1
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Bemani P, Mohammadi M, Hakakian A. Anti-ROR1 scFv-EndoG as a Novel Anti-Cancer Therapeutic Drug. Asian Pac J Cancer Prev 2018; 19:97-102. [PMID: 29373898 PMCID: PMC5844643 DOI: 10.22034/apjcp.2018.19.1.97] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Aim: Immunotoxins are proteins that consist of an antibody fragment linked to a toxin, used as agents for targeted
therapy of cancers. Although the most potent immunotoxins are made from bacterial and plant toxins, obstacles which
contribute to poor responses are immunogenicity in patients and rapid development of neutralizing antibodies. In the
present study we proposed a new therapeutic immunotoxin for targeted cancer therapy of ROR1 expressing cancers:
an anti ROR1 single chain fragment variable antibody (scFv)-endonuclease G (anti ROR1 scFv-EndoG). Methods:
The three-dimensional structure of anti ROR1 scFv-EndoG protein was modeled and structure validation tools were
employed to confirm the accuracy and reliability of the developed model. In addition, stability and integrity of the
model were assessed by molecular dynamic (MD) simulation. Results: All results suggested the protein model to
be acceptable and of good quality. Conclusions: Anti-ROR1 scFv-EndoG would be expected to bind to the ROR1
extracellular domain by its scFv portion and selectively deliver non-immunogenic human endonuclease G enzyme as
an end-stage apoptosis molecule into ROR1-expressing cancer cells and lead rapidly to apoptosis. We believe that anti
ROR1 and other anti-tumor antigen scFv-EndoG forms may be helpful for cancer therapy.
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Affiliation(s)
- Peyman Bemani
- Department of Immunology, Shiraz University of Medical Sciences, Shiraz, Iran. ,
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2
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Baslé A, Hewitt L, Koh A, Lamb HK, Thompson P, Burgess JG, Hall MJ, Hawkins AR, Murray H, Lewis RJ. Crystal structure of NucB, a biofilm-degrading endonuclease. Nucleic Acids Res 2018; 46:473-484. [PMID: 29165717 PMCID: PMC5758888 DOI: 10.1093/nar/gkx1170] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Accepted: 11/13/2017] [Indexed: 01/23/2023] Open
Abstract
Bacterial biofilms are a complex architecture of cells that grow on moist interfaces, and are held together by a molecular glue of extracellular proteins, sugars and nucleic acids. Biofilms are particularly problematic in human healthcare as they can coat medical implants and are thus a potential source of disease. The enzymatic dispersal of biofilms is increasingly being developed as a new strategy to treat this problem. Here, we have characterized NucB, a biofilm-dispersing nuclease from a marine strain of Bacillus licheniformis, and present its crystal structure together with the biochemistry and a mutational analysis required to confirm its active site. Taken together, these data support the categorization of NucB into a unique subfamily of the ββα metal-dependent non-specific endonucleases. Understanding the structure and function of NucB will facilitate its future development into an anti-biofilm therapeutic agent.
