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Dhiman R, Perera RS, Poojari CS, Wiedemann HTA, Kappl R, Kay CWM, Hub JS, Schrul B. Hairpin protein partitioning from the ER to lipid droplets involves major structural rearrangements. Nat Commun 2024; 15:4504. [PMID: 38802378 PMCID: PMC11130287 DOI: 10.1038/s41467-024-48843-8] [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: 01/28/2024] [Accepted: 05/15/2024] [Indexed: 05/29/2024] Open
Abstract
Lipid droplet (LD) function relies on proteins partitioning between the endoplasmic reticulum (ER) phospholipid bilayer and the LD monolayer membrane to control cellular adaptation to metabolic changes. It has been proposed that these hairpin proteins integrate into both membranes in a similar monotopic topology, enabling their passive lateral diffusion during LD emergence at the ER. Here, we combine biochemical solvent-accessibility assays, electron paramagnetic resonance spectroscopy and intra-molecular crosslinking experiments with molecular dynamics simulations, and determine distinct intramembrane positionings of the ER/LD protein UBXD8 in ER bilayer and LD monolayer membranes. UBXD8 is deeply inserted into the ER bilayer with a V-shaped topology and adopts an open-shallow conformation in the LD monolayer. Major structural rearrangements are required to enable ER-to-LD partitioning. Free energy calculations suggest that such structural transition is unlikely spontaneous, indicating that ER-to-LD protein partitioning relies on more complex mechanisms than anticipated and providing regulatory means for this trans-organelle protein trafficking.
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Affiliation(s)
- Ravi Dhiman
- Medical Biochemistry and Molecular Biology, Center for Molecular Signaling (PZMS), Faculty of Medicine, Saarland University, 66421, Homburg/Saar, Germany
| | - Rehani S Perera
- Medical Biochemistry and Molecular Biology, Center for Molecular Signaling (PZMS), Faculty of Medicine, Saarland University, 66421, Homburg/Saar, Germany
| | - Chetan S Poojari
- Theoretical Physics and Center for Biophysics, Saarland University, 66123, Saarbrücken, Germany
| | - Haakon T A Wiedemann
- Physical Chemistry and Chemistry Education, Saarland University, 66123, Saarbrücken, Germany
| | - Reinhard Kappl
- Department of Biophysics, Center for Integrative Physiology and Molecular Medicine (CIPMM), Faculty of Medicine, Saarland University, 66421, Homburg/Saar, Germany
| | - Christopher W M Kay
- Physical Chemistry and Chemistry Education, Saarland University, 66123, Saarbrücken, Germany
- London Centre for Nanotechnology, University College London, WC1H 0AH, London, UK
| | - Jochen S Hub
- Theoretical Physics and Center for Biophysics, Saarland University, 66123, Saarbrücken, Germany
| | - Bianca Schrul
- Medical Biochemistry and Molecular Biology, Center for Molecular Signaling (PZMS), Faculty of Medicine, Saarland University, 66421, Homburg/Saar, Germany.
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2
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Clarke A, Farr CV, El-Kasaby A, Szöllősi D, Freissmuth M, Sucic S, Stockner T. Probing binding and occlusion of substrate in the human creatine transporter-1 by computation and mutagenesis. Protein Sci 2024; 33:e4842. [PMID: 38032325 PMCID: PMC10751730 DOI: 10.1002/pro.4842] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Revised: 11/16/2023] [Accepted: 11/18/2023] [Indexed: 12/01/2023]
Abstract
In chordates, energy buffering is achieved in part through phosphocreatine, which requires cellular uptake of creatine by the membrane-embedded creatine transporter (CRT1/SLC6A8). Mutations in human slc6a8 lead to creatine transporter deficiency syndrome, for which there is only limited treatment. Here, we used a combined homology modeling, molecular dynamics, and experimental approach to generate a structural model of CRT1. Our observations support the following conclusions: contrary to previous proposals, C144, a key residue in the substrate binding site, is not present in a charged state. Similarly, the side chain D458 must be present in a protonated form to maintain the structural integrity of CRT1. Finally, we identified that the interaction chain Y148-creatine-Na+ is essential to the process of occlusion, which occurs via a "hold-and-pull" mechanism. The model should be useful to study the impact of disease-associated point mutations on the folding of CRT1 and identify approaches which correct folding-deficient mutants.
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Affiliation(s)
- Amy Clarke
- Institute of Pharmacology and the Gaston H. Glock Research Laboratories for Exploratory Drug Development, Center of Physiology and Pharmacology, Medical University of Vienna, Vienna, Austria
| | - Clemens V Farr
- Institute of Pharmacology and the Gaston H. Glock Research Laboratories for Exploratory Drug Development, Center of Physiology and Pharmacology, Medical University of Vienna, Vienna, Austria
| | - Ali El-Kasaby
- Institute of Pharmacology and the Gaston H. Glock Research Laboratories for Exploratory Drug Development, Center of Physiology and Pharmacology, Medical University of Vienna, Vienna, Austria
| | - Daniel Szöllősi
- Department of Theoretical and Computational Biophysics, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Michael Freissmuth
- Institute of Pharmacology and the Gaston H. Glock Research Laboratories for Exploratory Drug Development, Center of Physiology and Pharmacology, Medical University of Vienna, Vienna, Austria
| | - Sonja Sucic
- Institute of Pharmacology and the Gaston H. Glock Research Laboratories for Exploratory Drug Development, Center of Physiology and Pharmacology, Medical University of Vienna, Vienna, Austria
| | - Thomas Stockner
- Institute of Pharmacology and the Gaston H. Glock Research Laboratories for Exploratory Drug Development, Center of Physiology and Pharmacology, Medical University of Vienna, Vienna, Austria
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3
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Thakur GCN, Uday A, Jurkiewicz P. FRET-GP - A Local Measure of the Impact of Transmembrane Peptide on Lipids. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2023; 39:18390-18402. [PMID: 38048524 DOI: 10.1021/acs.langmuir.3c02505] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/06/2023]
Abstract
Reconstitution of a transmembrane protein in model lipid systems allows studying its structure and dynamics in isolation from the complexity of the natural environment. This approach also provides a well-defined environment for studying the interactions of proteins with lipids. In this work, we describe the FRET-GP method, which utilizes Förster resonance energy transfer (FRET) to specifically probe the nanoenvironment of a transmembrane domain. The tryptophan residues flanking this domain act as efficient FRET donors, while Laurdan acts as acceptor. The fluorescence of this solvatochromic probe is quantified using generalized polarization (GP) to report on lipid mobility in the vicinity of the transmembrane domain. We applied FRET-GP to study the transmembrane peptide WALP incorporated in liposomes. We found that the direct excitation of Laurdan to its second singlet state strongly contributes to GP values measured in FRET conditions. Removal of this parasitic contribution was essential for proper determination of GPFRET - the local analogue of classical GP parameter. The presence of WALP significantly increased both parameters but the local effects were considerably stronger (GPFRET ≫ GP). We conclude that WALP restricts lipid movement in its vicinity, inducing lateral inhomogeneity in membrane fluidity. WALP was also found to influence lipid phase transition. Our findings demonstrated that FRET-GP simultaneously provides local and global results, thereby enhancing the depth of information obtained from the measurement. We highlight the simplicity and sensitivity of the method, but also discuss its potential and limitations in studying protein-lipid interactions.
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Affiliation(s)
- Garima C N Thakur
- J. Heyrovský Institute of Physical Chemistry of the Academy of Sciences of the Czech Republic, v.v.i., Prague 182 00, Czech Republic
| | - Arunima Uday
- J. Heyrovský Institute of Physical Chemistry of the Academy of Sciences of the Czech Republic, v.v.i., Prague 182 00, Czech Republic
| | - Piotr Jurkiewicz
- J. Heyrovský Institute of Physical Chemistry of the Academy of Sciences of the Czech Republic, v.v.i., Prague 182 00, Czech Republic
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4
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Navratna V, Kumar A, Mosalaganti S. Structure of the human heparan-α-glucosaminide N-acetyltransferase (HGSNAT). BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.23.563672. [PMID: 37961489 PMCID: PMC10634761 DOI: 10.1101/2023.10.23.563672] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Degradation of heparan sulfate (HS), a glycosaminoglycan (GAG) comprised of repeating units of N-acetylglucosamine and glucuronic acid, begins in the cytosol and is completed in the lysosomes. Acetylation of the terminal non-reducing amino group of α-D-glucosamine of HS is essential for its complete breakdown into monosaccharides and free sulfate. Heparan-α-glucosaminide N-acetyltransferase (HGSNAT), a resident of the lysosomal membrane, catalyzes this essential acetylation reaction by accepting and transferring the acetyl group from cytosolic acetyl-CoA to terminal α-D-glucosamine of HS in the lysosomal lumen. Mutation-induced dysfunction in HGSNAT causes abnormal accumulation of HS within the lysosomes and leads to an autosomal recessive neurodegenerative lysosomal storage disorder called mucopolysaccharidosis IIIC (MPS IIIC). There are no approved drugs or treatment strategies to cure or manage the symptoms of, MPS IIIC. Here, we use cryo-electron microscopy (cryo-EM) to determine a high-resolution structure of the HGSNAT-acetyl-CoA complex in an open-to-lumen conformation, the first step in HGSNAT catalyzed acetyltransferase reaction. In addition, we map the known MPS IIIC mutations onto the structure and elucidate the molecular basis for mutation-induced HGSNAT dysfunction.
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Affiliation(s)
- Vikas Navratna
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan, 48109, United States
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, Michigan, 48109, United States
| | - Arvind Kumar
- Thermo Fisher Scientific, Waltham, Massachusetts, 02451, United States
| | - Shyamal Mosalaganti
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan, 48109, United States
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, Michigan, 48109, United States
- Department of Biophysics, College of Literature, Science and the Arts, University of Michigan, Ann Arbor, Michigan, 48109, United States
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5
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Yanagisawa H, Kita Y, Oda T, Kikkawa M. Cryo-EM elucidates the uroplakin complex structure within liquid-crystalline lipids in the porcine urothelial membrane. Commun Biol 2023; 6:1018. [PMID: 37805589 PMCID: PMC10560298 DOI: 10.1038/s42003-023-05393-x] [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: 06/19/2023] [Accepted: 09/27/2023] [Indexed: 10/09/2023] Open
Abstract
The urothelium, a distinct epithelial tissue lining the urinary tract, serves as an essential component in preserving urinary tract integrity and thwarting infections. The asymmetric unit membrane (AUM), primarily composed of the uroplakin complex, constitutes a critical permeability barrier in fulfilling this role. However, the molecular architectures of both the AUM and the uroplakin complex have remained enigmatic due to the paucity of high-resolution structural data. In this study, we utilized cryo-electron microscopy to elucidate the three-dimensional structure of the uroplakin complex within the porcine AUM. While the global resolution achieved was 3.5 Å, we acknowledge that due to orientation bias, the resolution in the vertical direction was determined to be 6.3 Å. Our findings unveiled that the uroplakin complexes are situated within hexagonally arranged crystalline lipid membrane domains, rich in hexosylceramides. Moreover, our research rectifies a misconception in a previous model by confirming the existence of a domain initially believed to be absent, and pinpointing the accurate location of a crucial Escherichia coli binding site implicated in urinary tract infections. These discoveries offer valuable insights into the molecular underpinnings governing the permeability barrier function of the urothelium and the orchestrated lipid phase formation within the plasma membrane.
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Affiliation(s)
- Haruaki Yanagisawa
- Department of Cell Biology and Anatomy, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Yoshihiro Kita
- Life Sciences Core Facility, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
- Department of Lipidomics, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Toshiyuki Oda
- Department of Anatomy and Structural Biology, Graduate School of Medicine, University of Yamanashi, 1110 Shimokato, Chuo, Yamanashi, 409-3898, Japan.
| | - Masahide Kikkawa
- Department of Cell Biology and Anatomy, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan.
