1
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Smith OB, Frkic RL, Rahman MG, Jackson CJ, Kaczmarski JA. Identification and Characterization of a Bacterial Periplasmic Solute Binding Protein That Binds l-Amino Acid Amides. Biochemistry 2024; 63:1322-1334. [PMID: 38696389 DOI: 10.1021/acs.biochem.4c00096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/04/2024]
Abstract
Periplasmic solute-binding proteins (SBPs) are key ligand recognition components of bacterial ATP-binding cassette (ABC) transporters that allow bacteria to import nutrients and metabolic precursors from the environment. Periplasmic SBPs comprise a large and diverse family of proteins, of which only a small number have been empirically characterized. In this work, we identify a set of 610 unique uncharacterized proteins within the SBP_bac_5 family that are found in conserved operons comprising genes encoding (i) ABC transport systems and (ii) putative amidases from the FmdA_AmdA family. From these uncharacterized SBP_bac_5 proteins, we characterize a representative periplasmic SBP from Mesorhizobium sp. A09 (MeAmi_SBP) and show that MeAmi_SBP binds l-amino acid amides but not the corresponding l-amino acids. An X-ray crystal structure of MeAmi_SBP bound to l-serinamide highlights the residues that impart distinct specificity for l-amino acid amides and reveals a structural Ca2+ binding site within one of the lobes of the protein. We show that the residues involved in ligand and Ca2+ binding are conserved among the 610 SBPs from experimentally uncharacterized FmdA_AmdA amidase-associated ABC transporter systems, suggesting these homologous systems are also likely to be involved in the sensing, uptake, and metabolism of l-amino acid amides across many Gram-negative nitrogen-fixing soil bacteria. We propose that MeAmi_SBP is involved in the uptake of such solutes to supplement pathways such as the citric acid cycle and the glutamine synthetase-glutamate synthase pathway. This work expands our currently limited understanding of microbial interactions with l-amino acid amides and bacterial nitrogen utilization.
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Affiliation(s)
- Oliver B Smith
- Research School of Chemistry, Australian National University, Canberra, Australian Capital Territory 2601, Australia
- ARC Centre of Excellence in Synthetic Biology, Australian National University, Canberra, Australian Capital Territory 2601, Australia
| | - Rebecca L Frkic
- Research School of Chemistry, Australian National University, Canberra, Australian Capital Territory 2601, Australia
- ARC Centre of Excellence for Innovations in Peptide & Protein Science, Australian National University, Canberra, Australian Capital Territory 2601, Australia
| | - Marina G Rahman
- ARC Centre of Excellence in Synthetic Biology, Australian National University, Canberra, Australian Capital Territory 2601, Australia
- Research School of Biology, Australian National University, Canberra, Australian Capital Territory 2601, Australia
| | - Colin J Jackson
- Research School of Chemistry, Australian National University, Canberra, Australian Capital Territory 2601, Australia
- ARC Centre of Excellence in Synthetic Biology, Australian National University, Canberra, Australian Capital Territory 2601, Australia
- ARC Centre of Excellence for Innovations in Peptide & Protein Science, Australian National University, Canberra, Australian Capital Territory 2601, Australia
- Research School of Biology, Australian National University, Canberra, Australian Capital Territory 2601, Australia
| | - Joe A Kaczmarski
- ARC Centre of Excellence in Synthetic Biology, Australian National University, Canberra, Australian Capital Territory 2601, Australia
- Research School of Biology, Australian National University, Canberra, Australian Capital Territory 2601, Australia
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2
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Rivera K, Tanaka KJ, Buechel ER, Origel O, Harrison A, Mason KM, Pinkett HW. Antimicrobial Peptide Recognition Motif of the Substrate Binding Protein SapA from Nontypeable Haemophilus influenzae. Biochemistry 2024; 63:294-311. [PMID: 38189237 PMCID: PMC10851439 DOI: 10.1021/acs.biochem.3c00562] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Revised: 12/11/2023] [Accepted: 12/13/2023] [Indexed: 01/09/2024]
Abstract
Nontypeable Haemophilus influenzae (NTHi) is an opportunistic pathogen associated with respiratory diseases, including otitis media and exacerbations of chronic obstructive pulmonary disease. NTHi exhibits resistance to killing by host antimicrobial peptides (AMPs) mediated by SapA, the substrate binding protein of the sensitivity to antimicrobial peptides (Sap) transporter. However, the specific mechanisms by which SapA selectively binds various AMPs such as defensins and cathelicidin are unknown. In this study, we report mutational analyses of both defensin AMPs and the SapA binding pocket to define the specificity of AMP recognition. Bactericidal assays revealed that NTHi lacking SapA are more susceptible to human beta defensins and LL-37, while remaining highly resistant to a human alpha defensin. In contrast to homologues, our research underscores the distinct specificity of NTHi SapA, which selectively recognizes and binds to peptides containing the charged-hydrophobic motif PKE and RRY. These findings provide valuable insight into the divergence of SapA among bacterial species and NTHi SapA's ability to selectively interact with specific AMPs to mediate resistance.
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Affiliation(s)
- Kristen
G. Rivera
- Department
of Molecular Biosciences, Northwestern University, Evanston, Illinois 60208, United States
| | - Kari J. Tanaka
- Department
of Molecular Biosciences, Northwestern University, Evanston, Illinois 60208, United States
| | - Evan R. Buechel
- Department
of Molecular Biosciences, Northwestern University, Evanston, Illinois 60208, United States
| | - Octavio Origel
- Department
of Molecular Biosciences, Northwestern University, Evanston, Illinois 60208, United States
| | - Alistair Harrison
- The
Center for Microbial Pathogenesis, The Abigail Wexner Research Institute
at Nationwide Children’s Hospital and College of Medicine,
Department of Pediatrics, The Ohio State
University, Columbus, Ohio 43205, United States
| | - Kevin M. Mason
- The
Center for Microbial Pathogenesis, The Abigail Wexner Research Institute
at Nationwide Children’s Hospital and College of Medicine,
Department of Pediatrics, The Ohio State
University, Columbus, Ohio 43205, United States
| | - Heather W. Pinkett
- Department
of Molecular Biosciences, Northwestern University, Evanston, Illinois 60208, United States
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3
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Ackroyd BK, Dodson EJ, Mehboob J, Dowle AA, Thomas GH, Wilkinson AJ. Structure and ligand binding in the putative anti-microbial peptide transporter protein, YejA. MICROBIOLOGY (READING, ENGLAND) 2024; 170:001430. [PMID: 38334478 PMCID: PMC10924461 DOI: 10.1099/mic.0.001430] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Accepted: 01/19/2024] [Indexed: 02/10/2024]
Abstract
YejABEF is an ATP-binding cassette transporter that is implicated in the sensitivity of Escherichia coli to anti-microbial peptides, the best-characterized example being microcin C, a peptide-nucleotide antibiotic that targets aspartyl-tRNA synthetase. Here the structure of the extracellular solute binding protein, YejA, has been determined, revealing an oligopeptide-binding protein fold enclosing a ligand-binding pocket larger than those of other peptide-binding proteins of known structure. Prominent electron density in this cavity defines an undecapeptide sequence LGEPRYAFNFN, an observation that is confirmed by mass spectrometry. In the structure, the peptide interactions with the protein are mediated by main chain hydrogen bonds with the exception of Arg5 whose guanidinium side chain makes a set of defining polar interactions with four YejA residues. More detailed characterization of purified recombinant YejA, by a combination of ESI and MALDI-mass spectrometry as well as thermal shift assays, reveals a set of YejA complexes containing overlapping peptides 10-19 residues in length. All contain the sequence LGEPRYAFN. Curiously, these peptides correspond to residues 8-26 of the mature YejA protein, which belong to a unique N-terminal extension that distinguishes YejA from other cluster C oligopeptide binding proteins of known structure. This 35-residue extension is well-ordered and packs across the surface of the protein. The undecapeptide ligand occupies only a fraction of the enclosed pocket volume suggesting the possibility that much larger peptides or peptide conjugates could be accommodated, though thermal shift assays of YejA binding to antimicrobial peptides and peptides unrelated to LGEPRYAFNFN have not provided evidence of binding. While the physiological significance of this 'auto-binding' is not clear, the experimental data suggest that it is not an artefact of the crystallization process and that it may have a function in the sensing of periplasmic or membrane stress.
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Affiliation(s)
- Bryony K. Ackroyd
- York Structural Biology Laboratory and York Biomedical Research Institute, Department of Chemistry, University of York, York YO10 5DD, UK
- Department of Biology and York Biomedical Research Institute, University of York, York YO10 5DD, UK
| | - Eleanor J. Dodson
- York Structural Biology Laboratory and York Biomedical Research Institute, Department of Chemistry, University of York, York YO10 5DD, UK
| | - Javeria Mehboob
- Department of Biology and York Biomedical Research Institute, University of York, York YO10 5DD, UK
| | - Adam A. Dowle
- Bioscience Technology Facility, Department of Biology, University of York, York YO10 5DD, UK
| | - Gavin H. Thomas
- Department of Biology and York Biomedical Research Institute, University of York, York YO10 5DD, UK
| | - Anthony J. Wilkinson
- York Structural Biology Laboratory and York Biomedical Research Institute, Department of Chemistry, University of York, York YO10 5DD, UK
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4
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Hughes AM, Darby JF, Dodson EJ, Wilson SJ, Turkenburg JP, Thomas GH, Wilkinson AJ. Peptide transport in Bacillus subtilis - structure and specificity in the extracellular solute binding proteins OppA and DppE. MICROBIOLOGY (READING, ENGLAND) 2022; 168. [PMID: 36748525 DOI: 10.1099/mic.0.001274] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
Abstract
Peptide transporters play important nutritional and cell signalling roles in Bacillus subtilis, which are pronounced during stationary phase adaptations and development. Three high-affinity ATP-binding cassette (ABC) family transporters are involved in peptide uptake - the oligopeptide permease (Opp), another peptide permease (App) and a less well-characterized dipeptide permease (Dpp). Here we report crystal structures of the extracellular substrate binding proteins, OppA and DppE, which serve the Opp and Dpp systems, respectively. The structure of OppA was determined in complex with endogenous peptides, modelled as Ser-Asn-Ser-Ser, and with the sporulation-promoting peptide Ser-Arg-Asn-Val-Thr, which bind with K d values of 0.4 and 2 µM, respectively, as measured by isothermal titration calorimetry. Differential scanning fluorescence experiments with a wider panel of ligands showed that OppA has highest affinity for tetra- and penta-peptides. The structure of DppE revealed the unexpected presence of a murein tripeptide (MTP) ligand, l-Ala-d-Glu-meso-DAP, in the peptide binding groove. The mode of MTP binding in DppE is different to that observed in the murein peptide binding protein, MppA, from Escherichia coli, suggesting independent evolution of these proteins from an OppA-like precursor. The presence of MTP in DppE points to a role for Dpp in the uptake and recycling of cell wall peptides, a conclusion that is supported by analysis of the genomic context of dpp, which revealed adjacent genes encoding enzymes involved in muropeptide catabolism in a gene organization that is widely conserved in Firmicutes.
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Affiliation(s)
- Adam M Hughes
- Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, UK
| | - John F Darby
- Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, UK
| | - Eleanor J Dodson
- Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, UK
| | - Samuel J Wilson
- Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, UK
| | - Johan P Turkenburg
- Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, UK
| | - Gavin H Thomas
- Department of Biology, University of York, York YO10 5DD, UK
| | - Anthony J Wilkinson
- Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, UK
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5
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Zainol MKM, Linforth RJC, Winzor DJ, Scott DJ. Thermodynamics of semi-specific ligand recognition: the binding of dipeptides to the E.coli dipeptide binding protein DppA. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2021; 50:1103-1110. [PMID: 34611772 PMCID: PMC8566422 DOI: 10.1007/s00249-021-01572-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 08/23/2021] [Accepted: 09/18/2021] [Indexed: 12/04/2022]
Abstract
This investigation of the temperature dependence of DppA interactions with a subset of three dipeptides (AA. AF and FA) by isothermal titration calorimetry has revealed the negative heat capacity (\documentclass[12pt]{minimal}
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\begin{document}$$\Delta {C}_{p}^{o}$$\end{document}ΔCpo) that is a characteristic of hydrophobic interactions. The observation of enthalpy–entropy compensation is interpreted in terms of the increased structuring of water molecules trapped in a hydrophobic environment, the enthalpic energy gain from which is automatically countered by the entropy decrease associated with consequent loss of water structure flexibility. Specificity for dipeptides stems from appropriate spacing of designated DppA aspartate and arginine residues for electrostatic interaction with the terminal amino and carboxyl groups of a dipeptide, after which the binding pocket closes to become completely isolated from the aqueous environment. Any differences in chemical reactivity of the dipeptide sidechains are thereby modulated by their occurrence in a hydrophobic environment where changes in the structural state of entrapped water molecules give rise to the phenomenon of enthalpy–entropy compensation. The consequent minimization of differences in the value of ΔG0 for all DppA–dipeptide interactions thus provides thermodynamic insight into the biological role of DppA as a transporter of all dipeptides across the periplasmic membrane.
