1
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Hartojo A, Doyle MT. β-barrel membrane proteins fold via hybrid-barrel intermediate states. Curr Opin Struct Biol 2024; 87:102830. [PMID: 38728831 DOI: 10.1016/j.sbi.2024.102830] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Revised: 03/15/2024] [Accepted: 04/22/2024] [Indexed: 05/12/2024]
Abstract
Gram-negative bacteria and eukaryotic organelles of bacterial origin contain outer membrane proteins that possess a transmembrane "β-barrel" domain. The conserved β-barrel assembly machine (BAM) and the sorting and assembly machine (SAM) are required for the folding and membrane insertion of β-barrels in Gram-negative bacteria and mitochondria, respectively. Although the mechanisms by which β-barrels are folded are incompletely understood, advances in cryo-electron microscopy (cryo-EM) have recently yielded unprecedented insights into their folding process. Here we highlight recent studies that show that both bacterial and mitochondrial β-barrels fold via the formation of remarkable "hybrid-barrel" intermediate states during their interaction with the folding machinery. We discuss how these results align with a general model of β-barrel folding.
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Affiliation(s)
- Alfred Hartojo
- Sydney Infectious Diseases Institute, The University of Sydney, Darlington, New South Wales, Australia; School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Darlington, New South Wales, Australia. https://twitter.com/AlfredHartojo29
| | - Matthew Thomas Doyle
- Sydney Infectious Diseases Institute, The University of Sydney, Darlington, New South Wales, Australia; School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Darlington, New South Wales, Australia.
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2
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Gutishvili G, Yang L, Gumbart JC. Seeing is believing: Illuminating the Gram-negative outer membrane with molecular dynamics simulations. Curr Opin Struct Biol 2024; 87:102828. [PMID: 38723580 DOI: 10.1016/j.sbi.2024.102828] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Revised: 04/14/2024] [Accepted: 04/15/2024] [Indexed: 07/29/2024]
Abstract
Recent advances in molecular dynamics (MD) simulations have led to rapid improvement in our understanding of the molecular details of the outer membranes (OMs) of Gram-negative bacteria. In this review, we highlight the latest discoveries from MD simulations of OMs, shedding light on the dynamic nature of these bacteria's first line of defense. With the focus on cutting-edge approaches, we explore the OM's sensitivity to structural features, including divalent cations and membrane composition, which have emerged as crucial determinants of antimicrobial passage. Additionally, studies have provided novel insights into outer-membrane proteins (OMPs), revealing their intricate roles in substrate translocation and their distinct interactions with lipopolysaccharides (LPS) in the OM. Finally, we explore the challenging process of β-barrel membrane protein insertion, showcasing recent findings that have enhanced our grasp of this fundamental biological phenomenon.
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Affiliation(s)
| | - Lixinhao Yang
- School of Chemistry and Biochemistry, 901 Atlantic Dr., Atlanta, GA, 30332, USA
| | - James C Gumbart
- School of Physics, 837 State St., Atlanta, GA, 30332, USA; School of Chemistry and Biochemistry, 901 Atlantic Dr., Atlanta, GA, 30332, USA.
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3
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Mellouk A, Jaouen P, Ruel LJ, Lê M, Martini C, Moraes TF, El Bakkouri M, Lagüe P, Boisselier E, Calmettes C. POTRA domains of the TamA insertase interact with the outer membrane and modulate membrane properties. Proc Natl Acad Sci U S A 2024; 121:e2402543121. [PMID: 38959031 PMCID: PMC11252910 DOI: 10.1073/pnas.2402543121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Accepted: 05/22/2024] [Indexed: 07/04/2024] Open
Abstract
The outer membrane (OM) of gram-negative bacteria serves as a vital organelle that is densely populated with OM proteins (OMPs) and plays pivotal roles in cellular functions and virulence. The assembly and insertion of these OMPs into the OM represent a fundamental process requiring specialized molecular chaperones. One example is the translocation and assembly module (TAM), which functions as a transenvelope chaperone promoting the folding of specific autotransporters, adhesins, and secretion systems. The catalytic unit of TAM, TamA, comprises a catalytic β-barrel domain anchored within the OM and three periplasmic polypeptide-transport-associated (POTRA) domains that recruit the TamB subunit. The latter acts as a periplasmic ladder that facilitates the transport of unfolded OMPs across the periplasm. In addition to their role in recruiting the auxiliary protein TamB, our data demonstrate that the POTRA domains mediate interactions with the inner surface of the OM, ultimately modulating the membrane properties. Through the integration of X-ray crystallography, molecular dynamic simulations, and biomolecular interaction methodologies, we located the membrane-binding site on the first and second POTRA domains. Our data highlight a binding preference for phosphatidylglycerol, a minor lipid constituent present in the OM, which has been previously reported to facilitate OMP assembly. In the context of the densely OMP-populated membrane, this association may serve as a mechanism to secure lipid accessibility for nascent OMPs through steric interactions with existing OMPs, in addition to creating favorable conditions for OMP biogenesis.