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Affiliation(s)
- Arnaud Baslé
- Institute for Cell and Molecular Biosciences, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Lorraine Hewitt
- Institute for Cell and Molecular Biosciences, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Alan Koh
- Centre for Bacterial Cell Biology, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4AX, UK
| | - Heather K Lamb
- Institute for Cell and Molecular Biosciences, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Paul Thompson
- Institute for Cell and Molecular Biosciences, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - J Grant Burgess
- Marine Biology, School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
| | - Michael J Hall
- Chemistry, School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
| | - Alastair R Hawkins
- Institute for Cell and Molecular Biosciences, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Heath Murray
- Centre for Bacterial Cell Biology, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4AX, UK
| | - Richard J Lewis
- Institute for Cell and Molecular Biosciences, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, UK,To whom correspondence should be addressed. Tel: +44 191 208 5482;
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3
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Maganti L, Ghosh M, Chakrabarti J. Molecular dynamics studies on conformational thermodynamics of Orai1-calmodulin complex. J Biomol Struct Dyn 2017; 36:3411-3419. [PMID: 28978262 DOI: 10.1080/07391102.2017.1388289] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Molecular understanding of bio-macromolecular binding is a challenging task due to large sizes of the molecules and presence of variety of interactions. Here, we study the molecular mechanism of calmodulin (CaM) binding to Orai1 that regulates Ca2+-dependent inactivation process in eukaryotic cells. Although experimental observations indicate that Orai1 binds to the C-terminal of Ca2+-loaded CaM, it is not decisive if N-domain of CaM interacts with Orai1. We address the issue of interaction of different domains of CaM with Orai1 using conformational thermodynamic changes, computed from histograms of dihedral angles over simulated trajectories of CaM, CaM-binding domain of Orai1 and complexes of CaM with Orai1. The changes for all residues of both C and N terminal domains of CaM upon Orai1 binding are compared. Our analysis shows that Orai1binds to both C-terminal and N-terminal domains of CaM, indicating 1:2 stoichiometry. The Orai1 binding to N-terminal domain of CaM is less stable than that to the C-terminal domain. The binding residues are primarily hydrophobic. These observations are in qualitative agreement to the experiments. The conformational thermodynamic changes thus provide a useful computational tool to provide atomic details of interactions in bio-macromolecular binding.
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Affiliation(s)
- Lakshmi Maganti
- a Department of Chemical, Biological and Macromolecular Sciences , S. N. Bose National Centre for Basic Sciences , Sector III, Block JD, Salt Lake, Kolkata 700106 , India
| | - Mahua Ghosh
- a Department of Chemical, Biological and Macromolecular Sciences , S. N. Bose National Centre for Basic Sciences , Sector III, Block JD, Salt Lake, Kolkata 700106 , India
| | - J Chakrabarti
- a Department of Chemical, Biological and Macromolecular Sciences , S. N. Bose National Centre for Basic Sciences , Sector III, Block JD, Salt Lake, Kolkata 700106 , India.,b Unit of Nanoscience and Technology-II and The Thematic Unit of Excellence on Computational Materials Science , S. N. Bose National Centre for Basic Sciences , Sector III, Block JD, Salt Lake, Kolkata 700106 , India
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4
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Oliva C, Sánchez-Murcia PA, Rico E, Bravo A, Menéndez M, Gago F, Jiménez-Ruiz A. Structure-based domain assignment in Leishmania infantum EndoG: characterization of a pH-dependent regulatory switch and a C-terminal extension that largely dictates DNA substrate preferences. Nucleic Acids Res 2017; 45:9030-9045. [PMID: 28911117 PMCID: PMC5587815 DOI: 10.1093/nar/gkx629] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Accepted: 07/11/2017] [Indexed: 11/28/2022] Open
Abstract
Mitochondrial endonuclease G from Leishmania infantum (LiEndoG) participates in the degradation of double-stranded DNA (dsDNA) during parasite cell death and is catalytically inactive at a pH of 8.0 or above. The presence, in the primary sequence, of an acidic amino acid-rich insertion exclusive to trypanosomatids and its spatial position in a homology-built model of LiEndoG led us to postulate that this peptide stretch might act as a pH sensor for self-inhibition. We found that a LiEndoG variant lacking residues 145–180 is indeed far more active than its wild-type counterpart at pH values >7.0. In addition, we discovered that (i) LiEndoG exists as a homodimer, (ii) replacement of Ser211 in the active-site SRGH motif with the canonical aspartate from the DRGH motif of other nucleases leads to a catalytically deficient enzyme, (iii) the activity of the S211D variant can be restored upon the concomitant replacement of Ala247 with Arg and (iv) a C-terminal extension is responsible for the observed preferential cleavage of single-stranded DNA (ssDNA) and ssDNA–dsDNA junctions. Taken together, our results support the view that LiEndoG is a multidomain molecular machine whose nuclease activity can be subtly modulated or even abrogated through architectural changes brought about by environmental conditions and interaction with other binding partners.
