1
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Alcorlo M, Abdullah MR, Steil L, Sotomayor F, López-de Oro L, de Castro S, Velázquez S, Kohler TP, Jiménez E, Medina A, Usón I, Keller LE, Bradshaw JL, McDaniel LS, Camarasa MJ, Völker U, Hammerschmidt S, Hermoso JA. Molecular and structural basis of oligopeptide recognition by the Ami transporter system in pneumococci. PLoS Pathog 2024; 20:e1011883. [PMID: 38838057 PMCID: PMC11192437 DOI: 10.1371/journal.ppat.1011883] [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: 12/07/2023] [Revised: 06/21/2024] [Accepted: 04/30/2024] [Indexed: 06/07/2024] Open
Abstract
ATP-binding cassette (ABC) transport systems are crucial for bacteria to ensure sufficient uptake of nutrients that are not produced de novo or improve the energy balance. The cell surface of the pathobiont Streptococcus pneumoniae (pneumococcus) is decorated with a substantial array of ABC transporters, critically influencing nasopharyngeal colonization and invasive infections. Given the auxotrophic nature of pneumococci for certain amino acids, the Ami ABC transporter system, orchestrating oligopeptide uptake, becomes indispensable in host compartments lacking amino acids. The system comprises five exposed Oligopeptide Binding Proteins (OBPs) and four proteins building the ABC transporter channel. Here, we present a structural analysis of all the OBPs in this system. Multiple crystallographic structures, capturing both open and closed conformations along with complexes involving chemically synthesized peptides, have been solved at high resolution providing insights into the molecular basis of their diverse peptide specificities. Mass spectrometry analysis of oligopeptides demonstrates the unexpected remarkable promiscuity of some of these proteins when expressed in Escherichia coli, displaying affinity for a wide range of peptides. Finally, a model is proposed for the complete Ami transport system in complex with its various OBPs. We further disclosed, through in silico modelling, some essential structural changes facilitating oligopeptide transport into the cellular cytoplasm. Thus, the structural analysis of the Ami system provides valuable insights into the mechanism and specificity of oligopeptide binding by the different OBPs, shedding light on the intricacies of the uptake mechanism and the in vivo implications for this human pathogen.
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Affiliation(s)
- Martín Alcorlo
- Department of Crystallography and Structural Biology, Institute of Physical-Chemistry “Blas Cabrera”, Spanish National Research Council (CSIC), Madrid; Spain
| | - Mohammed R. Abdullah
- Department of Molecular Genetics and Infection Biology, Interfaculty Institute for Genetics and Functional Genomics, Center for Functional Genomics of Microbes, University of Greifswald, Greifswald; Germany
| | - Leif Steil
- Department of Functional Genomics, Interfaculty Institute for Genetics and Functional Genomics, Center for Functional Genomics of Microbes, University Medicine Greifswald, Greifswald; Germany
| | - Francisco Sotomayor
- Department of Crystallography and Structural Biology, Institute of Physical-Chemistry “Blas Cabrera”, Spanish National Research Council (CSIC), Madrid; Spain
| | - Laura López-de Oro
- Department of Crystallography and Structural Biology, Institute of Physical-Chemistry “Blas Cabrera”, Spanish National Research Council (CSIC), Madrid; Spain
| | | | | | - Thomas P. Kohler
- Department of Molecular Genetics and Infection Biology, Interfaculty Institute for Genetics and Functional Genomics, Center for Functional Genomics of Microbes, University of Greifswald, Greifswald; Germany
| | - Elisabet Jiménez
- Crystallographic Methods, Institute of Molecular Biology of Barcelona (IBMB-CSIC), Barcelona Science Park, Helix Building, Barcelona; Spain
| | - Ana Medina
- Crystallographic Methods, Institute of Molecular Biology of Barcelona (IBMB-CSIC), Barcelona Science Park, Helix Building, Barcelona; Spain
| | - Isabel Usón
- Crystallographic Methods, Institute of Molecular Biology of Barcelona (IBMB-CSIC), Barcelona Science Park, Helix Building, Barcelona; Spain
- ICREA, Institució Catalana de Recerca i Estudis Avançats, Barcelona; Spain
| | - Lance E. Keller
- Center for Immunology and Microbial Research, University of Mississippi Medical Center, Jackson, Mississippi; United States of America
- Department of Cell and Molecular Biology, University of Mississippi Medical Center, Jackson, Mississippi; United States of America
| | - Jessica L. Bradshaw
- Department of Microbiology and Immunology, University of Mississippi Medical Center, Jackson, Mississippi; United States of America
| | - Larry S. McDaniel
- Center for Immunology and Microbial Research, University of Mississippi Medical Center, Jackson, Mississippi; United States of America
- Department of Cell and Molecular Biology, University of Mississippi Medical Center, Jackson, Mississippi; United States of America
| | | | - Uwe Völker
- Department of Functional Genomics, Interfaculty Institute for Genetics and Functional Genomics, Center for Functional Genomics of Microbes, University Medicine Greifswald, Greifswald; Germany
| | - Sven Hammerschmidt
- Department of Molecular Genetics and Infection Biology, Interfaculty Institute for Genetics and Functional Genomics, Center for Functional Genomics of Microbes, University of Greifswald, Greifswald; Germany
| | - Juan A. Hermoso
- Department of Crystallography and Structural Biology, Institute of Physical-Chemistry “Blas Cabrera”, Spanish National Research Council (CSIC), Madrid; Spain
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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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Liu Y, Zhang Y, Kang C, Tian D, Lu H, Xu B, Xia Y, Kashiwagi A, Westermann M, Hoischen C, Xu J, Yomo T. Comparative genomics hints at dispensability of multiple essential genes in two Escherichia coli L-form strains. Biosci Rep 2023; 43:BSR20231227. [PMID: 37819245 PMCID: PMC10600066 DOI: 10.1042/bsr20231227] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 10/09/2023] [Accepted: 10/11/2023] [Indexed: 10/13/2023] Open
Abstract
Despite the critical role of bacterial cell walls in maintaining cell shapes, certain environmental stressors can induce the transition of many bacterial species into a wall-deficient state called L-form. Long-term induced Escherichia coli L-forms lose their rod shape and usually hold significant mutations that affect cell division and growth. Besides this, the genetic background of L-form bacteria is still poorly understood. In the present study, the genomes of two stable L-form strains of E. coli (NC-7 and LWF+) were sequenced and their gene mutation status was determined and compared with their parental strains. Comparative genomic analysis between two L-forms reveals both unique adaptions and common mutated genes, many of which belong to essential gene categories not involved in cell wall biosynthesis, indicating that L-form genetic adaptation impacts crucial metabolic pathways. Missense variants from L-forms and Lenski's long-term evolution experiment (LTEE) were analyzed in parallel using an optimized DeepSequence pipeline to investigate predicted mutation effects (α) on protein functions. We report that the two L-form strains analyzed display a frequency of 6-10% (0% for LTEE) in mutated essential genes where the missense variants have substantial impact on protein functions (α<0.5). This indicates the emergence of different survival strategies in L-forms through changes in essential genes during adaptions to cell wall deficiency. Collectively, our results shed light on the detailed genetic background of two E. coli L-forms and pave the way for further investigations of the gene functions in L-form bacterial models.