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Affiliation(s)
- Mohamad K M Zainol
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, LE12 5RD, UK.,Faculty of Fisheries and Food Science, Universiti Malaysia Terengganu, Mengabang Telipot, 21030, Kuala Nerus, Terengganu, Malaysia
| | - Robert J C Linforth
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, LE12 5RD, UK
| | - Donald J Winzor
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, QLD, 4072, Australia
| | - David J Scott
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, LE12 5RD, UK. .,Rutherford Appleton Laboratory, Research Complex at Harwell, Oxfordshire, OX11 0FA, UK.
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6
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Kim H, Wu K, Lee C. Stress-Responsive Periplasmic Chaperones in Bacteria. Front Mol Biosci 2021; 8:678697. [PMID: 34046432 PMCID: PMC8144458 DOI: 10.3389/fmolb.2021.678697] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Accepted: 04/19/2021] [Indexed: 01/14/2023] Open
Abstract
Periplasmic proteins are involved in a wide range of bacterial functions, including motility, biofilm formation, sensing environmental cues, and small-molecule transport. In addition, a wide range of outer membrane proteins and proteins that are secreted into the media must travel through the periplasm to reach their final destinations. Since the porous outer membrane allows for the free diffusion of small molecules, periplasmic proteins and those that travel through this compartment are more vulnerable to external environmental changes, including those that result in protein unfolding, than cytoplasmic proteins are. To enable bacterial survival under various stress conditions, a robust protein quality control system is required in the periplasm. In this review, we focus on several periplasmic chaperones that are stress responsive, including Spy, which responds to envelope-stress, DegP, which responds to temperature to modulate chaperone/protease activity, HdeA and HdeB, which respond to acid stress, and UgpB, which functions as a bile-responsive chaperone.
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Affiliation(s)
- Hyunhee Kim
- Department of Biological Sciences, Ajou University, Suwon, South Korea
- Molecular, Cellular, and Developmental Biology, Howard Hughes Medical Institute, University of Michigan, Ann Arbor, MI, United States
| | - Kevin Wu
- Molecular, Cellular, and Developmental Biology, Howard Hughes Medical Institute, University of Michigan, Ann Arbor, MI, United States
- Department of Biophysics, University of Michigan, Ann Arbor, MI, United States
| | - Changhan Lee
- Department of Biological Sciences, Ajou University, Suwon, South Korea
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7
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Bioinformatics analysis and biochemical characterisation of ABC transporter-associated periplasmic substrate-binding proteins ModA and MetQ from Helicobacter pylori strain SS1. Biophys Chem 2021; 272:106577. [PMID: 33756269 DOI: 10.1016/j.bpc.2021.106577] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2021] [Revised: 02/23/2021] [Accepted: 03/06/2021] [Indexed: 12/29/2022]
Abstract
The human gastric pathogen Helicobacter pylori relies on the uptake of host-provided nutrients for its proliferation and pathogenicity. ABC transporters that mediate import of small molecules into the cytoplasm of H. pylori employ their cognate periplasmic substrate-binding proteins (SBPs) for ligand capture in the periplasm. The genome of the mouse-adapted strain SS1 of H. pylori encodes eight ABC transporter-associated SBPs, but little is known about their specificity or structure. In this study, we demonstrated that the SBP annotated as ModA binds molybdate (MoO42-, KD = 3.8 nM) and tungstate (WO42-, KD = 7.8 nM). In addition, we showed that MetQ binds D-methionine (KD = 9.5 μM), but not L-methionine, which suggests the existence of as yet unknown pathway for L-methionine uptake. Homology modelling has led to identification of the ligand-binding residues.
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8
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Groshong AM, McLain MA, Radolf JD. Host-specific functional compartmentalization within the oligopeptide transporter during the Borrelia burgdorferi enzootic cycle. PLoS Pathog 2021; 17:e1009180. [PMID: 33428666 PMCID: PMC7822543 DOI: 10.1371/journal.ppat.1009180] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 01/22/2021] [Accepted: 11/23/2020] [Indexed: 12/27/2022] Open
Abstract
Borrelia burgdorferi must acquire all of its amino acids (AAs) from its arthropod vector and vertebrate host. Previously, we determined that peptide uptake via the oligopeptide (Opp) ABC transporter is essential for spirochete viability in vitro and during infection. Our prior study also suggested that B. burgdorferi employs temporal regulation in concert with structural variation of oligopeptide-binding proteins (OppAs) to meet its AA requirements in each biological niche. Herein, we evaluated the contributions to the B. burgdorferi enzootic cycle of three of the spirochete's five OppAs (OppA1, OppA2, and OppA5). An oppA1 transposon (tn) mutant lysed in the hyperosmolar environment of the feeding tick, suggesting that OppA1 imports amino acids required for osmoprotection. The oppA2tn mutant displayed a profound defect in hematogenous dissemination in mice, yet persisted within skin while inducing only a minimal antibody response. These results, along with slightly decreased growth of the oppA2tn mutant within DMCs, suggest that OppA2 serves a minor nutritive role, while its dissemination defect points to an as yet uncharacterized signaling function. Previously, we identified a role for OppA5 in spirochete persistence within the mammalian host. We now show that the oppA5tn mutant displayed no defect during the tick phase of the cycle and could be tick-transmitted to naïve mice. Instead of working in tandem, however, OppA2 and OppA5 appear to function in a hierarchical manner; the ability of OppA5 to promote persistence relies upon the ability of OppA2 to facilitate dissemination. Structural homology models demonstrated variations within the binding pockets of OppA1, 2, and 5 indicative of different peptide repertoires. Rather than being redundant, B. burgdorferi's multiplicity of Opp binding proteins enables host-specific functional compartmentalization during the spirochete lifecycle.
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Affiliation(s)
- Ashley M. Groshong
- Department of Medicine, UConn Health, Farmington, Connecticut, United States of America
- Department of Pediatrics, UConn Health, Farmington, Connecticut, United States of America
- * E-mail:
| | - Melissa A. McLain
- Department of Medicine, UConn Health, Farmington, Connecticut, United States of America
| | - Justin D. Radolf
- Department of Medicine, UConn Health, Farmington, Connecticut, United States of America
- Department of Pediatrics, UConn Health, Farmington, Connecticut, United States of America
- Department of Molecular Biology and Biophysics, UConn Health, Farmington, Connecticut, United States of America
- Department of Genetics and Genome Science, UConn Health, Farmington, Connecticut, United States of America
- Department of Immunology, UConn Health, Farmington, Connecticut, United States of America
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9
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Lee C, Betschinger P, Wu K, Żyła DS, Glockshuber R, Bardwell JC. A metabolite binding protein moonlights as a bile-responsive chaperone. EMBO J 2020; 39:e104231. [PMID: 32882062 DOI: 10.15252/embj.2019104231] [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: 12/09/2019] [Revised: 07/12/2020] [Accepted: 07/17/2020] [Indexed: 12/27/2022] Open
Abstract
Bile salts are secreted into the gastrointestinal tract to aid in the absorption of lipids. In addition, bile salts show potent antimicrobial activity in part by mediating bacterial protein unfolding and aggregation. Here, using a protein folding sensor, we made the surprising discovery that the Escherichia coli periplasmic glycerol-3-phosphate (G3P)-binding protein UgpB can serve, in the absence of its substrate, as a potent molecular chaperone that exhibits anti-aggregation activity against bile salt-induced protein aggregation. The substrate G3P, which is known to accumulate in the later compartments of the digestive system, triggers a functional switch between UgpB's activity as a molecular chaperone and its activity as a G3P transporter. A UgpB mutant unable to bind G3P is constitutively active as a chaperone, and its crystal structure shows that it contains a deep surface groove absent in the G3P-bound wild-type UgpB. Our work illustrates how evolution may be able to convert threats into signals that first activate and then inactivate a chaperone at the protein level in a manner that bypasses the need for ATP.
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Affiliation(s)
- Changhan Lee
- Department of Molecular, Cellular, and Developmental Biology, Howard Hughes Medical Institute, University of Michigan, Ann Arbor, MI, USA
| | - Patrick Betschinger
- Department of Molecular, Cellular, and Developmental Biology, Howard Hughes Medical Institute, University of Michigan, Ann Arbor, MI, USA
| | - Kevin Wu
- Department of Molecular, Cellular, and Developmental Biology, Howard Hughes Medical Institute, University of Michigan, Ann Arbor, MI, USA.,Department of Biophysics, University of Michigan, Ann Arbor, MI, USA
| | - Dawid S Żyła
- Institute of Molecular Biology and Biophysics, Department of Biology, ETH Zurich, Zurich, Switzerland
| | - Rudi Glockshuber
- Institute of Molecular Biology and Biophysics, Department of Biology, ETH Zurich, Zurich, Switzerland
| | - James Ca Bardwell
- Department of Molecular, Cellular, and Developmental Biology, Howard Hughes Medical Institute, University of Michigan, Ann Arbor, MI, USA
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10
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Rodríguez-Arce I, Al-Jubair T, Euba B, Fernández-Calvet A, Gil-Campillo C, Martí S, Törnroth-Horsefield S, Riesbeck K, Garmendia J. Moonlighting of Haemophilus influenzae heme acquisition systems contributes to the host airway-pathogen interplay in a coordinated manner. Virulence 2019; 10:315-333. [PMID: 30973092 PMCID: PMC6550540 DOI: 10.1080/21505594.2019.1596506] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Revised: 02/18/2019] [Accepted: 03/12/2019] [Indexed: 01/30/2023] Open
Abstract
Nutrient iron sequestration is the most significant form of nutritional immunity and causes bacterial pathogens to evolve strategies of host iron scavenging. Cigarette smoking contains iron particulates altering lung and systemic iron homeostasis, which may enhance colonization in the lungs of patients suffering chronic obstructive pulmonary disease (COPD) by opportunistic pathogens such as nontypeable. NTHi is a heme auxotroph, and the NTHi genome contains multiple heme acquisition systems whose role in pulmonary infection requires a global understanding. In this study, we determined the relative contribution to NTHi airway infection of the four heme-acquisition systems HxuCBA, PE, SapABCDFZ, and HbpA-DppBCDF that are located at the bacterial outer membrane or the periplasm. Our computational studies provided plausible 3D models for HbpA, SapA, PE, and HxuA interactions with heme. Generation and characterization of single mutants in the hxuCBA, hpe, sapA, and hbpA genes provided evidence for participation in heme binding-storage and inter-bacterial donation. The hxuA, sapA, hbpA, and hpe genes showed differential expression and responded to heme. Moreover, HxuCBA, PE, SapABCDFZ, and HbpA-DppBCDF presented moonlighting properties related to resistance to antimicrobial peptides or glutathione import, together likely contributing to the NTHi-host airway interplay, as observed upon cultured airway epithelia and in vivo lung infection. The observed multi-functionality was shown to be system-specific, thus limiting redundancy. Together, we provide evidence for heme uptake systems as bacterial factors that act in a coordinated and multi-functional manner to subvert nutritional- and other sources of host innate immunity during NTHi airway infection.
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Affiliation(s)
| | - Tamim Al-Jubair
- Clinical Microbiology, Department of Translational Medicine, Faculty of Medicine, Lund University, Malmö, Sweden
- Department of Biomedical Sciences, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Begoña Euba
- Instituto de Agrobiotecnología, CSIC-Gobierno, Navarra, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), Madrid, Spain
| | | | | | - Sara Martí
- Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), Madrid, Spain
- Departamento Microbiología, Hospital Universitari Bellvitge, University of Barcelona, IDIBELL, Barcelona, Spain
| | - Susanna Törnroth-Horsefield
- Department of Biochemistry and Structural Biology, Center for Molecular Protein Science, Lund University, Lund, Sweden
| | - Kristian Riesbeck
- Clinical Microbiology, Department of Translational Medicine, Faculty of Medicine, Lund University, Malmö, Sweden
| | - Junkal Garmendia
- Instituto de Agrobiotecnología, CSIC-Gobierno, Navarra, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), Madrid, Spain
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11
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Molecular Basis of Unexpected Specificity of ABC Transporter-Associated Substrate-Binding Protein DppA from Helicobacter pylori. J Bacteriol 2019; 201:JB.00400-19. [PMID: 31358613 DOI: 10.1128/jb.00400-19] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Accepted: 07/22/2019] [Indexed: 12/16/2022] Open
Abstract
The gastric pathogen Helicobacter pylori has limited ability to use carbohydrates as a carbon source, relying instead on exogenous amino acids and peptides. Uptake of certain peptides by H. pylori requires an ATP binding cassette (ABC) transporter annotated dipeptide permease (Dpp). The transporter specificity is determined by its cognate substrate-binding protein DppA, which captures ligands in the periplasm and delivers them to the permease. Here, we show that, unlike previously characterized DppA proteins, H. pylori DppA binds, with micromolar affinity, peptides of diverse amino acid sequences ranging between two and eight residues in length. We present analysis of the 1.45-Å-resolution crystal structure of its complex with the tetrapeptide STSA, which provides a structural rationale for the observed broad specificity. Analysis of the molecular surface revealed a ligand-binding pocket that is large enough to accommodate peptides of up to nine residues in length. The structure suggests that H. pylori DppA is able to recognize a wide range of peptide sequences by forming interactions primarily with the peptide main chain atoms. The loop that terminates the peptide-binding pocket in DppAs from other bacteria is significantly shorter in the H. pylori protein, providing an explanation for its ability to bind longer peptides. The subsites accommodating the two N-terminal residues of the peptide ligand make the greatest contribution to the protein-ligand binding energy, in agreement with the observation that dipeptides bind with affinity close to that of longer peptides.IMPORTANCE The World Health Organization listed Helicobacter pylori as a high-priority pathogen for antibiotic development. The potential of using peptide transporters in drug design is well recognized. We discovered that the substrate-binding protein of the ABC transporter for peptides, termed dipeptide permease, is an unusual member of its family in that it directly binds peptides of diverse amino acid sequences, ranging between two and eight residues in length. We also provided a structural rationale for the observed broad specificity. Since the ability to import peptides as a source of carbon is critical for H. pylori, our findings will inform drug design strategies based on inhibition or fusion of membrane-impermeant antimicrobials with peptides.