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Affiliation(s)
- Abdelkader Mellouk
- Institut National de la Rechyuerche Scientifique (INRS), Centre Armand-Frappier Santé Biotechnologie, Laval, QCH7V 1B7, Canada
- Regroupement Québécois de recherche sur la fonction, la structure et l’ingénierie des protéines (PROTEO), Université du Québec à Montréal, Montréal, QCH2X 3Y7, Canada
| | - Paul Jaouen
- Regroupement Québécois de recherche sur la fonction, la structure et l’ingénierie des protéines (PROTEO), Université du Québec à Montréal, Montréal, QCH2X 3Y7, Canada
- Faculty of Medicine, Department of Ophthalmology and Otolaryngology—Head and Neck Surgery, centre hospitalier universitaire de Québec, Université Laval, Québec City, QCG1S 4L8, Canada
| | - Louis-Jacques Ruel
- Regroupement Québécois de recherche sur la fonction, la structure et l’ingénierie des protéines (PROTEO), Université du Québec à Montréal, Montréal, QCH2X 3Y7, Canada
- Département de Biochimie, de Microbiologie et de Bio-informatique, Université Laval, Québec City, QCG1V 0A6, Canada
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec City, QCG1V 0A6, Canada
| | - Michel Lê
- Institut National de la Rechyuerche Scientifique (INRS), Centre Armand-Frappier Santé Biotechnologie, Laval, QCH7V 1B7, Canada
- Regroupement Québécois de recherche sur la fonction, la structure et l’ingénierie des protéines (PROTEO), Université du Québec à Montréal, Montréal, QCH2X 3Y7, Canada
| | - Cyrielle Martini
- Institut National de la Rechyuerche Scientifique (INRS), Centre Armand-Frappier Santé Biotechnologie, Laval, QCH7V 1B7, Canada
- Regroupement Québécois de recherche sur la fonction, la structure et l’ingénierie des protéines (PROTEO), Université du Québec à Montréal, Montréal, QCH2X 3Y7, Canada
| | - Trevor F. Moraes
- Department of Biochemistry, University of Toronto, Toronto, ONM5G 1M1, Canada
| | - Majida El Bakkouri
- National Research Council Canada, Human Health Therapeutics, Montréal, QCH4P 2R2, Canada
| | - Patrick Lagüe
- Regroupement Québécois de recherche sur la fonction, la structure et l’ingénierie des protéines (PROTEO), Université du Québec à Montréal, Montréal, QCH2X 3Y7, Canada
- Département de Biochimie, de Microbiologie et de Bio-informatique, Université Laval, Québec City, QCG1V 0A6, Canada
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec City, QCG1V 0A6, Canada
| | - Elodie Boisselier
- Regroupement Québécois de recherche sur la fonction, la structure et l’ingénierie des protéines (PROTEO), Université du Québec à Montréal, Montréal, QCH2X 3Y7, Canada
- Faculty of Medicine, Department of Ophthalmology and Otolaryngology—Head and Neck Surgery, centre hospitalier universitaire de Québec, Université Laval, Québec City, QCG1S 4L8, Canada
| | - Charles Calmettes
- Institut National de la Rechyuerche Scientifique (INRS), Centre Armand-Frappier Santé Biotechnologie, Laval, QCH7V 1B7, Canada
- Regroupement Québécois de recherche sur la fonction, la structure et l’ingénierie des protéines (PROTEO), Université du Québec à Montréal, Montréal, QCH2X 3Y7, Canada
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4
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Hanson SE, Dowdy T, Larion M, Doyle MT, Bernstein HD. The patatin-like protein PlpD forms structurally dynamic homodimers in the Pseudomonas aeruginosa outer membrane. Nat Commun 2024; 15:4389. [PMID: 38782915 PMCID: PMC11116518 DOI: 10.1038/s41467-024-48756-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Accepted: 05/13/2024] [Indexed: 05/25/2024] Open
Abstract
Members of the Omp85 superfamily of outer membrane proteins (OMPs) found in Gram-negative bacteria, mitochondria and chloroplasts are characterized by a distinctive 16-stranded β-barrel transmembrane domain and at least one periplasmic POTRA domain. All previously studied Omp85 proteins promote critical OMP assembly and/or protein translocation reactions. Pseudomonas aeruginosa PlpD is the prototype of an Omp85 protein family that contains an N-terminal patatin-like (PL) domain that is thought to be translocated across the OM by a C-terminal β-barrel domain. Challenging the current dogma, we find that the PlpD PL-domain resides exclusively in the periplasm and, unlike previously studied Omp85 proteins, PlpD forms a homodimer. Remarkably, the PL-domain contains a segment that exhibits unprecedented dynamicity by undergoing transient strand-swapping with the neighboring β-barrel domain. Our results show that the Omp85 superfamily is more structurally diverse than currently believed and suggest that the Omp85 scaffold was utilized during evolution to generate novel functions.