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6
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Yanagisawa H, Kita Y, Oda T, Kikkawa M. Unveiling Liquid-Crystalline Lipids in the Urothelial Membrane through Cryo-EM. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.29.542358. [PMID: 37398191 PMCID: PMC10312457 DOI: 10.1101/2023.05.29.542358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
The urothelium, a distinct epithelial tissue lining the urinary tract, serves as an essential component in preserving urinary tract integrity and thwarting infections. The asymmetric unit membrane (AUM), primarily composed of the uroplakin complex, constitutes a critical permeability barrier in fulfilling this role. However, the molecular architectures of both the AUM and the uroplakin complex have remained enigmatic due to the paucity of high-resolution structural data. In this study, we utilized cryo-electron microscopy to elucidate the three-dimensional structure of the uroplakin complex within the porcine AUM. While the global resolution achieved was 3.5 Å, we acknowledge that due to orientation bias, the resolution in the vertical direction was determined to be 6.3 Å. Our findings unveiled that the uroplakin complexes are situated within hexagonally arranged crystalline lipid membrane domains, rich in hexosylceramides. Moreover, our research rectifies a misconception in a previous model by confirming the existence of a domain initially believed to be absent, and pinpointing the accurate location of a crucial Escherichia coli binding site implicated in urinary tract infections. These discoveries offer valuable insights into the molecular underpinnings governing the permeability barrier function of the urothelium and the orchestrated lipid phase formation within the plasma membrane.
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Affiliation(s)
- Haruaki Yanagisawa
- Department of Cell Biology and Anatomy, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Yoshihiro Kita
- Life Sciences Core Facility, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
- Department of Lipidomics, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Toshiyuki Oda
- Department of Anatomy and Structural Biology, Graduate School of Medicine, University of Yamanashi, 1110 Shimokato, Chuo, Yamanashi, 409-3898, Japan
| | - Masahide Kikkawa
- Department of Cell Biology and Anatomy, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
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7
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Oda T, Yanagisawa H, Kikkawa M, Kita Y. Unveiling Liquid-Crystalline Lipids in the Urothelial Membrane through Cryo-EM. RESEARCH SQUARE 2023:rs.3.rs-3080731. [PMID: 37503277 PMCID: PMC10371089 DOI: 10.21203/rs.3.rs-3080731/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
The urothelium, a distinct epithelial tissue lining the urinary tract, serves as an essential component in preserving urinary tract integrity and thwarting infections. The asymmetric unit membrane (AUM), primarily composed of the uroplakin complex, constitutes a critical permeability barrier in fulfilling this role. However, the molecular architectures of both the AUM and the uroplakin complex have remained enigmatic due to the paucity of high-resolution structural data. In this investigation, we employed cryo-electron microscopy to elucidate the three-dimensional structure of the uroplakin complex embedded within the porcine AUM at a resolution of 3.5 Å. Our findings unveiled that the uroplakin complexes are situated within hexagonally arranged crystalline lipid membrane domains, rich in hexosylceramides. Moreover, our research rectifies a misconception in a previous model by confirming the existence of a domain initially believed to be absent, and pinpointing the accurate location of a crucial Escherichia coli binding site implicated in urinary tract infections. These discoveries offer valuable insights into the molecular underpinnings governing the permeability barrier function of the urothelium and the orchestrated lipid phase formation within the plasma membrane.
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8
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Yeo WS, Dyzenhaus S, Torres VJ, Brinsmade SR, Bae T. Regulation of Bacterial Two-Component Systems by Cardiolipin. Infect Immun 2023; 91:e0004623. [PMID: 36975788 PMCID: PMC10112254 DOI: 10.1128/iai.00046-23] [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: 01/30/2023] [Accepted: 03/09/2023] [Indexed: 03/29/2023] Open
Abstract
The regulation of membrane protein activity for cellular functions is critically dependent on the composition of phospholipid membranes. Cardiolipin, a unique phospholipid found in bacterial membranes and mitochondrial membranes of eukaryotes, plays a crucial role in stabilizing membrane proteins and maintaining their function. In the human pathogen Staphylococcus aureus, the SaeRS two-component system (TCS) controls the expression of key virulence factors essential for the bacterium's virulence. The SaeS sensor kinase activates the SaeR response regulator via phosphoryl transfer to bind its gene target promoters. In this study, we report that cardiolipin is critical for sustaining the full activity of SaeRS and other TCSs in S. aureus. The sensor kinase protein SaeS binds directly to cardiolipin and phosphatidylglycerol, enabling SaeS activity. Elimination of cardiolipin from the membrane reduces SaeS kinase activity, indicating that bacterial cardiolipin is necessary for modulating the kinase activities of SaeS and other sensor kinases during infection. Moreover, the deletion of cardiolipin synthase genes cls1 and cls2 leads to reduced cytotoxicity to human neutrophils and lower virulence in a mouse model of infection. These findings suggest a model where cardiolipin modulates the kinase activity of SaeS and other sensor kinases after infection to adapt to the hostile environment of the host and expand our knowledge of how phospholipids contribute to membrane protein function.
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Affiliation(s)
- Won-Sik Yeo
- Department of Microbiology and Immunology, Indiana University School of Medicine-Northwest, Gary, Indiana, USA
| | - Sophie Dyzenhaus
- Department of Microbiology, New York University School of Medicine, New York, New York, USA
| | - Victor J. Torres
- Department of Microbiology, New York University School of Medicine, New York, New York, USA
| | | | - Taeok Bae
- Department of Microbiology and Immunology, Indiana University School of Medicine-Northwest, Gary, Indiana, USA
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9
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Jütte M, Abdighahroudi MS, Waldminghaus T, Lackner S, V Lutze H. Bacterial inactivation processes in water disinfection - mechanistic aspects of primary and secondary oxidants - A critical review. WATER RESEARCH 2023; 231:119626. [PMID: 36709565 DOI: 10.1016/j.watres.2023.119626] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 11/14/2022] [Accepted: 01/15/2023] [Indexed: 06/18/2023]
Abstract
Water disinfection during drinking water production is one of the most important processes to ensure safe drinking water, which is gaining even more importance due to the increasing impact of climate change. With specific reaction partners, chemical oxidants can form secondary oxidants, which can cause additional damage to bacteria. Cases in point are chlorine dioxide which forms free available chlorine (e.g., in the reaction with phenol) and ozone which can form hydroxyl radicals (e.g., during the reaction with natural organic matter). The present work reviews the complex interplay of all these reactive species which can occur in disinfection processes and their potential to affect disinfection processes. A quantitative overview of their disinfection strength based on inactivation kinetics and typical exposures is provided. By unifying the current data for different oxidants it was observable that cultivated wild strains (e.g., from wastewater treatment plants) are in general more resistant towards chemical oxidants compared to lab-cultivated strains from the same bacterium. Furthermore, it could be shown that for selective strains chlorine dioxide is the strongest disinfectant (highest maximum inactivation), however as a broadband disinfectant ozone showed the highest strength (highest average inactivation). Details in inactivation mechanisms regarding possible target structures and reaction mechanisms are provided. Thereby the formation of secondary oxidants and their role in inactivation of pathogens is decently discussed. Eventually, possible defense responses of bacteria and additional effects which can occur in vivo are discussed.
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Affiliation(s)
- Mischa Jütte
- Technical University of Darmstadt, Institute IWAR, Chair of environmental analytics and pollutants, Franziska-Braun-Straße 7, D-64287 Darmstadt, Germany
| | - Mohammad Sajjad Abdighahroudi
- Technical University of Darmstadt, Institute IWAR, Chair of environmental analytics and pollutants, Franziska-Braun-Straße 7, D-64287 Darmstadt, Germany
| | - Torsten Waldminghaus
- Technical University of Darmstadt, Centre for synthetic biology, Chair of molecular microbiology, Schnittspahnstraße 12, D-64287 Darmstadt, Germany
| | - Susanne Lackner
- Technical University of Darmstadt, Institute IWAR, Chair of water and environmental biotechnology, Franziska-Braun-Straße 7, D-64287 Darmstadt, Germany
| | - Holger V Lutze
- Technical University of Darmstadt, Institute IWAR, Chair of environmental analytics and pollutants, Franziska-Braun-Straße 7, D-64287 Darmstadt, Germany; IWW Water Centre, Moritzstraße 26, D-45476 Mülheim an der Ruhr, Germany; Centre for Water and Environmental Research (ZWU), Universitätsstraße 5, D-45141 Essen, Germany.
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10
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Kang K, Wang L, Song C. ProtRAP: Predicting Lipid Accessibility Together with Solvent Accessibility of Proteins in One Run. J Chem Inf Model 2023; 63:1058-1065. [PMID: 36693122 DOI: 10.1021/acs.jcim.2c01235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Solvent accessibility has been extensively used to characterize and predict the chemical properties of the surface residues of soluble proteins. However, there is not yet a widely accepted quantity of the same dimension for the study of lipid-accessible residues of membrane proteins. In this study, we propose that lipid accessibility, defined in a similar way to solvent accessibility, can be used to characterize the lipid-accessible residues of membrane proteins. Moreover, we developed a deep learning-based method, ProtRAP (Protein Relative Accessibility Predictor), to predict the relative lipid accessibility and relative solvent accessibility of residues from a given protein sequence, which can infer which residues are likely accessible to lipids, accessible to solvent, or buried in the protein interior in one run.
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Affiliation(s)
- Kai Kang
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing100871, China.,Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing100871, China
| | - Lei Wang
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing100871, China.,Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing100871, China
| | - Chen Song
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing100871, China.,Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing100871, China
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11
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The Role of Transmembrane Proteins in Plant Growth, Development, and Stress Responses. Int J Mol Sci 2022; 23:ijms232113627. [PMID: 36362412 PMCID: PMC9655316 DOI: 10.3390/ijms232113627] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 11/02/2022] [Accepted: 11/04/2022] [Indexed: 11/09/2022] Open
Abstract
Transmembrane proteins participate in various physiological activities in plants, including signal transduction, substance transport, and energy conversion. Although more than 20% of gene products are predicted to be transmembrane proteins in the genome era, due to the complexity of transmembrane domains they are difficult to reliably identify in the predicted protein, and they may have different overall three-dimensional structures. Therefore, it is challenging to study their biological function. In this review, we describe the typical structures of transmembrane proteins and their roles in plant growth, development, and stress responses. We propose a model illustrating the roles of transmembrane proteins during plant growth and response to various stresses, which will provide important references for crop breeding.
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12
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An in silico reverse vaccinology study of Brachyspira pilosicoli, the causative organism of intestinal spirochaetosis, to identify putative vaccine candidates. Process Biochem 2022. [DOI: 10.1016/j.procbio.2022.08.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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13
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Povilaitis SC, Fathizadeh A, Kogan M, Elber R, Webb LJ. Design of Peptides for Membrane Insertion: The Critical Role of Charge Separation. J Phys Chem B 2022; 126:6454-6463. [PMID: 35997537 PMCID: PMC9541189 DOI: 10.1021/acs.jpcb.2c04615] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A physical understanding of membrane permeation and translocation by small, positively charged molecules can illuminate cell penetrating peptide mechanisms of entry and inform drug design. We have previously investigated the permeation of the doubly charged peptide WKW and proposed a defect-assisted permeation mechanism where a small molecule with +2 charge can achieve a metastable state spanning the bilayer by forming a membrane defect with charges stabilized by phospholipid phosphate groups. Here, we investigate the membrane permeation of two doubly charged peptides, WWK and WWWK, with charges separated by different lengths. Through complementary experiments and molecular dynamics simulations, we show that membrane permeation was an order of magnitude more favorable when charges were separated by an ∼2-3 Å greater distance on WWWK compared to WWK. These results agree with the previously proposed defect-assisted permeation mechanism, where a greater distance between positive charges would require a less extreme membrane defect to stabilize the membrane-spanning metastable state. We discuss the implications of these results in understanding the membrane permeation of cell-penetrating peptides and other small, positively charged membrane permeants.
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Affiliation(s)
- Sydney C. Povilaitis
- Department of Chemistry, University of Texas at Austin, Austin, TX 78712, United States
| | - Arman Fathizadeh
- Oden Institute for Computational Engineering and Science, University of Texas at Austin, Austin, Texas 78712, United States
| | - Molly Kogan
- Department of Chemistry, University of Texas at Austin, Austin, TX 78712, United States
| | - Ron Elber
- Department of Chemistry, University of Texas at Austin, Austin, TX 78712, United States
- Oden Institute for Computational Engineering and Science, University of Texas at Austin, Austin, Texas 78712, United States
| | - Lauren J. Webb
- Department of Chemistry, University of Texas at Austin, Austin, TX 78712, United States
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14
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de Araujo AD, Hoang HN, Lim J, Mak JYW, Fairlie DP. Tuning Electrostatic and Hydrophobic Surfaces of Aromatic Rings to Enhance Membrane Association and Cell Uptake of Peptides. Angew Chem Int Ed Engl 2022; 61:e202203995. [PMID: 35523729 PMCID: PMC9543247 DOI: 10.1002/anie.202203995] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Indexed: 11/30/2022]
Abstract
Aromatic groups are key mediators of protein–membrane association at cell surfaces, contributing to hydrophobic effects and π‐membrane interactions. Here we show electrostatic and hydrophobic influences of aromatic ring substituents on membrane affinity and cell uptake of helical, cyclic and cell penetrating peptides. Hydrophobicity is important, but subtle changes in electrostatic surface potential, dipoles and polarizability also enhance association with phospholipid membranes and cell uptake. A combination of fluorine and sulfur substituents on an aromatic ring induces microdipoles that enhance cell uptake of 12‐residue peptide inhibitors of p53‐HDM2 interaction and of cell‐penetrating cyclic peptides. These aromatic motifs can be readily inserted into peptide sidechains to enhance their cell uptake.