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12
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Mitra A, Ko YH, Cingolani G, Niederweis M. Heme and hemoglobin utilization by Mycobacterium tuberculosis. Nat Commun 2019; 10:4260. [PMID: 31534126 PMCID: PMC6751184 DOI: 10.1038/s41467-019-12109-5] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Accepted: 08/21/2019] [Indexed: 12/31/2022] Open
Abstract
Iron is essential for growth of Mycobacterium tuberculosis (Mtb), but most iron in the human body is stored in heme within hemoglobin. Here, we demonstrate that the substrate-binding protein DppA of the inner membrane Dpp transporter is required for heme and hemoglobin utilization by Mtb. The 1.27 Å crystal structure of DppA shows a tetrapeptide bound in the protein core and a large solvent-exposed crevice for heme binding. Mutation of arginine 179 in this cleft eliminates heme binding to DppA and prevents heme utilization by Mtb. The outer membrane proteins PPE36 and PPE62 are also required for heme and hemoglobin utilization, indicating that these pathways converge at the cell surface of Mtb. Albumin, the most abundant blood protein, binds heme specifically and bypasses the requirements for PPE36, PPE62 and Dpp. Thus, our study reveals albumin-dependent and -independent heme uptake pathways, highlighting the importance of iron acquisition from heme for Mtb.
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Affiliation(s)
- Avishek Mitra
- Department of Microbiology, University of Alabama at Birmingham, 845 19th Street South, Birmingham, AL, 35294, USA
| | - Ying-Hui Ko
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, 233S. 10th Street, Philadelphia, PA, 19107, USA
| | - Gino Cingolani
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, 233S. 10th Street, Philadelphia, PA, 19107, USA. .,Institute of Biomembranes and Bioenergetics, National Research Council, Via Amendola 165/A, 70126, Bari, Italy.
| | - Michael Niederweis
- Department of Microbiology, University of Alabama at Birmingham, 845 19th Street South, Birmingham, AL, 35294, USA.
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Hughes A, Wilson S, Dodson EJ, Turkenburg JP, Wilkinson AJ. Crystal structure of the putative peptide-binding protein AppA from Clostridium difficile. Acta Crystallogr F Struct Biol Commun 2019; 75:246-253. [PMID: 30950825 PMCID: PMC6450515 DOI: 10.1107/s2053230x1900178x] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Accepted: 01/30/2019] [Indexed: 12/21/2022] Open
Abstract
Peptides play an important signalling role in Bacillus subtilis, where their uptake by one of two ABC-type oligopeptide transporters, Opp and App, is required for efficient sporulation. Homologues of these transporters in Clostridium difficile have been characterized, but their role, and hence that of peptides, in regulating sporulation in this organism is less clear. Here, the oligopeptide-binding receptor proteins for these transporters, CdAppA and CdOppA, have been purified and partially characterized, and the crystal structure of CdAppA has been determined in an open unliganded form. Peptide binding to either protein could not be observed in Thermofluor assays with a set of ten peptides of varying lengths and compositions. Re-examination of the protein sequences together with structure comparisons prompts the proposal that CdAppA is not a versatile peptide-binding protein but instead may bind a restricted set of peptides. Meanwhile, CdOppA is likely to be the receptor protein for a nickel-uptake system.
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Affiliation(s)
- Adam Hughes
- Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, England
| | - Samuel Wilson
- Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, England
| | - Eleanor J. Dodson
- Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, England
| | - Johan P. Turkenburg
- Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, England
| | - Anthony J. Wilkinson
- Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, England
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14
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Rahman MM, Machuca MA, Roujeinikova A. Preliminary X-ray crystallographic studies on the Helicobacter pylori ABC transporter glutamine-binding protein GlnH. Drug Discov Ther 2019; 13:52-58. [DOI: 10.5582/ddt.2019.01008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Mohammad M. Rahman
- Infection and Immunity Program, Monash Biomedicine Discovery Institute, Department of Microbiology, Monash University
| | - Mayra A. Machuca
- Infection and Immunity Program, Monash Biomedicine Discovery Institute, Department of Microbiology, Monash University
| | - Anna Roujeinikova
- Infection and Immunity Program, Monash Biomedicine Discovery Institute, Department of Microbiology, Monash University
- Department of Biochemistry and Molecular Biology, Monash University
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15
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Gangi Setty T, Mowers JC, Hobbs AG, Maiya SP, Syed S, Munson RS, Apicella MA, Subramanian R. Molecular characterization of the interaction of sialic acid with the periplasmic binding protein from Haemophilus ducreyi. J Biol Chem 2018; 293:20073-20084. [PMID: 30315109 DOI: 10.1074/jbc.ra118.005151] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Revised: 10/11/2018] [Indexed: 12/18/2022] Open
Abstract
The primary role of bacterial periplasmic binding proteins is sequestration of essential metabolites present at a low concentration in the periplasm and making them available for active transporters that transfer these ligands into the bacterial cell. The periplasmic binding proteins (SiaPs) from the tripartite ATP-independent periplasmic (TRAP) transport system that transports mammalian host-derived sialic acids have been well studied from different pathogenic bacteria, including Haemophilus influenzae, Fusobacterium nucleatum, Pasteurella multocida, and Vibrio cholerae SiaPs bind the sialic acid N-acetylneuraminic acid (Neu5Ac) with nanomolar affinity by forming electrostatic and hydrogen-bonding interactions. Here, we report the crystal structure of a periplasmic binding protein (SatA) of the ATP-binding cassette (ABC) transport system from the pathogenic bacterium Haemophilus ducreyi The structure of Hd-SatA in the native form and sialic acid-bound forms (with Neu5Ac and N-glycolylneuraminic acid (Neu5Gc)), determined to 2.2, 1.5, and 2.5 Å resolutions, respectively, revealed a ligand-binding site that is very different from those of the SiaPs of the TRAP transport system. A structural comparison along with thermodynamic studies suggested that similar affinities are achieved in the two classes of proteins through distinct mechanisms, one enthalpically driven and the other entropically driven. In summary, our structural and thermodynamic characterization of Hd-SatA reveals that it binds sialic acids with nanomolar affinity and that this binding is an entropically driven process. This information is important for future structure-based drug design against this pathogen and related bacteria.
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Affiliation(s)
- Thanuja Gangi Setty
- From the Institute for Stem Cell Biology and Regenerative Medicine, GKVK Post, Bangalore 560065, India,; the University of Trans-Disciplinary Health Sciences and Technology (TDU), Bengaluru, Karnataka 560064, India
| | - Jonathan C Mowers
- the Departments of Biochemistry and Carver College of Medicine, University of Iowa, Iowa City, Iowa 52242
| | - Aaron G Hobbs
- the Departments of Biochemistry and Carver College of Medicine, University of Iowa, Iowa City, Iowa 52242
| | - Shubha P Maiya
- From the Institute for Stem Cell Biology and Regenerative Medicine, GKVK Post, Bangalore 560065, India
| | - Sanaa Syed
- From the Institute for Stem Cell Biology and Regenerative Medicine, GKVK Post, Bangalore 560065, India
| | - Robert S Munson
- the Center for Microbial Interface Biology, Ohio State University, Columbus, Ohio 43210, and
| | - Michael A Apicella
- Microbiology and Immunology, Carver College of Medicine, University of Iowa, Iowa City, Iowa 52242
| | - Ramaswamy Subramanian
- From the Institute for Stem Cell Biology and Regenerative Medicine, GKVK Post, Bangalore 560065, India,; the Departments of Biochemistry and Carver College of Medicine, University of Iowa, Iowa City, Iowa 52242.
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Kuenzl T, Li-Blatter X, Srivastava P, Herdewijn P, Sharpe T, Panke S. Mutant Variants of the Substrate-Binding Protein DppA from Escherichia coli Enhance Growth on Nonstandard γ-Glutamyl Amide-Containing Peptides. Appl Environ Microbiol 2018; 84:e00340-18. [PMID: 29728377 PMCID: PMC6007095 DOI: 10.1128/aem.00340-18] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Accepted: 04/26/2018] [Indexed: 02/07/2023] Open
Abstract
The import of nonnatural molecules is a recurring problem in fundamental and applied aspects of microbiology. The dipeptide permease (Dpp) of Escherichia coli is an ABC-type multicomponent transporter system located in the cytoplasmic membrane, which is capable of transporting a wide range of di- and tripeptides with structurally and chemically diverse amino acid side chains into the cell. Given this low degree of specificity, Dpp was previously used as an entry gate to deliver natural and nonnatural cargo molecules into the cell by attaching them to amino acid side chains of peptides, in particular, the γ-carboxyl group of glutamate residues. However, the binding affinity of the substrate-binding protein dipeptide permease A (DppA), which is responsible for the initial binding of peptides in the periplasmic space, is significantly higher for peptides consisting of standard amino acids than for peptides containing side-chain modifications. Here, we used adaptive laboratory evolution to identify strains that utilize dipeptides containing γ-substituted glutamate residues more efficiently and linked this phenotype to different mutations in DppA. In vitro characterization of these mutants by thermal denaturation midpoint shift assays and isothermal titration calorimetry revealed significantly higher binding affinities of these variants toward peptides containing γ-glutamyl amides, presumably resulting in improved uptake and therefore faster growth in media supplemented with these nonstandard peptides.IMPORTANCE Fundamental and synthetic biology frequently suffer from insufficient delivery of unnatural building blocks or substrates for metabolic pathways into bacterial cells. The use of peptide-based transport vectors represents an established strategy to enable the uptake of such molecules as a cargo. We expand the scope of peptide-based uptake and characterize in detail the obtained DppA mutant variants. Furthermore, we highlight the potential of adaptive laboratory evolution to identify beneficial insertion mutations that are unlikely to be identified with existing directed evolution strategies.
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Affiliation(s)
- Tilmann Kuenzl
- Bioprocess Laboratory, Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | | | - Puneet Srivastava
- Laboratory of Medicinal Chemistry, Rega Institute for Medical Research, KU Leuven, Leuven, Belgium
| | - Piet Herdewijn
- Laboratory of Medicinal Chemistry, Rega Institute for Medical Research, KU Leuven, Leuven, Belgium
| | - Timothy Sharpe
- Biophysics Facility, Biozentrum, University of Basel, Basel, Switzerland
| | - Sven Panke
- Bioprocess Laboratory, Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
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Open Conformation of the Escherichia coli Periplasmic Murein Tripeptide Binding Protein, MppA, at High Resolution. BIOLOGY 2018; 7:biology7020030. [PMID: 29783769 PMCID: PMC6022919 DOI: 10.3390/biology7020030] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Revised: 05/11/2018] [Accepted: 05/11/2018] [Indexed: 01/28/2023]
Abstract
Periplasmic ligand-binding proteins (PBPs) bind ligands with a high affinity and specificity. They undergo a large conformational change upon ligand binding, and they have a robust protein fold. These physical features have made them ideal candidates for use in protein engineering projects to develop novel biosensors and signaling molecules. The Escherichia coli MppA (murein peptide permease A) PBP binds the murein tripeptide, l-alanyl-γ-d-glutamyl-meso-diaminopimelate, (l-Ala-γ-d-Glu-meso-Dap), which contains both a D-amino acid and a gamma linkage between two of the amino acids. We have solved a high-resolution X-ray crystal structure of E. coli MppA at 1.5 Å resolution in the unliganded, open conformation. Now, structures are available for this member of the PBP protein family in both the liganded/closed form and the unliganded/open form.
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18
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Kuenzl T, Sroka M, Srivastava P, Herdewijn P, Marlière P, Panke S. Overcoming the membrane barrier: Recruitment of γ-glutamyl transferase for intracellular release of metabolic cargo from peptide vectors. Metab Eng 2017; 39:60-70. [DOI: 10.1016/j.ymben.2016.10.016] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Revised: 09/21/2016] [Accepted: 10/25/2016] [Indexed: 11/25/2022]
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Kurkcuoglu Z, Doruker P. Ligand Docking to Intermediate and Close-To-Bound Conformers Generated by an Elastic Network Model Based Algorithm for Highly Flexible Proteins. PLoS One 2016; 11:e0158063. [PMID: 27348230 PMCID: PMC4922591 DOI: 10.1371/journal.pone.0158063] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2016] [Accepted: 06/09/2016] [Indexed: 01/03/2023] Open
Abstract
Incorporating receptor flexibility in small ligand-protein docking still poses a challenge for proteins undergoing large conformational changes. In the absence of bound structures, sampling conformers that are accessible by apo state may facilitate docking and drug design studies. For this aim, we developed an unbiased conformational search algorithm, by integrating global modes from elastic network model, clustering and energy minimization with implicit solvation. Our dataset consists of five diverse proteins with apo to complex RMSDs 4.7-15 Å. Applying this iterative algorithm on apo structures, conformers close to the bound-state (RMSD 1.4-3.8 Å), as well as the intermediate states were generated. Dockings to a sequence of conformers consisting of a closed structure and its "parents" up to the apo were performed to compare binding poses on different states of the receptor. For two periplasmic binding proteins and biotin carboxylase that exhibit hinge-type closure of two dynamics domains, the best pose was obtained for the conformer closest to the bound structure (ligand RMSDs 1.5-2 Å). In contrast, the best pose for adenylate kinase corresponded to an intermediate state with partially closed LID domain and open NMP domain, in line with recent studies (ligand RMSD 2.9 Å). The docking of a helical peptide to calmodulin was the most challenging case due to the complexity of its 15 Å transition, for which a two-stage procedure was necessary. The technique was first applied on the extended calmodulin to generate intermediate conformers; then peptide docking and a second generation stage on the complex were performed, which in turn yielded a final peptide RMSD of 2.9 Å. Our algorithm is effective in producing conformational states based on the apo state. This study underlines the importance of such intermediate states for ligand docking to proteins undergoing large transitions.