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MESH Headings
- Amino Acid Sequence
- Amino Acid Substitution
- Catalytic Domain
- Cloning, Molecular
- DNA Cleavage
- DNA, Protozoan/chemistry
- DNA, Protozoan/genetics
- DNA, Protozoan/metabolism
- DNA, Single-Stranded/chemistry
- DNA, Single-Stranded/genetics
- DNA, Single-Stranded/metabolism
- Endodeoxyribonucleases/chemistry
- Endodeoxyribonucleases/genetics
- Endodeoxyribonucleases/metabolism
- Escherichia coli/genetics
- Escherichia coli/metabolism
- Gene Expression
- Hydrogen-Ion Concentration
- Kinetics
- Leishmania infantum/chemistry
- Leishmania infantum/enzymology
- Models, Molecular
- Nucleic Acid Conformation
- Protein Binding
- Protein Conformation, alpha-Helical
- Protein Conformation, beta-Strand
- Protein Interaction Domains and Motifs
- Protein Multimerization
- Protozoan Proteins/chemistry
- Protozoan Proteins/genetics
- Protozoan Proteins/metabolism
- Recombinant Proteins/chemistry
- Recombinant Proteins/genetics
- Recombinant Proteins/metabolism
- Sequence Alignment
- Sequence Deletion
- Sequence Homology, Amino Acid
- Structure-Activity Relationship
- Substrate Specificity
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Affiliation(s)
- Cristina Oliva
- Departamento de Biología de Sistemas, Universidad de Alcalá, E-28805 Alcalá de Henares, Madrid, Spain
| | - Pedro A. Sánchez-Murcia
- Departamento de Ciencias Biomédicas y “Unidad Asociada IQM-CSIC”, Universidad de Alcalá, E-28805 Alcalá de Henares, Madrid, Spain
| | - Eva Rico
- Departamento de Biología de Sistemas, Universidad de Alcalá, E-28805 Alcalá de Henares, Madrid, Spain
| | - Ana Bravo
- Departamento de Ciencias Biomédicas y “Unidad Asociada IQM-CSIC”, Universidad de Alcalá, E-28805 Alcalá de Henares, Madrid, Spain
| | - Margarita Menéndez
- Instituto de Química Física Rocasolano, Consejo Superior de Investigaciones Científicas (CSIC), E-28006 Madrid, Spain
| | - Federico Gago
- Departamento de Ciencias Biomédicas y “Unidad Asociada IQM-CSIC”, Universidad de Alcalá, E-28805 Alcalá de Henares, Madrid, Spain
- To whom correspondence should be addressed. Tel: +34 918 855 109; Fax: +34 918 854 585; . Correspondence may also be addressed to Federico Gago. Tel: +34 918 854 514; Fax: +34 918 854 591;
| | - Antonio Jiménez-Ruiz
- Departamento de Biología de Sistemas, Universidad de Alcalá, E-28805 Alcalá de Henares, Madrid, Spain
- To whom correspondence should be addressed. Tel: +34 918 855 109; Fax: +34 918 854 585; . Correspondence may also be addressed to Federico Gago. Tel: +34 918 854 514; Fax: +34 918 854 591;
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5
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Improving the accuracy of high-throughput protein-protein affinity prediction may require better training data. BMC Bioinformatics 2017; 18:102. [PMID: 28361672 PMCID: PMC5374557 DOI: 10.1186/s12859-017-1533-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Background One goal of structural biology is to understand how a protein’s 3-dimensional conformation determines its capacity to interact with potential ligands. In the case of small chemical ligands, deconstructing a static protein-ligand complex into its constituent atom-atom interactions is typically sufficient to rapidly predict ligand affinity with high accuracy (>70% correlation between predicted and experimentally-determined affinity), a fact that is exploited to support structure-based drug design. We recently found that protein-DNA/RNA affinity can also be predicted with high accuracy using extensions of existing techniques, but protein-protein affinity could not be predicted with >60% correlation, even when the protein-protein complex was available. Methods X-ray and NMR structures of protein-protein complexes, their associated binding affinities and experimental conditions were obtained from different binding affinity and structural databases. Statistical models were implemented using a generalized linear model framework, including the experimental conditions as new model features. We