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Affiliation(s)
- Aline D. de Araujo
- Division of Chemistry and Structural Biology ARC Centre of Excellence for Innovations in Peptide & Protein Science Institute for Molecular Bioscience The University of Queensland Brisbane QLD 4072 Australia
| | - Huy N. Hoang
- Division of Chemistry and Structural Biology ARC Centre of Excellence for Innovations in Peptide & Protein Science Institute for Molecular Bioscience The University of Queensland Brisbane QLD 4072 Australia
| | - Junxian Lim
- Division of Chemistry and Structural Biology ARC Centre of Excellence for Innovations in Peptide & Protein Science Institute for Molecular Bioscience The University of Queensland Brisbane QLD 4072 Australia
| | - Jeffrey Y. W. Mak
- Division of Chemistry and Structural Biology ARC Centre of Excellence for Innovations in Peptide & Protein Science Institute for Molecular Bioscience The University of Queensland Brisbane QLD 4072 Australia
| | - David P. Fairlie
- Division of Chemistry and Structural Biology ARC Centre of Excellence for Innovations in Peptide & Protein Science Institute for Molecular Bioscience The University of Queensland Brisbane QLD 4072 Australia
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15
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Lazaratos M, Siemers M, Brown LS, Bondar AN. Conserved hydrogen-bond motifs of membrane transporters and receptors. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2022; 1864:183896. [PMID: 35217000 DOI: 10.1016/j.bbamem.2022.183896] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 02/04/2022] [Accepted: 02/16/2022] [Indexed: 01/18/2023]
Abstract
Membrane transporters and receptors often rely on conserved hydrogen bonds to assemble transient paths for ion transfer or long-distance conformational couplings. For transporters and receptors that use proton binding and proton transfer for function, inter-helical hydrogen bonds of titratable protein sidechains that could change protonation are of central interest to formulate hypotheses about reaction mechanisms. Knowledge of hydrogen bonds common at sites of potential interest for proton binding could thus inform and guide studies on functional mechanisms of protonation-coupled membrane proteins. Here we apply graph-theory approaches to identify hydrogen-bond motifs of carboxylate and histidine sidechains in a large data set of static membrane protein structures. We find that carboxylate-hydroxyl hydrogen bonds are present in numerous structures of the dataset, and can be part of more extended H-bond clusters that could be relevant to conformational coupling. Carboxylate-carboxyamide and imidazole-imidazole hydrogen bonds are represented in comparably fewer protein structures of the dataset. Atomistic simulations on two membrane transporters in lipid membranes suggest that many of the hydrogen bond motifs present in static protein structures tend to be robust, and can be part of larger hydrogen-bond clusters that recruit additional hydrogen bonds.
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Affiliation(s)
- Michalis Lazaratos
- Freie Universität Berlin, Department of Physics, Theoretical Molecular Biophysics, Arnimallee 14, D14195 Berlin, Germany
| | - Malte Siemers
- Freie Universität Berlin, Department of Physics, Theoretical Molecular Biophysics, Arnimallee 14, D14195 Berlin, Germany
| | - Leonid S Brown
- University of Guelph, Department of Physics, 50 Stone Road E., Guelph, Ontario N1G 2W1, Canada
| | - Ana-Nicoleta Bondar
- Freie Universität Berlin, Department of Physics, Theoretical Molecular Biophysics, Arnimallee 14, D14195 Berlin, Germany; University of Bucharest, Faculty of Physics, Atomiștilor 405, Măgurele 077125, Romania; Forschungszentrum Jülich, Institute for Neuroscience and Medicine and Institute for Advanced Simulations (IAS-5/INM-9), Computational Biomedicine, Wilhelm-Johnen Straße, 52428 Jülich, Germany.
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16
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de Araujo AD, Hoang HN, Lim J, Mak J, Fairlie DP. Tuning Electrostatic and Hydrophobic Surfaces of Aromatic Rings to Enhance Membrane Association and Cell Uptake of Peptides. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202203995] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Aline Dantes de Araujo
- The University of Queensland Institute for Molecular Bioscience Institute for Molecular Bioscience Institute for Molecular Bioscience, The University of Queensland 4072 Brisbane AUSTRALIA
| | - Huy N Hoang
- The University of Queensland Institute for Molecular Bioscience Institute for Molecular Bioscience Institute for Molecular Bioscience, The University of Queensland 4072 Brisbane AUSTRALIA
| | - Junxian Lim
- The University of Queensland Institute for Molecular Bioscience Institute for Molecular Bioscience Institute for Molecular Bioscience, The University of Queensland 4072 Brisbane AUSTRALIA
| | - Jeffrey Mak
- The University of Queensland Institute for Molecular Bioscience Institute for Molecular Bioscience Institute for Molecular Bioscience, The University of Queensland 4072 Brisbane AUSTRALIA
| | - David P Fairlie
- Institute for Molecular Bioscience Division of Chemistry and Structural Biology The University of Queensland 4072 Brisbane AUSTRALIA
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17
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Corin K, Bowie JU. How physical forces drive the process of helical membrane protein folding. EMBO Rep 2022; 23:e53025. [PMID: 35133709 PMCID: PMC8892262 DOI: 10.15252/embr.202153025] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 07/17/2021] [Accepted: 11/24/2021] [Indexed: 11/09/2022] Open
Abstract
Protein folding is a fundamental process of life with important implications throughout biology. Indeed, tens of thousands of mutations have been associated with diseases, and most of these mutations are believed to affect protein folding rather than function. Correct folding is also a key element of design. These factors have motivated decades of research on protein folding. Unfortunately, knowledge of membrane protein folding lags that of soluble proteins. This gap is partly caused by the greater technical challenges associated with membrane protein studies, but also because of additional complexities. While soluble proteins fold in a homogenous water environment, membrane proteins fold in a setting that ranges from bulk water to highly charged to apolar. Thus, the forces that drive folding vary in different regions of the protein, and this complexity needs to be incorporated into our understanding of the folding process. Here, we review our understanding of membrane protein folding biophysics. Despite the greater challenge, better model systems and new experimental techniques are starting to unravel the forces and pathways in membrane protein folding.
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Affiliation(s)
- Karolina Corin
- Department of Chemistry and BiochemistryMolecular Biology InstituteUCLA‐DOE InstituteUniversity of CaliforniaLos AngelesCAUSA
| | - James U Bowie
- Department of Chemistry and BiochemistryMolecular Biology InstituteUCLA‐DOE InstituteUniversity of CaliforniaLos AngelesCAUSA
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18
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Tamrakar A, Singh R, Kumar A, Makde RD, Ashish, Kodgire P. Biophysical characterization of the homodimers of HomA and HomB, outer membrane proteins of Helicobacter pylori. Sci Rep 2021; 11:24471. [PMID: 34963695 PMCID: PMC8714817 DOI: 10.1038/s41598-021-04039-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Accepted: 11/24/2021] [Indexed: 12/16/2022] Open
Abstract
Helicobacter pylori is a Gram-negative bacterium that causes chronic inflammations in the stomach area and is involved in ulcers, which can develop into gastric malignancies. H. pylori attaches and colonizes to the human epithelium using some of their outer membrane proteins (OMPs). HomB and HomA are the most studied OMPs from H. pylori as they play a crucial role in adherence, hyper biofilm formation, antibiotic resistance and are also associated with severe gastric malignancies. The role of HomA and HomB in pathogenesis concerning their structure and function has not been evaluated yet. In the present study, we explored the structural aspect of HomA and HomB proteins using various computational, biophysical and small-angle X-ray scattering (SAXS) techniques. Interestingly, the in-silico analysis revealed that HomA/B consists of 8 discontinuous N and C terminal β-strands forming a small β-barrel, along with a large surface-exposed globular domain. Further, biophysical experiments suggested that HomA and HomB are dimeric and most likely the cysteine residues present on surface-exposed loops participate in protein-protein interactions. Our study provides essential structural information of unexplored proteins of the Hom family that can help in a better understanding of H. pylori pathogenesis.
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Affiliation(s)
- Anubhav Tamrakar
- Discipline of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore, Madhya Pradesh, 453 552, India
| | - Rahul Singh
- High Pressure and Synchrotron Radiation Physics Division, Bhabha Atomic Research Center, Trombay, Mumbai, India
| | - Amit Kumar
- Discipline of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore, Madhya Pradesh, 453 552, India
| | - Ravindra D Makde
- High Pressure and Synchrotron Radiation Physics Division, Bhabha Atomic Research Center, Trombay, Mumbai, India
| | - Ashish
- Protein Science and Engineering Division, CSIR-Institute of Microbial Technology, Chandigarh, India
| | - Prashant Kodgire
- Discipline of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore, Madhya Pradesh, 453 552, India.
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19
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Abstract
Membrane proteins (MPs) play essential roles in numerous cellular processes. Because around 70% of the currently marketed drugs target MPs, a detailed understanding of their structure, binding properties, and functional dynamics in a physiologically relevant environment is crucial for a more detailed understanding of this important protein class. We here summarize the benefits of using lipid nanodiscs for NMR structural investigations and provide a detailed overview of the currently used lipid nanodisc systems as well as their applications in solution-state NMR. Despite the increasing use of other structural methods for the structure determination of MPs in lipid nanodiscs, solution NMR turns out to be a versatile tool to probe a wide range of MP features, ranging from the structure determination of small to medium-sized MPs to probing ligand and partner protein binding as well as functionally relevant dynamical signatures in a lipid nanodisc setting. We will expand on these topics by discussing recent NMR studies with lipid nanodiscs and work out a key workflow for optimizing the nanodisc incorporation of an MP for subsequent NMR investigations. With this, we hope to provide a comprehensive background to enable an informed assessment of the applicability of lipid nanodiscs for NMR studies of a particular MP of interest.
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Affiliation(s)
- Umut Günsel
- Bavarian NMR Center (BNMRZ) at the Department of Chemistry, Technical University of Munich, Ernst-Otto-Fischer-Strasse 2, 85748 Garching, Germany
| | - Franz Hagn
- Bavarian NMR Center (BNMRZ) at the Department of Chemistry, Technical University of Munich, Ernst-Otto-Fischer-Strasse 2, 85748 Garching, Germany.,Institute of Structural Biology, Helmholtz Zentrum München, Ingolstädter Landstraße 1, 85764 Neuherberg, Germany
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20
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Dubey S, Majumder P, Penmatsa A, Sardesai AA. Topological analyses of the L-lysine exporter LysO reveal a critical role for a conserved pair of intramembrane solvent-exposed acidic residues. J Biol Chem 2021; 297:101168. [PMID: 34487760 PMCID: PMC8498466 DOI: 10.1016/j.jbc.2021.101168] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 08/30/2021] [Accepted: 09/02/2021] [Indexed: 11/16/2022] Open
Abstract
LysO, a prototypical member of the LysO family, mediates export of L-lysine (Lys) and resistance to the toxic Lys antimetabolite, L-thialysine (Thl) in Escherichia coli. Here, we have addressed unknown aspects of LysO function pertaining to its membrane topology and the mechanism by which it mediates Lys/Thl export. Using substituted cysteine (Cys) accessibility, here we delineated the membrane topology of LysO. Our studies support a model in which both the N- and C-termini of LysO are present at the periplasmic face of the membrane with a transmembrane (TM) domain comprising eight TM segments (TMSs) between them. In addition, a feature of intramembrane solvent exposure in LysO is inferred with the identification of membrane-located solvent-exposed Cys residues. Isosteric substitutions of a pair of conserved acidic residues, one E233, located in the solvent-exposed TMS7 and the other D261, in a solvent-exposed intramembrane segment located between TMS7 and TMS8, abolished LysO function in vivo. Thl, but not Lys, elicited proton release in inside-out membrane vesicles, a process requiring the presence of both E233 and D261. We postulate that Thl may be exported in antiport with H+ and that Lys may be a low-affinity export substrate. Our findings are compatible with a physiological scenario wherein in vivo LysO exports the naturally occurring antimetabolite Thl with higher affinity over the essential cellular metabolite Lys, thus affording protection from Thl toxicity and limiting wasteful export of Lys.