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Affiliation(s)
- Zeynep Kurkcuoglu
- Department of Chemical Engineering and Polymer Research Center, Bogazici University, Bebek, Istanbul, 34342, Turkey
- * E-mail: (ZK); (PD)
| | - Pemra Doruker
- Department of Chemical Engineering and Polymer Research Center, Bogazici University, Bebek, Istanbul, 34342, Turkey
- * E-mail: (ZK); (PD)
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20
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El Sahili A, Li SZ, Lang J, Virus C, Planamente S, Ahmar M, Guimaraes BG, Aumont-Nicaise M, Vigouroux A, Soulère L, Reader J, Queneau Y, Faure D, Moréra S. A Pyranose-2-Phosphate Motif Is Responsible for Both Antibiotic Import and Quorum-Sensing Regulation in Agrobacterium tumefaciens. PLoS Pathog 2015; 11:e1005071. [PMID: 26244338 PMCID: PMC4526662 DOI: 10.1371/journal.ppat.1005071] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2015] [Accepted: 07/06/2015] [Indexed: 11/18/2022] Open
Abstract
Periplasmic binding proteins (PBPs) in association with ABC transporters select and import a wide variety of ligands into bacterial cytoplasm. They can also take up toxic molecules, as observed in the case of the phytopathogen Agrobacterium tumefaciens strain C58. This organism contains a PBP called AccA that mediates the import of the antibiotic agrocin 84, as well as the opine agrocinopine A that acts as both a nutrient and a signalling molecule for the dissemination of virulence genes through quorum-sensing. Here, we characterized the binding mode of AccA using purified agrocin 84 and synthetic agrocinopine A by X-ray crystallography at very high resolution and performed affinity measurements. Structural and affinity analyses revealed that AccA recognizes an uncommon and specific motif, a pyranose-2-phosphate moiety which is present in both imported molecules via the L-arabinopyranose moiety in agrocinopine A and the D-glucopyranose moiety in agrocin 84. We hypothesized that AccA is a gateway allowing the import of any compound possessing a pyranose-2-phosphate motif at one end. This was structurally and functionally confirmed by experiments using four synthetic compounds: agrocinopine 3'-O-benzoate, L-arabinose-2-isopropylphosphate, L-arabinose-2-phosphate and D-glucose-2-phosphate. By combining affinity measurements and in vivo assays, we demonstrated that both L-arabinose-2-phosphate and D-glucose-2-phosphate, which are the AccF mediated degradation products of agrocinopine A and agrocin 84 respectively, interact with the master transcriptional regulator AccR and activate the quorum-sensing signal synthesis and Ti plasmid transfer in A. tumefaciens C58. Our findings shed light on the role of agrocinopine and antibiotic agrocin 84 on quorum-sensing regulation in A. tumefaciens and reveal how the PBP AccA acts as vehicle for the importation of both molecules by means of a key-recognition motif. It also opens future possibilities for the rational design of antibiotic and anti-virulence compounds against A. tumefaciens or other pathogens possessing similar PBPs.
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Affiliation(s)
- Abbas El Sahili
- Institute for Integrative Biology of the Cell (I2BC), Department of Biophysics, Biochemistry and Structural Biology, CNRS CEA University Paris-Sud, Gif-sur-Yvette, France
- Institute for Integrative Biology of the Cell (I2BC), Department of Microbiology, CNRS CEA University Paris-Sud, Gif-sur-Yvette, France
| | - Si-Zhe Li
- Institut de Chimie et de Biochimie Moléculaires et Supramoléculaires, ICBMS, Université de Lyon, INSA Lyon, UMR 5246, CNRS, Université Lyon 1, INSA Lyon, CPE-Lyon, Bât J. Verne, Villeurbanne, France
| | - Julien Lang
- Institute for Integrative Biology of the Cell (I2BC), Department of Microbiology, CNRS CEA University Paris-Sud, Gif-sur-Yvette, France
| | - Cornelia Virus
- Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Sara Planamente
- Institute for Integrative Biology of the Cell (I2BC), Department of Biophysics, Biochemistry and Structural Biology, CNRS CEA University Paris-Sud, Gif-sur-Yvette, France
- Institute for Integrative Biology of the Cell (I2BC), Department of Microbiology, CNRS CEA University Paris-Sud, Gif-sur-Yvette, France
| | - Mohammed Ahmar
- Institut de Chimie et de Biochimie Moléculaires et Supramoléculaires, ICBMS, Université de Lyon, INSA Lyon, UMR 5246, CNRS, Université Lyon 1, INSA Lyon, CPE-Lyon, Bât J. Verne, Villeurbanne, France
| | | | - Magali Aumont-Nicaise
- Institute for Integrative Biology of the Cell (I2BC), Protein-Protein Interaction Platform, CNRS CEA University Paris-Sud, Orsay, France
| | - Armelle Vigouroux
- Institute for Integrative Biology of the Cell (I2BC), Department of Biophysics, Biochemistry and Structural Biology, CNRS CEA University Paris-Sud, Gif-sur-Yvette, France
| | - Laurent Soulère
- Institut de Chimie et de Biochimie Moléculaires et Supramoléculaires, ICBMS, Université de Lyon, INSA Lyon, UMR 5246, CNRS, Université Lyon 1, INSA Lyon, CPE-Lyon, Bât J. Verne, Villeurbanne, France
| | - John Reader
- Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Yves Queneau
- Institut de Chimie et de Biochimie Moléculaires et Supramoléculaires, ICBMS, Université de Lyon, INSA Lyon, UMR 5246, CNRS, Université Lyon 1, INSA Lyon, CPE-Lyon, Bât J. Verne, Villeurbanne, France
- * E-mail: (YQ); (DF); (SM)
| | - Denis Faure
- Institute for Integrative Biology of the Cell (I2BC), Department of Microbiology, CNRS CEA University Paris-Sud, Gif-sur-Yvette, France
- * E-mail: (YQ); (DF); (SM)
| | - Solange Moréra
- Institute for Integrative Biology of the Cell (I2BC), Department of Biophysics, Biochemistry and Structural Biology, CNRS CEA University Paris-Sud, Gif-sur-Yvette, France
- * E-mail: (YQ); (DF); (SM)
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McKinney DC, Bezdenejnih-Snyder N, Farrington K, Guo J, McLaughlin RE, Ruvinsky AM, Singh R, Basarab GS, Narayan S, Buurman ET. Illicit Transport via Dipeptide Transporter Dpp is Irrelevant to the Efficacy of Negamycin in Mouse Thigh Models of Escherichia coli Infection. ACS Infect Dis 2015; 1:222-30. [PMID: 27622650 DOI: 10.1021/acsinfecdis.5b00027] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Negamycin is a hydrophilic antimicrobial translation inhibitor that crosses the lipophilic inner membrane of Escherichia coli via at least two transport routes to reach its intracellular target. In a minimal salts medium, negamycin's peptidic nature allows illicit entry via a high-affinity route by hijacking the Dpp dipeptide transporter. Transport via a second, low-affinity route is energetically driven by the membrane potential, seemingly without the direct involvement of a transport protein. In mouse thigh models of E. coli infection, no evidence for Dpp-mediated transport of negamycin was found. The implication is that for the design of new negamycin-based analogs, the physicochemical properties required for cell entry via the low-affinity route need to be retained to achieve clinical success in the treatment of infectious diseases. Furthermore, clinical resistance to such analogs due to mutations affecting their ribosomal target or transport is expected to be rare and similar to that of aminoglycosides.
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Affiliation(s)
- David C. McKinney
- Departments of Chemistry, ‡Biosciences, and §Drug Metabolism and Pharmacokinetics, Infection Innovative Medicines Unit, AstraZeneca R&D Boston, 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States
| | - Natascha Bezdenejnih-Snyder
- Departments of Chemistry, ‡Biosciences, and §Drug Metabolism and Pharmacokinetics, Infection Innovative Medicines Unit, AstraZeneca R&D Boston, 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States
| | - Krista Farrington
- Departments of Chemistry, ‡Biosciences, and §Drug Metabolism and Pharmacokinetics, Infection Innovative Medicines Unit, AstraZeneca R&D Boston, 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States
| | - Jian Guo
- Departments of Chemistry, ‡Biosciences, and §Drug Metabolism and Pharmacokinetics, Infection Innovative Medicines Unit, AstraZeneca R&D Boston, 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States
| | - Robert E. McLaughlin
- Departments of Chemistry, ‡Biosciences, and §Drug Metabolism and Pharmacokinetics, Infection Innovative Medicines Unit, AstraZeneca R&D Boston, 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States
| | - Anatoly M. Ruvinsky
- Departments of Chemistry, ‡Biosciences, and §Drug Metabolism and Pharmacokinetics, Infection Innovative Medicines Unit, AstraZeneca R&D Boston, 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States
| | - Renu Singh
- Departments of Chemistry, ‡Biosciences, and §Drug Metabolism and Pharmacokinetics, Infection Innovative Medicines Unit, AstraZeneca R&D Boston, 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States
| | - Gregory S. Basarab
- Departments of Chemistry, ‡Biosciences, and §Drug Metabolism and Pharmacokinetics, Infection Innovative Medicines Unit, AstraZeneca R&D Boston, 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States
| | - Sridhar Narayan
- Departments of Chemistry, ‡Biosciences, and §Drug Metabolism and Pharmacokinetics, Infection Innovative Medicines Unit, AstraZeneca R&D Boston, 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States
| | - Ed T. Buurman
- Departments of Chemistry, ‡Biosciences, and §Drug Metabolism and Pharmacokinetics, Infection Innovative Medicines Unit, AstraZeneca R&D Boston, 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States
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Structural insights into the multispecific recognition of dipeptides of deep-sea gram-negative bacterium Pseudoalteromonas sp. strain SM9913. J Bacteriol 2015; 197:1125-34. [PMID: 25605306 DOI: 10.1128/jb.02600-14] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED Peptide uptake is important for nutrition supply for marine bacteria. It is also an important step in marine nitrogen cycling. However, how marine bacteria absorb peptides is still not fully understood. DppA is the periplasmic dipeptide binding protein of dipeptide permease (Dpp; an important peptide transporter in bacteria) and exclusively controls the substrate specificity of Dpp. Here, the substrate binding specificity of deep-sea Pseudoalteromonas sp. strain SM9913 DppA (PsDppA) was analyzed for 25 different dipeptides with various properties by using isothermal titration calorimetry measurements. PsDppA showed binding affinities for 8 dipeptides. To explain the multispecific substrate recognition mechanism of PsDppA, we solved the crystal structures of unliganded PsDppA and of PsDppA in complex with 4 different types of dipeptides (Ala-Phe, Met-Leu, Gly-Glu, and Val-Thr). PsDppA alternates between an "open" and a "closed" form during substrate binding. Structural analyses of the 4 PsDppA-substrate complexes combined with mutational assays indicate that PsDppA binds to different substrates through a precise mechanism: dipeptides are bound mainly by the interactions between their backbones and PsDppA, in particular by anchoring their N and C termini through ion-pair interactions; hydrophobic interactions are important in binding hydrophobic dipeptides; and Lys457 is necessary for the binding of dipeptides with a C-terminal glutamic acid or glutamine. Additionally, sequence alignment suggests that the substrate recognition mechanism of PsDppA may be common in Gram-negative bacteria. All together, our results provide structural insights into the multispecific substrate recognition mechanism of marine Gram-negative bacterial DppA, which provides a better understanding of the mechanisms of marine bacterial peptide uptake. IMPORTANCE Peptide uptake plays a significant role in nutrition supply for marine bacteria. It is also an important step in marine nitrogen cycling. However, how marine bacteria recognize and absorb peptides is still unclear. This study analyzed the substrate binding specificity of deep-sea Pseudoalteromonas sp. strain SM9913 DppA (PsDppA; the dipeptide-binding protein of dipeptide permease) and solved the crystal structures of unliganded PsDppA and PsDppA in complex with 4 different types of dipeptides. The multispecific recognition mechanism of PsDppA for dipeptides is explained based on structural and mutational analyses. We also find that the substrate-binding mechanism of PsDppA may be common in Gram-negative bacteria. This study sheds light on marine Gram-negative bacterial peptide uptake and marine nitrogen cycling.