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Affiliation(s)
- Yunfei Liu
- Laboratory of Biology and Information Science, School of Life Sciences, East China Normal University, Shanghai 200062, PR China
| | - Yueyue Zhang
- Laboratory of Biology and Information Science, School of Life Sciences, East China Normal University, Shanghai 200062, PR China
| | - Chen Kang
- School of Software Engineering, East China Normal University, Shanghai 200062, PR China
| | - Di Tian
- Laboratory of Biology and Information Science, School of Life Sciences, East China Normal University, Shanghai 200062, PR China
| | - Hui Lu
- Laboratory of Biology and Information Science, School of Life Sciences, East China Normal University, Shanghai 200062, PR China
| | - Boying Xu
- Laboratory of Biology and Information Science, School of Life Sciences, East China Normal University, Shanghai 200062, PR China
- Tongji University Cancer Center, Shanghai Tenth People’s Hospital, School of Medicine, Tongji University, Shanghai 200072, China
| | - Yang Xia
- Laboratory of Biology and Information Science, School of Life Sciences, East China Normal University, Shanghai 200062, PR China
| | - Akiko Kashiwagi
- Faculty of Agriculture and Life Science, Hirosaki University, Hirosaki 036-8561, Japan
| | - Martin Westermann
- Center for Electron Microscopy, Medical Faculty, Friedrich–Schiller–University Jena, Ziegelmühlenweg 1, D-07743 Jena, Germany
| | - Christian Hoischen
- CF Imaging, Leibniz Institute On Aging, Fritz–Lipmann–Institute (FLI), Beutenbergstraße 11, 07745 Jena, Germany
| | - Jian Xu
- Laboratory of Biology and Information Science, School of Life Sciences, East China Normal University, Shanghai 200062, PR China
| | - Tetsuya Yomo
- Laboratory of Biology and Information Science, School of Life Sciences, East China Normal University, Shanghai 200062, PR China
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4
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Omori A, Sasaki S, Kikukawa T, Shimono K, Miyauchi S. Elucidation of a Thermodynamical Feature Attributed to Substrate Binding to the Prokaryotic H +/Oligopeptide Cotransporter YdgR with Calorimetric Analysis: The Substrate Binding Driven by the Change in Entropy Implies the Release of Bound Water Molecules from the Binding Pocket. Biochemistry 2023. [PMID: 37163674 DOI: 10.1021/acs.biochem.2c00673] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Here, we have elucidated the substrate recognition mechanism by a prokaryotic H+/oligopeptide cotransporter, YdgR, using isothermal titration calorimetry. Under acidic conditions (pH 6.0), the binding of a dipeptide, Val-Ala, to YdgR elicited endothermic enthalpy, which compensated for the increase in entropy due to dipeptide binding. A series of dipeptides were used in the binding titration. The dipeptides represent Val-X and X-Val, where X is Ala, Ser, Val, Tyr, or Phe. Most dipeptides revealed endothermic enthalpy, which was completely compensated by the increase in entropy due to dipeptide binding. The change in enthalpy due to binding correlated well with the change in entropy, whereas the Gibbs free energy involved in the binding of the dipeptide to YdgR remained unchanged irrespective of dipeptide sequences, implying that the binding reaction was driven by entropy, that is, the release of bound water molecules in the binding pocket. It is also important to clarify that, based on the prediction of water molecules in the ligand-binding pocket of YdgR, the release of three bound water molecules in the putative substrate binding pocket occurred through binding to YdgR. In the comparison of Val-X and X-Val dipeptides, the N-terminal region of the binding pocket might contain more bound water molecules than the C-terminal region. In light of these findings, we suggest that bound water molecules might play an important role in substrate recognition and binding by YdgR.
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Affiliation(s)
- Akiko Omori
- Faculty of Pharmaceutical Sciences, Toho University, 2-2-1 Miyama, Funabashi, Chiba 274-8510, Japan
| | - Shotaro Sasaki
- Faculty of Pharmaceutical Sciences, Toho University, 2-2-1 Miyama, Funabashi, Chiba 274-8510, Japan
| | - Takashi Kikukawa
- Faculty of Advanced Life Science, Hokkaido University, Kita 10, Nishi 8, Kita-ku, Sapporo 060-0810, Japan
| | - Kazumi Shimono
- Faculty of Pharmaceutical Sciences, Toho University, 2-2-1 Miyama, Funabashi, Chiba 274-8510, Japan
- Faculty of Pharmaceutical Sciences, Sojo University, 4-22-1 Ikeda Nishi-ku, Kumamoto 860-0082, Japan
| | - Seiji Miyauchi
- Faculty of Pharmaceutical Sciences, Toho University, 2-2-1 Miyama, Funabashi, Chiba 274-8510, Japan
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5
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Thomas GH. Microbial Musings - Winter 2022. MICROBIOLOGY (READING, ENGLAND) 2022; 168:micro001310. [PMID: 36848206 PMCID: PMC10009517 DOI: 10.1099/mic.0.001310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Indexed: 03/01/2023]
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6
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Chai HH, Ham JS, Kim TH, Lim D. Identifying ligand-binding specificity of the oligopeptide receptor OppA from Bifidobacterium longum KACC91563 by structure-based molecular modeling. ARAB J CHEM 2022. [DOI: 10.1016/j.arabjc.2022.104198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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7
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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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8
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Abideen ZU, Ahmad A, Usman M, Majaz S, Ali W, Noreen S, Mahmood T, Nouroz F. Dynamics and conformational propensities of staphylococcal CntA. J Biomol Struct Dyn 2020; 39:4923-4935. [PMID: 32573341 DOI: 10.1080/07391102.2020.1782263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Enzymes use transition metals as co-factors for catalytic roles in biological processes. Notably, manganese, iron, cobalt, nickel, copper and zinc are abundantly used. Staphylococcus aureus, a commensal bacterium asymptomatically, lies on the human body causing variety of infections. S. aureus is equipped by advanced virulence-regulatory circuits of metal acquisition like Cnt that acquires metals at infection sites by utilizing a nicotianamine-like metallophore staphylopine. Despite significant growth in structural studies, how CntA of Cnt system transmits conformational signal upon staphylopine recognition remains elusive. Here, we analyzed the structural changes adopted by CntA during close-to-open transition by computational approaches. CntA uses a bi-domain architectural form of domain II which performed 37° rigid body rotation and 1.1 Å translation assisted by inter-domain hinge cluster residues. Important clustered communities were found regulating the conformational changes in CntA where communities 4 and 5 are found crucial. Besides open and close states, the fluctuating regions sampled two additional intermediate states which were considered close or open previously. CntA prefers fluctuating the non-conserved regions rather than conserved where domain II turned out to be rigid and maintains a stable fold. Overall, the CntA system is a potential target for structural biologist to hamper such conformational behaviors at family level.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Zain Ul Abideen
- Department of Bioinformatics, Hazara University, Mansehra, KPK, Pakistan
| | - Ashfaq Ahmad
- Department of Bioinformatics, Hazara University, Mansehra, KPK, Pakistan
| | - Muhammad Usman
- Department of Bioinformatics, Hazara University, Mansehra, KPK, Pakistan
| | - Sidra Majaz
- Department of Bioinformatics, Hazara University, Mansehra, KPK, Pakistan
| | - Waqar Ali
- Department of Bioinformatics, Hazara University, Mansehra, KPK, Pakistan
| | - Shumaila Noreen
- Department of Zoology, University of Peshawar, Peshawar, KPK, Pakistan
| | - Tariq Mahmood
- Department of Bioinformatics, Hazara University, Mansehra, KPK, Pakistan.,Department of Agriculture, Hazara University, Mansehra, KPK, Pakistan
| | - Faisal Nouroz
- Department of Bioinformatics, Hazara University, Mansehra, KPK, Pakistan.,Department of Botany, Hazara University, Mansehra, KPK, Pakistan
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9
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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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10
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Mishra KK, Singh SK, Kumar S, Singh G, Sarkar B, Madhusudhan MS, Das A. Water-Mediated Selenium Hydrogen-Bonding in Proteins: PDB Analysis and Gas-Phase Spectroscopy of Model Complexes. J Phys Chem A 2019; 123:5995-6002. [PMID: 31268326 DOI: 10.1021/acs.jpca.9b04159] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
High-resolution X-ray crystallography and two-dimensional NMR studies demonstrate that water-mediated conventional hydrogen-bonding interactions (N-H···N, O-H···N, etc.) bridging two or more amino acid residues contribute to the stability of proteins and protein-ligand complexes. In this work, we have investigated single water-mediated selenium hydrogen-bonding interactions (unconventional hydrogen-bonding) between amino acid residues in proteins through extensive protein data bank (PDB) analysis coupled with gas-phase spectroscopy and quantum chemical calculation of a model complex consisting of indole, dimethyl selenide, and water. Here, indole and dimethyl selenide represent the amino acid residues tryptophan and selenomethionine, respectively. The current investigation demonstrates that the most stable structure of the model complex observed in the IR spectroscopy mimics single water-mediated selenium hydrogen-bonded structural motifs present in the crystal structures of proteins. The present work establishes that water-mediated Se hydrogen-bonding interactions are ubiquitous in proteins and the number of these interactions observed in the PDB is more than that of direct Se hydrogen-bonds present there.