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Affiliation(s)
- Swati Dubey
- Laboratory of Bacterial Genetics, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India; Graduate Studies, Manipal Academy of Higher Education, Manipal, India
| | - Puja Majumder
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India
| | - Aravind Penmatsa
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India
| | - Abhijit A Sardesai
- Laboratory of Bacterial Genetics, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India.
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21
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Khazen G, Gyulkhandanian A, Issa T, Maroun RC. Getting to know each other: PPIMem, a novel approach for predicting transmembrane protein-protein complexes. Comput Struct Biotechnol J 2021; 19:5184-5197. [PMID: 34630938 PMCID: PMC8476896 DOI: 10.1016/j.csbj.2021.09.013] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 08/23/2021] [Accepted: 09/12/2021] [Indexed: 02/03/2023] Open
Abstract
Because of their considerable number and diversity, membrane proteins and their macromolecular complexes represent the functional units of cells. Their quaternary structure may be stabilized by interactions between the α-helices of different proteins in the hydrophobic region of the cell membrane. Membrane proteins equally represent potential pharmacological targets par excellence for various diseases. Unfortunately, their experimental 3D structure and that of their complexes with other intramembrane protein partners are scarce due to technical difficulties. To overcome this key problem, we devised PPIMem, a computational approach for the specific prediction of higher-order structures of α-helical transmembrane proteins. The novel approach involves proper identification of the amino acid residues at the interface of molecular complexes with a 3D structure. The identified residues compose then nonlinear interaction motifs that are conveniently expressed as mathematical regular expressions. These are efficiently implemented for motif search in amino acid sequence databases, and for the accurate prediction of intramembrane protein-protein complexes. Our template interface-based approach predicted 21,544 binary complexes between 1,504 eukaryotic plasma membrane proteins across 39 species. We compare our predictions to experimental datasets of protein-protein interactions as a first validation method. The online database that results from the PPIMem algorithm with the annotated predicted interactions are implemented as a web server and can be accessed directly at https://transint.univ-evry.fr.
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Affiliation(s)
- Georges Khazen
- Computer Science and Mathematics Department, Lebanese American University, Byblos, Lebanon
| | - Aram Gyulkhandanian
- Inserm U1204/Université d'Evry/Université Paris-Saclay, Structure-Activité des Biomolécules Normales et Pathologiques, 91025 Evry, France
| | - Tina Issa
- Computer Science and Mathematics Department, Lebanese American University, Byblos, Lebanon
| | - Rachid C Maroun
- Inserm U1204/Université d'Evry/Université Paris-Saclay, Structure-Activité des Biomolécules Normales et Pathologiques, 91025 Evry, France
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22
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Tryptophan, an Amino-Acid Endowed with Unique Properties and Its Many Roles in Membrane Proteins. CRYSTALS 2021. [DOI: 10.3390/cryst11091032] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Tryptophan is an aromatic amino acid with unique physico-chemical properties. It is often encountered in membrane proteins, especially at the level of the water/bilayer interface. It plays a role in membrane protein stabilization, anchoring and orientation in lipid bilayers. It has a hydrophobic character but can also engage in many types of interactions, such as π–cation or hydrogen bonds. In this review, we give an overview of the role of tryptophan in membrane proteins and a more detailed description of the underlying noncovalent interactions it can engage in with membrane partners.
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23
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Abstract
Pestiviruses are members of the family Flaviviridae, a group of enveloped viruses that bud at intracellular membranes. Pestivirus particles contain three glycosylated envelope proteins, Erns, E1, and E2. Among them, E1 is the least characterized concerning both biochemical features and function. E1 from bovine viral diarrhea virus (BVDV) strain CP7 was analyzed with regard to its intracellular localization and membrane topology. Here, it is shown that even in the absence of other viral proteins, E1 is not secreted or expressed at the cell surface but localizes predominantly in the endoplasmic reticulum (ER). Using engineered chimeric transmembrane domains with sequences from E1 and vesicular stomatitis virus G protein, the E1 ER-retention signal could be narrowed down to six fully conserved polar residues in the middle part of the transmembrane domain of E1. Retention was observed even when several of these polar residues were exchanged for alanine. Mutations with a strong impact on E1 retention prevented recovery of infectious viruses when tested in the viral context. Analysis of the membrane topology of E1 before and after the signal peptide cleavage via a selective permeabilization and an in vivo labeling approach revealed that mature E1 is a typical type I transmembrane protein with a single span transmembrane anchor at its C terminus, whereas it adopts a hairpin-like structure with the C terminus located in the ER lumen when the precleavage situation is mimicked by blocking the cleavage site between E1 and E2. IMPORTANCE The shortage of specific antibodies against E1, making detection and further analysis of E1 difficult, resulted in a lack of knowledge on E1 compared to Erns and E2 with regard to biosynthesis, structure, and function. It is known that pestiviruses bud intracellularly. Here, we show that E1 contains its own ER retention signal: six fully conserved polar residues in the middle part of the transmembrane domain are shown to be the determinants for ER retention of E1. Moreover, those six polar residues could serve as a functional group that intensely affect the generation of infectious viral particles. In addition, the membrane topology of E1 has been determined. In this context, we also identified dynamic changes in membrane topology of E1 with the carboxy terminus located on the luminal side of the ER in the precleavage state and relocation of this sequence upon signal peptidase cleavage. Our work provides the first systematic analysis of the pestiviral E1 protein with regard to its biochemical and functional characteristics.
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24
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Kumar GA, Sarkar P, Stepniewski TM, Jafurulla M, Singh SP, Selent J, Chattopadhyay A. A molecular sensor for cholesterol in the human serotonin 1A receptor. SCIENCE ADVANCES 2021; 7:7/30/eabh2922. [PMID: 34301606 PMCID: PMC8302130 DOI: 10.1126/sciadv.abh2922] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Accepted: 06/09/2021] [Indexed: 05/10/2023]
Abstract
The function of several G protein-coupled receptors (GPCRs) exhibits cholesterol sensitivity. Cholesterol sensitivity of GPCRs could be attributed to specific sequence and structural features, such as the cholesterol recognition/interaction amino acid consensus (CRAC) motif, that facilitate their cholesterol-receptor interaction. In this work, we explored the molecular basis of cholesterol sensitivity exhibited by the serotonin1A receptor, the most studied GPCR in the context of cholesterol sensitivity, by generating mutants of key residues in CRAC motifs in transmembrane helix 2 (TM2) and TM5 of the receptor. Our results show that a lysine residue (K101) in one of the CRAC motifs is crucial for sensing altered membrane cholesterol levels. Insights from all-atom molecular dynamics simulations showed that cholesterol-sensitive functional states of the serotonin1A receptor are associated with reduced conformational dynamics of extracellular loops of the receptor. These results constitute one of the first reports on the molecular mechanism underlying cholesterol sensitivity of GPCRs.
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Affiliation(s)
- G Aditya Kumar
- CSIR-Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad 500 007, India
| | - Parijat Sarkar
- CSIR-Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad 500 007, India
| | - Tomasz Maciej Stepniewski
- Research Programme on Biomedical Informatics (GRIB), Department of Experimental and Health Sciences of Pompeu Fabra University (UPF)-Hospital del Mar Medical Research Institute (IMIM), 08003 Barcelona, Spain
- Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, Warsaw, Poland
| | - Md Jafurulla
- CSIR-Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad 500 007, India
| | - Shishu Pal Singh
- National Centre for Biological Sciences, UAS-GKVK Campus, Bellary Road, Bengaluru 560 065, India
| | - Jana Selent
- Research Programme on Biomedical Informatics (GRIB), Department of Experimental and Health Sciences of Pompeu Fabra University (UPF)-Hospital del Mar Medical Research Institute (IMIM), 08003 Barcelona, Spain.
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25
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Jiménez-Vargas JM, Ramírez-Carreto S, Corzo G, Possani LD, Becerril B, Ortiz E. Structural and functional characterization of NDBP-4 family antimicrobial peptides from the scorpion Mesomexovis variegatus. Peptides 2021; 141:170553. [PMID: 33862164 DOI: 10.1016/j.peptides.2021.170553] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 04/06/2021] [Accepted: 04/08/2021] [Indexed: 12/13/2022]
Abstract
Six peptides, belonging to the NDBP-4 family of scorpion antimicrobial peptides were structurally and functionally characterized. The sequence of the mature peptides VpCT1, VpCT2, VpCT3 and VpCT4 was inferred by transcriptomic analysis of the venom gland of the scorpion Mesomexovis variegatus. Analysis of their amino acid sequences revealed patterns that are also present in previously reported peptides that show differences in their hemolytic and antimicrobial activities in vitro. Two other variants, VpCT3W and VpCTConsensus were designed to evaluate the effect of sequence changes of interest on their structure and activity. The synthesized peptides were evaluated by circular dichroism to confirm their α-helical conformation in a folding promoting medium. The peptides were assayed on two Gram-positive and three Gram-negative bacterial strains, and on two yeast strains. They preferentially inhibited the growth of Staphylococcus aureus, were mostly ineffective on Pseudomonas aeruginosa, and moderately inhibited the growth of Candida yeasts. All six peptides exhibited hemolytic activity on human erythrocytes in the range of 4.8-83.7 μM. VpCT3W displayed increased hemolytic and anti-yeast activities, but showed no change in antibacterial activity, relative to its parental peptide, suggesting that Trp6 may potentiate the interaction of VpCT3 with eukaryotic cell membranes. VpCTConsensus showed broader and enhanced antimicrobial activity relative to several of the natural peptides. The results presented here contribute new information on the structure and function of NDBP-4 antimicrobial peptides and provides clues for the design of less hemolytic and more effective antimicrobial peptides.
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Affiliation(s)
- Juana María Jiménez-Vargas
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Avenida Universidad, 2001, Colonia Chamilpa, Cuernavaca, Morelos, 62210, Mexico; Consejo Nacional de Ciencia y Tecnología (CONACyT), CDMX, Mexico
| | - Santos Ramírez-Carreto
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Avenida Universidad, 2001, Colonia Chamilpa, Cuernavaca, Morelos, 62210, Mexico
| | - Gerardo Corzo
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Avenida Universidad, 2001, Colonia Chamilpa, Cuernavaca, Morelos, 62210, Mexico
| | - Lourival D Possani
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Avenida Universidad, 2001, Colonia Chamilpa, Cuernavaca, Morelos, 62210, Mexico
| | - Baltazar Becerril
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Avenida Universidad, 2001, Colonia Chamilpa, Cuernavaca, Morelos, 62210, Mexico
| | - Ernesto Ortiz
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Avenida Universidad, 2001, Colonia Chamilpa, Cuernavaca, Morelos, 62210, Mexico.
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26
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Trenker R, Wu X, Nguyen JV, Wilcox S, Rubin AF, Call ME, Call MJ. Human and viral membrane-associated E3 ubiquitin ligases MARCH1 and MIR2 recognize different features of CD86 to downregulate surface expression. J Biol Chem 2021; 297:100900. [PMID: 34157285 PMCID: PMC8319528 DOI: 10.1016/j.jbc.2021.100900] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2020] [Revised: 06/16/2021] [Accepted: 06/18/2021] [Indexed: 11/23/2022] Open
Abstract
Immune-stimulatory ligands, such as major histocompatibility complex molecules and the T-cell costimulatory ligand CD86, are central to productive immunity. Endogenous mammalian membrane-associated RING-CHs (MARCH) act on these and other targets to regulate antigen presentation and activation of adaptive immunity, whereas virus-encoded homologs target the same molecules to evade immune responses. Substrate specificity is encoded in or near the membrane-embedded domains of MARCHs and the proteins they regulate, but the exact sequences that distinguish substrates from nonsubstrates are poorly understood. Here, we examined the requirements for recognition of the costimulatory ligand CD86 by two different MARCH-family proteins, human MARCH1 and Kaposi's sarcoma herpesvirus modulator of immune recognition 2 (MIR2), using deep mutational scanning. We identified a highly specific recognition surface in the hydrophobic core of the CD86 transmembrane (TM) domain (TMD) that is required for recognition by MARCH1 and prominently features a proline at position 254. In contrast, MIR2 requires no specific sequences in the CD86 TMD but relies primarily on an aspartic acid at position 244 in the CD86 extracellular juxtamembrane region. Surprisingly, MIR2 recognized CD86 with a TMD composed entirely of valine, whereas many different single amino acid substitutions in the context of the native TM sequence conferred MIR2 resistance. These results show that the human and viral proteins evolved completely different recognition modes for the same substrate. That some TM sequences are incompatible with MIR2 activity, even when no specific recognition motif is required, suggests a more complicated mechanism of immune modulation via CD86 than was previously appreciated.