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Affiliation(s)
- Sarah E Hanson
- Genetics and Biochemistry Branch, National Institutes of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Tyrone Dowdy
- Neuro-Oncology Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Mioara Larion
- Neuro-Oncology Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Matthew Thomas Doyle
- Genetics and Biochemistry Branch, National Institutes of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, 20892, USA.
- Sydney Infectious Diseases Institute and School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, 2006, Australia.
| | - Harris D Bernstein
- Genetics and Biochemistry Branch, National Institutes of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, 20892, USA.
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5
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George A, Patil AG, Mahalakshmi R. ATP-independent assembly machinery of bacterial outer membranes: BAM complex structure and function set the stage for next-generation therapeutics. Protein Sci 2024; 33:e4896. [PMID: 38284489 PMCID: PMC10804688 DOI: 10.1002/pro.4896] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 12/28/2023] [Accepted: 12/31/2023] [Indexed: 01/30/2024]
Abstract
Diderm bacteria employ β-barrel outer membrane proteins (OMPs) as their first line of communication with their environment. These OMPs are assembled efficiently in the asymmetric outer membrane by the β-Barrel Assembly Machinery (BAM). The multi-subunit BAM complex comprises the transmembrane OMP BamA as its functional subunit, with associated lipoproteins (e.g., BamB/C/D/E/F, RmpM) varying across phyla and performing different regulatory roles. The ability of BAM complex to recognize and fold OM β-barrels of diverse sizes, and reproducibly execute their membrane insertion, is independent of electrochemical energy. Recent atomic structures, which captured BAM-substrate complexes, show the assembly function of BamA can be tailored, with different substrate types exhibiting different folding mechanisms. Here, we highlight common and unique features of its interactome. We discuss how this conserved protein complex has evolved the ability to effectively achieve the directed assembly of diverse OMPs of wide-ranging sizes (8-36 β-stranded monomers). Additionally, we discuss how darobactin-the first natural membrane protein inhibitor of Gram-negative bacteria identified in over five decades-selectively targets and specifically inhibits BamA. We conclude by deliberating how a detailed deduction of BAM complex-associated regulation of OMP biogenesis and OM remodeling will open avenues for the identification and development of effective next-generation therapeutics against Gram-negative pathogens.
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Affiliation(s)
- Anjana George
- Molecular Biophysics Laboratory, Department of Biological SciencesIndian Institute of Science Education and ResearchBhopalIndia
| | - Akanksha Gajanan Patil
- Molecular Biophysics Laboratory, Department of Biological SciencesIndian Institute of Science Education and ResearchBhopalIndia
| | - Radhakrishnan Mahalakshmi
- Molecular Biophysics Laboratory, Department of Biological SciencesIndian Institute of Science Education and ResearchBhopalIndia
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6
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Gopinath A, Rath T, Morgner N, Joseph B. Lateral gating mechanism and plasticity of the β-barrel assembly machinery complex in micelles and Escherichia coli. PNAS NEXUS 2024; 3:pgae019. [PMID: 38312222 PMCID: PMC10833450 DOI: 10.1093/pnasnexus/pgae019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Accepted: 01/08/2024] [Indexed: 02/06/2024]
Abstract
The β-barrel assembly machinery (BAM) mediates the folding and insertion of the majority of outer membrane proteins (OMPs) in gram-negative bacteria. BAM is a penta-heterooligomeric complex consisting of the central β-barrel BamA and four interacting lipoproteins BamB, C, D, and E. The conformational switching of BamA between inward-open (IO) and lateral-open (LO) conformations is required for substrate recognition and folding. However, the mechanism for the lateral gating or how the structural details observed in vitro correspond with the cellular environment remains elusive. In this study, we addressed these questions by characterizing the conformational heterogeneity of BamAB, BamACDE, and BamABCDE complexes in detergent micelles and/or Escherichia coli using pulsed dipolar electron spin resonance spectroscopy (PDS). We show that the binding of BamB does not induce any visible changes in BamA, and the BamAB complex exists in the IO conformation. The BamCDE complex induces an IO to LO transition through a coordinated movement along the BamA barrel. However, the extracellular loop 6 (L6) is unaffected by the presence of lipoproteins and exhibits large segmental dynamics extending to the exit pore. PDS experiments with the BamABCDE complex in intact E. coli confirmed the dynamic behavior of both the lateral gate and the L6 in the native environment. Our results demonstrate that the BamCDE complex plays a key role in the function by regulating lateral gating in BamA.