evaluated the potential for new features to improve affinity prediction models by calculating the Pearson correlation between predicted and experimental binding affinities on the training and test data after model fitting and after cross-validation. Differences in accuracy were assessed using two-sample t test and nonparametric Mann–Whitney U test. Results Here we evaluate a range of potential factors that may interfere with accurate protein-protein affinity prediction. We find that X-ray crystal resolution has the strongest single effect on protein-protein affinity prediction. Limiting our analyses to only high-resolution complexes (≤2.5 Å) increased the correlation between predicted and experimental affinity from 54 to 68% (p = 4.32x10−3). In addition, incorporating information on the experimental conditions under which affinities were measured (pH, temperature and binding assay) had significant effects on prediction accuracy. We also highlight a number of potential errors in large structure-affinity databases, which could affect both model training and accuracy assessment. Conclusions The results suggest that the accuracy of statistical models for protein-protein affinity prediction may be limited by the information present in databases used to train new models. Improving our capacity to integrate large-scale structural and functional information may be required to substantively advance our understanding of the general principles by which a protein’s structure determines its function. Electronic supplementary material The online version of this article (doi:10.1186/s12859-017-1533-z) contains supplementary material, which is available to authorized users.
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6
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Melo R, Fieldhouse R, Melo A, Correia JDG, Cordeiro MNDS, Gümüş ZH, Costa J, Bonvin AMJJ, Moreira IS. A Machine Learning Approach for Hot-Spot Detection at Protein-Protein Interfaces. Int J Mol Sci 2016; 17:E1215. [PMID: 27472327 PMCID: PMC5000613 DOI: 10.3390/ijms17081215] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Revised: 07/11/2016] [Accepted: 07/18/2016] [Indexed: 12/17/2022] Open
Abstract
Understanding protein-protein interactions is a key challenge in biochemistry. In this work, we describe a more accurate methodology to predict Hot-Spots (HS) in protein-protein interfaces from their native complex structure compared to previous published Machine Learning (ML) techniques. Our model is trained on a large number of complexes and on a significantly larger number of different structural- and evolutionary sequence-based features. In particular, we added interface size, type of interaction between residues at the interface of the complex, number of different types of residues at the interface and the Position-Specific Scoring Matrix (PSSM), for a total of 79 features. We used twenty-seven algorithms from a simple linear-based function to support-vector machine models with different cost functions. The best model was achieved by the use of the conditional inference random forest (c-forest) algorithm with a dataset pre-processed by the normalization of features and with up-sampling of the minor class. The method has an overall accuracy of 0.80, an F1-score of 0.73, a sensitivity of 0.76 and a specificity of 0.82 for the independent test set.
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Affiliation(s)
- Rita Melo
- Centro de Ciências e Tecnologias Nucleares, Instituto Superior Técnico, Universidade de Lisboa, Estrada Nacional 10 (ao km 139,7), 2695-066 Bobadela LRS, Portugal.
- CNC-Center for Neuroscience and Cell Biology; Rua Larga, Faculdade de Medicina, Polo I, 1ºandar, Universidade de Coimbra, 3004-504 Coimbra, Portugal.
| | - Robert Fieldhouse
- Department of Genetics and Genomics and Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
| | - André Melo
- REQUIMTE (Rede de Química e Tecnologia), Faculdade de Ciências da Universidade do Porto, Departamento de Química e Bioquímica, Rua do Campo Alegre, 4169-007 Porto, Portugal.