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Affiliation(s)
- Raphael Trenker
- Structural Biology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia; Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia
| | - Xinyu Wu
- Structural Biology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia; Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia
| | - Julie V Nguyen
- Structural Biology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
| | - Stephen Wilcox
- Structural Biology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia; Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia; Genomics Laboratory, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
| | - Alan F Rubin
- Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia; Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
| | - Matthew E Call
- Structural Biology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia; Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia.
| | - Melissa J Call
- Structural Biology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia; Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia.
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27
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Bondar AN. Proton-Binding Motifs of Membrane-Bound Proteins: From Bacteriorhodopsin to Spike Protein S. Front Chem 2021; 9:685761. [PMID: 34136464 PMCID: PMC8203321 DOI: 10.3389/fchem.2021.685761] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Accepted: 05/18/2021] [Indexed: 11/13/2022] Open
Abstract
Membrane-bound proteins that change protonation during function use specific protein groups to bind and transfer protons. Knowledge of the identity of the proton-binding groups is of paramount importance to decipher the reaction mechanism of the protein, and protonation states of prominent are studied extensively using experimental and computational approaches. Analyses of model transporters and receptors from different organisms, and with widely different biological functions, indicate common structure-sequence motifs at internal proton-binding sites. Proton-binding dynamic hydrogen-bond networks that are exposed to the bulk might provide alternative proton-binding sites and proton-binding pathways. In this perspective article I discuss protonation coupling and proton binding at internal and external carboxylate sites of proteins that use proton transfer for function. An inter-helical carboxylate-hydroxyl hydrogen-bond motif is present at functionally important sites of membrane proteins from archaea to the brain. External carboxylate-containing H-bond clusters are observed at putative proton-binding sites of protonation-coupled model proteins, raising the question of similar functionality in spike protein S.
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Affiliation(s)
- Ana-Nicoleta Bondar
- Freie Universität Berlin, Department of Physics, Theoretical Molecular Biophysics Group, Berlin, Germany
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28
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Kuroki K, Sakai T, Masuda T, Kawano K, Futaki S. Membrane anchoring of a curvature-inducing peptide, EpN18, promotes membrane translocation of octaarginine. Bioorg Med Chem Lett 2021; 43:128103. [PMID: 33984474 DOI: 10.1016/j.bmcl.2021.128103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 04/29/2021] [Accepted: 05/05/2021] [Indexed: 11/25/2022]
Abstract
EpN18 is a curvature-inducing peptide, which loosens lipid packing upon interaction with the cell membrane, and facilitates cell-membrane penetration by arginine-rich cell-penetrating peptides, including octaarginine (R8). In the present study, we conjugated the N-terminal of EpN18 with a pyrenebutyryl (pBu) moiety, which acts as an anchoring unit that increases membrane interactions. Enhanced lipid-packing loosening and cytosolic translocation of R8 were observed by the pBu anchoring of EpN18.
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Affiliation(s)
- Kakeru Kuroki
- Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Takayuki Sakai
- Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Toshihiro Masuda
- Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Kenichi Kawano
- Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Shiroh Futaki
- Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan.
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29
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Marx DC, Fleming KG. Membrane proteins enter the fold. Curr Opin Struct Biol 2021; 69:124-130. [PMID: 33975156 DOI: 10.1016/j.sbi.2021.03.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 03/15/2021] [Accepted: 03/21/2021] [Indexed: 11/19/2022]
Abstract
Membrane proteins have historically been recalcitrant to biophysical folding studies. However, recent adaptations of methods from the soluble protein folding field have found success in their applications to transmembrane proteins composed of both α-helical and β-barrel conformations. Avoiding aggregation is critical for the success of these experiments. Altogether these studies are leading to discoveries of folding trajectories, foundational stabilizing forces and better-defined endpoints that enable more accurate interpretation of thermodynamic data. Increased information on membrane protein folding in the cell shows that the emerging biophysical principles are largely recapitulated even in the complex biological environment.
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Affiliation(s)
- Dagan C Marx
- TC Jenkins Department of Biophysics, Johns Hopkins University, 3400 N. Charles Street, Baltimore, MD, 21218, United States
| | - Karen G Fleming
- TC Jenkins Department of Biophysics, Johns Hopkins University, 3400 N. Charles Street, Baltimore, MD, 21218, United States.
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30
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Beytur S. Marker residue types at the structural regions of transmembrane alpha-helical and beta-barrel interfaces. Proteins 2021; 89:1145-1157. [PMID: 33890696 DOI: 10.1002/prot.26087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Revised: 04/13/2021] [Accepted: 04/16/2021] [Indexed: 11/11/2022]
Abstract
Membrane proteins play a variety of biological functions to the survival of organisms and functionalities of these proteins are often due to their homo- or hetero-complexation. Encoded by ~30% of the genome in most organisms, they represent the target of over half of nowadays drugs. Spanning the entirety of the cell membrane, transmembrane proteins are the most common type of membrane proteins and can be classified by secondary structures: alpha-helical and beta-barrel structures. Protein-protein interaction (PPI) have been widely studied for globular proteins and many computational tools are available for predicting PPI sites and construct models of complexes. Here, the structural regions of a non-redundant set of 232 alpha-helical and 37 beta-barrel transmembrane complexes and their interfaces are analyzed. Using the residue composition, frequency and propensity, this study brings the light on the marker residue types located at the structural regions of alpha-helical and beta-barrel transmembrane homomeric protein complexes and of their interfaces. This study also shows the necessity to relate the frequency to the composition into a ratio for immediately figuring out residue types presenting high frequencies at the interface and/or at one of its structural regions despite being a minor contributor compared to other residue types to that location's residue composition.
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Affiliation(s)
- Sercan Beytur
- Faculty of Engineering and Natural Sciences, Department of Bioinformatics and Genetics, Kadir Has University, Istanbul, Turkey
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31
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Thibado JK, Tano JY, Lee J, Salas-Estrada L, Provasi D, Strauss A, Marcelo Lamim Ribeiro J, Xiang G, Broichhagen J, Filizola M, Lohse MJ, Levitz J. Differences in interactions between transmembrane domains tune the activation of metabotropic glutamate receptors. eLife 2021; 10:e67027. [PMID: 33880992 PMCID: PMC8102066 DOI: 10.7554/elife.67027] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Accepted: 04/19/2021] [Indexed: 12/16/2022] Open
Abstract
The metabotropic glutamate receptors (mGluRs) form a family of neuromodulatory G-protein-coupled receptors that contain both a seven-helix transmembrane domain (TMD) and a large extracellular ligand-binding domain (LBD) which enables stable dimerization. Although numerous studies have revealed variability across subtypes in the initial activation steps at the level of LBD dimers, an understanding of inter-TMD interaction and rearrangement remains limited. Here, we use a combination of single molecule fluorescence, molecular dynamics, functional assays, and conformational sensors to reveal that distinct TMD assembly properties drive differences between mGluR subtypes. We uncover a variable region within transmembrane helix 4 (TM4) that contributes to homo- and heterodimerization in a subtype-specific manner and tunes orthosteric, allosteric, and basal activation. We also confirm a critical role for a conserved inter-TM6 interface in stabilizing the active state during orthosteric or allosteric activation. Together this study shows that inter-TMD assembly and dynamic rearrangement drive mGluR function with distinct properties between subtypes.
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Affiliation(s)
- Jordana K Thibado
- Physiology, Biophysics and Systems Biology Graduate Program, Weill Cornell Graduate School of Medical SciencesNew YorkUnited States
| | | | - Joon Lee
- Department of Biochemistry, Weill Cornell MedicineNew YorkUnited States
| | - Leslie Salas-Estrada
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount SinaiNew YorkUnited States
| | - Davide Provasi
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount SinaiNew YorkUnited States
| | - Alexa Strauss
- Tri-Institutional PhD Program in Chemical BiologyNew YorkUnited States
| | | | - Guoqing Xiang
- Department of Biochemistry, Weill Cornell MedicineNew YorkUnited States
| | | | - Marta Filizola
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount SinaiNew YorkUnited States
| | - Martin J Lohse
- Max Delbrück Center for Molecular MedicineBerlinGermany
- ISAR Bioscience InstitutePlanegg-MunichGermany
| | - Joshua Levitz
- Physiology, Biophysics and Systems Biology Graduate Program, Weill Cornell Graduate School of Medical SciencesNew YorkUnited States
- Department of Biochemistry, Weill Cornell MedicineNew YorkUnited States
- Tri-Institutional PhD Program in Chemical BiologyNew YorkUnited States
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32
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Matos-Filipe P, Preto AJ, Koukos PI, Mourão J, Bonvin AMJJ, Moreira IS. MENSAdb: a thorough structural analysis of membrane protein dimers. Database (Oxford) 2021; 2021:baab013. [PMID: 33822911 PMCID: PMC8023553 DOI: 10.1093/database/baab013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Revised: 01/19/2021] [Accepted: 03/01/2021] [Indexed: 11/14/2022]
Abstract
Membrane proteins (MPs) are key players in a variety of different cellular processes and constitute the target of around 60% of all Food and Drug Administration-approved drugs. Despite their importance, there is still a massive lack of relevant structural, biochemical and mechanistic information mainly due to their localization within the lipid bilayer. To help fulfil this gap, we developed the MEmbrane protein dimer Novel Structure Analyser database (MENSAdb). This interactive web application summarizes the evolutionary and physicochemical properties of dimeric MPs to expand the available knowledge on the fundamental principles underlying their formation. Currently, MENSAdb contains features of 167 unique MPs (63% homo- and 37% heterodimers) and brings insights into the conservation of residues, accessible solvent area descriptors, average B-factors, intermolecular contacts at 2.5 Å and 4.0 Å distance cut-offs, hydrophobic contacts, hydrogen bonds, salt bridges, π-π stacking, T-stacking and cation-π interactions. The regular update and organization of all these data into a unique platform will allow a broad community of researchers to collect and analyse a large number of features efficiently, thus facilitating their use in the development of prediction models associated with MPs. Database URL: http://www.moreiralab.com/resources/mensadb.
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Affiliation(s)
- Pedro Matos-Filipe
- Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra 3005-504, Portugal
| | - António J Preto
- Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra 3005-504, Portugal
- PhD Programme in Experimental Biology and Biomedicine, Institute for Interdisciplinary Research, University of Coimbra, Coimbra, 3030-789, Portugal
| | - Panagiotis I Koukos
- Bijvoet Centre for Biomolecular Research, Faculty of Science—Chemistry, Utrecht University, Utrecht, 3584, CH, Netherlands
| | - Joana Mourão
- Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra 3005-504, Portugal
| | - Alexandre M J J Bonvin
- Bijvoet Centre for Biomolecular Research, Faculty of Science—Chemistry, Utrecht University, Utrecht, 3584, CH, Netherlands
| | - Irina S Moreira
- Department of Life Sciences, University of Coimbra, Coimbra, 3000-456, Portugal
- Center for Neuroscience and Cell Biology, Center for Innovative Biomedicine and Biotechnology, University of Coimbra, Coimbra, Portugal
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33
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Huang Y, Liu Y, Li Y, Liu Y, Zhang C, Wen H, Zhao L, Song Y, Wang L, Wang Z. Role of key amino acids in the transmembrane domain of the Newcastle disease virus fusion protein. Biosci Trends 2021; 15:16-23. [PMID: 33504738 DOI: 10.5582/bst.2020.03317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Newcastle disease (ND), caused by the Newcastle disease virus (NDV), is transmitted by poultry with severe infectivity and a high fatality rate. The fusion (F) protein on the NDV envelope facilitates the merger of the viral and host cell membranes with the help of the homologous hemagglutinin-neuraminidase protein (HN). The transmembrane (TM) domains of viral fusion proteins are typically required for fusion, but the key amino acids in NDV F TM domains have not been identified. Site-directed mutagenesis was utilized to change the conserved amino acids at 500, 501, 502, 505, 510, 513, 516, 519, and 520 to alanine. It was found that mutants L519 and V520 had an interrupted protein expression, decreased to below 10%, and mutants A500, I505, V513, and V516 had a hypoactive impact on fusion activity, decreased to 85.38%, 67.05%, 55.38% and 51.13% of wt F, respectively. The results indicated that the TM domain plays a vital part in the fusion activity of the NDV F protein.