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Pletzer D, Lafon C, Braun Y, Köhler T, Page MGP, Mourez M, Weingart H. High-throughput screening of dipeptide utilization mediated by the ABC transporter DppBCDF and its substrate-binding proteins DppA1-A5 in Pseudomonas aeruginosa. PLoS One 2014; 9:e111311. [PMID: 25338022 PMCID: PMC4206461 DOI: 10.1371/journal.pone.0111311] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2014] [Accepted: 09/23/2014] [Indexed: 11/18/2022] Open
Abstract
In this study, we show that the dppBCDF operon of Pseudomonas aeruginosa PA14 encodes an ABC transporter responsible for the utilization of di/tripeptides. The substrate specificity of ABC transporters is determined by its associated substrate-binding proteins (SBPs). Whereas in E. coli only one protein, DppA, determines the specificity of the transporter, five orthologous SBPs, DppA1-A5 are present in P. aeruginosa. Multiple SBPs might broaden the substrate specificity by increasing the transporter capacity. We utilized the Biolog phenotype MicroArray technology to investigate utilization of di/tripeptides in mutants lacking either the transport machinery or all of the five SBPs. This high-throughput method enabled us to screen hundreds of dipeptides with various side-chains, and subsequently, to determine the substrate profile of the dipeptide permease. The substrate spectrum of the SBPs was elucidated by complementation of a penta mutant, deficient of all five SBPs, with plasmids carrying individual SBPs. It became apparent that some dipeptides were utilized with different affinity for each SBP. We found that DppA2 shows the highest flexibility on substrate recognition and that DppA2 and DppA4 have a higher tendency to utilize tripeptides. DppA5 was not able to complement the penta mutant under our screening conditions. Phaseolotoxin, a toxic tripeptide inhibiting the enzyme ornithine carbamoyltransferase, is also transported into P. aeruginosa via the DppBCDF permease. The SBP DppA1, and with much greater extend DppA3, are responsible for delivering the toxin to the permease. Our results provide a first overview of the substrate pattern of the ABC dipeptide transport machinery in P. aeruginosa.
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Affiliation(s)
- Daniel Pletzer
- Jacobs University Bremen, School of Engineering and Science, Bremen, Germany
| | - Corinne Lafon
- Sanofi-Aventis R&D, Infectious Diseases Therapeutic Unit, Toulouse, France
| | - Yvonne Braun
- Jacobs University Bremen, School of Engineering and Science, Bremen, Germany
| | - Thilo Köhler
- Department of Microbiology and Molecular Medicine and Service of Infectious Diseases, University Hospital Geneva, Geneva, Switzerland
| | | | - Michael Mourez
- Sanofi-Aventis R&D, Infectious Diseases Therapeutic Unit, Toulouse, France
| | - Helge Weingart
- Jacobs University Bremen, School of Engineering and Science, Bremen, Germany
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Giaouris E, Samoilis G, Chorianopoulos N, Ercolini D, Nychas GJ. Differential protein expression patterns between planktonic and biofilm cells of Salmonella enterica serovar Enteritidis PT4 on stainless steel surface. Int J Food Microbiol 2013; 162:105-13. [PMID: 23376784 DOI: 10.1016/j.ijfoodmicro.2012.12.023] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2012] [Revised: 12/27/2012] [Accepted: 12/28/2012] [Indexed: 10/27/2022]
Abstract
In the present study, the proteome of a strain of S. enterica serovar Enteritidis PT4, grown either as biofilm on stainless steel surface or as free-floating (planktonic) in Brain Heart (BH) broth, was investigated in order to detect the strong differences in whole-cell protein expression patterns between the two growth styles. The proteins extracted from both types of cells were subjected to 2-D PAGE, followed by in-gel tryptic digestion, extraction, subsequent MALDI-TOF mass spectrometry (MS) analysis and finally database searches for protein identification. Using this approach, 30 proteins were identified as differentially expressed between the two growth modes on an "on-off" basis, that is, proteins that were detected in one case but not in the other. In particular, 20 and 10 proteins were identified in biofilm and planktonic-grown cells, respectively. The group of proteins whose expression was visible only during biofilm growth included proteins involved in global regulation and stress response (ArcA, BtuE, Dps, OsmY, SspA, TrxA, YbbN and YhbO), nutrient transport (Crr, DppA, Fur and SufC), degradation and energy metabolism (GcvT, GpmA, RibB), detoxification (SseA and YibF), DNA metabolism (SSB), curli production (CsgF), and murein synthesis (MipA). To summarize, this study demonstrates that biofilm growth of S. Enteritidis causes distinct changes in protein expression and offers valuable new data regarding some of the proteins presumably involved in this process. The putative role of these proteins in the maintenance of a biofilm community in Salmonella and other bacteria is discussed.
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Affiliation(s)
- Efstathios Giaouris
- Department of Food Science and Nutrition, University of the Aegean, Mitropoliti Ioakeim 2, Myrina, 81400 Lemnos, Greece.
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25
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Lassaux P, Peri C, Ferrer-Navarro M, Gourlay LJ, Gori A, Conchillo-Solé O, Rinchai D, Lertmemongkolchai G, Longhi R, Daura X, Colombo G, Bolognesi M. A structure-based strategy for epitope discovery in Burkholderia pseudomallei OppA antigen. Structure 2012; 21:167-175. [PMID: 23159127 DOI: 10.1016/j.str.2012.10.005] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2012] [Revised: 09/10/2012] [Accepted: 10/04/2012] [Indexed: 10/27/2022]
Abstract
We present an approach integrating structural and computational biology with immunological tests to identify epitopes in the OppA antigen from the Gram-negative pathogen Burkholderia pseudomallei, the etiological agent of melioidosis. The crystal structure of OppA(Bp), reported here at 2.1 Å resolution, was the basis for a computational analysis that identified three potential epitopes. In parallel, antigen proteolysis and immunocapturing allowed us to identify three additional peptides. All six potential epitopes were synthesized as free peptides and tested for their immunoreactivity against sera from healthy seronegative, healthy seropositive, and recovered melioidosis patients. Three synthetic peptides allowed the different patient groups to be distinguished, underlining the potential of this approach. Extension of the computational analysis, including energy-based decomposition methods, allowed rationalizing results of the predictive analyses and the immunocapture epitope mapping. Our results illustrate a structure-based epitope discovery process, whose application may expand our perspectives in the diagnostic and vaccine design fields.
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Affiliation(s)
- Patricia Lassaux
- Department of Biosciences, University of Milan, Milan 20133, Italy
| | - Claudio Peri
- Consiglio Nazionale delle Ricerche, Institute for Chemistry of Molecular Recognition, Department of Computational Biology, Milan 20131, Italy
| | - Mario Ferrer-Navarro
- Institute of Biotechnology and Biomedicine, Universitat Autònoma de Barcelona, Bellaterra 08193, Spain
| | - Louise J Gourlay
- Department of Biosciences, University of Milan, Milan 20133, Italy
| | - Alessandro Gori
- Consiglio Nazionale delle Ricerche, Institute for Chemistry of Molecular Recognition, Department of Computational Biology, Milan 20131, Italy
| | - Oscar Conchillo-Solé
- Institute of Biotechnology and Biomedicine, Universitat Autònoma de Barcelona, Bellaterra 08193, Spain
| | - Darawan Rinchai
- Center for Research and Development of Medical Diagnostic Laboratories, Faculty of Associated Medical Sciences, Khon Kaen University, Khon Kaen 40002, Thailand
| | - Ganjana Lertmemongkolchai
- Center for Research and Development of Medical Diagnostic Laboratories, Faculty of Associated Medical Sciences, Khon Kaen University, Khon Kaen 40002, Thailand
| | - Renato Longhi
- Consiglio Nazionale delle Ricerche, Institute for Chemistry of Molecular Recognition, Department of Computational Biology, Milan 20131, Italy
| | - Xavier Daura
- Institute of Biotechnology and Biomedicine, Universitat Autònoma de Barcelona, Bellaterra 08193, Spain; Catalan Institution for Research and Advanced Studies, Barcelona 08010, Spain
| | - Giorgio Colombo
- Consiglio Nazionale delle Ricerche, Institute for Chemistry of Molecular Recognition, Department of Computational Biology, Milan 20131, Italy.
| | - Martino Bolognesi
- Department of Biosciences, University of Milan, Milan 20133, Italy; Consiglio Nazionale delle Ricerche, Institute of Biophysics, University of Milan, Milan 20133, Italy.
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Suenaga A, Okimoto N, Hirano Y, Fukui K. An efficient computational method for calculating ligand binding affinities. PLoS One 2012; 7:e42846. [PMID: 22916168 PMCID: PMC3423425 DOI: 10.1371/journal.pone.0042846] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2012] [Accepted: 07/12/2012] [Indexed: 11/19/2022] Open
Abstract
Virtual compound screening using molecular docking is widely used in the discovery of new lead compounds for drug design. However, the docking scores are not sufficiently precise to represent the protein-ligand binding affinity. Here, we developed an efficient computational method for calculating protein-ligand binding affinity, which is based on molecular mechanics generalized Born/surface area (MM-GBSA) calculations and Jarzynski identity. Jarzynski identity is an exact relation between free energy differences and the work done through non-equilibrium process, and MM-GBSA is a semimacroscopic approach to calculate the potential energy. To calculate the work distribution when a ligand is pulled out of its binding site, multiple protein-ligand conformations are randomly generated as an alternative to performing an explicit single-molecule pulling simulation. We assessed the new method, multiple random conformation/MM-GBSA (MRC-MMGBSA), by evaluating ligand-binding affinities (scores) for four target proteins, and comparing these scores with experimental data. The calculated scores were qualitatively in good agreement with the experimental binding affinities, and the optimal docking structure could be determined by ranking the scores of the multiple docking poses obtained by the molecular docking process. Furthermore, the scores showed a strong linear response to experimental binding free energies, so that the free energy difference of the ligand binding (ΔΔG) could be calculated by linear scaling of the scores. The error of calculated ΔΔG was within ≈ ± 1.5 kcal.mol(-1) of the experimental values. Particularly, in the case of flexible target proteins, the MRC-MMGBSA scores were more effective in ranking ligands than those generated by the MM-GBSA method using a single protein-ligand conformation. The results suggest that, owing to its lower computational costs and greater accuracy, the MRC-MMGBSA offers efficient means to rank the ligands, in the post-docking process, according to their binding affinities, and to compare these directly with the experimental values.
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Affiliation(s)
- Atsushi Suenaga
- Computational Biology Research Center, National Institute of Advanced Industrial Science and Technology, Koto-ku, Tokyo, Japan.
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Chivers PT, Benanti EL, Heil-Chapdelaine V, Iwig JS, Rowe JL. Identification of Ni-(L-His)₂ as a substrate for NikABCDE-dependent nickel uptake in Escherichia coli. Metallomics 2012; 4:1043-50. [PMID: 22885853 DOI: 10.1039/c2mt20139a] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Nickel is an important cofactor for several microbial enzymes. The ATP-dependent NikABCDE transporter is one of several types of uptake pathways known to be important for nickel acquisition in microbes. The Escherichia coli NikA periplasmic binding protein is structurally homologous to the di- and oligopeptide binding proteins, DppA and OppA. This structural similarity raises interesting questions regarding the evolutionary relationships between the recognition of nickel ions and short peptides. We find that in defined minimal growth medium NikABCDE transports nickel ions in the presence of exogenously added L-histidine (L-His), but not D-histidine. Both nickel uptake in cells and nickel binding to purified NikA showed an L-His concentration dependence consistent with recognition of a Ni-(L-His)₂ complex. This discovery reveals parallels to the transport of other metal complexes, notably iron, and suggests the structural diversity of nickel transporters may arise from the need to recognize extracellular nickel complexed with different organic ligands, whether they be exogenously or endogenously produced. Further, these results suggest that experiments examining the physiology and ecology of nickel-requiring microbes should account for the possibility that the growth medium may not support nickel uptake.
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Affiliation(s)
- Peter T Chivers
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110, USA.