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Affiliation(s)
| | | | | | | | - Biplab Sarkar
- Department of Chemistry , North Eastern Hill University , Shillong , Meghalaya 793022 , India
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11
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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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12
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Norcross S, Sunderraj A, Tantama M. pH- and Temperature-Dependent Peptide Binding to the Lactococcus lactis Oligopeptide-Binding Protein A Measured with a Fluorescence Anisotropy Assay. ACS OMEGA 2019; 4:2812-2822. [PMID: 30842982 PMCID: PMC6396125 DOI: 10.1021/acsomega.8b02427] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Accepted: 01/22/2019] [Indexed: 05/03/2023]
Abstract
Bacterial ATP-binding cassette transporters are a superfamily of transport systems involved in the import of various molecules including amino acids, ions, sugars, and peptides. In the lactic acid bacteria Lactococcus lactis, the oligopeptide-binding protein A (OppA) binds peptides for import to support nitrogen metabolism and cell growth. The OppA protein is of great interest because it can bind peptides over a broad variety of lengths and sequences; however, current methods to study peptide binding have employed low throughput, endpoint, or low dynamic range techniques. Therefore, in this study, we developed a fluorescence anisotropy-based peptide-binding assay that can be readily employed to quantify OppA function. To test the utility of our assay, we characterized the pH dependence of oligopeptide binding because L. lactis is commonly used in fermentation and often must survive in low pH environments caused by lactic acid export. We determined that OppA affinity increases as pH or temperature decreases, and circular dichroism spectroscopy further indicated that acidic conditions increase the thermal stability of the protein, increasing the unfolding transition temperature by 10 °C from pH 8 to pH 6. Thus, our fluorescence anisotropy assay provides an easy technique to measure peptide binding, and it can be used to understand molecular aspects of OppA function under stress conditions experienced during fermentation and other biotechnology applications.
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Affiliation(s)
- Stevie Norcross
- Department
of Chemistry, Institute for Integrative Neuroscience, and Institute for
Inflammation, Immunology, and Infectious Disease, Purdue University, 560 Oval Drive Box 68, West Lafayette, Indiana 47907, United States
| | - Ashwin Sunderraj
- Department
of Chemistry, Institute for Integrative Neuroscience, and Institute for
Inflammation, Immunology, and Infectious Disease, Purdue University, 560 Oval Drive Box 68, West Lafayette, Indiana 47907, United States
| | - Mathew Tantama
- Department
of Chemistry, Institute for Integrative Neuroscience, and Institute for
Inflammation, Immunology, and Infectious Disease, Purdue University, 560 Oval Drive Box 68, West Lafayette, Indiana 47907, United States
- E-mail: . Phone: 765-494-5312
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13
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Fixation of atmospheric CO2 and recognition of anions/hydrated anions: Differential binding mode in protonated vs. neutral tripodal urea/thiourea receptors. Inorganica Chim Acta 2019. [DOI: 10.1016/j.ica.2018.11.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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14
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Minhas GS, Bawdon D, Herman R, Rudden M, Stone AP, James AG, Thomas GH, Newstead S. Structural basis of malodour precursor transport in the human axilla. eLife 2018; 7:e34995. [PMID: 29966586 PMCID: PMC6059767 DOI: 10.7554/elife.34995] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Accepted: 06/23/2018] [Indexed: 01/10/2023] Open
Abstract
Mammals produce volatile odours that convey different types of societal information. In Homo sapiens, this is now recognised as body odour, a key chemical component of which is the sulphurous thioalcohol, 3-methyl-3-sulfanylhexan-1-ol (3M3SH). Volatile 3M3SH is produced in the underarm as a result of specific microbial activity, which act on the odourless dipeptide-containing malodour precursor molecule, S-Cys-Gly-3M3SH, secreted in the axilla (underarm) during colonisation. The mechanism by which these bacteria recognise S-Cys-Gly-3M3SH and produce body odour is still poorly understood. Here we report the structural and biochemical basis of bacterial transport of S-Cys-Gly-3M3SH by Staphylococcus hominis, which is converted to the sulphurous thioalcohol component 3M3SH in the bacterial cytoplasm, before being released into the environment. Knowledge of the molecular basis of precursor transport, essential for body odour formation, provides a novel opportunity to design specific inhibitors of malodour production in humans.
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Affiliation(s)
- Gurdeep S Minhas
- Department of BiochemistryUniversity of OxfordOxfordUnited Kingdom
| | - Daniel Bawdon
- Department of BiologyUniversity of YorkYorkUnited Kingdom
| | - Reyme Herman
- Department of BiologyUniversity of YorkYorkUnited Kingdom
| | | | - Andrew P Stone
- Department of BiologyUniversity of YorkYorkUnited Kingdom
| | | | - Gavin H Thomas
- Department of BiologyUniversity of YorkYorkUnited Kingdom
| | - Simon Newstead
- Department of BiochemistryUniversity of OxfordOxfordUnited Kingdom
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15
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Abstract
Copper-binding metallophores, or chalkophores, play a role in microbial copper homeostasis that is analogous to that of siderophores in iron homeostasis. The best-studied chalkophores are members of the methanobactin (Mbn) family-ribosomally produced, posttranslationally modified natural products first identified as copper chelators responsible for copper uptake in methane-oxidizing bacteria. To date, Mbns have been characterized exclusively in those species, but there is genomic evidence for their production in a much wider range of bacteria. This review addresses the current state of knowledge regarding the function, biosynthesis, transport, and regulation of Mbns. While the roles of several proteins in these processes are supported by substantial genetic and biochemical evidence, key aspects of Mbn manufacture, handling, and regulation remain unclear. In addition, other natural products that have been proposed to mediate copper uptake as well as metallophores that have biologically relevant roles involving copper binding, but not copper uptake, are discussed.