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Affiliation(s)
- Yanan Huang
- Department of Virology, School of Public Health, Cheeloo College of Medicine, Shandong University, Ji'nan, Shandong, China
| | - Yaqing Liu
- Department of Virology, School of Public Health, Cheeloo College of Medicine, Shandong University, Ji'nan, Shandong, China
| | - Yanguo Li
- Department of Health Management and Services, Cangzhou Medical College, Cangzhou, Hebei, China
| | - Ying Liu
- Department of Virology, School of Public Health, Cheeloo College of Medicine, Shandong University, Ji'nan, Shandong, China
| | - Chi Zhang
- Department of Virology, School of Public Health, Cheeloo College of Medicine, Shandong University, Ji'nan, Shandong, China
| | - Hongling Wen
- Department of Virology, School of Public Health, Cheeloo College of Medicine, Shandong University, Ji'nan, Shandong, China
| | - Li Zhao
- Department of Virology, School of Public Health, Cheeloo College of Medicine, Shandong University, Ji'nan, Shandong, China
| | - Yanyan Song
- Department of Virology, School of Public Health, Cheeloo College of Medicine, Shandong University, Ji'nan, Shandong, China
| | - Liyang Wang
- Department of Clinical Laboratory, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Ji'nan, Shandong, China
| | - Zhiyu Wang
- Department of Virology, School of Public Health, Cheeloo College of Medicine, Shandong University, Ji'nan, Shandong, China
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34
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Daniele-Silva A, Rodrigues SDCS, Dos Santos ECG, Queiroz Neto MFD, Rocha HADO, Silva-Júnior AAD, Resende JM, Araújo RM, Fernandes-Pedrosa MDF. NMR three-dimensional structure of the cationic peptide Stigmurin from Tityus stigmurus scorpion venom: In vitro antioxidant and in vivo antibacterial and healing activity. Peptides 2021; 137:170478. [PMID: 33359395 DOI: 10.1016/j.peptides.2020.170478] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Revised: 12/15/2020] [Accepted: 12/16/2020] [Indexed: 01/05/2023]
Abstract
Infectious diseases and the rapid development of pathogens resistant to conventional drugs are a serious global public health problem, which motivates the search for new pharmacological agents. In this context, cationic peptides without disulfide bridges from different species of scorpion venom have been the target of scientific studies due to their multifunctional activities. Stigmurin is a linear peptide composed of 17 amino acid residues (Phe-Phe-Ser-Leu-Ile-Pro-Ser-Leu-Val-Gly-Gly-Leu-Ile-Ser-Ala-Phe-Lys-NH2), which is present in the venom gland of the scorpion Tityus stigmurus. Here we present investigations of the in vitro antioxidant action of Stigmurin together with the in vivo antibacterial and healing activity of this peptide in a wound infection model induced by Staphylococcus aureus. In addition, we have reports for the first time of the three-dimensional structure determined by NMR spectroscopy of a peptide without disulfide bridges present in scorpion venom from the Tityus genus. Stigmurin showed hydroxyl radical scavenging above 70 % at 10 μM and antibiotic action in the skin wound, reducing the number of viable microorganisms by 67.2 % on the 7 day after infection. Stigmurin (1 μg / μL) increased the retraction rate of the lesion, with wound area reduction of 43 % on the second day after skin injury, which indicates its ability to induce tissue repair. Stigmurin in trifluoroethanol:water exhibited a random conformation at the N-terminus region (Phe1 to Pro6), with a helical structure from Ser7 to Phe16. This structural information, allied with the multifunctional activity of Stigmurin, makes it an attractive candidate for the design of novel therapeutic agents.
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Affiliation(s)
- Alessandra Daniele-Silva
- Laboratório de Tecnologia e Biotecnologia Farmacêutica, Departamento de Farmácia, Universidade Federal do Rio Grande do Norte, Natal, Brazil
| | - Suedson de Carvalho Silva Rodrigues
- Laboratório de Isolamento e Síntese de Compostos Orgânicos, Instituto de Química, Universidade Federal do Rio Grande do Norte, Natal, Brazil
| | | | - Moacir Fernandes de Queiroz Neto
- Laboratório de Biotecnologia de Polímeros Naturais, Departamento de Bioquímica, Universidade Federal do Rio Grande do Norte, Natal, Brazil
| | - Hugo Alexandre de Oliveira Rocha
- Laboratório de Biotecnologia de Polímeros Naturais, Departamento de Bioquímica, Universidade Federal do Rio Grande do Norte, Natal, Brazil
| | - Arnóbio Antônio da Silva-Júnior
- Laboratório de Tecnologia e Biotecnologia Farmacêutica, Departamento de Farmácia, Universidade Federal do Rio Grande do Norte, Natal, Brazil
| | - Jarbas Magalhães Resende
- Laboratório de Síntese e Estrutura de Peptídeos, Departamento de Química, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Renata Mendonça Araújo
- Laboratório de Isolamento e Síntese de Compostos Orgânicos, Instituto de Química, Universidade Federal do Rio Grande do Norte, Natal, Brazil
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35
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Vorobieva AA, White P, Liang B, Horne JE, Bera AK, Chow CM, Gerben S, Marx S, Kang A, Stiving AQ, Harvey SR, Marx DC, Khan GN, Fleming KG, Wysocki VH, Brockwell DJ, Tamm LK, Radford SE, Baker D. De novo design of transmembrane β barrels. Science 2021; 371:eabc8182. [PMID: 33602829 PMCID: PMC8064278 DOI: 10.1126/science.abc8182] [Citation(s) in RCA: 58] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2020] [Accepted: 12/07/2020] [Indexed: 12/12/2022]
Abstract
Transmembrane β-barrel proteins (TMBs) are of great interest for single-molecule analytical technologies because they can spontaneously fold and insert into membranes and form stable pores, but the range of pore properties that can be achieved by repurposing natural TMBs is limited. We leverage the power of de novo computational design coupled with a "hypothesis, design, and test" approach to determine TMB design principles, notably, the importance of negative design to slow β-sheet assembly. We design new eight-stranded TMBs, with no homology to known TMBs, that insert and fold reversibly into synthetic lipid membranes and have nuclear magnetic resonance and x-ray crystal structures very similar to the computational models. These advances should enable the custom design of pores for a wide range of applications.
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Affiliation(s)
- Anastassia A Vorobieva
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA
| | - Paul White
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, USA
| | - Binyong Liang
- Department of Molecular Physiology and Biological Physics and Center for Membrane and Cell Physiology, University of Virginia, Charlottesville, VA 22903, USA
| | - Jim E Horne
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, USA
| | - Asim K Bera
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Cameron M Chow
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Stacey Gerben
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Sinduja Marx
- Department of Molecular Engineering and Sciences, University of Washington, Seattle, WA 98195, USA
| | - Alex Kang
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Alyssa Q Stiving
- Department of Chemistry and Biochemistry, Resource for Native Mass Spectrometry Guided Structural Biology, The Ohio State University, Columbus, OH 43210, USA
| | - Sophie R Harvey
- Department of Chemistry and Biochemistry, Resource for Native Mass Spectrometry Guided Structural Biology, The Ohio State University, Columbus, OH 43210, USA
| | - Dagan C Marx
- TC Jenkins Department of Biophysics Johns Hopkins University, Baltimore, MD 21218, USA
| | - G Nasir Khan
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, USA
| | - Karen G Fleming
- TC Jenkins Department of Biophysics Johns Hopkins University, Baltimore, MD 21218, USA
| | - Vicki H Wysocki
- Department of Chemistry and Biochemistry, Resource for Native Mass Spectrometry Guided Structural Biology, The Ohio State University, Columbus, OH 43210, USA
| | - David J Brockwell
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, USA
| | - Lukas K Tamm
- Department of Molecular Physiology and Biological Physics and Center for Membrane and Cell Physiology, University of Virginia, Charlottesville, VA 22903, USA
| | - Sheena E Radford
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, USA
| | - David Baker
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA.
- Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
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36
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Izci M, Maksoudian C, Manshian BB, Soenen SJ. The Use of Alternative Strategies for Enhanced Nanoparticle Delivery to Solid Tumors. Chem Rev 2021; 121:1746-1803. [PMID: 33445874 PMCID: PMC7883342 DOI: 10.1021/acs.chemrev.0c00779] [Citation(s) in RCA: 193] [Impact Index Per Article: 64.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2020] [Indexed: 02/08/2023]
Abstract
Nanomaterial (NM) delivery to solid tumors has been the focus of intense research for over a decade. Classically, scientists have tried to improve NM delivery by employing passive or active targeting strategies, making use of the so-called enhanced permeability and retention (EPR) effect. This phenomenon is made possible due to the leaky tumor vasculature through which NMs can leave the bloodstream, traverse through the gaps in the endothelial lining of the vessels, and enter the tumor. Recent studies have shown that despite many efforts to employ the EPR effect, this process remains very poor. Furthermore, the role of the EPR effect has been called into question, where it has been suggested that NMs enter the tumor via active mechanisms and not through the endothelial gaps. In this review, we provide a short overview of the EPR and mechanisms to enhance it, after which we focus on alternative delivery strategies that do not solely rely on EPR in itself but can offer interesting pharmacological, physical, and biological solutions for enhanced delivery. We discuss the strengths and shortcomings of these different strategies and suggest combinatorial approaches as the ideal path forward.
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Affiliation(s)
- Mukaddes Izci
- NanoHealth
and Optical Imaging Group, Translational Cell and Tissue Research
Unit, Department of Imaging and Pathology, KU Leuven, Herestraat 49, B3000 Leuven, Belgium
| | - Christy Maksoudian
- NanoHealth
and Optical Imaging Group, Translational Cell and Tissue Research
Unit, Department of Imaging and Pathology, KU Leuven, Herestraat 49, B3000 Leuven, Belgium
| | - Bella B. Manshian
- Translational
Cell and Tissue Research Unit, Department of Imaging and Pathology, KU Leuven, Herestraat 49, B3000 Leuven, Belgium
| | - Stefaan J. Soenen
- NanoHealth
and Optical Imaging Group, Translational Cell and Tissue Research
Unit, Department of Imaging and Pathology, KU Leuven, Herestraat 49, B3000 Leuven, Belgium
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37
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Synthetic Peptide ΔM4-Induced Cell Death Associated with Cytoplasmic Membrane Disruption, Mitochondrial Dysfunction and Cell Cycle Arrest in Human Melanoma Cells. Molecules 2020; 25:molecules25235684. [PMID: 33276536 PMCID: PMC7730669 DOI: 10.3390/molecules25235684] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Revised: 11/16/2020] [Accepted: 11/25/2020] [Indexed: 12/31/2022] Open
Abstract
Melanoma is the most dangerous and lethal form of skin cancer, due to its ability to spread to different organs if it is not treated at an early stage. Conventional chemotherapeutics are failing as a result of drug resistance and weak tumor selectivity. Therefore, efforts to evaluate novel molecules for the treatment of skin cancer are necessary. Antimicrobial peptides have become attractive anticancer agents because they execute their biological activity with features such as a high potency of action, a wide range of targets, and high target specificity and selectivity. In the present study, the antiproliferative activity of the synthetic peptide ΔM4 on A375 human melanoma cells and spontaneously immortalized HaCaT human keratinocytes was investigated. The cytotoxic effect of ΔM4 treatment was evaluated through propidium iodide uptake by flow cytometry. The results indicated selective toxicity in A375 cells and, in order to further investigate the mode of action, assays were carried out to evaluate morphological changes, mitochondrial function, and cell cycle progression. The findings indicated that ΔM4 exerts its antitumoral effects by multitarget action, causing cell membrane disruption, a change in the mitochondrial transmembrane potential, an increase of reactive oxygen species, and cell cycle accumulation in S-phase. Further exploration of the peptide may be helpful in the design of novel anticancer peptides.