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Vergauwen B, Van der Meeren R, Dansercoer A, Savvides SN. Delineation of the Pasteurellaceae-specific GbpA-family of glutathione-binding proteins. BMC BIOCHEMISTRY 2011; 12:59. [PMID: 22087650 PMCID: PMC3295651 DOI: 10.1186/1471-2091-12-59] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/12/2011] [Accepted: 11/16/2011] [Indexed: 01/27/2023]
Abstract
BACKGROUND The Gram-negative bacterium Haemophilus influenzae is a glutathione auxotroph and acquires the redox-active tripeptide by import. The dedicated glutathione transporter belongs to the ATP-binding cassette (ABC)-transporter superfamily and displays more than 60% overall sequence identity with the well-studied dipeptide (Dpp) permease of Escherichia coli. The solute binding protein (SBP) that mediates glutathione transport in H. influenzae is a lipoprotein termed GbpA and is 54% identical to E. coli DppA, a well-studied member of family 5 SBP's. The discovery linking GbpA to glutathione import came rather unexpectedly as this import-priming SBP was previously annotated as a heme-binding protein (HbpA), and was thought to mediate heme acquisition. Nonetheless, although many SBP's have been implicated in more than one function, a prominent physiological role for GbpA and its partner permease in heme acquisition appears to be very unlikely. Here, we sought to characterize five representative GbpA homologs in an effort to delineate the novel GbpA-family of glutathione-specific family 5 SBPs and to further clarify their functional role in terms of ligand preferences. RESULTS Lipoprotein and non-lipoprotein GbpA homologs were expressed in soluble form and substrate specificity was evaluated via a number of ligand binding assays. A physiologically insignificant affinity for hemin was observed for all five GbpA homologous test proteins. Three out of five test proteins were found to bind glutathione and some of its physiologically relevant derivatives with low- or submicromolar affinity. None of the tested SBP family 5 allocrites interacted with the remaining two GbpA test proteins. Structure-based sequence alignments and phylogenetic analysis show that the two binding-inert GbpA homologs clearly form a separate phylogenetic cluster. To elucidate a structure-function rationale for this phylogenetic differentiation, we determined the crystal structure of one of the GbpA family outliers from H. parasuis. Comparisons thereof with the previously determined structure of GbpA in complex with oxidized glutathione reveals the structural basis for the lack of allocrite binding capacity, thereby explaining the outlier behavior. CONCLUSIONS Taken together, our studies provide for the first time a collective functional look on a novel, Pasteurellaceae-specific, SBP subfamily of glutathione binding proteins, which we now term GbpA proteins. Our studies strongly implicate GbpA family SBPs in the priming step of ABC-transporter-mediated translocation of useful forms of glutathione across the inner membrane, and rule out a general role for GbpA proteins in heme acquisition.
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Affiliation(s)
- Bjorn Vergauwen
- Unit for Structural Biology, Laboratory for Protein Biochemistry and Biomolecular Engineering, Department of Biochemistry and Microbiology, Ghent University, 9000 Ghent, Belgium.
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Maqbool A, Levdikov VM, Blagova EV, Hervé M, Horler RSP, Wilkinson AJ, Thomas GH. Compensating stereochemical changes allow murein tripeptide to be accommodated in a conventional peptide-binding protein. J Biol Chem 2011; 286:31512-21. [PMID: 21705338 PMCID: PMC3173086 DOI: 10.1074/jbc.m111.267179] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The oligopeptide permease (Opp) of Escherichia coli is an ATP-binding cassette transporter that uses the substrate-binding protein (SBP) OppA to bind peptides and deliver them to the membrane components (OppBCDF) for transport. OppA binds conventional peptides 2-5 residues in length regardless of their sequence, but does not facilitate transport of the cell wall component murein tripeptide (Mtp, L-Ala-γ-D-Glu-meso-Dap), which contains a D-amino acid and a γ-peptide linkage. Instead, MppA, a homologous substrate-binding protein, forms a functional transporter with OppBCDF for uptake of this unusual tripeptide. Here we have purified MppA and demonstrated biochemically that it binds Mtp with high affinity (K(D) ∼ 250 nM). The crystal structure of MppA in complex with Mtp has revealed that Mtp is bound in a relatively extended conformation with its three carboxylates projecting from one side of the molecule and its two amino groups projecting from the opposite face. Specificity for Mtp is conferred by charge-charge and dipole-charge interactions with ionic and polar residues of MppA. Comparison of the structure of MppA-Mtp with structures of conventional tripeptides bound to OppA, reveals that the peptide ligands superimpose remarkably closely given the profound differences in their structures. Strikingly, the effect of the D-stereochemistry, which projects the side chain of the D-Glu residue at position 2 in the direction of the main chain in a conventional tripeptide, is compensated by the formation of a γ-linkage to the amino group of diaminopimelic acid, mimicking the peptide bond between residues 2 and 3 of a conventional tripeptide.
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Affiliation(s)
- Abbas Maqbool
- Department of Biology (Area 10), University of York, York YO10 5YW, United Kingdom
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Heme utilization by nontypeable Haemophilus influenzae is essential and dependent on Sap transporter function. J Bacteriol 2011; 193:2527-35. [PMID: 21441512 DOI: 10.1128/jb.01313-10] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Bacterial strategies of innate immune evasion and essential metabolic functions are critical for commensal-host homeostasis. Previously, we showed that Sap translocator function is necessary for nontypeable Haemophilus influenzae (NTHI) behaviors that mediate diseases of the human airway. Antimicrobial peptide (AP) lethality is limited by binding mediated by the Sap complex. SapA shares homology with the dipeptide-binding protein (DppA) and the heme-binding lipoprotein (HbpA), both of which have previously been shown to bind the iron-containing compound heme, whose acquisition is essential for Haemophilus survival. Computational modeling revealed conserved SapA residues, similarly modeled to mediate heme binding in HbpA. Here, we directly demonstrate that SapA bound heme and was essential for heme utilization by iron-starved NTHI. Further, the Sap translocator permease mediated heme transport into the bacterial cytoplasm, thus defining a heretofore unknown mechanism of intracytoplasmic membrane heme transport in Haemophilus. Since we demonstrate multiple ligand specificity for the SapA-binding protein, we tested whether APs would compete with heme for SapA binding. We showed that human β-defensins 2 and 3, human cathelicidin LL-37, human neutrophil protein 1, and melittin displaced heme bound to SapA, thus supporting a hierarchy wherein immune evasion supercedes even the needed iron acquisition functions of the Sap system.
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Domains III and I-2{alpha}, at the entrance of the binding cleft, play an important role in cold adaptation of the periplasmic dipeptide-binding protein (DppA) from the deep-sea psychrophilic bacterium Pseudoalteromonas sp. strain SM9913. Appl Environ Microbiol 2010; 76:4354-61. [PMID: 20453143 DOI: 10.1128/aem.02884-09] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The peptide transporter from a cold-adapted bacterium has never been reported. In the present study, the dpp operon from the psychrophilic bacterium Pseudoalteromonas sp. strain SM9913 was cloned and analyzed. The dipeptide binding protein DppA of SM9913 was overexpressed in Escherichia coli, and its cold adaptation characteristics were studied. The recombinant DppA of SM9913 (PsDppA) displayed the highest ligand-binding affinity at 15 degrees C, whereas the recombinant DppA of E. coli (EcDppA) displayed the highest ligand-binding affinity at 35 degrees C. Thermal and guanidium hydrochloride unfolding analyses indicated that PsDppA has more structural instability than EcDppA. Six domain-exchanged mutants of PsDppA were expressed and purified. Analyses of these mutants indicated that domains III, I-2, and I-3 of PsDppA were less stable than those from EcDppA and that domains III and I-2 made a significant contribution to the high binding affinity of PsDppA at low temperatures. Structural and sequence analyses suggested that the state transition-involved regions in domain III and the alpha part of domain I-2 are the hot spots of optimization during cold adaptation and that decreasing the side-chain size in these regions is an important strategy for the cold adaptation of PsDppA.
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Repellent taxis in response to nickel ion requires neither Ni2+ transport nor the periplasmic NikA binding protein. J Bacteriol 2010; 192:2633-7. [PMID: 20233931 DOI: 10.1128/jb.00854-09] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Ni(2+) and Co(2+) are sensed as repellents by the Escherichia coli Tar chemoreceptor. The periplasmic Ni(2+) binding protein, NikA, has been suggested to sense Ni(2+). We show here that neither NikA nor the membrane-bound NikB and NikC proteins of the Ni(2+) transport system are required for repellent taxis in response to Ni(2+).
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Mackenzie AK, Valegård K, Iqbal A, Caines ME, Kershaw NJ, Jensen SE, Schofield CJ, Andersson I. Crystal Structures of an Oligopeptide-Binding Protein from the Biosynthetic Pathway of the β-Lactamase Inhibitor Clavulanic Acid. J Mol Biol 2010; 396:332-44. [DOI: 10.1016/j.jmb.2009.11.045] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2009] [Revised: 11/17/2009] [Accepted: 11/18/2009] [Indexed: 11/30/2022]
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Cuneo MJ, Beese LS, Hellinga HW. Ligand-induced conformational changes in a thermophilic ribose-binding protein. BMC STRUCTURAL BIOLOGY 2008; 8:50. [PMID: 19019243 PMCID: PMC2630998 DOI: 10.1186/1472-6807-8-50] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/20/2008] [Accepted: 11/19/2008] [Indexed: 01/07/2023]
Abstract
BACKGROUND Members of the periplasmic binding protein (PBP) superfamily are involved in transport and signaling processes in both prokaryotes and eukaryotes. Biological responses are typically mediated by ligand-induced conformational changes in which the binding event is coupled to a hinge-bending motion that brings together two domains in a closed form. In all PBP-mediated biological processes, downstream partners recognize the closed form of the protein. This motion has also been exploited in protein engineering experiments to construct biosensors that transduce ligand binding to a variety of physical signals. Understanding the mechanistic details of PBP conformational changes, both global (hinge bending, twisting, shear movements) and local (rotamer changes, backbone motion), therefore is not only important for understanding their biological function but also for protein engineering experiments. RESULTS Here we present biochemical characterization and crystal structure determination of the periplasmic ribose-binding protein (RBP) from the hyperthermophile Thermotoga maritima in its ribose-bound and unliganded state. The T. maritima RBP (tmRBP) has 39% sequence identity and is considerably more resistant to thermal denaturation (app Tm value is 108 degrees C) than the mesophilic Escherichia coli homolog (ecRBP) (app Tm value is 56 degrees C). Polar ligand interactions and ligand-induced global conformational changes are conserved among ecRBP and tmRBP; however local structural rearrangements involving side-chain motions in the ligand-binding site are not conserved. CONCLUSION Although the large-scale ligand-induced changes are mediated through similar regions, and are produced by similar backbone movements in tmRBP and ecRBP, the small-scale ligand-induced structural rearrangements differentiate the mesophile and thermophile. This suggests there are mechanistic differences in the manner by which these two proteins bind their ligands and are an example of how two structurally similar proteins utilize different mechanisms to form a ligand-bound state.
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Affiliation(s)
- Matthew J Cuneo
- The Department of Biochemistry, Duke University Medical Center, Durham, North Carolina, 27710, USA
| | - Lorena S Beese
- The Department of Biochemistry, Duke University Medical Center, Durham, North Carolina, 27710, USA
| | - Homme W Hellinga
- The Department of Biochemistry, Duke University Medical Center, Durham, North Carolina, 27710, USA
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Doeven MK, van den Bogaart G, Krasnikov V, Poolman B. Probing receptor-translocator interactions in the oligopeptide ABC transporter by fluorescence correlation spectroscopy. Biophys J 2008; 94:3956-65. [PMID: 18212011 PMCID: PMC2367188 DOI: 10.1529/biophysj.107.120964] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2007] [Accepted: 12/21/2007] [Indexed: 11/18/2022] Open
Abstract
The oligopeptide transporter Opp is a five-component ABC uptake system. The extracytoplasmic lipid-anchored substrate-binding protein (or receptor) OppA delivers peptides to an integral membrane complex OppBCDF (or translocator), where, on ATP binding and hydrolysis, translocation across the membrane takes place. OppA and OppBCDF were labeled with fluorescent probes, reconstituted into giant unilamellar vesicles, and the receptor-translocator interactions were investigated by fluorescence correlation spectroscopy. Lateral mobility of OppA was reduced on incorporation of OppBCDF into giant unilamellar vesicles, and decreased even further on the addition of peptide. Fluorescence cross-correlation measurements revealed that OppBCDF distinguished liganded from unliganded OppA, binding only the former. Addition of ATP or its nonhydrolyzable analog AMP-PNP resulted in release of OppA from OppBCDF. In vanadate-trapped "transition state" conditions, OppA also was not bound by OppBCDF. A model is presented in which ATP-binding to OppDF results in donation of peptide to OppBC and simultaneous release of OppA. ATP-hydrolysis would complete the peptide translocation and reset the transporter for another catalytic cycle. Implications in terms of a general transport mechanism for ABC importers and exporters are discussed.
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Affiliation(s)
- Mark K Doeven
- Department of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9747 AG Groningen, The Netherlands
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Létoffé S, Delepelaire P, Wandersman C. The housekeeping dipeptide permease is the Escherichia coli heme transporter and functions with two optional peptide binding proteins. Proc Natl Acad Sci U S A 2006; 103:12891-6. [PMID: 16905647 PMCID: PMC1568943 DOI: 10.1073/pnas.0605440103] [Citation(s) in RCA: 102] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2006] [Indexed: 01/25/2023] Open
Abstract
Heme, a major iron source, is transported through the outer membrane of Gram-negative bacteria by specific heme/hemoprotein receptors and through the inner membrane by heme-specific, periplasmic, binding protein-dependent, ATP-binding cassette permeases. Escherichia coli K12 does not use exogenous heme, and no heme uptake genes have been identified. Nevertheless, a recombinant E. coli strain expressing just one foreign heme outer membrane receptor can use exogenous heme as an iron source. This result suggests either that heme might be able to cross the cytoplasmic membrane in the absence of specific carrier or that there is a functional inner membrane heme transporter. Here, we show that to use heme iron E. coli requires the dipeptide inner membrane ATP-binding cassette transporter (DppBCDF) and either of two periplasmic binding proteins: MppA, the L-alanyl-gamma-D-glutamyl-meso-diaminopimelate binding protein, or DppA, the dipeptide binding protein. Thus, wild-type E. coli has a peptide/heme permease despite being unable to use exogenous heme. DppA, which shares sequence similarity with the Haemophilus influenzae heme-binding protein HbpA, and MppA are functional heme-binding proteins. Peptides compete with heme for binding both "in vitro" and "in vivo."