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Affiliation(s)
- Aathira Gopinath
- Department of Physics, Freie Universität Berlin, Berlin, 14195, Germany
- Institute of Biophysics, Goethe Universität Frankfurt, Frankfurt, 60438, Germany
| | - Tobias Rath
- Institute of Physical and Theoretical Chemistry, Goethe Universität Frankfurt, Frankfurt, 60438, Germany
| | - Nina Morgner
- Institute of Physical and Theoretical Chemistry, Goethe Universität Frankfurt, Frankfurt, 60438, Germany
| | - Benesh Joseph
- Department of Physics, Freie Universität Berlin, Berlin, 14195, Germany
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7
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Yeow J, Luo M, Chng SS. Molecular mechanism of phospholipid transport at the bacterial outer membrane interface. Nat Commun 2023; 14:8285. [PMID: 38092770 PMCID: PMC10719372 DOI: 10.1038/s41467-023-44144-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 12/01/2023] [Indexed: 12/17/2023] Open
Abstract
The outer membrane (OM) of Gram-negative bacteria is an asymmetric lipid bilayer with outer leaflet lipopolysaccharides and inner leaflet phospholipids (PLs). This unique lipid asymmetry renders the OM impermeable to external insults, including antibiotics and bile salts. To maintain this barrier, the OmpC-Mla system removes mislocalized PLs from the OM outer leaflet, and transports them to the inner membrane (IM); in the first step, the OmpC-MlaA complex transfers PLs to the periplasmic chaperone MlaC, but mechanistic details are lacking. Here, we biochemically and structurally characterize the MlaA-MlaC transient complex. We map the interaction surfaces between MlaA and MlaC in Escherichia coli, and show that electrostatic interactions are important for MlaC recruitment to the OM. We further demonstrate that interactions with MlaC modulate conformational states in MlaA. Finally, we solve a 2.9-Å cryo-EM structure of a disulfide-trapped OmpC-MlaA-MlaC complex in nanodiscs, reinforcing the mechanism of MlaC recruitment, and highlighting membrane thinning as a plausible strategy for directing lipids for transport. Our work offers critical insights into retrograde PL transport by the OmpC-Mla system in maintaining OM lipid asymmetry.
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Affiliation(s)
- Jiang Yeow
- Department of Chemistry, Faculty of Science, National University of Singapore, Singapore, 117543, Singapore
| | - Min Luo
- Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore, 117558, Singapore
- Center for Bioimaging Sciences, Department of Biological Sciences, National University of Singapore, Singapore, 117557, Singapore
| | - Shu-Sin Chng
- Department of Chemistry, Faculty of Science, National University of Singapore, Singapore, 117543, Singapore.
- Singapore Center for Environmental Life Sciences Engineering, National University of Singapore (SCELSE-NUS), Singapore, 117456, Singapore.
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8
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Shen C, Chang S, Luo Q, Chan KC, Zhang Z, Luo B, Xie T, Lu G, Zhu X, Wei X, Dong C, Zhou R, Zhang X, Tang X, Dong H. Structural basis of BAM-mediated outer membrane β-barrel protein assembly. Nature 2023; 617:185-193. [PMID: 37100902 DOI: 10.1038/s41586-023-05988-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Accepted: 03/21/2023] [Indexed: 04/28/2023]
Abstract
The outer membrane structure is common in Gram-negative bacteria, mitochondria and chloroplasts, and contains outer membrane β-barrel proteins (OMPs) that are essential interchange portals of materials1-3. All known OMPs share the antiparallel β-strand topology4, implicating a common evolutionary origin and conserved folding mechanism. Models have been proposed for bacterial β-barrel assembly machinery (BAM) to initiate OMP folding5,6; however, mechanisms by which BAM proceeds to complete OMP assembly remain unclear. Here we report intermediate structures of BAM assembling an OMP substrate, EspP, demonstrating sequential conformational dynamics of BAM during the late stages of OMP assembly, which is further supported by molecular dynamics simulations. Mutagenic in vitro and in vivo assembly assays reveal functional residues of BamA and EspP for barrel hybridization, closure and release. Our work provides novel insights into the common mechanism of OMP assembly.