| | - João D G Correia
- Centro de Ciências e Tecnologias Nucleares, Instituto Superior Técnico, Universidade de Lisboa, Estrada Nacional 10 (ao km 139,7), 2695-066 Bobadela LRS, Portugal.
| | - Maria Natália D S Cordeiro
- REQUIMTE (Rede de Química e Tecnologia), Faculdade de Ciências da Universidade do Porto, Departamento de Química e Bioquímica, Rua do Campo Alegre, 4169-007 Porto, Portugal.
| | - Zeynep H Gümüş
- Department of Genetics and Genomics and Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
| | - Joaquim Costa
- CMUP/FCUP, Centro de Matemática da Universidade do Porto, Faculdade de Ciências, Rua do Campo Alegre, 4169-007 Porto, Portugal.
| | - Alexandre M J J Bonvin
- Bijvoet Center for Biomolecular Research, Faculty of Science-Chemistry, Utrecht University, Utrecht 3584CH, The Netherlands.
| | - Irina S Moreira
- CNC-Center for Neuroscience and Cell Biology; Rua Larga, Faculdade de Medicina, Polo I, 1ºandar, Universidade de Coimbra, 3004-504 Coimbra, Portugal.
- Bijvoet Center for Biomolecular Research, Faculty of Science-Chemistry, Utrecht University, Utrecht 3584CH, The Netherlands.
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7
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Yüksel D, Bianco PR, Kumar K. De novo design of protein mimics of B-DNA. MOLECULAR BIOSYSTEMS 2016; 12:169-77. [PMID: 26568416 PMCID: PMC4699573 DOI: 10.1039/c5mb00524h] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Structural mimicry of DNA is utilized in nature as a strategy to evade molecular defences mounted by host organisms. One such example is the protein Ocr - the first translation product to be expressed as the bacteriophage T7 infects E. coli. The structure of Ocr reveals an intricate and deliberate arrangement of negative charges that endows it with the ability to mimic ∼24 base pair stretches of B-DNA. This uncanny resemblance to DNA enables Ocr to compete in binding the type I restriction modification (R/M) system, and neutralizes the threat of hydrolytic cleavage of viral genomic material. Here, we report the de novo design and biophysical characterization of DNA mimicking peptides, and describe the inhibitory action of the designed helical bundles on a type I R/M enzyme, EcoR124I. This work validates the use of charge patterning as a design principle for creation of protein mimics of DNA, and serves as a starting point for development of therapeutic peptide inhibitors against human pathogens that employ molecular camouflage as part of their invasion stratagem.
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Affiliation(s)
- Deniz Yüksel
- Department of Chemistry, Tufts University, 62 Talbot Avenue, Medford, MA 02155, USA.
| | - Piero R Bianco
- Department of Microbiology and Immunology, University at Buffalo, The State University of New York, Buffalo, NY 14214, USA.
| | - Krishna Kumar
- Department of Chemistry, Tufts University, 62 Talbot Avenue, Medford, MA 02155, USA. and Cancer Center, Tufts Medical Center, Boston, MA 02111, USA
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8
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Sikdar S, Chakrabarti J, Ghosh M. A microscopic insight from conformational thermodynamics to functional ligand binding in proteins. MOLECULAR BIOSYSTEMS 2015; 10:3280-9. [PMID: 25310453 DOI: 10.1039/c4mb00434e] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
We show that the thermodynamics of metal ion-induced conformational changes aid to understand the functions of protein complexes. This is illustrated in the case of a metalloprotein, alpha-lactalbumin (aLA), a divalent metal ion binding protein. We use the histograms of dihedral angles of the protein, generated from all-atom molecular dynamics simulations, to calculate conformational thermodynamics. The thermodynamically destabilized and disordered residues in different conformational states of a protein are proposed to serve as binding sites for ligands. This is tested for β-1,4-galactosyltransferase (β4GalT) binding to the Ca(2+)-aLA complex, in which the binding residues are known. Among the binding residues, the C-terminal residues like aspartate (D) 116, glutamine (Q) 117, tryptophan (W) 118 and leucine (L) 119 are destabilized and disordered and can dock β4GalT onto Ca(2+)-aLA. No such thermodynamically favourable binding residues can be identified in the case of the Mg(2+)-aLA complex. We apply similar analysis to oleic acid binding and predict that the Ca(2+)-aLA complex can bind to oleic acid through the basic histidine (H) 32 of the A2 helix and the hydrophobic residues, namely, isoleucine (I) 59, W60 and I95, of the interfacial cleft. However, the number of destabilized and disordered residues in Mg(2+)-aLA are few, and hence, the oleic acid binding to Mg(2+)-bound aLA is less stable than that to the Ca(2+)-aLA complex. Our analysis can be generalized to understand the functionality of other ligand bound proteins.
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Affiliation(s)
- Samapan Sikdar
- Department of Chemical, Biological and Macromolecular Sciences, S. N. Bose National Centre for Basic Sciences, Sector III, Block JD, Salt Lake, Kolkata 700098, India.
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9
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Moon AF, Gaudu P, Pedersen LC. Structural characterization of the virulence factor nuclease A from Streptococcus agalactiae. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2014; 70:2937-49. [PMID: 25372684 PMCID: PMC4220975 DOI: 10.1107/s1399004714019725] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/27/2014] [Accepted: 09/01/2014] [Indexed: 12/28/2022]
Abstract
The group B pathogen Streptococcus agalactiae commonly populates the human gut and urogenital tract, and is a major cause of infection-based mortality in neonatal infants and in elderly or immunocompromised adults. Nuclease A (GBS_NucA), a secreted DNA/RNA nuclease, serves as a virulence factor for S. agalactiae, facilitating bacterial evasion of the human innate immune response. GBS_NucA efficiently degrades the DNA matrix component of neutrophil extracellular traps (NETs), which attempt to kill and clear invading bacteria during the early stages of infection. In order to better understand the mechanisms of DNA substrate binding and catalysis of GBS_NucA, the high-resolution structure of a catalytically inactive mutant (H148G) was solved by X-ray crystallography. Several mutants on the surface of GBS_NucA which might influence DNA substrate binding and catalysis were generated and evaluated using an imidazole chemical rescue technique. While several of these mutants severely inhibited nuclease activity, two mutants (K146R and Q183A) exhibited significantly increased activity. These structural and biochemical studies have greatly increased our understanding of the mechanism of action of GBS_NucA in bacterial virulence and may serve as a foundation for the structure-based drug design of antibacterial compounds targeted to S. agalactiae.
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Affiliation(s)
- Andrea F. Moon
- Laboratory of Structural Biology, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA
| | - Philippe Gaudu
- INRA, UMR1319 Micalis, Domaine de Vilvert, Jouy-en-Josas, France; AgroParisTech, UMR Micalis, Jouy-en-Josas, France
| | - Lars C. Pedersen
- Laboratory of Structural Biology, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA
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10
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Shah S, Heddle JG. Squaring up to DNA: pentapeptide repeat proteins and DNA mimicry. Appl Microbiol Biotechnol 2014; 98:9545-60. [PMID: 25343976 DOI: 10.1007/s00253-014-6151-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2014] [Revised: 10/08/2014] [Accepted: 10/09/2014] [Indexed: 02/01/2023]
Abstract
Pentapeptide repeats are a class of proteins characterized by the presence of multiple repeating sequences five amino acids in length. The sequences fold into a right-handed β-helix with a roughly square-shaped cross section. Pentapeptide repeat proteins include a number of examples which are thought to function as structural mimics of DNA and act to competitively bind to the type II topoisomerase DNA gyrase, an important antibacterial target. DNA gyrase-targeting pentapeptide repeat proteins can both inhibit DNA gyrase-a potentially useful therapeutic property-and contribute to resistance to quinolone antibacterials (by acting to prevent them forming a lethal complex with the DNA and enzyme). Pentapeptide repeat proteins are therefore of wide interest not only because of their unusual structure, function, and potential as an antibacterial target, but also because knowledge of their mechanism of action may lead to both a greater understanding of the details of DNA gyrase function as well as being a useful template for the design of new DNA gyrase inhibitors. However, many puzzling aspects as to how these DNA mimics function and indeed even their ability to act as DNA mimics itself remains open to question. This review summarizes the current state of knowledge regarding pentapeptide repeat proteins, focusing on those that are thought to mimic DNA, and speculates on potential structure-function relationships which may account for their differing specificities.
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Affiliation(s)
- Shama Shah
- Heddle Initiative Research Unit, RIKEN, 2-1, Hirosawa, Wako, Saitama, 351-0198, Japan
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11
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Yugandhar K, Gromiha MM. Protein–protein binding affinity prediction from amino acid sequence. Bioinformatics 2014; 30:3583-9. [DOI: 10.1093/bioinformatics/btu580] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
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12
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Wang HC, Ho CH, Hsu KC, Yang JM, Wang AHJ. DNA mimic proteins: functions, structures, and bioinformatic analysis. Biochemistry 2014; 53:2865-74. [PMID: 24766129 DOI: 10.1021/bi5002689] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
DNA mimic proteins have DNA-like negative surface charge distributions, and they function by occupying the DNA binding sites of DNA binding proteins to prevent these sites from being accessed by DNA. DNA mimic proteins control the activities of a variety of DNA binding proteins and are involved in a wide range of cellular mechanisms such as chromatin assembly, DNA repair, transcription regulation, and gene recombination. However, the sequences and structures of DNA mimic proteins are diverse, making them difficult to predict by bioinformatic search. To date, only a few DNA mimic proteins have been reported. These DNA mimics were not found by searching for functional motifs in their sequences but were revealed only by structural analysis of their charge distribution. This review highlights the biological roles and structures of 16 reported DNA mimic proteins. We also discuss approaches that might be used to discover new DNA mimic proteins.
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Affiliation(s)
- Hao-Ching Wang
- Graduate Institute of Translational Medicine, College of Medical Science and Technology, Taipei Medical University , Taipei 110, Taiwan
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13
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Das A, Chakrabarti J, Ghosh M. Thermodynamics of interfacial changes in a protein–protein complex. ACTA ACUST UNITED AC 2014; 10:437-45. [DOI: 10.1039/c3mb70249a] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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14
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Das A, Chakrabarti J, Ghosh M. Conformational contribution to thermodynamics of binding in protein-peptide complexes through microscopic simulation. Biophys J 2013; 104:1274-84. [PMID: 23528087 DOI: 10.1016/j.bpj.2012.12.058] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2012] [Revised: 12/31/2012] [Accepted: 12/31/2012] [Indexed: 11/17/2022] Open
Abstract
We extract the thermodynamics of conformational changes in biomacromolecular complexes from the distributions of the dihedral angles of the macromolecules. These distributions are obtained from the equilibrium configurations generated via all-atom molecular dynamics simulations. The conformational thermodynamics data we obtained for calmodulin-peptide complexes using our methodology corroborate well with the experimentally observed conformational and binding entropies. The conformational free-energy changes and their contributions for different peptide-binding regions of calmodulin are evaluated microscopically.
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Affiliation(s)
- Amit Das
- Department of Chemical, Biological and Macromolecular Sciences, S. N. Bose National Centre for Basic Sciences, Salt Lake, Kolkata, India
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Midon M, Gimadutdinow O, Meiss G, Friedhoff P, Pingoud A. Chemical Rescue of Active Site Mutants of S. pneumoniae Surface Endonuclease EndA and Other Nucleases of the HNH Family by Imidazole. Chembiochem 2012; 13:713-21. [DOI: 10.1002/cbic.201100775] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2011] [Indexed: 11/08/2022]
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16
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Korczynska JE, Turkenburg JP, