0c01176] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Dissolved organic matter (DOM) plays a significant role in the transport and transformation of pollutants in the aquatic environment. However, the experimental characterization of DOM has been limited mainly to bulk properties, and the molecular-level interactions among various components of DOM remain to be fully characterized. Here, we use molecular dynamics (MD) simulations to probe the structural properties of model DOM systems at atomic detail. The 200 ns simulations, validated by available experimental data, reveal processes and mechanisms by which chemical species (cations, peptides, lipids, lignin, carbohydrates, and some low-molecular-weight aliphatic and aromatic compounds) aggregate to form complex DOM. The DOM aggregates are dynamic, consisting of a hydrophobic core and amphiphilic exterior. The lipid tails and other hydrophobic fragments form the core, with hydrophilic and amphiphilic groups exposed to water, making DOM accessible to both polar and nonpolar species. Thus, the lipid component acts as a nucleator, whereas cations (especially Ca2+) connect the molecular fragments on the surface by coordinating with the O-containing functional groups of DOM. The structural details revealed here provide new insights including surface accessible atoms, overall assemblage, and interactions among the molecules of DOM for understanding the kinetics and mechanisms through which DOM interacts with metal and other contaminants.
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Affiliation(s)
- Deepa Devarajan
- UT/ORNL Center for Molecular Biophysics, Biosciences Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, Tennessee 37831-6309, United States
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Liyuan Liang
- UT/ORNL Center for Molecular Biophysics, Biosciences Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, Tennessee 37831-6309, United States
- Department of Earth and Planetary Sciences, University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Baohua Gu
- Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831-6309, United States
| | - Scott C Brooks
- Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831-6309, United States
| | - Jerry M Parks
- UT/ORNL Center for Molecular Biophysics, Biosciences Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, Tennessee 37831-6309, United States
| | - Jeremy C Smith
- UT/ORNL Center for Molecular Biophysics, Biosciences Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, Tennessee 37831-6309, United States
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee 37996, United States
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26
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Ishida T, Parks JM, Smith JC. Insight into the Catalytic Mechanism of GH11 Xylanase: Computational Analysis of Substrate Distortion Based on a Neutron Structure. J Am Chem Soc 2020; 142:17966-17980. [PMID: 32959658 DOI: 10.1021/jacs.0c02148] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The reaction mechanism of biomass decomposition by xylanases remains the subject of debate. To clarify the mechanism we investigated the glycosylation step of GH11 xylanase, an enzyme that catalyzes the hydrolysis of lignocellulosic hemicellulose (xylan). Making use of a recent neutron crystal structure, which revealed the protonation states of relevant residues, we used ab initio quantum mechanics/molecular mechanics (QM/MM) calculations to determine the detailed reaction mechanism of the glycosylation step. In particular, our focus is on the controversial question of whether or not an oxocarbenium ion intermediate is formed on the reaction pathway. The calculations support the validity of a basic retaining mechanism within a double-displacement scheme. The estimated free energy barrier of this reaction is ∼18 kcal/mol with QM/MM-CCSD(T)/6-31(+)G**//MP2/6-31+G**/AMBER calculations, and the rate-determining step of the glycosylation is scission of the glycosidic bond after proton transfer from the acidic Glu177. The estimated lifetime of the oxocarbenium ion intermediate (on the order of tens of ps) and the secondary kinetic isotope effect suggest that there is no accumulation of this intermediate on the reaction path, although the intermediate can be transiently formed. In the enzyme-substrate (ES) complex, the carbohydrate structure of the xylose residue at the -1 subsite has a rather distorted (skewed) geometry, and this xylose unit at the active site has an apparent half-chair conformation when the oxocarbenium ion intermediate is formed. The major catalytic role of the protein environment is to orient residues that take part in the initial proton transfer. Because of a fine alignment of catalytic residues, the enzyme can accelerate the glycosylation reaction without paying a reorganization energy penalty.
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Affiliation(s)
- Toyokazu Ishida
- Research Center for Computational Design of Advanced Functional Materials (CD-FMat), National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba Central 2, 1-1-1 Umezono, Tsukuba 305-8568, Japan
| | - Jerry M Parks
- Center for Molecular Biophysics (CMB), Biosciences Division, Oak Ridge National Laboratory (ORNL), 1 Bethel Valley Road, Oak Ridge, Tennessee 37831-6309, United States
| | - Jeremy C Smith
- Center for Molecular Biophysics (CMB), Biosciences Division, Oak Ridge National Laboratory (ORNL), 1 Bethel Valley Road, Oak Ridge, Tennessee 37831-6309, United States
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27
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Aranha MP, Jewel YSM, Beckman RA, Weiner LM, Mitchell JC, Parks JM, Smith JC. Combining Three-Dimensional Modeling with Artificial Intelligence to Increase Specificity and Precision in Peptide-MHC Binding Predictions. J Immunol 2020; 205:1962-1977. [PMID: 32878910 PMCID: PMC7511449 DOI: 10.4049/jimmunol.1900918] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Accepted: 08/01/2020] [Indexed: 02/06/2023]
Abstract
The reliable prediction of the affinity of candidate peptides for the MHC is important for predicting their potential antigenicity and thus influences medical applications, such as decisions on their inclusion in T cell-based vaccines. In this study, we present a rapid, predictive computational approach that combines a popular, sequence-based artificial neural network method, NetMHCpan 4.0, with three-dimensional structural modeling. We find that the ensembles of bound peptide conformations generated by the programs MODELLER and Rosetta FlexPepDock are less variable in geometry for strong binders than for low-affinity peptides. In tests on 1271 peptide sequences for which the experimental dissociation constants of binding to the well-characterized murine MHC allele H-2Db are known, by applying thresholds for geometric fluctuations the structure-based approach in a standalone manner drastically improves the statistical specificity, reducing the number of false positives. Furthermore, filtering candidates generated with NetMHCpan 4.0 with the structure-based predictor led to an increase in the positive predictive value (PPV) of the peptides correctly predicted to bind very strongly (i.e., K d < 100 nM) from 40 to 52% (p = 0.027). The combined method also significantly improved the PPV when tested on five human alleles, including some with limited data for training. Overall, an average increase of 10% in the PPV was found over the standalone sequence-based method. The combined method should be useful in the rapid design of effective T cell-based vaccines.
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Affiliation(s)
- Michelle P Aranha
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, TN 37916
- Center for Molecular Biophysics, Oak Ridge National Laboratory, Oak Ridge, TN 37830
| | - Yead S M Jewel
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, TN 37916
- Center for Molecular Biophysics, Oak Ridge National Laboratory, Oak Ridge, TN 37830
| | - Robert A Beckman
- Innovation Center for Biomedical Informatics, Georgetown University Medical Center, Washington, DC 20007
- Department of Biostatistics, Bioinformatics, and Biomathematics, Georgetown University Medical Center, Washington, DC 20007
- Department of Oncology and Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC 20057
| | - Louis M Weiner
- Department of Oncology and Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC 20057
| | - Julie C Mitchell
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37830
| | - Jerry M Parks
- Center for Molecular Biophysics, Oak Ridge National Laboratory, Oak Ridge, TN 37830
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37830
| | - Jeremy C Smith
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, TN 37916;
- Center for Molecular Biophysics, Oak Ridge National Laboratory, Oak Ridge, TN 37830
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28
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Pavlova A, Lynch DL, Daidone I, Zanetti-Polzi L, Smith MD, Chipot C, Kneller DW, Kovalevsky A, Coates L, Golosov AA, Dickson CJ, Velez-Vega C, Duca JS, Vermaas JV, Pang YT, Acharya A, Parks JM, Smith JC, Gumbart JC. Inhibitor binding influences the protonation states of histidines in SARS-CoV-2 main protease. bioRxiv 2020. [PMID: 32935106 DOI: 10.1101/2020.09.07.286344] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The main protease (M pro ) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is an attractive target for antiviral therapeutics. Recently, many high-resolution apo and inhibitor-bound structures of M pro , a cysteine protease, have been determined, facilitating structure-based drug design. M pro plays a central role in the viral life cycle by catalyzing the cleavage of SARS-CoV-2 polyproteins. In addition to the catalytic dyad His41-Cys145, M pro contains multiple histidines including His163, His164, and His172. The protonation states of these histidines and the catalytic nu-cleophile Cys145 have been debated in previous studies of SARS-CoV M pro , but have yet to be investigated for SARS-CoV-2. In this work we have used molecular dynamics simulations to determine the structural stability of SARS-CoV-2 M pro as a function of the protonation assignments for these residues. We simulated both the apo and inhibitor-bound enzyme and found that the conformational stability of the binding site, bound inhibitors, and the hydrogen bond networks of M pro are highly sensitive to these assignments. Additionally, the two inhibitors studied, the peptidomimetic N3 and an α -ketoamide, display distinct His41/His164 protonation-state-dependent stabilities. While the apo and the N3-bound systems favored N δ (HD) and N ϵ (HE) protonation of His41 and His164, respectively, the α -ketoamide was not stably bound in this state. Our results illustrate the importance of using appropriate histidine protonation states to accurately model the structure and dynamics of SARS-CoV-2 M pro in both the apo and inhibitor-bound states, a necessary prerequisite for drug-design efforts.
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29
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Acharya A, Agarwal R, Baker M, Baudry J, Bhowmik D, Boehm S, Byler KG, Coates L, Chen SY, Cooper CJ, Demerdash O, Daidone I, Eblen JD, Ellingson S, Forli S, Glaser J, Gumbart JC, Gunnels J, Hernandez O, Irle S, Larkin J, Lawrence TJ, LeGrand S, Liu SH, Mitchell JC, Park G, Parks JM, Pavlova A, Petridis L, Poole D, Pouchard L, Ramanathan A, Rogers D, Santos-Martins D, Scheinberg A, Sedova A, Shen S, Smith JC, Smith MD, Soto C, Tsaris A, Thavappiragasam M, Tillack AF, Vermaas JV, Vuong VQ, Yin J, Yoo S, Zahran M, Zanetti-Polzi L. Supercomputer-Based Ensemble Docking Drug Discovery Pipeline with Application to Covid-19. ChemRxiv 2020:12725465. [PMID: 33200117 PMCID: PMC7668744 DOI: 10.26434/chemrxiv.12725465] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Revised: 07/29/2020] [Indexed: 01/18/2023]
Abstract
We present a supercomputer-driven pipeline for in-silico drug discovery using enhanced sampling molecular dynamics (MD) and ensemble docking. We also describe preliminary results obtained for 23 systems involving eight protein targets of the proteome of SARS CoV-2. THe MD performed is temperature replica-exchange enhanced sampling, making use of the massively parallel supercomputing on the SUMMIT supercomputer at Oak Ridge National Laboratory, with which more than 1ms of enhanced sampling MD can be generated per day. We have ensemble docked repurposing databases to ten configurations of each of the 23 SARS CoV-2 systems using AutoDock Vina. We also demonstrate that using Autodock-GPU on SUMMIT, it is possible to perform exhaustive docking of one billion compounds in under 24 hours. Finally, we discuss preliminary results and planned improvements to the pipeline, including the use of quantum mechanical (QM), machine learning, and AI methods to cluster MD trajectories and rescore docking poses.
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Affiliation(s)
- A Acharya
- School of Physics, Georgia Institute of Technology, Atlanta, GA 30332
| | - R Agarwal
- UT/ORNL Center for Molecular Biophysics, Oak Ridge National Laboratory, TN, 37830
- The University of Tennessee, Knoxville. Department of Biochemistry & Cellular and Molecular Biology, 309 Ken and Blaire Mossman Bldg. 1311 Cumberland Avenue Knoxville, TN, 37996
- Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, TN, 37996
| | - M Baker
- Computer Science and Mathematics Division, Oak Ridge National Lab, Oak Ridge, TN 37830
| | - J Baudry
- The University of Alabama in Huntsville, Department of Biological Sciences. 301 Sparkman Drive, Huntsville, AL 35899
| | - D Bhowmik
- Computational Sciences and Engineering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831
| | - S Boehm
- Computer Science and Mathematics Division, Oak Ridge National Lab, Oak Ridge, TN 37830
| | - K G Byler
- The University of Alabama in Huntsville, Department of Biological Sciences. 301 Sparkman Drive, Huntsville, AL 35899
| | - L Coates
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831
| | - S Y Chen
- Computational Science Initiative, Brookhaven National Laboratory, Upton, NY 11973
| | - C J Cooper
- UT/ORNL Center for Molecular Biophysics, Oak Ridge National Laboratory, TN, 37830
- Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, TN, 37996
| | - O Demerdash
- Biosciences Division, Oak Ridge National Lab, Oak Ridge, TN 37830
| | - I Daidone
- Department of Physical and Chemical Sciences, University of L'Aquila, I-67010 L'Aquila, Italy
| | - J D Eblen
- UT/ORNL Center for Molecular Biophysics, Oak Ridge National Laboratory, TN, 37830
- The University of Tennessee, Knoxville. Department of Biochemistry & Cellular and Molecular Biology, 309 Ken and Blaire Mossman Bldg. 1311 Cumberland Avenue Knoxville, TN, 37996
| | - S Ellingson
- University of Kentucky, Division of Biomedical Informatics, College of Medicine, UK Medical Center MN 150, Lexington KY, 40536
| | - S Forli
- Scripps Research, La Jolla, CA, 92037
| | - J Glaser
- National Center for Computational Sciences, Oak Ridge National Laboratory, Oak Ridge, TN 37830
| | - J C Gumbart
- School of Physics, Georgia Institute of Technology, Atlanta, GA 30332
| | - J Gunnels
- HPC Engineering, Amazon Web Services, Seattle, WA 98121
| | - O Hernandez
- Computer Science and Mathematics Division, Oak Ridge National Lab, Oak Ridge, TN 37830
| | - S Irle
- Computational Sciences and Engineering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831
- Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee, Knoxville, TN 37996
| | - J Larkin
- NVIDIA Corporation, Santa Clara, CA 95051
| | - T J Lawrence
- Biosciences Division, Oak Ridge National Lab, Oak Ridge, TN 37830
| | - S LeGrand
- NVIDIA Corporation, Santa Clara, CA 95051
| | - S-H Liu
- UT/ORNL Center for Molecular Biophysics, Oak Ridge National Laboratory, TN, 37830
- The University of Tennessee, Knoxville. Department of Biochemistry & Cellular and Molecular Biology, 309 Ken and Blaire Mossman Bldg. 1311 Cumberland Avenue Knoxville, TN, 37996
| | - J C Mitchell
- Biosciences Division, Oak Ridge National Lab, Oak Ridge, TN 37830
| | - G Park
- Computational Science Initiative, Brookhaven National Laboratory, Upton, NY 11973
| | - J M Parks
- UT/ORNL Center for Molecular Biophysics, Oak Ridge National Laboratory, TN, 37830
- The University of Tennessee, Knoxville. Department of Biochemistry & Cellular and Molecular Biology, 309 Ken and Blaire Mossman Bldg. 1311 Cumberland Avenue Knoxville, TN, 37996
- Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, TN, 37996
| | - A Pavlova
- School of Physics, Georgia Institute of Technology, Atlanta, GA 30332
| | - L Petridis
- UT/ORNL Center for Molecular Biophysics, Oak Ridge National Laboratory, TN, 37830
- The University of Tennessee, Knoxville. Department of Biochemistry & Cellular and Molecular Biology, 309 Ken and Blaire Mossman Bldg. 1311 Cumberland Avenue Knoxville, TN, 37996
| | - D Poole
- NVIDIA Corporation, Santa Clara, CA 95051
| | - L Pouchard
- Computational Science Initiative, Brookhaven National Laboratory, Upton, NY 11973
| | - A Ramanathan
- Data Science and Learning Division, Argonne National Lab, Lemont, IL 60439
| | - D Rogers
- National Center for Computational Sciences, Oak Ridge National Laboratory, Oak Ridge, TN 37830
| | | | | | - A Sedova
- Biosciences Division, Oak Ridge National Lab, Oak Ridge, TN 37830
| | - S Shen
- UT/ORNL Center for Molecular Biophysics, Oak Ridge National Laboratory, TN, 37830
- The University of Tennessee, Knoxville. Department of Biochemistry & Cellular and Molecular Biology, 309 Ken and Blaire Mossman Bldg. 1311 Cumberland Avenue Knoxville, TN, 37996
- Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, TN, 37996
| | - J C Smith
- UT/ORNL Center for Molecular Biophysics, Oak Ridge National Laboratory, TN, 37830
- The University of Tennessee, Knoxville. Department of Biochemistry & Cellular and Molecular Biology, 309 Ken and Blaire Mossman Bldg. 1311 Cumberland Avenue Knoxville, TN, 37996
| | - M D Smith
- UT/ORNL Center for Molecular Biophysics, Oak Ridge National Laboratory, TN, 37830
- The University of Tennessee, Knoxville. Department of Biochemistry & Cellular and Molecular Biology, 309 Ken and Blaire Mossman Bldg. 1311 Cumberland Avenue Knoxville, TN, 37996
| | - C Soto
- Computational Science Initiative, Brookhaven National Laboratory, Upton, NY 11973
| | - A Tsaris
- National Center for Computational Sciences, Oak Ridge National Laboratory, Oak Ridge, TN 37830
| | | | | | - J V Vermaas
- National Center for Computational Sciences, Oak Ridge National Laboratory, Oak Ridge, TN 37830
| | - V Q Vuong
- Computational Sciences and Engineering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831
- Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee, Knoxville, TN 37996
| | - J Yin
- National Center for Computational Sciences, Oak Ridge National Laboratory, Oak Ridge, TN 37830
| | - S Yoo
- Computational Science Initiative, Brookhaven National Laboratory, Upton, NY 11973
| | - M Zahran
- Department of Biological Sciences, New York City College of Technology, The City University of New York (CUNY), Brooklyn, NY 11201
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30
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Cooper CJ, Zheng K, Rush KW, Johs A, Sanders BC, Pavlopoulos GA, Kyrpides NC, Podar M, Ovchinnikov S, Ragsdale SW, Parks JM. Structure determination of the HgcAB complex using metagenome sequence data: insights into microbial mercury methylation. Commun Biol 2020; 3:320. [PMID: 32561885 PMCID: PMC7305189 DOI: 10.1038/s42003-020-1047-5] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [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: 01/27/2020] [Accepted: 05/27/2020] [Indexed: 11/09/2022] Open
Abstract
Bacteria and archaea possessing the hgcAB gene pair methylate inorganic mercury (Hg) to form highly toxic methylmercury. HgcA consists of a corrinoid binding domain and a transmembrane domain, and HgcB is a dicluster ferredoxin. However, their detailed structure and function have not been thoroughly characterized. We modeled the HgcAB complex by combining metagenome sequence data mining, coevolution analysis, and Rosetta structure calculations. In addition, we overexpressed HgcA and HgcB in Escherichia coli, confirmed spectroscopically that they bind cobalamin and [4Fe-4S] clusters, respectively, and incorporated these cofactors into the structural model. Surprisingly, the two domains of HgcA do not interact with each other, but HgcB forms extensive contacts with both domains. The model suggests that conserved cysteines in HgcB are involved in shuttling HgII, methylmercury, or both. These findings refine our understanding of the mechanism of Hg methylation and expand the known repertoire of corrinoid methyltransferases in nature. Connor J. Cooper et al. expressed HgcA and HgcB in Escherichia coli and modeled the structure of the HgcAB complex by combining metagenome sequence data, coevolution analysis, and ab initio structure calculations. This study provides insights into the biochemical mechanism of mercury (Hg) methylation.
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Affiliation(s)
- Connor J Cooper
- Graduate School of Genome Science and Technology, University of Tennessee, F225 Walters Life Science, Knoxville, TN, 37996, USA.,Biosciences Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN, 37831-6038, USA
| | - Kaiyuan Zheng
- Department of Biological Chemistry, University of Michigan Medical School, 1150 West Medical Center Drive, Ann Arbor, MI, 48109-0606, USA
| | - Katherine W Rush
- Department of Biological Chemistry, University of Michigan Medical School, 1150 West Medical Center Drive, Ann Arbor, MI, 48109-0606, USA
| | - Alexander Johs
- Environmental Sciences Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN, 37831-6038, USA
| | - Brian C Sanders
- Biosciences Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN, 37831-6038, USA
| | - Georgios A Pavlopoulos
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA.,Institute for Fundamental Biomedical Research, Biomedical Science Research Center "Alexander Fleming", 34 Fleming Street, 16672, Vari, Greece
| | - Nikos C Kyrpides
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA.,Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory Berkeley, California, USA
| | - Mircea Podar
- Graduate School of Genome Science and Technology, University of Tennessee, F225 Walters Life Science, Knoxville, TN, 37996, USA.,Biosciences Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN, 37831-6038, USA
| | - Sergey Ovchinnikov
- John Harvard Distinguished Science Fellowship Program, Harvard University, Cambridge, MA, 02138, USA
| | - Stephen W Ragsdale
- Department of Biological Chemistry, University of Michigan Medical School, 1150 West Medical Center Drive, Ann Arbor, MI, 48109-0606, USA
| | - Jerry M Parks
- Graduate School of Genome Science and Technology, University of Tennessee, F225 Walters Life Science, Knoxville, TN, 37996, USA. .,Biosciences Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN, 37831-6038, USA.
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31
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Affiliation(s)
- Jerry M Parks
- From the University of Tennessee-Oak Ridge National Laboratory Center for Molecular Biophysics, Biosciences Division, Oak Ridge National Laboratory, Oak Ridge (J.M.P., J.C.S.), and the Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville (J.C.S.)
| | - Jeremy C Smith
- From the University of Tennessee-Oak Ridge National Laboratory Center for Molecular Biophysics, Biosciences Division, Oak Ridge National Laboratory, Oak Ridge (J.M.P., J.C.S.), and the Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville (J.C.S.)
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32
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Hwang H, Hazel A, Lian P, Smith JC, Gumbart JC, Parks JM. A Minimal Membrane Metal Transport System: Dynamics and Energetics of mer Proteins. J Comput Chem 2020; 41:528-537. [PMID: 31721253 PMCID: PMC7263448 DOI: 10.1002/jcc.26098] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [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: 06/05/2019] [Revised: 09/17/2019] [Accepted: 10/14/2019] [Indexed: 12/28/2022]
Abstract
The mer operon in bacteria encodes a set of proteins and enzymes that impart resistance to environmental mercury toxicity by importing Hg2+ and reducing it to volatile Hg(0). Because the reduction occurs in the cytoplasm, mercuric ions must first be transported across the cytoplasmic membrane by one of a few known transporters. MerF is the smallest of these, containing only two transmembrane helices and two pairs of vicinal cysteines that coordinate mercuric ions. In this work, we use molecular dynamics simulations to characterize the dynamics of MerF in its apo and Hg2+ -bound states. We find that the apo state positions one of the cysteine pairs closer to the periplasmic side of the membrane, while in the bound state the same pair approaches the cytoplasmic side. This finding is consistent with the functional requirement of accepting Hg2+ from the periplasmic space, sequestering it on acceptance, and transferring it to the cytoplasm. Conformational changes in the TM helices facilitate the functional interaction of the two cysteine pairs. Free-energy calculations provide a barrier of 16 kcal/mol for the association of the periplasmic Hg2+ -bound protein MerP with MerF and 7 kcal/mol for the subsequent association of MerF's two cysteine pairs. Despite the significant conformational changes required to move the binding site across the membrane, coarse-grained simulations of multiple copies of MerF support the expectation that it functions as a monomer. Our results demonstrate how conformational changes and binding thermodynamics could lead to such a small membrane protein acting as an ion transporter. Published 2019. This article is a U.S. Government work and is in the public domain in the USA.
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Affiliation(s)
- Hyea Hwang
- School of Materials Science and Engineering, Georgia Institute of Technology, Atlanta, GA 30332
- UT/ORNL Center for Molecular Biophysics, Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831
| | - Anthony Hazel
- School of Physics, Georgia Institute of Technology, Atlanta, GA 30332
| | - Peng Lian
- UT/ORNL Center for Molecular Biophysics, Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, 37996
| | - Jeremy C. Smith
- UT/ORNL Center for Molecular Biophysics, Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, TN, 37996
| | - James C. Gumbart
- School of Physics, Georgia Institute of Technology, Atlanta, GA 30332
| | - Jerry M. Parks
- UT/ORNL Center for Molecular Biophysics, Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831
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33
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Green AT, Moniruzzaman M, Cooper CJ, Walker JK, Smith JC, Parks JM, Zgurskaya HI. Discovery of multidrug efflux pump inhibitors with a novel chemical scaffold. Biochim Biophys Acta Gen Subj 2020; 1864:129546. [PMID: 32032658 DOI: 10.1016/j.bbagen.2020.129546] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Revised: 01/21/2020] [Accepted: 01/30/2020] [Indexed: 12/12/2022]
Abstract
Multidrug efflux is a major contributor to antibiotic resistance in Gram-negative bacterial pathogens. Inhibition of multidrug efflux pumps is a promising approach for reviving the efficacy of existing antibiotics. Previously, inhibitors targeting both the efflux transporter AcrB and the membrane fusion protein AcrA in the Escherichia coli AcrAB-TolC efflux pump were identified. Here we use existing physicochemical property guidelines to generate a filtered library of compounds for computational docking. We then experimentally test the top candidate coumpounds using in vitro binding assays and in vivo potentiation assays in bacterial strains with controllable permeability barriers. We thus identify a new class of inhibitors of E. coli AcrAB-TolC. Six molecules with a shared scaffold were found to potentiate the antimicrobial activity of erythromycin and novobiocin in hyperporinated E. coli cells. Importantly, these six molecules were also active in wild-type strains of both Acinetobacter baumannii and Klebsiella pneumoniae, potentiating the activity of erythromycin and novobiocin up to 8-fold.
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Affiliation(s)
- Adam T Green
- UT/ORNL Center for Molecular Biophysics, Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA; Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, TN, 37996, USA
| | - Mohammad Moniruzzaman
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK 73019, USA
| | - Connor J Cooper
- UT/ORNL Center for Molecular Biophysics, Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA; Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, TN, 37996, USA
| | - John K Walker
- Department of Pharmacology and Physiology, Saint Louis University School of Medicine and the Henry and Amelia Nasrallah Center for Neuroscience, Saint Louis, MO, 63104, USA
| | - Jeremy C Smith
- UT/ORNL Center for Molecular Biophysics, Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA; Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, TN, 37996, USA; Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, TN 37996, USA
| | - Jerry M Parks
- UT/ORNL Center for Molecular Biophysics, Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA; Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, TN, 37996, USA.
| | - Helen I Zgurskaya
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK 73019, USA.
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34
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Gumbart JC, Ferreira J, hwang S, Hazel A, Parks JM, Smith JC, Beeby M, Zgurskaya H. Modeling the Placement of the AcrAB-TolC Multidrug Efflux Pump in the Bacterial Cell Envelope. Biophys J 2020. [DOI: 10.1016/j.bpj.2019.11.251] [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: 10/25/2022] Open
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35
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Hazel AJ, Abdali N, Leus IV, Parks JM, Smith JC, Zgurskaya HI, Gumbart JC. Conformational Dynamics of AcrA Govern Multidrug Efflux Pump Assembly. ACS Infect Dis 2019; 5:1926-1935. [PMID: 31517484 DOI: 10.1021/acsinfecdis.9b00273] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Multidrug efflux pumps of pathogenic, Gram-negative bacteria comprise an innate resistance mechanism and are key contributors to the emerging global pandemic of antibiotic resistance. Several increasingly detailed cryo-electron microscopy maps have been resolved of an entire efflux pump complex, AcrAB-TolC, resulting in atomistic structural models. Using a recent model, we have carried out nearly 40 μs of molecular dynamics simulations to study one of the key components of the protein complex AcrA, the membrane fusion protein that connects the inner-membrane-bound AcrB to the outer-membrane-bound TolC. We determined a three-dimensional potential of mean force (PMF) for AcrA, which displays two main conformational basins representing assembly competent and incompetent states. Corresponding experiments show that stabilizing mutations at an interdomain interface shift the dynamic equilibrium between these states to the incompetent one, disrupting pump assembly and function and resensitizing bacteria to existing antibiotics. The modulation of AcrA dynamics through pharmacological intervention therefore presents a promising route for the development of new antibiotics.
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Affiliation(s)
- Anthony J. Hazel
- School of Physics, Georgia Institute of Technology, 837 State Street NW, Atlanta, Georgia 30332, United States
| | - Narges Abdali
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Norman, Oklahoma 73019, United States
| | - Inga V. Leus
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Norman, Oklahoma 73019, United States
| | - Jerry M. Parks
- UT/ORNL Center for Molecular Biophysics, Biosciences Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, Tennessee 37831, United States
| | - Jeremy C. Smith
- UT/ORNL Center for Molecular Biophysics, Biosciences Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, Tennessee 37831, United States
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, 1311 Cumberland Avenue, Knoxville, Tennessee 37996, United States
| | - Helen I. Zgurskaya
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Norman, Oklahoma 73019, United States
| | - James C. Gumbart
- School of Physics, Georgia Institute of Technology, 837 State Street NW, Atlanta, Georgia 30332, United States
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36
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Lian P, Guo L, Devarajan D, Parks JM, Painter SL, Brooks SC, Smith JC. The AQUA-MER databases and aqueous speciation server: A web resource for multiscale modeling of mercury speciation. J Comput Chem 2019; 41:147-155. [PMID: 31603259 DOI: 10.1002/jcc.26081] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Revised: 09/09/2019] [Accepted: 09/10/2019] [Indexed: 02/06/2023]
Abstract
To assess the chemical reactivity, toxicity, and mobility of pollutants in the environment, knowledge of their species distributions is critical. Because their direct measurement is often infeasible, speciation modeling is widely adopted. Mercury (Hg) is a representative pollutant for which study of its speciation benefits from modeling. However, Hg speciation modeling is often hindered by a lack of reliable thermodynamic constants. Although computational chemistry (e.g., density functional theory [DFT]) can generate these constants, methods for directly coupling DFT and speciation modeling are not available. Here, we combine computational chemistry and continuum-scale modeling with curated online databases to ameliorate the problem of unreliable inputs to Hg speciation modeling. Our AQUA-MER databases and web server (https://aquamer.ornl.gov) provides direct speciation results by combining web-based interfaces to a speciation calculator, databases of thermodynamic constants, and a computational chemistry toolkit to estimate missing constants. Although Hg is presented as a concrete use case, AQUA-MER can also be readily applied to other elements. © 2019 Wiley Periodicals, Inc.
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Affiliation(s)
- Peng Lian
- UT/ORNL Center for Molecular Biophysics, Biosciences Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, Tennessee, 37831.,Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee, 37996
| | - Luanjing Guo
- UT/ORNL Center for Molecular Biophysics, Biosciences Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, Tennessee, 37831.,Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee, 37996
| | - Deepa Devarajan
- UT/ORNL Center for Molecular Biophysics, Biosciences Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, Tennessee, 37831.,Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee, 37996
| | - Jerry M Parks
- UT/ORNL Center for Molecular Biophysics, Biosciences Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, Tennessee, 37831
| | - Scott L Painter
- Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, 37831
| | - Scott C Brooks
- Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, 37831
| | - Jeremy C Smith
- UT/ORNL Center for Molecular Biophysics, Biosciences Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, Tennessee, 37831.,Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee, 37996
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37
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Close DM, Cooper CJ, Wang X, Chirania P, Gupta M, Ossyra JR, Giannone RJ, Engle N, Tschaplinski TJ, Smith JC, Hedstrom L, Parks JM, Michener JK. Horizontal transfer of a pathway for coumarate catabolism unexpectedly inhibits purine nucleotide biosynthesis. Mol Microbiol 2019; 112:1784-1797. [PMID: 31532038 DOI: 10.1111/mmi.14393] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/16/2019] [Indexed: 11/28/2022]
Abstract
A microbe's ecological niche and biotechnological utility are determined by its specific set of co-evolved metabolic pathways. The acquisition of new pathways, through horizontal gene transfer or genetic engineering, can have unpredictable consequences. Here we show that two different pathways for coumarate catabolism failed to function when initially transferred into Escherichia coli. Using laboratory evolution, we elucidated the factors limiting activity of the newly acquired pathways and the modifications required to overcome these limitations. Both pathways required host mutations to enable effective growth with coumarate, but the necessary mutations differed. In one case, a pathway intermediate inhibited purine nucleotide biosynthesis, and this inhibition was relieved by single amino acid replacements in IMP dehydrogenase. A strain that natively contains this coumarate catabolism pathway, Acinetobacter baumannii, is resistant to inhibition by the relevant intermediate, suggesting that natural pathway transfers have faced and overcome similar challenges. Molecular dynamics simulation of the wild type and a representative single-residue mutant provide insight into the structural and dynamic changes that relieve inhibition. These results demonstrate how deleterious interactions can limit pathway transfer, that these interactions can be traced to specific molecular interactions between host and pathway, and how evolution or engineering can alleviate these limitations.
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Affiliation(s)
- Dan M Close
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Connor J Cooper
- Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, TN, 37996, USA
| | - Xingyou Wang
- Graduate Program in Chemistry, Brandeis University, 415 South Street, Waltham, MA, 02454, USA
| | - Payal Chirania
- Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, TN, 37996, USA.,Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37830, USA
| | - Madhulika Gupta
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - John R Ossyra
- Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, TN, 37996, USA
| | - Richard J Giannone
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37830, USA.,BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN, 37830, USA.,Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, 37830, USA
| | - Nancy Engle
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA.,BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN, 37830, USA.,Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, 37830, USA
| | - Timothy J Tschaplinski
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA.,BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN, 37830, USA.,Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, 37830, USA
| | - Jeremy C Smith
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA.,Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee Knoxville, Knoxville, Tennessee, 37996, USA
| | - Lizbeth Hedstrom
- Department of Biology, Brandeis University, 415 South Street, Waltham, MA, 02454, USA.,Department of Chemistry, Brandeis University, 415 South Street, Waltham, MA, 02454, USA
| | - Jerry M Parks
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA.,Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, TN, 37996, USA
| | - Joshua K Michener
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA.,BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN, 37830, USA.,Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, 37830, USA
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38
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Cross KL, Campbell JH, Balachandran M, Campbell AG, Cooper SJ, Griffen A, Heaton M, Joshi S, Klingeman D, Leys E, Yang Z, Parks JM, Podar M. Targeted isolation and cultivation of uncultivated bacteria by reverse genomics. Nat Biotechnol 2019; 37:1314-1321. [PMID: 31570900 PMCID: PMC6858544 DOI: 10.1038/s41587-019-0260-6] [Citation(s) in RCA: 164] [Impact Index Per Article: 32.8] [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: 01/20/2019] [Accepted: 08/15/2019] [Indexed: 12/16/2022]
Abstract
Most microorganisms from all taxonomic levels are uncultured. Single-cell
genomes and metagenomes continue to increase the known diversity of
Bacteria and Archaea, but while
‘omics can be used to infer physiological or ecological roles for species
in a community, most of those hypothetical roles remain unvalidated. Here we
report an approach to capture specific microorganisms from complex communities
into pure cultures using genome-informed antibody engineering. We apply our
reverse genomics approach to isolate and sequence single cells and to cultivate
three different species-level lineages of human oral Saccharibacteria/TM7. Using
our pure cultures we show that all three saccharibacteria species are epibionts
of diverse Actinobacteria. We also isolate and cultivate human
oral SR1 bacteria, which are members of a lineage of previously uncultured
bacteria. Reverse-genomics-enabled cultivation of microorganisms can be applied
to any species from any environment and has the potential to unlock the
isolation, cultivation and characterization of species from as-yet-uncultured
branches of the microbial tree of life.
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Affiliation(s)
- Karissa L Cross
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA.,Department of Microbiology, University of Tennessee, Knoxville, TN, USA
| | - James H Campbell
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA.,Department of Natural Sciences, Northwest Missouri State University, Maryville, MO, USA
| | | | - Alisha G Campbell
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA.,Genome Science and Technology Program, University of Tennessee, Knoxville, TN, USA.,Department of Natural Sciences, Northwest Missouri State University, Maryville, MO, USA
| | - Sarah J Cooper
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA.,Genome Science and Technology Program, University of Tennessee, Knoxville, TN, USA
| | - Ann Griffen
- College of Dentistry, The Ohio State University, Columbus, OH, USA
| | | | - Snehal Joshi
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Dawn Klingeman
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Eugene Leys
- College of Dentistry, The Ohio State University, Columbus, OH, USA
| | - Zamin Yang
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Jerry M Parks
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA.,Genome Science and Technology Program, University of Tennessee, Knoxville, TN, USA
| | - Mircea Podar
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA. .,Department of Microbiology, University of Tennessee, Knoxville, TN, USA. .,Genome Science and Technology Program, University of Tennessee, Knoxville, TN, USA.
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Hu X, Smith MD, Humphreys BM, Green AT, Parks JM, Baudry JY, Smith JC. Ligand-Dependent Sodium Ion Dynamics within the A 2A Adenosine Receptor: A Molecular Dynamics Study. J Phys Chem B 2019; 123:7947-7954. [PMID: 31483659 DOI: 10.1021/acs.jpcb.9b04474] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Sodium ions have long been known to reduce the binding of agonists in many class-A GPCRs while having little effect on antagonist binding. Here, using long-time scale classical all-atom molecular dynamics simulations, we explore, in atomic detail, the motion of sodium ions within the ligand-binding pocket of the A2A adenosine receptor (A2A-AR) both in the presence and absence of ligands and in the active and inactive state. We identify novel secondary ion binding sites within the pocket and find that the types of ion motions within the pocket are highly dependent on the presence and type of ligand within the pocket. Our results provide a first step toward developing a molecular understanding of the impact of sodium ions on class-A GPCRs.
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Affiliation(s)
- Xiaohu Hu
- Department of Pharmacological Sciences , Icahn School of Medicine at Mount Sinai , New York , New York 10029 , United States.,Center for Molecular Biophysics, Biosciences Division , Oak Ridge National Laboratory , Oak Ridge , Tennessee 37830 , United States
| | - Micholas Dean Smith
- Center for Molecular Biophysics, Biosciences Division , Oak Ridge National Laboratory , Oak Ridge , Tennessee 37830 , United States
| | - Bailey M Humphreys
- Center for Molecular Biophysics, Biosciences Division , Oak Ridge National Laboratory , Oak Ridge , Tennessee 37830 , United States
| | - Adam T Green
- Center for Molecular Biophysics, Biosciences Division , Oak Ridge National Laboratory , Oak Ridge , Tennessee 37830 , United States
| | - Jerry M Parks
- Center for Molecular Biophysics, Biosciences Division , Oak Ridge National Laboratory , Oak Ridge , Tennessee 37830 , United States
| | - Jerome Y Baudry
- Biological Sciences Department , University of Alabama in Huntsville , Huntsville , Alabama 35899 , United States
| | - Jeremy C Smith
- Center for Molecular Biophysics, Biosciences Division , Oak Ridge National Laboratory , Oak Ridge , Tennessee 37830 , United States
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40
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Ajina R, Zuo A, Moussa M, Cooper SJ, Shen Y, Johnson QR, Parks JM, Smith JC, Fertig E, Catalfamo M, Jablonski SA, Weiner LM. Abstract 4584: Malignant pancreatic cancer cells respond to immune selection pressure to foster immunosuppression. Cancer Res 2019. [DOI: 10.1158/1538-7445.am2019-4584] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Background:
Host immunity is relevant to pancreatic cancer (PC). Pancreatic tumors are infiltrated with a high number of immune cells, and they play a potential important role in disease evolution. However, there is no FDA approved immunotherapy for PC yet, suggesting that a deeper understanding of immune-cancer interaction is needed. The aim of this study was to investigate the effects of immune selection pressure on malignant pancreatic epithelial cells and on subsequent cancer immune evasion mechanisms.
Materials and Methods:
1 X105 mT3-2D murine pancreatic cancer cells (Kras+/G12D, p53+/-R172H (Boj et al. 2015)) were injected subcutaneously into syngeneic C57BL/6J (WT), B6.CB17-Prkdcscid/SzJ (SCID) and T cell-depleted WT mice (10 mice/group). Tumor growth was monitored over time. 1 cm3 tumors then were harvested, processed and studied. To consider the complex biology of pancreatic cancer immunology, we analyzed tumor specimens in their entirety by histopathological evaluation, multiple color flow cytometry, NanoString nCounter, and global proteomics profiling. Furthermore, to evaluate the influence of immune selection pressure on neoplastic cells, we selectively analyzed malignant epithelial cell gene expression in the cell line, and in cells isolated from tumors grown in WT and SCID mice, respectively, by RNAseq on mT3-2D-GFP+ fluorescence-activated cell sorter (FACS)-sorted cells. Also, whole exome sequencing was performed on WT tumors.
Results
Here we demonstrate that mT3-2D tumors engrafted in WT mice grow more slowly as compared with syngeneic SCID and T cell-depleted tumors, demonstrating that the reduced mT3-2D tumor growth rate in WT mice is T cell dependent. Putative cancer neoantigens were identified from whole exome sequences with pVACtools. Supporting evidence of tumor immunogenicity came from the observation that WT tumors are moderately infiltrated with T cells, by IHC and flow cytometry. Proteomics and NanoString nCounter analysis demonstrated the selective presence of myeloid suppressive cells in WT tumors, supporting their role in immune evasion. Notably, RNAseq showed selective upregulation of malignant epithelial cell-derived genes known to stimulate this immunosuppressive phenotype, including myeloid- and complement-related genes.
Conclusion
Despite the immunogenicity of the WT tumors and the infiltration of T cells in this PC model, T cell immunity incompletely controls tumor growth. Malignant epithelial cells mediate this cancer immunosuppressive phenotype in response to immune selection pressure, suggesting novel translational opportunities.
References:
Boj SF, Hwang C-I, Baker LA, Chio IIC, Engle DD, Corbo V, Jager M, Ponz-Sarvise M, Tiriac H, Spector MS, et al. 2015. Organoid models of human and mouse ductal pancreatic cancer. Cell 160:324–338.
Citation Format: Reham Ajina, Annie Zuo, Maha Moussa, Sarah J. Cooper, Yue Shen, Quentin R. Johnson, Jerry M. Parks, Jeremy C. Smith, Elana Fertig, Marta Catalfamo, Sandra A. Jablonski, Louis M. Weiner. Malignant pancreatic cancer cells respond to immune selection pressure to foster immunosuppression [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 4584.
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Affiliation(s)
| | - Annie Zuo
- 1Georgetown University, Washington, DC
| | | | | | - Yue Shen
- 2University of Tennessee, Knoxville, TN
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An J, Zhang L, Lu X, Pelletier DA, Pierce EM, Johs A, Parks JM, Gu B. Mercury Uptake by Desulfovibrio desulfuricans ND132: Passive or Active? Environ Sci Technol 2019; 53:6264-6272. [PMID: 31075193 DOI: 10.1021/acs.est.9b00047] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Recent studies have identified HgcAB proteins as being responsible for mercury [Hg(II)] methylation by certain anaerobic microorganisms. However, it remains controversial whether microbes take up Hg(II) passively or actively. Here, we examine the dynamics of concurrent Hg(II) adsorption, uptake, and methylation by both viable and inactivated cells (heat-killed or starved) or spheroplasts of the sulfate-reducing bacterium Desulfovibrio desulfuricans ND132 in laboratory incubations. We show that, without addition of thiols, >60% of the added Hg(II) (25 nM) was taken up passively in 48 h by live and inactivated cells and also by cells treated with the proton gradient uncoupler, carbonylcyanide-3-chlorophenylhydrazone (CCCP). Inactivation abolished Hg(II) methylation, but the cells continued taking up Hg(II), likely through competitive binding or ligand exchange of Hg(II) by intracellular proteins or thiol-containing cellular components. Similarly, treatment with CCCP impaired the ability of spheroplasts to methylate Hg(II) but did not stop Hg(II) uptake. Spheroplasts showed a greater capacity to adsorb Hg(II) than whole cells, and the level of cytoplasmic membrane-bound Hg(II) correlated well with MeHg production, as Hg(II) methylation is associated with cytoplasmic HgcAB. Our results indicate that active metabolism is not required for cellular Hg(II) uptake, thereby providing an improved understanding of Hg(II) bioavailability for methylation.
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Affiliation(s)
- Jing An
- Environmental Sciences Division , Oak Ridge National Laboratory , Oak Ridge , Tennessee 37831 , United States
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology , Chinese Academy of Sciences , Shenyang 110016 , China
| | - Lijie Zhang
- Environmental Sciences Division , Oak Ridge National Laboratory , Oak Ridge , Tennessee 37831 , United States
| | - Xia Lu
- Environmental Sciences Division , Oak Ridge National Laboratory , Oak Ridge , Tennessee 37831 , United States
| | - Dale A Pelletier
- Biosciences Division , Oak Ridge National Laboratory , Oak Ridge , Tennessee 37831 , United States
| | - Eric M Pierce
- Environmental Sciences Division , Oak Ridge National Laboratory , Oak Ridge , Tennessee 37831 , United States
| | - Alexander Johs
- Environmental Sciences Division , Oak Ridge National Laboratory , Oak Ridge , Tennessee 37831 , United States
| | - Jerry M Parks
- Biosciences Division , Oak Ridge National Laboratory , Oak Ridge , Tennessee 37831 , United States
| | - Baohua Gu
- Environmental Sciences Division , Oak Ridge National Laboratory , Oak Ridge , Tennessee 37831 , United States
- Department of Biosystems Engineering and Soil Science , University of Tennessee , Knoxville , Tennessee 37996 , United States
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Abstract
Mercury (Hg) is a global environmental contaminant. Major anthropogenic sources of Hg emission include gold mining and the burning of fossil fuels. Once deposited in aquatic environments, Hg can undergo redox reactions, form complexes with ligands, and adsorb onto particles. It can also be methylated by microorganisms. Mercury, especially its methylated form methylmercury, can be taken up by organisms, where it bioaccumulates and biomagnifies in the food chain, leading to detrimental effects on ecosystem and human health. In support of the recently enforced Minamata Convention on Mercury, a legally binding international convention aimed at reducing the anthropogenic emission of-and human exposure to-Hg, its global biogeochemical cycle must be understood. Thus, a detailed understanding of the molecular-level interactions of Hg is crucial. The ongoing rapid development of hardware and methods has brought computational chemistry to a point that it can usefully inform environmental science. This is particularly true for Hg, which is difficult to handle experimentally due to its ultratrace concentrations in the environment and its toxicity. The current account provides a synopsis of the application of computational chemistry to filling several major knowledge gaps in environmental Hg chemistry that have not been adequately addressed experimentally. Environmental Hg chemistry requires defining the factors that determine the relative affinities of different ligands for Hg species, as they are critical for understanding its speciation, transformation and bioaccumulation in the environment. Formation constants and the nature of bonding have been determined computationally for environmentally relevant Hg(II) complexes such as chlorides, hydroxides, sulfides and selenides, in various physical phases. Quantum chemistry has been used to determine the driving forces behind the speciation of Hg with hydrochalcogenide and halide ligands. Of particular importance is the detailed characterization of solvation effects. Indeed, the aqueous phase reverses trends in affinities found computationally in the gas phase. Computation has also been used to investigate complexes of methylmercury with (seleno)amino acids, providing a molecular-level understanding of the toxicological antagonism between Hg and selenium (Se). Furthermore, evidence is emerging that ice surfaces play an important role in Hg transport and transformation in polar and alpine regions. Therefore, the diffusion of Hg and its ions through an idealized ice surface has been characterized. Microorganisms are major players in environmental mercury cycling. Some methylate inorganic Hg species, whereas others demethylate methylmercury. Quantum chemistry has been used to investigate catalytic mechanisms of enzymatic Hg methylation and demethylation. The complex interplay between the myriad chemical reactions and transport properties both in and outside microbial cells determines net biogeochemical cycling. Prospects for scaling up molecular work to obtain a mechanistic understanding of Hg cycling with comprehensive multiscale biogeochemical modeling are also discussed.
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Affiliation(s)
- Abu Asaduzzaman
- Department of Chemistry, University of Manitoba, Winnipeg, MB Canada, R3T 2N2
- School of Science, Engineering and Technology, Penn State Harrisburg, 777 West Harrisburg Pike, Middletown, Pennsylvania 17057, United States
| | - Demian Riccardi
- University of Tennessee/Oak Ridge National Laboratory Center for Molecular Biophysics, Biosciences Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, Tennessee 37831-6309, United States
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee Knoxville, Knoxville, Tennessee 37996, United States
| | - Akef T. Afaneh
- Department of Chemistry, University of Manitoba, Winnipeg, MB Canada, R3T 2N2
- Department of Chemistry, Faculty of Science, Al-Balqa Applied University, P.O. Box 19117,
postal code 19117, Al-Salt, Jordan
| | - Connor J. Cooper
- Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Jeremy C. Smith
- University of Tennessee/Oak Ridge National Laboratory Center for Molecular Biophysics, Biosciences Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, Tennessee 37831-6309, United States
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee Knoxville, Knoxville, Tennessee 37996, United States
| | - Feiyue Wang
- Centre for Earth Observation Science and Department of Environment and Geography, University of Manitoba, Winnipeg, MB Canada, R3T 2N2
| | - Jerry M. Parks
- University of Tennessee/Oak Ridge National Laboratory Center for Molecular Biophysics, Biosciences Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, Tennessee 37831-6309, United States
- Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Georg Schreckenbach
- Department of Chemistry, University of Manitoba, Winnipeg, MB Canada, R3T 2N2
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Hwang S, Paracini N, Parks JM, Lakey JH, Gumbart JC. Distribution of Mechanical Stress in the Escherichia Coli Cell Envelope. Biophys J 2019. [DOI: 10.1016/j.bpj.2018.11.913] [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: 10/27/2022] Open
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44
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Darzynkiewicz ZM, Green AT, Abdali N, Hazel A, Fulton RL, Kimball J, Gryczynski Z, Gumbart JC, Parks JM, Smith JC, Zgurskaya HI. Identification of Binding Sites for Efflux Pump Inhibitors of the AcrAB-TolC Component AcrA. Biophys J 2019; 116:648-658. [PMID: 30691677 DOI: 10.1016/j.bpj.2019.01.010] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Revised: 01/06/2019] [Accepted: 01/07/2019] [Indexed: 01/02/2023] Open
Abstract
The overexpression of multidrug efflux pumps is an important mechanism of clinical resistance in Gram-negative bacteria. Recently, four small molecules were discovered that inhibit efflux in Escherichia coli and interact with the AcrAB-TolC efflux pump component AcrA. However, the binding site(s) for these molecules was not determined. Here, we combine ensemble docking and molecular dynamics simulations with tryptophan fluorescence spectroscopy, site-directed mutagenesis, and antibiotic susceptibility assays to probe binding sites and effects of binding of these molecules. We conclude that clorobiocin and SLU-258 likely bind at a site located between the lipoyl and β-barrel domains of AcrA.
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Affiliation(s)
| | - Adam T Green
- UT/ORNL Center for Molecular Biophysics, Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee; Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, Tennessee
| | - Narges Abdali
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma
| | - Anthony Hazel
- School of Physics, Georgia Institute of Technology, Atlanta, Georgia
| | - Ronnie L Fulton
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma
| | - Joseph Kimball
- Department of Physics and Astronomy, Texas Christian University, Fort Worth, Texas
| | - Zygmunt Gryczynski
- Department of Physics and Astronomy, Texas Christian University, Fort Worth, Texas; Department of Microbiology, Immunology, and Genetics, University of North Texas Health Science Center, Fort Worth, Texas
| | - James C Gumbart
- School of Physics, Georgia Institute of Technology, Atlanta, Georgia
| | - Jerry M Parks
- UT/ORNL Center for Molecular Biophysics, Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee; Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, Tennessee
| | - Jeremy C Smith
- UT/ORNL Center for Molecular Biophysics, Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee; Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, Tennessee; Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee
| | - Helen I Zgurskaya
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma.
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45
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Qian C, Chen H, Johs A, Lu X, An J, Pierce EM, Parks JM, Elias DA, Hettich RL, Gu B. Quantitative Proteomic Analysis of Biological Processes and Responses of the Bacterium Desulfovibrio desulfuricans ND132 upon Deletion of Its Mercury Methylation Genes. Proteomics 2018; 18:e1700479. [PMID: 30009483 DOI: 10.1002/pmic.201700479] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2017] [Revised: 05/17/2018] [Indexed: 11/10/2022]
Abstract
Recent studies of microbial mercury (Hg) methylation revealed a key gene pair, hgcAB, which is essential for methylmercury (MeHg) production in the environment. However, many aspects of the mechanism and biological processes underlying Hg methylation, as well as any additional physiological functions of the hgcAB genes, remain unknown. Here, quantitative proteomics are used to identify changes in potential functional processes related to hgcAB gene deletion in the Hg-methylating bacterium Desulfovibrio desulfuricans ND132. Global proteomics analyses indicate that the wild type and ΔhgcAB strains are similar with respect to the whole proteome and the identified number of proteins, but differ significantly in the abundance of specific proteins. The authors observe changes in the abundance of proteins related to the glycolysis pathway and one-carbon metabolism, suggesting that the hgcAB gene pair is linked to carbon metabolism. Unexpectedly, the authors find that the deletion of hgcAB significantly impacts a range of metal transport proteins, specifically membrane efflux pumps such as those associated with heavy metal copper (Cu) export, leading to decreased Cu uptake in the ΔhgcAB mutant. This observation indicates possible linkages between this set of proteins and metal homeostasis in the cell. However, hgcAB gene expression is not induced by Hg, as evidenced by similarly low abundance of HgcA and HgcB proteins in the absence or presence of Hg (500 nm). Taken together, these results suggest an apparent link between HgcAB, one-carbon metabolism, and metal homeostasis, thereby providing insights for further exploration of biochemical mechanisms and biological functions of microbial Hg methylation.
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Affiliation(s)
- Chen Qian
- Chemical Sciences Division, Oak Ridge National Laboratory, 37831 Oak Ridge, TN, USA.,Graduate School of Genome Science and Technology, University of Tennessee, 37996 Knoxville, TN, USA
| | - Hongmei Chen
- Environmental Sciences Division, Oak Ridge National Laboratory, 37831 Oak Ridge, TN, USA
| | - Alexander Johs
- Environmental Sciences Division, Oak Ridge National Laboratory, 37831 Oak Ridge, TN, USA
| | - Xia Lu
- Environmental Sciences Division, Oak Ridge National Laboratory, 37831 Oak Ridge, TN, USA
| | - Jing An
- Environmental Sciences Division, Oak Ridge National Laboratory, 37831 Oak Ridge, TN, USA
| | - Eric M Pierce
- Environmental Sciences Division, Oak Ridge National Laboratory, 37831 Oak Ridge, TN, USA
| | - Jerry M Parks
- Biosciences Division, Oak Ridge National Laboratory, 37831 Oak Ridge, TN, USA
| | - Dwayne A Elias
- Biosciences Division, Oak Ridge National Laboratory, 37831 Oak Ridge, TN, USA
| | - Robert L Hettich
- Chemical Sciences Division, Oak Ridge National Laboratory, 37831 Oak Ridge, TN, USA.,Graduate School of Genome Science and Technology, University of Tennessee, 37996 Knoxville, TN, USA
| | - Baohua Gu
- Environmental Sciences Division, Oak Ridge National Laboratory, 37831 Oak Ridge, TN, USA
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46
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Cooper CJ, Krishnamoorthy G, Wolloscheck D, Walker JK, Rybenkov VV, Parks JM, Zgurskaya HI. Molecular Properties That Define the Activities of Antibiotics in Escherichia coli and Pseudomonas aeruginosa. ACS Infect Dis 2018; 4:1223-1234. [PMID: 29756762 DOI: 10.1021/acsinfecdis.8b00036] [Citation(s) in RCA: 48] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The permeability barrier of Gram-negative cell envelopes is the major obstacle in the discovery and development of new antibiotics. In Gram-negative bacteria, these difficulties are exacerbated by the synergistic interaction between two biochemically distinct phenomena, the low permeability of the outer membrane (OM) and active multidrug efflux. In this study, we used Pseudomonas aeruginosa and Escherichia coli strains with controllable permeability barriers, achieved through hyperporination of the OMs and varied efflux capacities, to evaluate the contributions of each of the barriers to protection from antibacterials. We analyzed antibacterial activities of β-lactams and fluoroquinolones, antibiotics that are optimized for targets in the periplasm and the cytoplasm, respectively, and performed a machine learning-based analysis to identify physicochemical descriptors that best classify their relative potencies. Our results show that the molecular properties selected by active efflux and the OM barriers are different for the two species. Antibiotic activity in P. aeruginosa was better classified by electrostatic and surface area properties, whereas topology, physical properties, and atom or bond counts best capture the behavior in E. coli. In several cases, descriptor values that correspond to active antibiotics also correspond to significant barrier effects, highlighting the synergy between the two barriers where optimizing for one barrier promotes strengthening of the other barrier. Thus, both barriers should be considered when optimizing antibiotics for favorable OM permeability, efflux evasion, or both.