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Affiliation(s)
- Chongrong Shen
- State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, China
| | - Shenghai Chang
- Department of Biophysics of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Center of Cryo Electron Microscopy, Zhejiang University, Hangzhou, China
- Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou, China
- Department of Pathology of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Qinghua Luo
- State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, China
- Frontiers Medical Center, Tianfu Jincheng Laboratory, West China Hospital, Sichuan University, Chengdu, China
| | - Kevin Chun Chan
- Institute of Quantitative Biology, College of Life Sciences, Cancer Center, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
- Shanghai Institute for Advanced Study, Zhejiang University, Shanghai, China
| | - Zhibo Zhang
- State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, China
| | - Bingnan Luo
- State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, China
| | - Teng Xie
- Institute of Quantitative Biology, College of Life Sciences, Cancer Center, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Guangwen Lu
- State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, China
| | - Xiaofeng Zhu
- College of Life Science, Sichuan University, Chengdu, China
| | - Xiawei Wei
- State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, China
| | - Changjiang Dong
- School of Pharmaceutical Sciences, Wuhan University, Wuhan, China
| | - Ruhong Zhou
- Institute of Quantitative Biology, College of Life Sciences, Cancer Center, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China.
- Shanghai Institute for Advanced Study, Zhejiang University, Shanghai, China.
- Department of Chemistry, Columbia University, New York, NY, USA.
| | - Xing Zhang
- Department of Biophysics of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China.
- Center of Cryo Electron Microscopy, Zhejiang University, Hangzhou, China.
- Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou, China.
- Department of Pathology of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China.
| | - Xiaodi Tang
- State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, China.
| | - Haohao Dong
- State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, China.
- Department of Pathology of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China.
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9
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Hanson SE, Doyle MT, Bernstein HD. The patatin-like protein PlpD forms novel structurally dynamic homodimers in the Pseudomonas aeruginosa outer membrane. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.17.537245. [PMID: 37333265 PMCID: PMC10274916 DOI: 10.1101/2023.04.17.537245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
Members of the Omp85 superfamily of outer membrane proteins (OMPs) found in Gram-negative bacteria, mitochondria and chloroplasts are characterized by a distinctive 16-stranded β-barrel transmembrane domain and at least one periplasmic POTRA domain. All previously studied Omp85 proteins promote critical OMP assembly and/or protein translocation reactions. Pseudomonas aeruginosa PlpD is the prototype of an Omp85 protein family that contains an N-terminal patatin-like (PL) domain that is thought to be translocated across the OM by a C-terminal β-barrel domain. Challenging the current dogma, we found that the PlpD PL-domain resides exclusively in the periplasm and, unlike previously studied Omp85 proteins, PlpD forms a homodimer. Remarkably, the PL-domain contains a segment that exhibits unprecedented dynamicity by undergoing transient strand-swapping with the neighboring β-barrel domain. Our results show that the Omp85 superfamily is more structurally diverse than currently believed and suggest that the Omp85 scaffold was utilized during evolution to generate novel functions.
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Affiliation(s)
- Sarah E. Hanson
- Genetics and Biochemistry Branch, National Institutes of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892 USA
| | | | - Harris D. Bernstein
- Genetics and Biochemistry Branch, National Institutes of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892 USA
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10
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Abstract
Several antibacterial compounds have recently been discovered that potentially inhibit the activity of BamA, an essential subunit of a heterooligomer (the barrel assembly machinery or BAM) that assembles outer membrane proteins (OMPs) in Gram-negative bacteria, but their mode of action is unclear. To address this issue, we examined the effect of three inhibitors on the biogenesis of a model E. coli OMP (EspP) in vivo. We found that darobactin potently inhibited the interaction of a conserved C-terminal sequence motif (the “β signal”) with BamA, but had no effect on assembly if added at a postbinding stage. In contrast, Polyphor peptide 7 and MRL-494 inhibited both binding and at least one later step of assembly. Taken together with previous studies that analyzed the binding of darobactin and Polyphor peptide 7 to BamA in vitro, our results strongly suggest that the two compounds inhibit BAM function by distinct competitive and allosteric mechanisms. In addition to providing insights into the properties of the antibacterial compounds, our results also provide direct experimental evidence that supports a model in which the binding of the β signal to BamA initiates the membrane insertion of OMPs.