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Affiliation(s)
- Grace E Kenney
- Department of Molecular Biosciences, Northwestern University, Evanston, Illinois 60208, USA; ,
| | - Amy C Rosenzweig
- Department of Molecular Biosciences, Northwestern University, Evanston, Illinois 60208, USA; ,
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, USA
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16
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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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17
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Song L, Zhang Y, Chen W, Gu T, Zhang SY, Ji Q. Mechanistic insights into staphylopine-mediated metal acquisition. Proc Natl Acad Sci U S A 2018; 115:3942-3947. [PMID: 29581261 PMCID: PMC5899449 DOI: 10.1073/pnas.1718382115] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Metal acquisition is vital to pathogens for successful infection within hosts. Staphylopine (StP), a broad-spectrum metallophore biosynthesized by the major human pathogen, Staphylococcus aureus, plays a central role in transition-metal acquisition and bacterial virulence. The StP-like biosynthesis loci are present in various pathogens, and the proteins responsible for StP/metal transportation have been determined. However, the molecular mechanisms of how StP/metal complexes are recognized and transported remain unknown. We report multiple structures of the extracytoplasmic solute-binding protein CntA from the StP/metal transportation system in apo form and in complex with StP and three different metals. We elucidated a sophisticated metal-bound StP recognition mechanism and determined that StP/metal binding triggers a notable interdomain conformational change in CntA. Furthermore, CRISPR/Cas9-mediated single-base substitution mutations and biochemical analysis highlight the importance of StP/metal recognition for StP/metal acquisition. These discoveries provide critical insights into the study of novel metal-acquisition mechanisms in microbes.
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Affiliation(s)
- Liqiang Song
- School of Physical Science and Technology, ShanghaiTech University, 201210 Shanghai, China
| | - Yifei Zhang
- School of Physical Science and Technology, ShanghaiTech University, 201210 Shanghai, China
| | - Weizhong Chen
- School of Physical Science and Technology, ShanghaiTech University, 201210 Shanghai, China
| | - Tongnian Gu
- School of Physical Science and Technology, ShanghaiTech University, 201210 Shanghai, China
| | - Shu-Yu Zhang
- School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, 200240 Shanghai, China
| | - Quanjiang Ji
- School of Physical Science and Technology, ShanghaiTech University, 201210 Shanghai, China;
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18
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Peptide Uptake Is Essential for Borrelia burgdorferi Viability and Involves Structural and Regulatory Complexity of its Oligopeptide Transporter. mBio 2017; 8:mBio.02047-17. [PMID: 29259089 PMCID: PMC5736914 DOI: 10.1128/mbio.02047-17] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Borrelia burgdorferi is an extreme amino acid (AA) auxotroph whose genome encodes few free AA transporters and an elaborate oligopeptide transport system (B. burgdorferi Opp [BbOpp]). BbOpp consists of five oligopeptide-binding proteins (OBPs), two heterodimeric permeases, and a heterodimeric nucleotide-binding domain (NBD). Homology modeling based on the crystal structure of liganded BbOppA4 revealed that each OBP likely binds a distinct range of peptides. Transcriptional analyses demonstrated that the OBPs are differentially and independently regulated whereas the permeases and NBDs are constitutively expressed. A conditional NBD mutant failed to divide in the absence of inducer and replicated in an IPTG (isopropyl-β-d-thiogalactopyranoside) concentration-dependent manner. NBD mutants grown without IPTG exhibited an elongated morphotype lacking division septa, often with flattening at the cell center due to the absence of flagellar filaments. Following cultivation in dialysis membrane chambers, NBD mutants recovered from rats not receiving IPTG also displayed an elongated morphotype. The NBD mutant was avirulent by needle inoculation, but infectivity was partially restored by oral administration of IPTG to infected mice. We conclude that peptides are a major source of AAs for B. burgdorferi both in vitro and in vivo and that peptide uptake is essential for regulation of morphogenesis, cell division, and virulence. Borrelia burgdorferi, the causative agent of Lyme disease, is an extreme amino acid (AA) auxotroph with a limited repertoire of annotated single-AA transporters. A major issue is how the spirochete meets its AA requirements as it transits between its arthropod vector and mammalian reservoir. While previous studies have confirmed that the B. burgdorferi oligopeptide transport (opp) system is capable of importing peptides, the importance of the system for viability and pathogenesis has not been established. Here, we evaluated the opp system structurally and transcriptionally to elucidate its ability to import a wide range of peptides during the spirochete’s enzootic cycle. Additionally, using a novel mutagenesis strategy to abrogate opp transporter function, we demonstrated that peptide uptake is essential for bacterial viability, morphogenesis, and infectivity. Our studies revealed a novel link between borrelial physiology and virulence and suggest that peptide uptake serves an intracellular signaling function regulating morphogenesis and division.
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19
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Lee XA, Verma C, Sim AY. Designing dual inhibitors of Mdm2/MdmX: Unexpected coupling of water with gatekeeper Y100/99. Proteins 2017; 85:1493-1506. [DOI: 10.1002/prot.25310] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2016] [Revised: 03/28/2017] [Accepted: 04/17/2017] [Indexed: 01/06/2023]
Affiliation(s)
- Xiong An Lee
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR); Matrix 138671 Singapore
| | - Chandra Verma
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR); Matrix 138671 Singapore
- Department of Biological Sciences; National University of Singapore; 117543 Singapore
- School of Biological Sciences; Nanyang Technological University; 637551 Singapore
| | - Adelene Y.L Sim
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR); Matrix 138671 Singapore
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20
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The substrate-binding protein in bacterial ABC transporters: dissecting roles in the evolution of substrate specificity. Biochem Soc Trans 2016; 43:1011-7. [PMID: 26517916 DOI: 10.1042/bst20150135] [Citation(s) in RCA: 93] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
ATP-binding cassette (ABC) transporters, although being ubiquitous in biology, often feature a subunit that is limited primarily to bacteria and archaea. This subunit, the substrate-binding protein (SBP), is a key determinant of the substrate specificity and high affinity of ABC uptake systems in these organisms. Most prokaryotes have many SBP-dependent ABC transporters that recognize a broad range of ligands from metal ions to amino acids, sugars and peptides. Herein, we review the structure and function of a number of more unusual SBPs, including an ABC transporter involved in the transport of rare furanose forms of sugars and an SBP that has evolved to specifically recognize the bacterial cell wall-derived murein tripeptide (Mtp). Both these examples illustrate that subtle changes in binding-site architecture, including changes in side chains not directly involved in ligand co-ordination, can result in significant alteration of substrate range in novel and unpredictable ways.