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Affiliation(s)
- Sylvie Létoffé
- Unité des Membranes Bactériennes, Département de Microbiologie Fondamentale et Médicale, Institut Pasteur, Centre National de la Recherche Scientifique, Unité de Recherche Associée 2172, 75724 Paris Cedex 15, France
| | - Philippe Delepelaire
- Unité des Membranes Bactériennes, Département de Microbiologie Fondamentale et Médicale, Institut Pasteur, Centre National de la Recherche Scientifique, Unité de Recherche Associée 2172, 75724 Paris Cedex 15, France
| | - Cécile Wandersman
- Unité des Membranes Bactériennes, Département de Microbiologie Fondamentale et Médicale, Institut Pasteur, Centre National de la Recherche Scientifique, Unité de Recherche Associée 2172, 75724 Paris Cedex 15, France
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Cuneo MJ, Changela A, Warren JJ, Beese LS, Hellinga HW. The crystal structure of a thermophilic glucose binding protein reveals adaptations that interconvert mono and di-saccharide binding sites. J Mol Biol 2006; 362:259-70. [PMID: 16904687 DOI: 10.1016/j.jmb.2006.06.084] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2006] [Revised: 06/20/2006] [Accepted: 06/27/2006] [Indexed: 11/19/2022]
Abstract
Periplasmic binding proteins (PBPs) comprise a protein superfamily that is involved in prokaryotic solute transport and chemotaxis. These proteins have been used to engineer reagentless biosensors to detect natural or non-natural ligands. There is considerable interest in obtaining very stable members of this superfamily from thermophilic bacteria to use as robust engineerable parts in biosensor development. Analysis of the recently determined genome sequence of Thermus thermophilus revealed the presence of more than 30 putative PBPs in this thermophile. One of these is annotated as a glucose binding protein (GBP) based on its genetic linkage to genes that are homologous to an ATP-binding cassette glucose transport system, although the PBP sequence is homologous to periplasmic maltose binding proteins (MBPs). Here we present the cloning, over-expression, characterization of cognate ligands, and determination of the X-ray crystal structure of this gene product. We find that it is a very stable (apo-protein Tm value is 100(+/- 2) degrees C; complexes 106(+/- 3) degrees C and 111(+/- 1) degrees C for glucose and galactose, respectively) glucose (Kd value is 0.08(+/- 0.03) microM) and galactose (Kd value is 0.94(+/- 0.04) microM) binding protein. Determination of the X-ray crystal structure revealed that this T. thermophilus glucose binding protein (ttGBP) is structurally homologous to MBPs rather than other GBPs. The di or tri-saccharide ligands in MBPs are accommodated in long relatively shallow grooves. In the ttGBP binding site, this groove is partially filled by two loops and an alpha-helix, which create a buried binding site that allows binding of only monosaccharides. Comparison of ttGBP and MBP provides a clear example of structural adaptations by which the size of ligand binding sites can be controlled in the PBP super family.
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Affiliation(s)
- Matthew J Cuneo
- The Department of Biochemistry, Duke University Medical Center, Durham, NC 27710, USA
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38
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Marland Z, Beddoe T, Zaker-Tabrizi L, Lucet IS, Brammananth R, Whisstock JC, Wilce MCJ, Coppel RL, Crellin PK, Rossjohn J. Hijacking of a Substrate-binding Protein Scaffold for use in Mycobacterial Cell Wall Biosynthesis. J Mol Biol 2006; 359:983-97. [PMID: 16698034 DOI: 10.1016/j.jmb.2006.04.012] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2006] [Revised: 03/28/2006] [Accepted: 04/05/2006] [Indexed: 11/30/2022]
Abstract
The waxy cell wall is crucial to the survival of mycobacteria within the infected host. The cell wall is a complex structure rich in unusual molecules that includes two related lipoglycans, the phosphatidylinositol mannosides (PIMs) and lipoarabinomannans (LAMs). Many proteins implicated in the PIM/LAM biosynthetic pathway, while attractive therapeutic targets, are poorly defined. The 2.4A resolution crystal structure of an essential lipoprotein, LpqW, implicated in LAM biosynthesis is reported here. LpqW adopts a scaffold reminiscent of the distantly related, promiscuous substrate-binding proteins of the ATP-binding cassette import system. Nevertheless, the unique closed conformation of LpqW suggests that mycobacteria and other closely related pathogens have hijacked this scaffold for use in key processes of cell wall biosynthesis. In silico docking provided a plausible model in which the candidate PIM ligand binds within a marked electronegative region located on the surface of LpqW. We suggest that LpqW represents an archetypal lipoprotein that channels intermediates from a pathway for mature PIM production into a pathway for LAM biosynthesis, thus controlling the relative abundance of these two important components of the cell wall.
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Affiliation(s)
- Zara Marland
- The Protein Crystallography Unit, Department of Biochemistry and Molecular Biology, School of Biomedical Sciences, Monash University, Clayton, Vic. 3800, Australia
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39
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Jacobsen ID, Meens J, Baltes N, Gerlach GF. Differential expression of non-cytoplasmic Actinobacillus pleuropneumoniae proteins induced by addition of bronchoalveolar lavage fluid. Vet Microbiol 2005; 109:245-56. [PMID: 15979826 DOI: 10.1016/j.vetmic.2005.05.013] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2005] [Revised: 05/04/2005] [Accepted: 05/09/2005] [Indexed: 10/25/2022]
Abstract
Actinobacillus (A.) pleuropneumoniae is the causative agent of a porcine pleuropneumonia occurring worldwide. In order to identify novel non-cytoplasmic putative virulence-associated proteins, we prepared fractions enriched in surface-associated proteins for differential proteome analysis by two-dimensional (2D) gel electrophoresis and quadrupole time-of-flight mass spectrometry (Q-Tof MS). Bacteria grown under standard culture conditions were compared to an ex vivo model based on the addition of bronchoalveolar lavage fluid (BALF) to the culture media. Twelve proteins were found to be upregulated upon induction with BALF, among them a superoxide dismutase, a parvulin-like peptidy-prolyl isomerase, a polynucleotide phosphorylase and the highly immunogenic lipoprotein OmlA. Four of the proteins upregulated by BALF were additionally constitutively expressed by an isogenic A. pleuropneumoniae fur deletion mutant and could be identified by Q-Tof MS as the heat shock protein GroES, a putative dipeptide transporter, a putative metal ion transporter and a conserved protein of unknown function. In silico analysis of the putative promoter regions of the encoding genes revealed putative Fur boxes upstream of two genes, one of which encodes part of a putative metal ion transporter. An isogenic mutant with a deletion in this protein was constructed and designated as A. pleuropneumoniae Deltafui. Analysis of the mutant in an aerosol infection model revealed symptoms indistinguishable from those seen upon infection with wild type A. pleuropneumoniae. This result implies that not all proteins upregulated by BALF are directly involved in A. pleuropneumoniae virulence.
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Affiliation(s)
- Ilse D Jacobsen
- Institute for Microbiology, Department of Infectious Diseases, University of Veterinary Medicine Hannover, Foundation, Hannover, Germany
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Doeven MK, Kok J, Poolman B. Specificity and selectivity determinants of peptide transport in Lactococcus lactis and other microorganisms. Mol Microbiol 2005; 57:640-9. [PMID: 16045610 DOI: 10.1111/j.1365-2958.2005.04698.x] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Peptide transport in microorganisms is important for nutrition of the cell and various signalling processes including regulation of gene expression, sporulation, chemotaxis, competence and virulence development. Peptide transport is mediated via different combinations of ion-linked and ATP-binding cassette (ABC) transporters, the latter utilizing single or multiple peptide-binding proteins with overlapping specificities. The paradigm for research on peptide transport is Lactococcus lactis, in which the uptake of peptides containing essential amino acids is vital for growth on milk proteins. Differential expression and characteristics of peptide-binding proteins in several Lactococcus lactis strains resulted in apparent conflicts with older literature. Recent developments and new data now make the pieces of the puzzle fall back into place again and confirm the view that the oligopeptide-binding proteins determine the uptake selectivity of their cognate ABC transporters. Besides reviewing the current data on binding specificity and transport selectivity of peptide transporters in L. lactis, the possible implications for peptide utilization by other bacterial species are discussed.
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Affiliation(s)
- Mark K Doeven
- Department of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen, the Netherlands
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41
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Williams WA, Zhang RG, Zhou M, Joachimiak G, Gornicki P, Missiakas D, Joachimiak A. The membrane-associated lipoprotein-9 GmpC from Staphylococcus aureus binds the dipeptide GlyMet via side chain interactions. Biochemistry 2005; 43:16193-202. [PMID: 15610013 PMCID: PMC2792005 DOI: 10.1021/bi048877o] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Bacterial dipeptide ABC transporters function to import a wide range of dipeptide substrates. This ability to transport a wide variety of dipeptides is conferred by the cognate substrate binding protein (SBP) of these transporters. SBPs bind dipeptides with little regard for their amino acid content. Here, we report the 1.7 A resolution structure of lipoprotein-9 (SA0422) of Staphylococcus aureus in complex with the dipeptide glycylmethionine. Experimental characterization of the subcellular location of the protein confirmed that SA0422 is an acylated, peripheral membrane protein. This is the first structure determined for an SBP of a Gram-positive dipeptide ABC transporter. Usually, binding of dipeptides occurs in a binding pocket that is largely hydrated and able to accommodate the side chains of several different amino acid residues. Unlike any other known SBP, lipoprotein-9 binds the side chains of the glycylmethionine dipeptide through very specific interactions. Lipoprotein-9 shares significant structural and sequence homology with the MetQ family of methionine SBP. Sequence comparisons between MetQ-like proteins and lipoprotein-9 suggest that the residues forming the tight interactions with the methionine side chains of the ligand are highly conserved between lipoprotein-9 and MetQ homologues, while the residues involved in coordinating the glycine residue are not. Modeling of the Vibrio cholerae MetQ and lipoprotein-9 binding pockets can account for lipoprotein-9 substrate specificity toward glycylmethionine. For this reason, we have designated lipoprotein-9 GmpC, for glycylmethionine binding protein.
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Affiliation(s)
- Wade A. Williams
- Committee on Microbiology, University of Chicago, 920 East 58 Street, Chicago, Illinois 60637
- Department of Molecular Genetics and Cell Biology, University of Chicago, 920 East 58 Street, Chicago, Illinois 60637
| | - Rong-gaung Zhang
- Structural Biology Center, Biosciences, Argonne National Laboratory, 9700 South Cass Avenue, Building 202, Argonne, Illinois 60439
| | - Min Zhou
- Structural Biology Center, Biosciences, Argonne National Laboratory, 9700 South Cass Avenue, Building 202, Argonne, Illinois 60439
| | - Grazyna Joachimiak
- Structural Biology Center, Biosciences, Argonne National Laboratory, 9700 South Cass Avenue, Building 202, Argonne, Illinois 60439
| | - Piotr Gornicki
- Department of Biochemistry and Molecular Biology, University of Chicago, 920 East 58 Street, Chicago, Illinois 60637
| | - Dominique Missiakas
- Committee on Microbiology, University of Chicago, 920 East 58 Street, Chicago, Illinois 60637
- Department of Molecular Genetics and Cell Biology, University of Chicago, 920 East 58 Street, Chicago, Illinois 60637
- To whom correspondence should be addressed. D.M.: phone, (773) 834-8161; fax, (773) 834-8150; . A.J.: phone, (630) 252-3926; fax, (630) 252-6126;
| | - Andrzej Joachimiak
- Department of Molecular Genetics and Cell Biology, University of Chicago, 920 East 58 Street, Chicago, Illinois 60637
- Structural Biology Center, Biosciences, Argonne National Laboratory, 9700 South Cass Avenue, Building 202, Argonne, Illinois 60439
- To whom correspondence should be addressed. D.M.: phone, (773) 834-8161; fax, (773) 834-8150; . A.J.: phone, (630) 252-3926; fax, (630) 252-6126;
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Levdikov VM, Blagova EV, Brannigan JA, Wright L, Vagin AA, Wilkinson AJ. The Structure of the Oligopeptide-binding Protein, AppA, from Bacillus subtilis in Complex with a Nonapeptide. J Mol Biol 2005; 345:879-92. [PMID: 15588833 DOI: 10.1016/j.jmb.2004.10.089] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2004] [Revised: 10/28/2004] [Accepted: 10/29/2004] [Indexed: 10/26/2022]
Abstract
Besides their role as a source of amino acids for Bacillus subtilis, exogenous peptides play important roles in the signalling pathways leading to the development of competence and sporulation. B.subtilis has three peptide transport systems all belonging to the ATP-binding cassette family, a dipeptide permease (Dpp) and two oligopeptide permeases (Opp and App) with overlapping specificity. These comprise a membrane-spanning channel through which the peptide passes, a pair of ATPases which couple ATP hydrolysis to peptide translocation and a lipid-modified, membrane-anchored extracellular "binding-protein" that serves as the receptor for the system. Here, we present the crystal structure of a soluble form of the peptide-binding protein AppA, which has been solved to 1.6 A spacing by anomalous scattering and molecular replacement methods. The structure reveals a protein made of two distinct lobes with a topology similar to those of DppA from Escherichia coli and OppA from Salmonella typhimurium. Examination of the interlobe region reveals an enlarged pocket, containing electron density defining a nonapeptide ligand. The main-chain of the peptide is well defined and makes a series of polar contacts with the protein including salt-bridges at both its termini. The side-chain density is ambiguous in places, consistent with the interpretation that a population of peptides is bound, whose average electron density resembles the amino acid sequence N-VDSKNTSSW-C.