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11
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Doyle MT, Bernstein HD. Function of the Omp85 Superfamily of Outer Membrane Protein Assembly Factors and Polypeptide Transporters. Annu Rev Microbiol 2022; 76:259-279. [PMID: 35650668 DOI: 10.1146/annurev-micro-033021-023719] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The Omp85 protein superfamily is found in the outer membrane (OM) of all gram-negative bacteria and eukaryotic organelles of bacterial origin. Members of the family catalyze both the membrane insertion of β-barrel proteins and the translocation of proteins across the OM. Although the mechanism(s) by which these proteins function is unclear, striking new insights have emerged from recent biochemical and structural studies. In this review we discuss the entire Omp85 superfamily but focus on the function of the best-studied member, BamA, which is an essential and highly conserved component of the bacterial barrel assembly machinery (BAM). Because BamA has multiple functions that overlap with those of other Omp85 proteins, it is likely the prototypical member of the Omp85 superfamily. Furthermore, BamA has become a protein of great interest because of the recent discovery of small-molecule inhibitors that potentially represent an important new class of antibiotics. Expected final online publication date for the Annual Review of Microbiology, Volume 76 is September 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Matthew Thomas Doyle
- Genetics and Biochemistry Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, USA; ,
| | - Harris D Bernstein
- Genetics and Biochemistry Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, USA; ,
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12
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Doyle MT, Jimah JR, Dowdy T, Ohlemacher SI, Larion M, Hinshaw JE, Bernstein HD. Cryo-EM structures reveal multiple stages of bacterial outer membrane protein folding. Cell 2022; 185:1143-1156.e13. [PMID: 35294859 DOI: 10.1016/j.cell.2022.02.016] [Citation(s) in RCA: 40] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 12/01/2021] [Accepted: 02/13/2022] [Indexed: 02/08/2023]
Abstract
Transmembrane β barrel proteins are folded into the outer membrane (OM) of Gram-negative bacteria by the β barrel assembly machinery (BAM) via a poorly understood process that occurs without known external energy sources. Here, we used single-particle cryo-EM to visualize the folding dynamics of a model β barrel protein (EspP) by BAM. We found that BAM binds the highly conserved "β signal" motif of EspP to correctly orient β strands in the OM during folding. We also found that the folding of EspP proceeds via "hybrid-barrel" intermediates in which membrane integrated β sheets are attached to the essential BAM subunit, BamA. The structures show an unprecedented deflection of the membrane surrounding the EspP intermediates and suggest that β sheets progressively fold toward BamA to form a β barrel. Along with in vivo experiments that tracked β barrel folding while the OM tension was modified, our results support a model in which BAM harnesses OM elasticity to accelerate β barrel folding.
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Affiliation(s)
- Matthew Thomas Doyle
- Genetics and Biochemistry Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - John R Jimah
- Laboratory of Cell and Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Tyrone Dowdy
- Neuro-Oncology Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Shannon I Ohlemacher
- Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Mioara Larion
- Neuro-Oncology Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jenny E Hinshaw
- Laboratory of Cell and Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA.
| | - Harris D Bernstein
- Genetics and Biochemistry Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA.
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13
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Horne JE, Radford SE. Roll out the barrel! Outer membrane tension resolves an unexpected folding intermediate. Cell 2022; 185:1107-1109. [DOI: 10.1016/j.cell.2022.03.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Revised: 02/25/2022] [Accepted: 02/28/2022] [Indexed: 12/01/2022]
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14
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A noncanonical chaperone interacts with drug efflux pumps during their assembly into bacterial outer membranes. PLoS Biol 2022; 20:e3001523. [PMID: 35061668 PMCID: PMC8809574 DOI: 10.1371/journal.pbio.3001523] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 02/02/2022] [Accepted: 12/22/2021] [Indexed: 11/19/2022] Open
Abstract
Bacteria have membrane-spanning efflux pumps to secrete toxic compounds ranging from heavy metal ions to organic chemicals, including antibiotic drugs. The overall architecture of these efflux pumps is highly conserved: with an inner membrane energy-transducing subunit coupled via an adaptor protein to an outer membrane conduit subunit that enables toxic compounds to be expelled into the environment. Here, we map the distribution of efflux pumps across bacterial lineages to show these proteins are more widespread than previously recognised. Complex phylogenetics support the concept that gene cassettes encoding the subunits for these pumps are commonly acquired by horizontal gene transfer. Using TolC as a model protein, we demonstrate that assembly of conduit subunits into the outer membrane uses the chaperone TAM to physically organise the membrane-embedded staves of the conduit subunit of the efflux pump. The characteristics of this assembly pathway have impact for the acquisition of efflux pumps across bacterial species and for the development of new antimicrobial compounds that inhibit efflux pump function. A crosslinking study reveals novel insights into how the chaperone TAM helps Gram-negative bacteria insert the drug efflux pump subunit TolC into their outer membrane. Bioinformatic analyses show that TolC-like proteins can be found in all LPS-containing bacteria, but also in some monodermic Firmicutes.