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Affiliation(s)
- Connor J. Cooper
- Graduate School of Genome Science and Technology, University of Tennessee, F225 Walters Life Science, Knoxville, Tennessee 37996, United States
| | - Ganesh Krishnamoorthy
- Department of Chemistry and Biochemistry, Stephenson Life Sciences Research Center, University of Oklahoma, 101 Stephenson Parkway, Norman, Oklahoma 73019, United States
| | - David Wolloscheck
- Department of Chemistry and Biochemistry, Stephenson Life Sciences Research Center, University of Oklahoma, 101 Stephenson Parkway, Norman, Oklahoma 73019, United States
| | - John K. Walker
- Department of Pharmacological & Physiological Science, Saint Louis University School of Medicine, St. Louis, Missouri 63104, United States
| | - Valentin V. Rybenkov
- Department of Chemistry and Biochemistry, Stephenson Life Sciences Research Center, University of Oklahoma, 101 Stephenson Parkway, Norman, Oklahoma 73019, United States
| | - Jerry M. Parks
- Graduate School of Genome Science and Technology, University of Tennessee, F225 Walters Life Science, Knoxville, Tennessee 37996, United States
- Biosciences Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, Tennessee 37831-6309, United States
| | - Helen I. Zgurskaya
- Department of Chemistry and Biochemistry, Stephenson Life Sciences Research Center, University of Oklahoma, 101 Stephenson Parkway, Norman, Oklahoma 73019, United States
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Mueser TC, Dajnowicz S, Kovalevsky A, Parks JM. Neutron diffraction studies of pyridoxal-5′-phosphate-dependent enzymes. Acta Crystallogr A Found Adv 2018. [DOI: 10.1107/s0108767318099634] [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: 11/11/2022] Open
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48
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Kanzler CR, Lian P, Trainer EL, Yang X, Govind N, Parks JM, Graham AM. Emerging investigator series: methylmercury speciation and dimethylmercury production in sulfidic solutions. Environ Sci Process Impacts 2018; 20:584-594. [PMID: 29388993 DOI: 10.1039/c7em00533d] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Alkylated mercury species (monomethylmercury, MeHg, and dimethylmercury, DMeHg) exhibit significant bioaccumulation, and pose significant risks to ecosystems and human health. Although decades of research have been devoted to understanding MeHg formation and degradation, little is known about the DMeHg formation in aquatic systems. Here, we combine complementary experimental and computational approaches to examine MeHg speciation and DMeHg formation in sulfidic aqueous solutions, with an emphasis on the formation and decomposition of the binuclear bis(methylmercuric(ii)) sulfide complex (CH3Hg)2S. Experimental data indicate that the reaction 2CH3Hg+ + HS- ⇄ (CH3Hg)2S + H+ has a log K = 26.0 ± 0.2. Thus, the binuclear (CH3Hg)2S complex is likely to be the dominant MeHg species under high MeHg concentrations typically used in experimental investigations of MeHg degradation by sulfate-reducing bacteria (SRB). Our finding of a significant abiotic removal mechanism for MeHg in sulfidic solutions through the formation of relatively insoluble (CH3Hg)2S suggests careful reexamination of reported "oxidative demethylation" of MeHg by SRB and perhaps other obligate anaerobes. We provide evidence for slow decomposition of (CH3Hg)2S to DMeHg and HgS, with a first-order rate constant k = 1.5 ± 0.4 × 10-6 h-1. Quantum chemical calculations suggest that the reaction proceeds by a novel mechanism involving rearrangement of the (CH3Hg)2S complex facilitated by strong Hg-Hg interactions that activate a methyl group for intramolecular transfer. Predictions of DMeHg formation rates under a variety of field and laboratory conditions indicate that this pathway for DMeHg formation will be significant in laboratory experiments utilizing high MeHg concentrations, favoring (CH3Hg)2S formation. In natural systems with relatively high MeHg/[H2S]T ratios (the oxic/anoxic interface, for example), DMeHg production may be observed, and warrants further investigation.
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49
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Lian P, Johnston RC, Parks JM, Smith JC. Quantum Chemical Calculation of pKas of Environmentally Relevant Functional Groups: Carboxylic Acids, Amines, and Thiols in Aqueous Solution. J Phys Chem A 2018; 122:4366-4374. [DOI: 10.1021/acs.jpca.8b01751] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Peng Lian
- UT/ORNL Center for Molecular Biophysics, Biosciences Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, Tennessee 37831-6309, United States
| | - Ryne C. Johnston
- UT/ORNL Center for Molecular Biophysics, Biosciences Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, Tennessee 37831-6309, United States
| | - Jerry M. Parks
- UT/ORNL Center for Molecular Biophysics, Biosciences Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, Tennessee 37831-6309, United States
| | - Jeremy C. Smith
- UT/ORNL Center for Molecular Biophysics, Biosciences Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, Tennessee 37831-6309, United States
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50
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Goins CM, Dajnowicz S, Smith MD, Parks JM, Ronning DR. Mycolyltransferase from Mycobacterium tuberculosis in covalent complex with tetrahydrolipstatin provides insights into antigen 85 catalysis. J Biol Chem 2018; 293:3651-3662. [PMID: 29352107 PMCID: PMC5846135 DOI: 10.1074/jbc.ra117.001681] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2017] [Indexed: 01/07/2023] Open
Abstract
Mycobacterium tuberculosis antigen 85 (Ag85) enzymes catalyze the transfer of mycolic acid (MA) from trehalose monomycolate to produce the mycolyl arabinogalactan (mAG) or trehalose dimycolate (TDM). These lipids define the protective mycomembrane of mycobacteria. The current model of substrate binding within the active sites of Ag85s for the production of TDM is not sterically and geometrically feasible; additionally, this model does not account for the production of mAG. Furthermore, this model does not address how Ag85s limit the hydrolysis of the acyl-enzyme intermediate while catalyzing acyl transfer. To inform an updated model, we obtained an Ag85 acyl-enzyme intermediate structure that resembles the mycolated form. Here, we present a 1.45-Å X-ray crystal structure of M. tuberculosis Ag85C covalently modified by tetrahydrolipstatin (THL), an esterase inhibitor that suppresses M. tuberculosis growth and mimics structural attributes of MAs. The mode of covalent inhibition differs from that observed in the reversible inhibition of the human fatty-acid synthase by THL. Similarities between the Ag85-THL structure and previously determined Ag85C structures suggest that the enzyme undergoes structural changes upon acylation, and positioning of the peptidyl arm of THL limits hydrolysis of the acyl-enzyme adduct. Molecular dynamics simulations of the modeled mycolated-enzyme form corroborate the structural analysis. From these findings, we propose an alternative arrangement of substrates that rectifies issues with the previous model and suggest a direct role for the β-hydroxy of MA in the second half-reaction of Ag85 catalysis. This information affords the visualization of a complete mycolyltransferase catalytic cycle.
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Affiliation(s)
- Christopher M. Goins
- From the Department of Chemistry and Biochemistry, University of Toledo, Toledo, Ohio 43606-3390
| | - Steven Dajnowicz
- From the Department of Chemistry and Biochemistry, University of Toledo, Toledo, Ohio 43606-3390, ,Biology and Soft Matter Division and
| | - Micholas D. Smith
- University of Tennessee and Oak Ridge National Laboratory (UT/ORNL) Center for Molecular Biophysics, Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, and ,Department of Biochemistry, Cellular, and Molecular Biology, University of Tennessee, Knoxville, Tennessee 37996
| | - Jerry M. Parks
- University of Tennessee and Oak Ridge National Laboratory (UT/ORNL) Center for Molecular Biophysics, Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, and
| | - Donald R. Ronning
- From the Department of Chemistry and Biochemistry, University of Toledo, Toledo, Ohio 43606-3390, , To whom correspondence should be addressed:
Dept. of Chemistry and Biochemistry, University of Toledo, 2801 W. Bancroft St., Toledo, OH 43606-3390. Tel.:
419-530-1585; E-mail:
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