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21
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Maurer M, de Beer SBA, Oostenbrink C. Calculation of Relative Binding Free Energy in the Water-Filled Active Site of Oligopeptide-Binding Protein A. Molecules 2016; 21:499. [PMID: 27092480 PMCID: PMC5881882 DOI: 10.3390/molecules21040499] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Revised: 03/30/2016] [Accepted: 04/11/2016] [Indexed: 11/19/2022] Open
Abstract
The periplasmic oligopeptide binding protein A (OppA) represents a well-known example of water-mediated protein-ligand interactions. Here, we perform free-energy calculations for three different ligands binding to OppA, using a thermodynamic integration approach. The tripeptide ligands share a high structural similarity (all have the sequence KXK), but their experimentally-determined binding free energies differ remarkably. Thermodynamic cycles were constructed for the ligands, and simulations conducted in the bound and (freely solvated) unbound states. In the unbound state, it was observed that the difference in conformational freedom between alanine and glycine leads to a surprisingly slow convergence, despite their chemical similarity. This could be overcome by increasing the softness parameter during alchemical transformations. Discrepancies remained in the bound state however, when comparing independent simulations of the three ligands. These difficulties could be traced to a slow relaxation of the water network within the active site. Fluctuations in the number of water molecules residing in the binding cavity occur mostly on a timescale larger than the simulation time along the alchemical path. After extensive simulations, relative binding free energies that were converged to within thermal noise could be obtained, which agree well with available experimental data.
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Affiliation(s)
- Manuela Maurer
- Institute of Molecular Modeling and Simulation, University of Natural Resources and Life Sciences, Muthgasse 18, A-1190 Vienna, Austria.
| | - Stephanie B A de Beer
- Institute of Molecular Modeling and Simulation, University of Natural Resources and Life Sciences, Muthgasse 18, A-1190 Vienna, Austria.
| | - Chris Oostenbrink
- Institute of Molecular Modeling and Simulation, University of Natural Resources and Life Sciences, Muthgasse 18, A-1190 Vienna, Austria.
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22
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Michel J, Verdonk ML, Essex JW. Protein-Ligand Complexes: Computation of the Relative Free Energy of Different Scaffolds and Binding Modes. J Chem Theory Comput 2015; 3:1645-55. [PMID: 26627610 DOI: 10.1021/ct700081t] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
A methodology for the calculation of the free energy difference between a pair of molecules of arbitrary topology is proposed. The protocol relies on a dual-topology paradigm, a softening of the intermolecular interactions, and a constraint that prevents the perturbed molecules from drifting away from each other at the end states. The equivalence and the performance of the methodology against a single-topology approach are demonstrated on a pair of harmonic oscillators, the calculation of the relative solvation free energy of ethane and methanol, and the relative binding free energy of two congeneric inhibitors of cyclooxygenase 2. The stability of two alternative binding modes of an inhibitor of cyclin-dependent kinase 2 is then investigated. Finally, the relative binding free energy of two structurally different inhibitors of cyclin-dependent kinase 2 is calculated. The proposed methodology allows the study of a range of problems that are beyond the reach of traditional relative free energy calculation protocols and should prove useful in drug design studies.
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Affiliation(s)
- Julien Michel
- School of Chemistry, University of Southampton, Highfield, Southampton, SO17 1BJ, United Kingdom, and Astex Therapeutics Ltd., 436 Cambridge Science Park, Cambridge, CB4 0QA, United Kingdom
| | - Marcel L Verdonk
- School of Chemistry, University of Southampton, Highfield, Southampton, SO17 1BJ, United Kingdom, and Astex Therapeutics Ltd., 436 Cambridge Science Park, Cambridge, CB4 0QA, United Kingdom
| | - Jonathan W Essex
- School of Chemistry, University of Southampton, Highfield, Southampton, SO17 1BJ, United Kingdom, and Astex Therapeutics Ltd., 436 Cambridge Science Park, Cambridge, CB4 0QA, United Kingdom
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23
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Minkiewicz P, Darewicz M, Iwaniak A, Sokołowska J, Starowicz P, Bucholska J, Hrynkiewicz M. Common Amino Acid Subsequences in a Universal Proteome--Relevance for Food Science. Int J Mol Sci 2015; 16:20748-73. [PMID: 26340620 PMCID: PMC4613229 DOI: 10.3390/ijms160920748] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2015] [Revised: 08/18/2015] [Accepted: 08/24/2015] [Indexed: 02/06/2023] Open
Abstract
A common subsequence is a fragment of the amino acid chain that occurs in more than one protein. Common subsequences may be an object of interest for food scientists as biologically active peptides, epitopes, and/or protein markers that are used in comparative proteomics. An individual bioactive fragment, in particular the shortest fragment containing two or three amino acid residues, may occur in many protein sequences. An individual linear epitope may also be present in multiple sequences of precursor proteins. Although recent recommendations for prediction of allergenicity and cross-reactivity include not only sequence identity, but also similarities in secondary and tertiary structures surrounding the common fragment, local sequence identity may be used to screen protein sequence databases for potential allergens in silico. The main weakness of the screening process is that it overlooks allergens and cross-reactivity cases without identical fragments corresponding to linear epitopes. A single peptide may also serve as a marker of a group of allergens that belong to the same family and, possibly, reveal cross-reactivity. This review article discusses the benefits for food scientists that follow from the common subsequences concept.
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Affiliation(s)
- Piotr Minkiewicz
- Department of Food Biochemistry, University of Warmia and Mazury in Olsztyn, Plac Cieszyński 1, Olsztyn-Kortowo 10-726, Poland.
| | - Małgorzata Darewicz
- Department of Food Biochemistry, University of Warmia and Mazury in Olsztyn, Plac Cieszyński 1, Olsztyn-Kortowo 10-726, Poland.
| | - Anna Iwaniak
- Department of Food Biochemistry, University of Warmia and Mazury in Olsztyn, Plac Cieszyński 1, Olsztyn-Kortowo 10-726, Poland.
| | - Jolanta Sokołowska
- Department of Food Biochemistry, University of Warmia and Mazury in Olsztyn, Plac Cieszyński 1, Olsztyn-Kortowo 10-726, Poland.
| | - Piotr Starowicz
- Department of Food Biochemistry, University of Warmia and Mazury in Olsztyn, Plac Cieszyński 1, Olsztyn-Kortowo 10-726, Poland.
| | - Justyna Bucholska
- Department of Food Biochemistry, University of Warmia and Mazury in Olsztyn, Plac Cieszyński 1, Olsztyn-Kortowo 10-726, Poland.
| | - Monika Hrynkiewicz
- Department of Food Biochemistry, University of Warmia and Mazury in Olsztyn, Plac Cieszyński 1, Olsztyn-Kortowo 10-726, Poland.