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15
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Gopinath A, Joseph B. Conformational Flexibility of the Protein Insertase BamA in the Native Asymmetric Bilayer Elucidated by ESR Spectroscopy. Angew Chem Int Ed Engl 2022; 61:e202113448. [PMID: 34761852 PMCID: PMC9299766 DOI: 10.1002/anie.202113448] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Indexed: 12/15/2022]
Abstract
The β-barrel assembly machinery (BAM) consisting of the central β-barrel BamA and four other lipoproteins mediates the folding of the majority of the outer membrane proteins. BamA is placed in an asymmetric bilayer and its lateral gate is suggested to be the functional hotspot. Here we used in situ pulsed electron-electron double resonance spectroscopy to characterize BamA in the native outer membrane. In the detergent micelles, the data is consistent with mainly an inward-open conformation of BamA. The native membrane considerably enhanced the conformational heterogeneity. The lateral gate and the extracellular loop 3 exist in an equilibrium between different conformations. The outer membrane provides a favorable environment for occupying multiple conformational states independent of the lipoproteins. Our results reveal a highly dynamic behavior of the lateral gate and other key structural elements and provide direct evidence for the conformational modulation of a membrane protein in situ.
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Affiliation(s)
- Aathira Gopinath
- Institute of BiophysicsDepartment of PhysicsCenter for Biomolecular Magnetic Resonance (BMRZ)Goethe University FrankfurtMax-von-Laue-Str. 160438Frankfurt/MainGermany
| | - Benesh Joseph
- Institute of BiophysicsDepartment of PhysicsCenter for Biomolecular Magnetic Resonance (BMRZ)Goethe University FrankfurtMax-von-Laue-Str. 160438Frankfurt/MainGermany
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16
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Plasticity within the barrel domain of BamA mediates a hybrid-barrel mechanism by BAM. Nat Commun 2021; 12:7131. [PMID: 34880256 PMCID: PMC8655018 DOI: 10.1038/s41467-021-27449-4] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Accepted: 11/22/2021] [Indexed: 12/26/2022] Open
Abstract
In Gram-negative bacteria, the biogenesis of β-barrel outer membrane proteins is mediated by the β-barrel assembly machinery (BAM). The mechanism employed by BAM is complex and so far- incompletely understood. Here, we report the structures of BAM in nanodiscs, prepared using polar lipids and native membranes, where we observe an outward-open state. Mutations in the barrel domain of BamA reveal that plasticity in BAM is essential, particularly along the lateral seam of the barrel domain, which is further supported by molecular dynamics simulations that show conformational dynamics in BAM are modulated by the accessory proteins. We also report the structure of BAM in complex with EspP, which reveals an early folding intermediate where EspP threads from the underside of BAM and incorporates into the barrel domain of BamA, supporting a hybrid-barrel budding mechanism in which the substrate is folded into the membrane sequentially rather than as a single unit.
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17
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Gopinath A, Joseph B. Conformational Flexibility of the Protein Insertase BamA in the Native Asymmetric Bilayer Elucidated by ESR Spectroscopy. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202113448] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Aathira Gopinath
- Institute of Biophysics Department of Physics Center for Biomolecular Magnetic Resonance (BMRZ) Goethe University Frankfurt Max-von-Laue-Str. 1 60438 Frankfurt/Main Germany
| | - Benesh Joseph
- Institute of Biophysics Department of Physics Center for Biomolecular Magnetic Resonance (BMRZ) Goethe University Frankfurt Max-von-Laue-Str. 1 60438 Frankfurt/Main Germany
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18
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The role of membrane destabilisation and protein dynamics in BAM catalysed OMP folding. Nat Commun 2021; 12:4174. [PMID: 34234105 PMCID: PMC8263589 DOI: 10.1038/s41467-021-24432-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Accepted: 06/08/2021] [Indexed: 02/06/2023] Open
Abstract
The folding of β-barrel outer membrane proteins (OMPs) in Gram-negative bacteria is catalysed by the β-barrel assembly machinery (BAM). How lateral opening in the β-barrel of the major subunit BamA assists in OMP folding, and the contribution of membrane disruption to BAM catalysis remain unresolved. Here, we use an anti-BamA monoclonal antibody fragment (Fab1) and two disulphide-crosslinked BAM variants (lid-locked (LL), and POTRA-5-locked (P5L)) to dissect these roles. Despite being lethal in vivo, we show that all complexes catalyse folding in vitro, albeit less efficiently than wild-type BAM. CryoEM reveals that while Fab1 and BAM-P5L trap an open-barrel state, BAM-LL contains a mixture of closed and contorted, partially-open structures. Finally, all three complexes globally destabilise the lipid bilayer, while BamA does not, revealing that the BAM lipoproteins are required for this function. Together the results provide insights into the role of BAM structure and lipid dynamics in OMP folding.