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Affiliation(s)
- Vladimir M Levdikov
- Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5YW, UK
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43
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Sherman DB, Zhang S, Pitner JB, Tropsha A. Evaluation of the relative stability of liganded versus ligand-free protein conformations using Simplicial Neighborhood Analysis of Protein Packing (SNAPP) method. Proteins 2004; 56:828-38. [PMID: 15281134 PMCID: PMC2778290 DOI: 10.1002/prot.20131] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Many proteins change their conformation upon ligand binding. For instance, bacterial periplasmic binding proteins (bPBPs), which transport nutrients into the cytoplasm, generally consist of two globular domains connected by strands, forming a hinge. During ligand binding, hinge motion changes the conformation from the open to the closed form. Both forms can be crystallized without a ligand, suggesting that the energy difference between them is small. We applied Simplicial Neighborhood Analysis of Protein Packing (SNAPP) as a method to evaluate the relative stability of open and closed forms in bPBPs. Using united residue representation of amino acids, SNAPP performs Delaunay tessellation of the protein, producing an aggregate of space-filling, irregular tetrahedra with nearest neighbor residues at the vertices. The SNAPP statistical scoring function is derived from log-likelihood scores for all possible quadruplet compositions of amino acids found in a representative subset of the Protein Data Bank, and the sum of the scores for a given protein provides the total SNAPP score. Results of scoring for bPBPs suggest that in most cases, the unliganded form is more stable than the liganded form, and this conclusion is corroborated by similar observations of other proteins undergoing conformation changes upon binding their ligands. The results of these studies suggest that the SNAPP method can be used to predict the relative stability of accessible protein conformations. Furthermore, the SNAPP method allows delineation of the role of individual residues in protein stabilization, thereby providing new testable hypotheses for rational site-directed mutagenesis in the context of protein engineering.
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Affiliation(s)
| | - Shuxing Zhang
- The Laboratory for Molecular Modeling, Division of Medicinal Chemistry and Natural Products, School of Pharmacy, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-7360
| | - J. Bruce Pitner
- BD Technologies, 21 Davis Dr., Research Triangle Park, NC 27709
| | - Alexander Tropsha
- The Laboratory for Molecular Modeling, Division of Medicinal Chemistry and Natural Products, School of Pharmacy, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-7360
- Corresponding author, School of Pharmacy, Campus Box 7360, 327 Beard Hall, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-7360. Telephone (919) 966-2955, FAX: (919) 966-0204,
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44
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Abstract
Thiol-disulfide interconversions play a crucial role in the chemistry of biological systems. They participate in the major systems that control the cellular redox potential and prevent oxidative damage. In addition, thiol-disulfide exchange reactions serve as molecular switches in a growing number of redox-regulated proteins. We developed a differential thiol-trapping technique combined with two-dimensional gel analysis, which in combination with genetic studies, allowed us to obtain a snapshot of the in vivo thiol status of cellular proteins. We determined the redox potential of protein thiols in vivo, identified and dissected the in vivo substrate proteins of the major cellular thiol-disulfide oxidoreductases, and discovered proteins that undergo thiol modifications during oxidative stress. Under normal growth conditions most cytosolic proteins had reduced cysteines, confirming existing dogmas. Among the few partly oxidized cytosolic proteins that we detected were proteins that are known to form disulfide bond intermediates transiently during their catalytic cycle (e.g., dihydrolipoyl transacetylase and lipoamide dehydrogenase). Most proteins with highly oxidized thiols were periplasmic proteins and were found to be in vivo substrates of the disulfide-bond-forming protein DsbA. We discovered a substantial number of redox-sensitive cytoplasmic proteins, whose thiol groups were significantly oxidized in strains lacking thioredoxin A. These included detoxifying enzymes as well as many metabolic enzymes with active-site cysteines that were not known to be substrates for thioredoxin. H2O2-induced oxidative stress resulted in the specific oxidation of thiols of proteins involved in detoxification of H2O2 and of enzymes of cofactor and amino acid biosynthesis pathways such as thiolperoxidase, GTP-cyclohydrolase I, and the cobalamin-independent methionine synthase MetE. Remarkably, a number of these proteins were previously or are now shown to be redox regulated. A differential thiol-trapping technique combined with two- dimensional gel analysis has been developed and used to visualize thiol-disulfide exchange reactions, which act as switches in redox-regulated proteins
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Affiliation(s)
- Lars I Leichert
- 1Department of Molecular, Cellular, and Developmental Biology, University of MichiganAnn Arbor, MichiganUnited States of America
| | - Ursula Jakob
- 1Department of Molecular, Cellular, and Developmental Biology, University of MichiganAnn Arbor, MichiganUnited States of America
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45
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Solomon J, Su L, Shyn S, Grossman AD. Isolation and characterization of mutants of the Bacillus subtilis oligopeptide permease with altered specificity of oligopeptide transport. J Bacteriol 2003; 185:6425-33. [PMID: 14563878 PMCID: PMC219414 DOI: 10.1128/jb.185.21.6425-6433.2003] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Bacterial oligopeptide permeases are members of the large family of ATP binding cassette transporters and typically import peptides of 3 to 5 amino acids, apparently independently of sequence. Oligopeptide permeases are needed for bacteria to utilize peptides as nutrient sources and are sometimes involved in signal transduction pathways. The Bacillus subtilis oligopeptide permease stimulates competence development and the initiation of sporulation, at least in part, by importing specific signaling peptides. We isolated rare, partly functional mutations in B. subtilis opp. The mutants were resistant to a toxic tripeptide but still retained the ability to sporulate and/or become competent. The mutations, mostly in the oligopeptide binding protein located on the cell surface, affected residues whose alteration appears to change the specificity of oligopeptide transport.
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Affiliation(s)
- Jonathan Solomon
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA.
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46
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Sanz Y, Toldrá F, Renault P, Poolman B. Specificity of the second binding protein of the peptide ABC-transporter (Dpp) ofLactococcus lactisIL1403. FEMS Microbiol Lett 2003; 227:33-8. [PMID: 14568145 DOI: 10.1016/s0378-1097(03)00662-1] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
The genome sequence of Lactococcus lactis IL1403 revealed the presence of a putative peptide-binding protein-dependent ABC-transporter (Dpp). The genes for two peptide-binding proteins (dppA and dppP) precede the membrane components, which include two transmembrane protein genes (dppB and dppC) and two ATP-binding protein genes (dppD and dppF). In this work, the gene specifying the second peptide-binding protein (DppP) was cloned under the control of the nisin promoter. The protein fused to a carboxyl-terminal histidine tag (DppP-His(6)) was purified and its binding properties were determined by monitoring the intrinsic fluorescence changes observed upon ligand binding. The major features of peptide binding to DppP-His(6) include: (i) a requirement for a free N-terminal alpha-amino group in the ligand; (ii) a high affinity for di-, tri- and tetra-peptides; (iii) affinity constants for peptide binding independent of pH; and (iv) a high affinity for D-isomer-containing peptides. Remarkably, the features (ii), (iii) and (iv) differ from those previously reported for DppA-His(6), suggesting that DppP-His(6) is a more versatile peptide-binding protein that could have additional functions.
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Affiliation(s)
- Yolanda Sanz
- Instituto de Agroqui;mica y Tecnologi;a de Alimentos (C.S.I.C.), Apartado 73, 46100, Valencia, Burjasot, Spain.
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de Lorimier RM, Smith JJ, Dwyer MA, Looger LL, Sali KM, Paavola CD, Rizk SS, Sadigov S, Conrad DW, Loew L, Hellinga HW. Construction of a fluorescent biosensor family. Protein Sci 2002; 11:2655-75. [PMID: 12381848 PMCID: PMC2373719 DOI: 10.1110/ps.021860] [Citation(s) in RCA: 262] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Bacterial periplasmic binding proteins (bPBPs) are specific for a wide variety of small molecule ligands. bPBPs undergo a large, ligand-mediated conformational change that can be linked to reporter functions to monitor ligand concentrations. This mechanism provides the basis of a general system for engineering families of reagentless biosensors that share a common physical signal transduction functionality and detect many different analytes. We demonstrate the facility of designing optical biosensors based on fluorophore conjugates using 8 environmentally sensitive fluorophores and 11 bPBPs specific for diverse ligands, including sugars, amino acids, anions, cations, and dipeptides. Construction of reagentless fluorescent biosensors relies on identification of sites that undergo a local conformational change in concert with the global, ligand-mediated hinge-bending motion. Construction of cysteine mutations at these locations then permits site-specific coupling of environmentally sensitive fluorophores that report ligand binding as changes in fluorescence intensity. For 10 of the bPBPs presented in this study, the three-dimensional receptor structure was used to predict the location of reporter sites. In one case, a bPBP sensor specific for glutamic and aspartic acid was designed starting from genome sequence information and illustrates the potential for discovering novel binding functions in the microbial genosphere using bioinformatics.
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Affiliation(s)
- Robert M de Lorimier
- Department of Biochemistry, Duke University Medical Center, Durham, North Carolina 27710, USA
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48
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Gupta S, Payne JW. Evaluation of the conformational propensities of peptide isosteres as a basis for selecting bioactive pseudopeptides. THE JOURNAL OF PEPTIDE RESEARCH : OFFICIAL JOURNAL OF THE AMERICAN PEPTIDE SOCIETY 2001; 58:546-61. [PMID: 12005424 DOI: 10.1034/j.1399-3011.2001.00954.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Our aim was to compare the repertoires of conformers formed by the model zwitterionic peptides AA and AAA in aqueous solution with the conformational profiles of a range of their peptide isosteres, so as to facilitate selection of isosteres for synthesis and testing as biologically stable surrogates of bioactive di- and tripeptides. Comparisons were based upon the results of conformational analysis using a random search approach implemented within the SYBYL molecular modelling package, using zwitterionic molecules, simulated aqueous solvation using a dielectric constant of 80 and allowing all torsions to vary. For each compound, individual conformers were grouped on the basis of specific combinations of psi, phi and omega torsions and, using their energies, the aggregated percentage for each group was calculated using a Boltzmann distribution and displayed using a 3D pseudo Ramachandran plot relating percentage conformer to psi and phi torsions. Retroamide, N-methylamide and thioamide isosteres showed the best match to natural peptides and to the molecular recognition parameters defined for substrates of peptide transporters. The results should aid rational design of therapeutic agents in various areas, e.g. oral delivery of drugs by peptide transporters and of peptidase inhibitors. This approach may usefully be applied to various biochemical and pharmaceutical topics.
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Affiliation(s)
- S Gupta
- School of Biological Sciences, University of Wales Bangor, UK
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49
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Payne JW, Payne GM, Gupta S, Marshall NJ, Grail BM. Conformational limitations of glycylsarcosine as a prototypic substrate for peptide transporters. BIOCHIMICA ET BIOPHYSICA ACTA 2001; 1514:65-75. [PMID: 11513805 DOI: 10.1016/s0005-2736(01)00364-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
Peptide transporters are present in all species to absorb the small peptides that occur ubiquitously as products of proteolysis. The broad substrate specificities of these systems allow them to be exploited therapeutically for delivery of peptidomimetic drugs in microbes and man. To this end, glycylsarcosine is currently used as a standard substrate for assaying peptidomimetic transport by peptide transporters. However, in this study we find it is unsuitable as a general substrate, based on assays of its transport by model bacterial peptide transporters and computer-based conformational analysis of its structure. Of the two generic transporters for di- and tripeptides, exemplified by Dpp and Tpp in Escherichia coli, only Dpp can transport glycylsarcosine. The explanation for this finding came from molecular modelling, which indicated that glycylsarcosine can adopt only a restricted range of conformers compared with typical dipeptides, and that of the conformers with a trans peptide bond, the majority have the specific psi and phi backbone torsion angles needed for molecular recognition and transport by Dpp but none possessed psi and phi torsions required for recognition by Tpp; moreover, 38% of its conformers have cis peptide bonds that are not substrates for any peptide transporter. Thus, using glycylsarcosine as substrate in competition assays with compounds that typically form conformers recognised by both types of peptide transporter will underestimate their transport. These findings have implications for assays of oral availability of peptidomimetic drugs such as beta-lactams, ACE inhibitors and anti-viral compounds, for which glycylsarcosine is routinely used.
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Affiliation(s)
- J W Payne
- School of Biological Sciences, University of Wales, Bangor, Gwynedd LL57 2UW, UK.
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Abstract
In this review our knowledge of ATP binding cassette (ABC) transporters specific for peptides is discussed. Besides serving a role in nutrition of the cell, the systems participate in various signaling processes that allow (micro)organisms to monitor the local environment. In bacteria, these include regulation of gene expression, competence development, sporulation, DNA transfer by conjugation, chemotaxis, and virulence development, and the role of ABC transporters in each of these processes is discussed. Particular attention is paid to the specificity determinants of peptide receptors and transporters in relation to their structure and to the mechanisms of peptide binding.
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Affiliation(s)
- F J Detmers
- Department of Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, The Netherlands
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