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24
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Montoya-Rodríguez A, Gómez-Favela MA, Reyes-Moreno C, Milán-Carrillo J, González de Mejía E. Identification of Bioactive Peptide Sequences from Amaranth (Amaranthus hypochondriacus) Seed Proteins and Their Potential Role in the Prevention of Chronic Diseases. Compr Rev Food Sci Food Saf 2015; 14:139-158. [DOI: 10.1111/1541-4337.12125] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2014] [Accepted: 12/01/2014] [Indexed: 12/21/2022]
Affiliation(s)
- Alvaro Montoya-Rodríguez
- Programa Regional del Noroeste para el Doctorado en Biotecnología, FCQB-UAS; Ciudad Univ; AP 1354, CP 80000 Culiacán Sinaloa México
- Dept. of Food Science and Human Nutrition; Univ. of Illinois at Urbana-Champaign; IL 61801 U.S.A
| | - Mario A. Gómez-Favela
- Programa Regional del Noroeste para el Doctorado en Biotecnología, FCQB-UAS; Ciudad Univ; AP 1354, CP 80000 Culiacán Sinaloa México
| | - Cuauhtémoc Reyes-Moreno
- Programa Regional del Noroeste para el Doctorado en Biotecnología, FCQB-UAS; Ciudad Univ; AP 1354, CP 80000 Culiacán Sinaloa México
| | - Jorge Milán-Carrillo
- Programa Regional del Noroeste para el Doctorado en Biotecnología, FCQB-UAS; Ciudad Univ; AP 1354, CP 80000 Culiacán Sinaloa México
| | - Elvira González de Mejía
- Dept. of Food Science and Human Nutrition; Univ. of Illinois at Urbana-Champaign; IL 61801 U.S.A
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25
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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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26
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De S, Groaz E, Herdewijn P. Tailoring Peptide-Nucleotide Conjugates (PNCs) for Nucleotide Delivery in Bacterial Cells. European J Org Chem 2014. [DOI: 10.1002/ejoc.201301781] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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27
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Cavazos A, Gonzalez de Mejia E. Identification of Bioactive Peptides from Cereal Storage Proteins and Their Potential Role in Prevention of Chronic Diseases. Compr Rev Food Sci Food Saf 2013; 12:364-380. [DOI: 10.1111/1541-4337.12017] [Citation(s) in RCA: 116] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2013] [Accepted: 03/27/2013] [Indexed: 01/11/2023]
Affiliation(s)
- Ariel Cavazos
- Dept. of Food Science and Human Nutrition; Univ. of Illinois at Urbana Champaign; 228 ERML; 1201 W. Gregory Drive; Urbana; IL 61801; U.S.A
| | - Elvira Gonzalez de Mejia
- Dept. of Food Science and Human Nutrition; Univ. of Illinois at Urbana Champaign; 228 ERML; 1201 W. Gregory Drive; Urbana; IL 61801; U.S.A
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28
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Basu A, Das G. Encapsulation of a discrete cyclic halide water tetramer [X2(H2O)2]2-, X = Cl-/Br- within a dimeric capsular assembly of a tripodal amide receptor. Chem Commun (Camb) 2013; 49:3997-9. [PMID: 23563509 DOI: 10.1039/c3cc40955d] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
A conformationally flexible C3v symmetric N-bridged tripodal amide receptor encapsulates a tetrameric halide water cluster [X2(H2O)2](2-) (X = Cl(-)/Br(-)) within its dimeric capsular assembly and forms a non-capsular 1D polymeric assembly with higher homologous iodide anions upon protonation.
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Affiliation(s)
- Arghya Basu
- Department of Chemistry, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India
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29
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Audie J, Swanson J. Advances in the Prediction of Protein-Peptide Binding Affinities: Implications for Peptide-Based Drug Discovery. Chem Biol Drug Des 2012; 81:50-60. [DOI: 10.1111/cbdd.12076] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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30
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Higgins KA, Carr CE, Maroney MJ. Specific metal recognition in nickel trafficking. Biochemistry 2012; 51:7816-32. [PMID: 22970729 DOI: 10.1021/bi300981m] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Nickel is an essential metal for a number of bacterial species that have developed systems for acquiring, delivering, and incorporating the metal into target enzymes and controlling the levels of nickel in cells to prevent toxic effects. As with other transition metals, these trafficking systems must be able to distinguish between the desired metal and other transition metal ions with similar physical and chemical properties. Because there are few enzymes (targets) that require nickel for activity (e.g., Escherichia coli transports nickel for hydrogenases made under anaerobic conditions, and Helicobacter pylori requires nickel for hydrogenase and urease that are essential for acid viability), the "traffic pattern" for nickel is relatively simple, and nickel trafficking therefore presents an opportunity to examine a system for the mechanisms that are used to distinguish nickel from other metals. In this review, we describe the details known for examples of uptake permeases, metallochaperones and proteins involved in metallocenter assembly, and nickel metalloregulators. We also illustrate a variety of mechanisms, including molecular recognition in the case of NikA protein and examples of allosteric regulation for HypA, NikR, and RcnR, employed to generate specific biological responses to nickel ions.
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Affiliation(s)
- Khadine A Higgins
- Department of Chemistry, University of Massachusetts, Amherst, Massachusetts 01003, USA
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31
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Affiliation(s)
- David J Huggins
- Department of Oncology, Hutchison/MRC Research Centre, University of Cambridge, Hills Road, Cambridge, CB2 0XZ, United Kingdom.
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32
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Saeed MA, Pramanik A, Wong BM, Haque SA, Powell DR, Chand DK, Hossain MA. Self-assembly of ordered water tetramers in an encapsulated [Br(H2O)12]− complex. Chem Commun (Camb) 2012; 48:8631-3. [DOI: 10.1039/c2cc30767g] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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Escherichia coli Peptide Binding Protein OppA Has a Preference for Positively Charged Peptides. J Mol Biol 2011; 414:75-85. [DOI: 10.1016/j.jmb.2011.09.043] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2011] [Revised: 09/20/2011] [Accepted: 09/26/2011] [Indexed: 11/18/2022]
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Cappel D, Wahlström R, Brenk R, Sotriffer CA. Probing the Dynamic Nature of Water Molecules and Their Influences on Ligand Binding in a Model Binding Site. J Chem Inf Model 2011; 51:2581-94. [DOI: 10.1021/ci200052j] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Daniel Cappel
- Institute of Pharmacy and Food Chemistry, Julius-Maximilians University Würzburg, Am Hubland, D-97074 Würzburg, Germany
| | - Rickard Wahlström
- College of Life Sciences, Division of Chemical Biology and Drug Discovery, James Black Centre, University of Dundee, Dow Street, Dundee DD1 5EH, Scotland, United Kingdom
| | - Ruth Brenk
- College of Life Sciences, Division of Chemical Biology and Drug Discovery, James Black Centre, University of Dundee, Dow Street, Dundee DD1 5EH, Scotland, United Kingdom
| | - Christoph A. Sotriffer
- Institute of Pharmacy and Food Chemistry, Julius-Maximilians University Würzburg, Am Hubland, D-97074 Würzburg, Germany
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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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Gauto DF, Di Lella S, Estrin DA, Monaco HL, Martí MA. Structural basis for ligand recognition in a mushroom lectin: solvent structure as specificity predictor. Carbohydr Res 2011; 346:939-48. [PMID: 21453906 DOI: 10.1016/j.carres.2011.02.016] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2010] [Revised: 02/07/2011] [Accepted: 02/16/2011] [Indexed: 11/29/2022]
Abstract
Lectins are able to recognize specific carbohydrate structures through their carbohydrate recognition domain (CRD). The lectin from the mushroom Agaricus bisporus (ABL) has the remarkable ability of selectively recognizing the TF-antigen, composed of Galβ1-3GalNAc, Ser/Thr linked to proteins, specifically exposed in neoplastic tissues. Strikingly, the recently solved crystal structure of tetrameric ABL in the presence of TF-antigen and other carbohydrates showed that each monomer has two CRDs, each being able to bind specifically to different monosaccharides that differ only in the configuration of a single hydroxyl, like N-acetyl-d-galactosamine (GalNAc) and N-acetyl-d-glucosamine (GlcNAc). Understanding how lectin CRDs bind and discriminate mono and/or (poly)-saccharides is an important issue in glycobiology, with potential impact in the design of better and selective lectin inhibitors with potential therapeutic properties. In this work, and based on the unusual monosaccharide epimeric specificity of the ABL CRDs, we have performed molecular dynamics simulations of the natural (crystallographic) and inverted (changing GalNAc for GlcNAc and vice-versa) ABL-monosaccharide complexes in order to understand the selective ligand recognition properties of each CRD. We also performed a detailed analysis of the CRD local solvent structure, using previously developed methodology, and related it with the recognition mechanism. Our results provide a detailed picture of each ABL CRD specificity, allowing a better understanding of the carbohydrate selective recognition process in this particular lectin.
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Affiliation(s)
- Diego F Gauto
- Departamento de Química Inorgánica, Analítica, y Química Física, INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pabellón II, C1428EHA Ciudad de Buenos Aires, Argentina, Argentina
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37
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Specific intermolecular interactions of conserved water molecules with amino acids in the Galectin-1 carbohydrate recognition domain. J Mol Struct 2010. [DOI: 10.1016/j.molstruc.2010.03.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Tian F, Yang L, Lv F, Luo X, Pan Y. Why OppA protein can bind sequence-independent peptides? A combination of QM/MM, PB/SA, and structure-based QSAR analyses. Amino Acids 2010; 40:493-503. [DOI: 10.1007/s00726-010-0661-9] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2010] [Accepted: 06/12/2010] [Indexed: 01/21/2023]
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39
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Saeed MA, Wong BM, Fronczek FR, Venkatraman R, Hossain MA. Formation of an Amine-Water Cyclic Pentamer: A New Type of Water Cluster in a Polyazacryptand. CRYSTAL GROWTH & DESIGN 2010; 10:1486-1488. [PMID: 20495666 PMCID: PMC2873190 DOI: 10.1021/cg100161a] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Structural analysis of an adduct of a thiophene-based cryptand with tosylic acid shows the formation of a hybrid amine-water cyclic pentamer composed of four water molecules and one protonated amine in the charged hydrophobic cavity. The bulky tosylate groups remain outside the cavity, making the ligand favorable for hosting water molecules. Ab initio calculations based on density functional theory (DFT) confirm that the hybrid amine-water pentamer is stabilized inside the hydrophobic cavity of the cryptand.
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Affiliation(s)
- Musabbir A. Saeed
- Department of Chemistry and Biochemistry, Jackson State University, Jackson, MS 39212
| | - Bryan M. Wong
- Materials Chemistry Department, Sandia National Laboratories, Livermore, CA 94551
| | - Frank R. Fronczek
- Department of Chemistry, Louisiana State University, Baton Rouge, LA 70803
| | - Ramaiyer Venkatraman
- Department of Chemistry and Biochemistry, Jackson State University, Jackson, MS 39212
| | - Md. Alamgir Hossain
- Department of Chemistry and Biochemistry, Jackson State University, Jackson, MS 39212
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40
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Picon A, García-Casado M, Nuñez M. Proteolytic activities, peptide utilization and oligopeptide transport systems of wild Lactococcus lactis strains. Int Dairy J 2010. [DOI: 10.1016/j.idairyj.2009.10.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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41
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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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42
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Gauto DF, Di Lella S, Guardia CMA, Estrin DA, Martí MA. Carbohydrate-binding proteins: Dissecting ligand structures through solvent environment occupancy. J Phys Chem B 2009; 113:8717-24. [PMID: 19485380 DOI: 10.1021/jp901196n] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Formation of protein ligand complexes is a fundamental phenomenon in biochemistry. During the process, significant solvent reorganization is produced along the contact surface and many water molecules strongly bound to the protein's ligand binding site must be displaced. Both the thermodynamics and kinetics of this process are complex and a clear understanding at the microscopic level has been not achieved so far. Special attention has been paid to the structure of water molecules on carbohydrate recognition sites of various proteins, and many studies support the idea that displacement of these water molecules should have a crucial effect on the binding free energy. Molecular dynamics (MD) simulations in explicit water solvent is a very promising approach for this type of studies. Using MD simulations combined with statistical mechanics analysis, thermodynamic properties of these water molecules can be computed and analyzed in a comparative view. Using this idea, we developed a set of analysis tools to link solvation with ligand binding in a key carbohydrate binding protein, human galectin-1 (hGal-1). Specifically, we defined water sites (WS) in terms of the thermodynamic properties of water molecules strongly bound to protein surfaces. In the present work, we selected a group of proteins whose ligand bound complexes have been already structurally characterized in order to extend the analysis of the role of the surface associated water molecules in the ligand binding and recognition process. The selected proteins are concanavalin-A (Con-A), galectin-3 (Gal-3), cyclophilin-A (Cyp-A), and two modules CBM40 and CBM32 of the multimodular bacterial sialidase. Our results show that the probability of finding water molecules inside the WS, p(v), with respect to the bulk density is directly correlated to the likeliness of finding an hydroxyl group of the ligand in the protein-ligand complex. This information can be used to analyze in detail the solvation structure of the carbohydrate recognition domain (CRD) and its relation to the possible protein ligand complexes and suggests addition of OH-containing functional groups to displace water from high p(v) WS to enhance drugs, specially glycomimetic-drugs, protein affinity, and/or specificity.
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Affiliation(s)
- Diego F Gauto
- Departamento de Quimica Inorganica, Analitica, y Quimica Fisica, INQUIMAE-CONICET, Universidad de Buenos Aires, Argentina
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43
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Cuneo MJ, Changela A, Beese LS, Hellinga HW. Structural Adaptations that Modulate Monosaccharide, Disaccharide, and Trisaccharide Specificities in Periplasmic Maltose-Binding Proteins. J Mol Biol 2009; 389:157-66. [DOI: 10.1016/j.jmb.2009.04.008] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2009] [Revised: 04/02/2009] [Accepted: 04/03/2009] [Indexed: 11/25/2022]
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44
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The Thermodynamics of Protein–Ligand Interaction and Solvation: Insights for Ligand Design. J Mol Biol 2008; 384:1002-17. [DOI: 10.1016/j.jmb.2008.09.073] [Citation(s) in RCA: 249] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2008] [Revised: 09/26/2008] [Accepted: 09/26/2008] [Indexed: 11/21/2022]
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45
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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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46
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Silva-Sánchez C, de la Rosa APB, León-Galván MF, de Lumen BO, de León-Rodríguez A, de Mejía EG. Bioactive peptides in amaranth (Amaranthus hypochondriacus) seed. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2008; 56:1233-40. [PMID: 18211015 DOI: 10.1021/jf072911z] [Citation(s) in RCA: 131] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Amaranth seeds are rich in protein with a high nutritional value, but little is known about their bioactive compounds that could benefit health. The objectives of this research were to investigate the presence, characterization, and the anticarcinogenic properties of the peptide lunasin in amaranth seeds. Furthermore, to predict and identify other peptides in amaranth seed with potential biological activities. ELISA showed an average concentration of 11.1 microg lunasin equivalent/g total extracted protein in four genotypes of mature amaranth seeds. Glutelin fraction had the highest lunasin concentration (3.0 microg/g). Lunasin was also identified in albumin, prolamin and globulin amaranth protein fractions and even in popped amaranth seeds. Western blot analysis revealed a band at 18.5 kDa, and MALDI-TOF analysis showed that this peptide matched more than 60% of the soybean lunasin peptide sequence. Glutelin extracts digested with trypsin, showed the induction of apoptosis against HeLa cells. Prediction of other bioactive peptides in amaranth globulins and glutelins were mainly antihypertensive. This is the first study that reports the presence of a lunasin-like peptide and other potentially bioactive peptides in amaranth protein fractions.
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Affiliation(s)
- C Silva-Sánchez
- Molecular Biology Division, Instituto Potosino de Investigación Científica y Tecnológica, San Luis Potosí, S.L.P., Mexico
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47
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Marchand A, Marchand D, Busson R, Marlière P, Herdewijn P. Synthesis of a pyridoxine-peptide based delivery system for nucleotides. Chem Biodivers 2007; 4:1450-65. [PMID: 17638325 DOI: 10.1002/cbdv.200790123] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
As a first step in the development of a nucleotide delivery system making use of oligopeptide permease, we have synthesized pyridoxine-peptide-nucleotide conjugates. The nucleotides are bonded on serine residues. The peptides terminate with a pyroglutamate residue. In the first example, the pyridoxine moiety is connected at the end of the peptides, while, in the second example, the pyridoxine moiety is bonded at an aspartic acid residue in a middle position of the peptide. Nucleotides are introduced as phosphoramidites. The synthetic strategy involves a series of protection, deprotection, and coupling reactions, and integrates peptide, nucleotide, and pyridoxine chemistry. The final deprotection step was carried out in basic conditions using 10% K2CO3 in MeOH.
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Affiliation(s)
- Arnaud Marchand
- Laboratory of Medicinal Chemistry, Rega Institute for Medical Research, KU Leuven, Minderbroedersstraat 10, B-3000 Leuven, Belgium
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48
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Müller A, León-Kempis MDR, Dodson E, Wilson KS, Wilkinson AJ, Kelly DJ. A Bacterial Virulence Factor with a Dual Role as an Adhesin and a Solute-binding Protein: The Crystal Structure at 1.5 Å Resolution of the PEB1a Protein from the Food-borne Human Pathogen Campylobacter jejuni. J Mol Biol 2007; 372:160-71. [PMID: 17631313 DOI: 10.1016/j.jmb.2007.06.041] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2007] [Revised: 06/13/2007] [Accepted: 06/14/2007] [Indexed: 12/20/2022]
Abstract
The PEB1a protein is an antigenic factor exposed on the surface of the food-borne human pathogen Campylobacter jejuni, which has a major role in adherence and host colonisation. PEB1a is also the periplasmic binding protein component of an aspartate/glutamate ABC transporter essential for optimal microaerobic growth on these dicarboxylic amino acids. Here, we report the crystal structure of PEB1a at 1.5 A resolution. The protein has a typical two-domain alpha/beta structure, characteristic of periplasmic extracytoplasmic solute receptors and a chain topology related to the type II subfamily. An aspartate ligand, clearly defined by electron density in the interdomain cleft, forms extensive polar interactions with the protein, the majority of which are made with the larger domain. Arg89 and Asp174 form ion-pairing interactions with the main chain alpha-carboxyl and alpha-amino-groups, respectively, of the ligand, while Arg67, Thr82, Lys19 and Tyr156 co-ordinate the ligand side-chain carboxyl group. Lys19 and Arg67 line a positively charged groove, which favours binding of Asp over the neutral Asn. The ligand-binding cleft is of sufficient depth to accommodate a glutamate. This is the first structure of an ABC-type aspartate-binding protein, and explains the high affinity of the protein for aspartate and glutamate, and its much weaker binding of asparagine and glutamine. Stopped-flow fluorescence spectroscopy indicates a simple bimolecular mechanism of ligand binding, with high association rate constants. Sequence alignments and phylogenetic analyses revealed PEB1a homologues in some Gram-positive bacteria. The alignments suggest a more distant homology with GltI from Escherichia coli, a known glutamate and aspartate-binding protein, but Lys19 and Tyr156 are not conserved in GltI. Our results provide a structural basis for understanding both the solute transport and adhesin/virulence functions of PEB1a.
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Affiliation(s)
- Axel Müller
- Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York YO10 5YW, UK
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Kurashima-Ito K, Moromisato K, Nishimura K, Wälchli M, Tame JRH, Ito Y. Backbone 1H, 13C and 15N assignments of a 59 kDa Salmonella typhimurium periplasmic oligopeptide binding protein, OppA. BIOMOLECULAR NMR ASSIGNMENTS 2007; 1:37-39. [PMID: 19636820 DOI: 10.1007/s12104-007-9008-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2006] [Accepted: 02/22/2007] [Indexed: 05/28/2023]
Abstract
Salmonella typhimurium OppA is the periplasmic oligopeptide-binding protein. Backbone resonances of OppA(D419N) on its own were assigned for approximately 90% of residues. Missing residues are localised around the ligand-binding site, suggesting conformational flexibility in the unliganded state.
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Affiliation(s)
- Kaori Kurashima-Ito
- Research Group for Bio-supramolecular Structure-Function, RIKEN, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
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Li Z, Lazaridis T. The effect of water displacement on binding thermodynamics: concanavalin A. J Phys Chem B 2007; 109:662-70. [PMID: 16851059 DOI: 10.1021/jp0477912] [Citation(s) in RCA: 95] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Interactions at the binding interface of biomolecular complexes are often mediated by ordered water molecules. In this work, we considered two concanavalin A-carbohydrate complexes. In the first, a water molecule is buried at the binding interface. In the second, this water molecule is displaced by a modification of the ligand (Clarke, C.; Woods, R. J.; Gluska, J.; Cooper, A.; Nutley, M. A.; Boons, G. J. J. Am. Chem. Soc. 2001, 123, 12238-12247). We computed the contribution of this water molecule to the thermodynamic properties using statistical mechanical formulas for the energy and entropy and molecular dynamics simulations. Other contributions to the binding affinity, including desolvation, entropy of conformational restriction, and interaction between the ligand and protein, were also computed. The thermodynamic consequences of displacement of the ordered water molecule by ligand modification were in qualitative agreement with experimental data. The free energy contribution of the water molecule (-17.2 kcal/mol; -19.2 enthalpic and +2 entropic) was nearly equivalent to the additional protein-ligand interactions in trimannoside 2 (-18.9 kcal/mol). The two structural ions interact more strongly with the water than with the hydroxyl of trimannoside 2, thus favoring trimannoside 1. The contributions from desolvation and conformational entropy are much smaller but significant, compared to the binding free energy difference. The picture that emerges is that the final outcome of water displacement is sensitive to the details of the binding site and cannot be predicted by simple empirical rules.
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Affiliation(s)
- Zheng Li
- Department of Chemistry, City College of CUNY, New York, New York 10031, USA
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