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19
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Steinberg R, Koch HG. The largely unexplored biology of small proteins in pro- and eukaryotes. FEBS J 2021; 288:7002-7024. [PMID: 33780127 DOI: 10.1111/febs.15845] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 03/11/2021] [Accepted: 03/26/2021] [Indexed: 12/29/2022]
Abstract
The large abundance of small open reading frames (smORFs) in prokaryotic and eukaryotic genomes and the plethora of smORF-encoded small proteins became only apparent with the constant advancements in bioinformatic, genomic, proteomic, and biochemical tools. Small proteins are typically defined as proteins of < 50 amino acids in prokaryotes and of less than 100 amino acids in eukaryotes, and their importance for cell physiology and cellular adaptation is only beginning to emerge. In contrast to antimicrobial peptides, which are secreted by prokaryotic and eukaryotic cells for combatting pathogens and competitors, small proteins act within the producing cell mainly by stabilizing protein assemblies and by modifying the activity of larger proteins. Production of small proteins is frequently linked to stress conditions or environmental changes, and therefore, cells seem to use small proteins as intracellular modifiers for adjusting cell metabolism to different intra- and extracellular cues. However, the size of small proteins imposes a major challenge for the cellular machinery required for protein folding and intracellular trafficking and recent data indicate that small proteins can engage distinct trafficking pathways. In the current review, we describe the diversity of small proteins in prokaryotes and eukaryotes, highlight distinct and common features, and illustrate how they are handled by the protein trafficking machineries in prokaryotic and eukaryotic cells. Finally, we also discuss future topics of research on this fascinating but largely unexplored group of proteins.
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Affiliation(s)
- Ruth Steinberg
- Institute for Biochemistry and Molecular Biology, Zentrum für Biochemie und Molekulare Medizin (ZMBZ), Faculty of Medicine, Albert-Ludwigs-Universität Freiburg, Germany
| | - Hans-Georg Koch
- Institute for Biochemistry and Molecular Biology, Zentrum für Biochemie und Molekulare Medizin (ZMBZ), Faculty of Medicine, Albert-Ludwigs-Universität Freiburg, Germany
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20
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Diederichs KA, Buchanan SK, Botos I. Building Better Barrels - β-barrel Biogenesis and Insertion in Bacteria and Mitochondria. J Mol Biol 2021; 433:166894. [PMID: 33639212 PMCID: PMC8292188 DOI: 10.1016/j.jmb.2021.166894] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Revised: 02/18/2021] [Accepted: 02/18/2021] [Indexed: 01/20/2023]
Abstract
β-barrel proteins are folded and inserted into outer membranes by multi-subunit protein complexes that are conserved across different types of outer membranes. In Gram-negative bacteria this complex is the barrel-assembly machinery (BAM), in mitochondria it is the sorting and assembly machinery (SAM) complex, and in chloroplasts it is the outer envelope protein Oep80. Mitochondrial β-barrel precursor proteins are translocated from the cytoplasm to the intermembrane space by the translocase of the outer membrane (TOM) complex, and stabilized by molecular chaperones before interaction with the assembly machinery. Outer membrane bacterial BamA interacts with four periplasmic accessory proteins, whereas mitochondrial Sam50 interacts with two cytoplasmic accessory proteins. Despite these major architectural differences between BAM and SAM complexes, their core proteins, BamA and Sam50, seem to function the same way. Based on the new SAM complex structures, we propose that the mitochondrial β-barrel folding mechanism follows the budding model with barrel-switching aiding in the release of new barrels. We also built a new molecular model for Tom22 interacting with Sam37 to identify regions that could mediate TOM-SAM supercomplex formation.
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Affiliation(s)
- Kathryn A Diederichs
- Laboratory of Molecular Biology, National Institute of Diabetes & Digestive & Kidney Diseases, National Institutes of Health, 9000 Rockville Pike, Bethesda, MD 20892, USA
| | - Susan K Buchanan
- Laboratory of Molecular Biology, National Institute of Diabetes & Digestive & Kidney Diseases, National Institutes of Health, 9000 Rockville Pike, Bethesda, MD 20892, USA
| | - Istvan Botos
- Laboratory of Molecular Biology, National Institute of Diabetes & Digestive & Kidney Diseases, National Institutes of Health, 9000 Rockville Pike, Bethesda, MD 20892, USA.
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