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38
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The Landscape of Pseudomonas aeruginosa Membrane-Associated Proteins. Cells 2020; 9:cells9112421. [PMID: 33167383 PMCID: PMC7694347 DOI: 10.3390/cells9112421] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Revised: 10/29/2020] [Accepted: 11/01/2020] [Indexed: 12/15/2022] Open
Abstract
Background: Pseudomonas aeruginosa cell envelope-associated proteins play a relevant role in infection mechanisms. They can contribute to the antibiotic resistance of the bacterial cells and be involved in the interaction with host cells. Thus, studies contributing to elucidating these key molecular elements are of great importance to find alternative therapeutics. Methods: Proteins and peptides were extracted by different methods and analyzed by Multidimensional Protein Identification Technology (MudPIT) approach. Proteomic data were processed by Discoverer2.1 software and multivariate statistics, i.e., Linear Discriminant Analysis (LDA), while the Immune Epitope Database (IEDB) resources were used to predict antigenicity and immunogenicity of experimental identified peptides and proteins. Results: The combination of 29 MudPIT runs allowed the identification of 10,611 peptides and 2539 distinct proteins. Following application of extraction methods enriching specific protein domains, about 15% of total identified peptides were classified in trans inner-membrane, inner-membrane exposed, trans outer-membrane and outer-membrane exposed. In this scenario, nine outer membrane proteins (OprE, OprI, OprF, OprD, PagL, OprG, PA1053, PAL and PA0833) were predicted to be highly antigenic. Thus, they were further processed and epitopes target of T cells (MHC Class I and Class II) and B cells were predicted. Conclusion: The present study represents one of the widest characterizations of the P. aeruginosa membrane-associated proteome. The feasibility of our method may facilitates the investigation of other bacterial species whose envelope exposed protein domains are still unknown. Besides, the stepwise prioritization of proteome, by combining experimental proteomic data and reverse vaccinology, may be useful for reducing the number of proteins to be tested in vaccine development.
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39
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Ruiz CA, Chaney ME, Imamura M, Imai H, Tosi AJ. Predicted structural differences of four fertility-related Y-chromosome proteins in Macaca mulatta, M. fascicularis, and their Indochinese hybrids. Proteins 2020; 89:361-370. [PMID: 33146441 DOI: 10.1002/prot.26021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Revised: 10/22/2020] [Accepted: 10/25/2020] [Indexed: 11/10/2022]
Abstract
Species in the genus Macaca typically live in multimale-multifemale social groups with male macaques exhibiting some of the largest testis: body weight ratios among primates. Males are believed to experience intense levels of sperm competition. Several spermatogenesis genes are located on the Y-chromosome and, interestingly, occasional hybridization between two species has led to the introgression of the rhesus macaque (Macaca mulatta) Y-chromosome deep into the range of the long-tailed macaque (M. fascicularis). These observations have led to the prediction that the successful introgression of the rhesus Y-haplotype is due to functional differences in spermatogenesis genes compared to those of the native long-tailed Y-haplotype. We examine here four Y-chromosomal loci-RBMY, XKRY, and two nearly identical copies of CDY-and their corresponding protein sequences. The genes were surveyed in representative animals from north of, south of, and within the rhesus x long-tailed introgression zone. Our results show a series of non-synonymous amino acid substitutions present between the two Y-haplotypes. Protein structure modeling via I-TASSER revealed different folding patterns between the two species' Y-proteins, and functional predictions via TreeSAAP further reveal physicochemical differences as a result of non-synonymous substitutions. These differences inform our understanding of the evolution of primate Y-proteins involved in spermatogenesis and, in turn, have biomedical implications for human male fertility.
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Affiliation(s)
- Cody A Ruiz
- Department of Anthropology, Kent State University, Kent, Ohio, USA.,School of Biomedical Sciences, Kent State University, Kent, Ohio, USA
| | - Morgan E Chaney
- Department of Anthropology, Kent State University, Kent, Ohio, USA.,School of Biomedical Sciences, Kent State University, Kent, Ohio, USA
| | - Masanori Imamura
- Department of Cellular and Molecular Biology, Primate Research Institute, Kyoto University, Inuyama, Japan
| | - Hiroo Imai
- Department of Cellular and Molecular Biology, Primate Research Institute, Kyoto University, Inuyama, Japan
| | - Anthony J Tosi
- Department of Anthropology, Kent State University, Kent, Ohio, USA.,School of Biomedical Sciences, Kent State University, Kent, Ohio, USA
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McKay MJ, Greathouse DV, Koeppe RE. Flanking aromatic residue competition influences transmembrane peptide helix dynamics. FEBS Lett 2020; 594:4280-4291. [DOI: 10.1002/1873-3468.13926] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Revised: 08/31/2020] [Accepted: 09/02/2020] [Indexed: 01/18/2023]
Affiliation(s)
- Matthew J. McKay
- Department of Chemistry and Biochemistry University of Arkansas Fayetteville AR USA
| | - Denise V. Greathouse
- Department of Chemistry and Biochemistry University of Arkansas Fayetteville AR USA
| | - Roger E. Koeppe
- Department of Chemistry and Biochemistry University of Arkansas Fayetteville AR USA
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Chiasson MA, Rollins NJ, Stephany JJ, Sitko KA, Matreyek KA, Verby M, Sun S, Roth FP, DeSloover D, Marks DS, Rettie AE, Fowler DM. Multiplexed measurement of variant abundance and activity reveals VKOR topology, active site and human variant impact. eLife 2020; 9:e58026. [PMID: 32870157 PMCID: PMC7462613 DOI: 10.7554/elife.58026] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Accepted: 07/28/2020] [Indexed: 01/05/2023] Open
Abstract
Vitamin K epoxide reductase (VKOR) drives the vitamin K cycle, activating vitamin K-dependent blood clotting factors. VKOR is also the target of the widely used anticoagulant drug, warfarin. Despite VKOR's pivotal role in coagulation, its structure and active site remain poorly understood. In addition, VKOR variants can cause vitamin K-dependent clotting factor deficiency or alter warfarin response. Here, we used multiplexed, sequencing-based assays to measure the effects of 2,695 VKOR missense variants on abundance and 697 variants on activity in cultured human cells. The large-scale functional data, along with an evolutionary coupling analysis, supports a four transmembrane domain topology, with variants in transmembrane domains exhibiting strongly deleterious effects on abundance and activity. Functionally constrained regions of the protein define the active site, and we find that, of four conserved cysteines putatively critical for function, only three are absolutely required. Finally, 25% of human VKOR missense variants show reduced abundance or activity, possibly conferring warfarin sensitivity or causing disease.
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Affiliation(s)
- Melissa A Chiasson
- Department of Genome Sciences, University of WashingtonSeattleUnited States
| | - Nathan J Rollins
- Department of Systems Biology, Harvard Medical SchoolBostonUnited States
| | - Jason J Stephany
- Department of Genome Sciences, University of WashingtonSeattleUnited States
| | - Katherine A Sitko
- Department of Genome Sciences, University of WashingtonSeattleUnited States
| | - Kenneth A Matreyek
- Department of Genome Sciences, University of WashingtonSeattleUnited States
| | - Marta Verby
- Donnelly Centre and Departments of Molecular Genetics and Computer Science, University of Toronto, and Lunenfeld-Tanenbaum Research Institute, Sinai Health SystemTorontoCanada
| | - Song Sun
- Donnelly Centre and Departments of Molecular Genetics and Computer Science, University of Toronto, and Lunenfeld-Tanenbaum Research Institute, Sinai Health SystemTorontoCanada
| | - Frederick P Roth
- Donnelly Centre and Departments of Molecular Genetics and Computer Science, University of Toronto, and Lunenfeld-Tanenbaum Research Institute, Sinai Health SystemTorontoCanada
| | | | - Debora S Marks
- Department of Systems Biology, Harvard Medical SchoolBostonUnited States
| | - Allan E Rettie
- Department of Medicinal Chemistry, University of WashingtonSeattleUnited States
| | - Douglas M Fowler
- Department of Genome Sciences, University of WashingtonSeattleUnited States
- Department of Bioengineering, University of WashingtonSeattleUnited States
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42
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Aguayo-Ortiz R, Espinoza-Fonseca LM. Linking Biochemical and Structural States of SERCA: Achievements, Challenges, and New Opportunities. Int J Mol Sci 2020; 21:ijms21114146. [PMID: 32532023 PMCID: PMC7313052 DOI: 10.3390/ijms21114146] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Revised: 06/05/2020] [Accepted: 06/08/2020] [Indexed: 02/07/2023] Open
Abstract
Sarcoendoplasmic reticulum calcium ATPase (SERCA), a member of the P-type ATPase family of ion and lipid pumps, is responsible for the active transport of Ca2+ from the cytoplasm into the sarcoplasmic reticulum lumen of muscle cells, into the endoplasmic reticulum (ER) of non-muscle cells. X-ray crystallography has proven to be an invaluable tool in understanding the structural changes of SERCA, and more than 70 SERCA crystal structures representing major biochemical states (defined by bound ligand) have been deposited in the Protein Data Bank. Consequently, SERCA is one of the best characterized components of the calcium transport machinery in the cell. Emerging approaches in the field, including spectroscopy and molecular simulation, now help integrate and interpret this rich structural information to understand the conformational transitions of SERCA that occur during activation, inhibition, and regulation. In this review, we provide an overview of the crystal structures of SERCA, focusing on identifying metrics that facilitate structure-based categorization of major steps along the catalytic cycle. We examine the integration of crystallographic data with different biophysical approaches and computational methods to link biochemical and structural states of SERCA that are populated in the cell. Finally, we discuss the challenges and new opportunities in the field, including structural elucidation of functionally important and novel regulatory complexes of SERCA, understanding the structural basis of functional divergence among homologous SERCA regulators, and bridging the gap between basic and translational research directed toward therapeutic modulation of SERCA.
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Fluorine-19 NMR spectroscopy of fluorinated analogs of tritrpticin highlights a distinct role for Tyr residues in antimicrobial peptides. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2020; 1862:183260. [DOI: 10.1016/j.bbamem.2020.183260] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 02/17/2020] [Accepted: 02/19/2020] [Indexed: 02/08/2023]
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Yadavalli SS, Goh T, Carey JN, Malengo G, Vellappan S, Nickels BE, Sourjik V, Goulian M, Yuan J. Functional determinants of a small protein controlling a broadly conserved bacterial sensor kinase. J Bacteriol 2020; 202:JB.00305-20. [PMID: 32482726 PMCID: PMC8404706 DOI: 10.1128/jb.00305-20] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Accepted: 05/22/2020] [Indexed: 12/14/2022] Open
Abstract
The PhoQ/PhoP two-component system plays a vital role in the regulation of Mg2+ homeostasis, resistance to acid and hyperosmotic stress, cationic antimicrobial peptides, and virulence in Escherichia coli, Salmonella and related bacteria. Previous studies have shown that MgrB, a 47 amino acid membrane protein that is part of the PhoQ/PhoP regulon, inhibits the histidine kinase PhoQ. MgrB is part of a negative feedback loop modulating this two-component system that prevents hyperactivation of PhoQ and may also provide an entry point for additional input signals for the PhoQ/PhoP pathway. To explore the mechanism of action of MgrB, we have analyzed the effects of point mutations, C-terminal truncations and transmembrane region swaps on MgrB activity. In contrast with two other known membrane protein regulators of histidine kinases in E. coli, we find that the MgrB TM region is necessary for PhoQ inhibition. Our results indicate that the TM region mediates interactions with PhoQ and that W20 is a key residue for PhoQ/MgrB complex formation. Additionally, mutations of the MgrB cytosolic region suggest that the two N-terminal lysines play an important role in regulating PhoQ activity. Alanine scanning mutagenesis of the periplasmic region of MgrB further indicates that, with the exception of a few highly conserved residues, most residues are not essential for MgrB's function as a PhoQ inhibitor. Our results indicate that the regulatory function of the small protein MgrB depends on distinct contributions from multiple residues spread across the protein. Interestingly, the TM region also appears to interact with other non-cognate histidine kinases in a bacterial two-hybrid assay, suggesting a potential route for evolving new small protein modulators of histidine kinases.
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Affiliation(s)
- Srujana S Yadavalli
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
- Department of Genetics and Waksman Institute of Microbiology, Rutgers University, Piscataway, NJ 08854, USA
| | - Ted Goh
- Department of Biology, Swarthmore College, Swarthmore, Pennsylvania 19081, USA
- Boston University School of Medicine, Boston, Massachusetts 02118, USA
| | - Jeffrey N Carey
- Biochemistry and Molecular Biophysics Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Gabriele Malengo
- Max Planck Institute for Terrestrial Microbiology, 35043 Marburg, Germany
- LOEWE Center for Synthetic Microbiology (SYNMIKRO), 35043 Marburg, Germany
| | - Sangeevan Vellappan
- Molecular Biosciences Graduate Program, Rutgers University, Piscataway NJ 08854
| | - Bryce E Nickels
- Department of Genetics and Waksman Institute of Microbiology, Rutgers University, Piscataway, NJ 08854, USA
| | - Victor Sourjik
- Max Planck Institute for Terrestrial Microbiology, 35043 Marburg, Germany
- LOEWE Center for Synthetic Microbiology (SYNMIKRO), 35043 Marburg, Germany
| | - Mark Goulian
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
- Department of Physics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Jing Yuan
- Max Planck Institute for Terrestrial Microbiology, 35043 Marburg, Germany
- LOEWE Center for Synthetic Microbiology (SYNMIKRO), 35043 Marburg, Germany
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Armbruster KM, Komazin G, Meredith TC. Bacterial lyso-form lipoproteins are synthesized via an intramolecular acyl chain migration. J Biol Chem 2020; 295:10195-10211. [PMID: 32471867 DOI: 10.1074/jbc.ra120.014000] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 05/22/2020] [Indexed: 01/08/2023] Open
Abstract
All bacterial lipoproteins share a variably acylated N-terminal cysteine residue. Gram-negative bacterial lipoproteins are triacylated with a thioether-linked diacylglycerol moiety and an N-acyl chain. The latter is transferred from a membrane phospholipid donor to the α-amino terminus by the enzyme lipoprotein N-acyltransferase (Lnt), using an active-site cysteine thioester covalent intermediate. Many Gram-positive Firmicutes also have N-acylated lipoproteins, but the enzymes catalyzing N-acylation remain uncharacterized. The integral membrane protein Lit (lipoprotein intramolecular transacylase) from the opportunistic nosocomial pathogen Enterococcus faecalis synthesizes a specific lysoform lipoprotein (N-acyl S-monoacylglycerol) chemotype by an unknown mechanism that helps this bacterium evade immune recognition by the Toll-like receptor 2 family complex. Here, we used a deuterium-labeled lipoprotein substrate with reconstituted Lit to investigate intramolecular acyl chain transfer. We observed that Lit transfers the sn-2 ester-linked lipid from the diacylglycerol moiety to the α-amino terminus without forming a covalent thioester intermediate. Utilizing Mut-Seq to analyze an alanine scan library of Lit alleles, we identified two stretches of functionally important amino acid residues containing two conserved histidines. Topology maps based on reporter fusion assays and cysteine accessibility placed both histidines in the extracellular half of the cytoplasmic membrane. We propose a general acid base-promoted catalytic mechanism, invoking direct nucleophilic attack by the substrate α-amino group on the sn-2 ester to form a cyclic tetrahedral intermediate that then collapses to produce lyso-lipoprotein. Lit is a unique example of an intramolecular transacylase differentiated from that catalyzed by Lnt, and provides insight into the heterogeneity of bacterial lipoprotein biosynthetic systems.
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Affiliation(s)
- Krista M Armbruster
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania, USA
| | - Gloria Komazin
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania, USA
| | - Timothy C Meredith
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania, USA .,The Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park Pennsylvania, USA
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Role of an Aromatic-Aromatic Interaction in the Assembly and Trafficking of the Zebrafish Panx1a Membrane Channel. Biomolecules 2020; 10:biom10020272. [PMID: 32053881 PMCID: PMC7072349 DOI: 10.3390/biom10020272] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Revised: 01/29/2020] [Accepted: 02/05/2020] [Indexed: 12/28/2022] Open
Abstract
Pannexin 1 (Panx1) is a ubiquitously expressed hexameric integral membrane protein known to function as an adenosine triphosphate (ATP) release channel. Panx1 proteins exist in unglycosylated core form (Gly0). They undergo critical post-translational modifications forming the high mannose glycosylation state (Gly1) in the endoplasmic reticulum (ER) and the complex glycosylation state (Gly2) in the Golgi apparatus. The regulation of transition from the ER to the cell membrane is not fully understood. Using site-specific mutagenesis, dye uptake assays, and interaction testing, we identified two conserved aromatic residues, Trp123 and Tyr205, in the transmembrane domains 2 and 3 of the zebrafish panx1a protein. Results suggest that both residues primarily govern the assembly of panx1a subunits into channels, with mutant proteins failing to interact. The results provide insight into a mechanism enabling regulation of Panx1 oligomerization, glycosylation, and trafficking.
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Comparing Interfacial Trp, Interfacial His and pH Dependence for the Anchoring of Tilted Transmembrane Helical Peptides. Biomolecules 2020; 10:biom10020273. [PMID: 32053887 PMCID: PMC7072424 DOI: 10.3390/biom10020273] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Revised: 02/07/2020] [Accepted: 02/10/2020] [Indexed: 11/27/2022] Open
Abstract
Charged and aromatic amino acid residues, being enriched toward the terminals of membrane-spanning helices in membrane proteins, help to stabilize particular transmembrane orientations. Among them, histidine is aromatic and can be positively charge at low pH. To enable investigations of the underlying protein-lipid interactions, we have examined the effects of single or pairs of interfacial histidine residues using the constructive low-dynamic GWALP23 (acetyl-GG2ALW5LALALALALALALW19LAG22A-amide) peptide framework by incorporating individual or paired histidines at locations 2, 5, 19 or 22. Analysis of helix orientation by means of solid-state 2H NMR spectra of labeled alanine residues reveals marked differences with H2,22 compared to W2,22. Nevertheless, the properties of membrane-spanning H2,22WALP23 helices show little pH dependence and are similar to those having Gly, Arg or Lys at positions 2 and 22. The presence of H5 or H19 influences the helix rotational preference but not the tilt magnitude. H5 affects the helical integrity, as residue 7 unwinds from the core helix; yet once again the helix orientation and dynamic properties show little sensitivity to pH. The overall results reveal that the detailed properties of transmembrane helices depend upon the precise locations of interfacial histidine residues.
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Hassan SAEM, Ahmed SAEF, Helmy AH, Youssef NF. Spectrofluorimetric study on fluorescence quenching of tyrosine and l-tryptophan by the aniracetam cognition enhancer drug: quenching mechanism using Stern-Volmer and double-log plots. LUMINESCENCE 2020; 35:728-737. [PMID: 31994341 DOI: 10.1002/bio.3778] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Revised: 01/06/2020] [Accepted: 01/07/2020] [Indexed: 11/05/2022]
Abstract
A novel approach on fluorescence quenching of tyrosine and l-tryptophan is presented for spectrofluorimetric determination of aniracetam in drug substances and products. The quenching mechanism was investigated using Stern-Volmer plots and ultraviolet spectra figures of quencher-fluorophore mixtures. Binding constant and stoichiometry were calculated using double-log plots. The spectrofluorimetric method was optimized for the experimental conditions affecting fluorescence quenching including fluorophore concentration, diluent, and reaction time. Moreover, the pH-rate profile of aniracetam was studied using simple kinetics and found to be stable within the pH range 5-8. Fluorescence quenching of tyrosine and l-tryptophan were observed on addition of aniracetam in aqueous medium at pH 5.5-6.5. Aniracetam quenched the fluorescence of tyrosine and l-tryptophan in the concentration range 1-20 μg/ml and 0.3-20 μg/ml, respectively, with binomial relationships between quenching values (ΔF) and aniracetam concentration. Limits of detection were found to be 0.10 μg/ml for tyrosine-aniracetam and 0.14 μg/ml for l-tryptophan-aniracetam. Method validation was performed as per ICH guidelines and demonstrated that the developed spectrofluorimetric method was accurate, precise, specific, and suitable for analysis of aniracetam in routine quality control laboratories. All experimental materials and solvents used are eco-friendly, indicating that the cited spectrofluorimetric procedure is an excellent green method.
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Affiliation(s)
| | | | - Aya Hosam Helmy
- Pharmaceutical Chemistry Department, National Organization for Drug Control and Research (NODCAR), Giza, Egypt
| | - Nadia Fayek Youssef
- Pharmaceutical Chemistry Department, National Organization for Drug Control and Research (NODCAR), Giza, Egypt
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The Mechanism of Bidirectional pH Taxis in Bacillus subtilis. J Bacteriol 2020; 202:JB.00491-19. [PMID: 31685537 DOI: 10.1128/jb.00491-19] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Accepted: 10/30/2019] [Indexed: 01/19/2023] Open
Abstract
We investigated pH taxis in Bacillus subtilis This bacterium was found to perform bidirectional taxis in response to external pH gradients, enabling it to preferentially migrate to neutral environments. We next investigated the chemoreceptors involved in sensing pH gradients. We identified four chemoreceptors involved in sensing pH: McpA and TlpA for sensing acidic environments and McpB and TlpB for sensing alkaline ones. In addition, TlpA was found to also weakly sense alkaline environments. By analyzing chimeras between McpA and TlpB, the principal acid- and base-sensing chemoreceptors, we identified four critical amino acid residues-Thr199, Gln200, His273, and Glu274 on McpA and Lys199, Glu200, Gln273, and Asp274 on TlpB-involved in sensing pH. Swapping these four residues between McpA and TlpB converted the former into a base receptor and the latter into an acid receptor. Based on the results, we propose that disruption of hydrogen bonding between the adjacent residues upon pH changes induces signaling. Collectively, our results further our understanding of chemotaxis in B. subtilis and provide a new model for pH sensing in bacteria.IMPORTANCE Many bacteria can sense the pH in their environment and then use this information to direct their movement toward more favorable locations. In this study, we investigated the pH sensing mechanism in Bacillus subtilis This bacterium preferentially migrates to neutral environments. It employs four chemoreceptors to sense pH. Two are involved in sensing acidic environments, and two are involved in sensing alkaline ones. To identify the mechanism for pH sensing, we constructed receptor chimeras of acid- and base-sensing chemoreceptors. By analyzing the responses of these chimeric receptors, we were able to identify four critical amino acid residues involved in pH sensing and propose a model for the pH sensing mechanism in B. subtilis.
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50
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Iyer BR, Gupta S, Noordeen H, Ravi R, Pawar MD, George A, Mahalakshmi R. Molecular Switch between Structural Compaction and Thermodynamic Stability by the Xxx-Pro Interface in Transmembrane β-Barrels. Biochemistry 2020; 59:303-314. [PMID: 31777252 DOI: 10.1021/acs.biochem.9b00731] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Transmembrane β-barrel scaffolds found in outer membrane proteins are formed and stabilized by a defined pattern of interstrand intraprotein H-bonds, in hydrophobic lipid bilayers. Introducing the conformationally constrained proline in β-barrels can cause significant destabilization of these structural regions that require H-bonding, with proline additionally acting as a secondary structure breaker. Membrane protein β-barrels are therefore expected to show poor tolerance to the presence of a transmembrane proline. Here, we assign a thermodynamic measure for the extent to which a single proline can be tolerated at the C-terminal interface of the model transmembrane β-barrel PagP. We find that proline drastically destabilizes PagP by 7.0 kcal mol-1 with respect to wild-type PagP (F161 → P161). Interestingly, strategic modulation of the preceding residue can modify the measured energetics. Placing a hydrophobic or bulky side chain as the preceding residue increases the thermodynamic stability by ≤8.0 kcal mol-1. While polar substituents at the preceding residue decrease the PagP stability, these residues demonstrate stronger tertiary packing interactions in the barrel and retain the catalytic activity of native PagP. This biophysical interplay between enhanced thermodynamic stability and attaining a structurally compact functional β-barrel scaffold highlights the detrimental effect caused by proline incorporation. Our findings also reveal alternative mechanisms that protein sequences can employ to salvage the structural integrity of transmembrane protein structures.
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Affiliation(s)
- Bharat Ramasubramanian Iyer
- Molecular Biophysics Laboratory, Department of Biological Sciences , Indian Institute of Science Education and Research , Bhopal 462066 , India
| | - Swadha Gupta
- Molecular Biophysics Laboratory, Department of Biological Sciences , Indian Institute of Science Education and Research , Bhopal 462066 , India
| | - Henna Noordeen
- Molecular Biophysics Laboratory, Department of Biological Sciences , Indian Institute of Science Education and Research , Bhopal 462066 , India
| | - Roshika Ravi
- Molecular Biophysics Laboratory, Department of Biological Sciences , Indian Institute of Science Education and Research , Bhopal 462066 , India
| | - Meera Daulatrao Pawar
- Molecular Biophysics Laboratory, Department of Biological Sciences , Indian Institute of Science Education and Research , Bhopal 462066 , India
| | - Anjana George
- Molecular Biophysics Laboratory, Department of Biological Sciences , Indian Institute of Science Education and Research , Bhopal 462066 , India
| | - Radhakrishnan Mahalakshmi
- Molecular Biophysics Laboratory, Department of Biological Sciences , Indian Institute of Science Education and Research , Bhopal 462066 , India
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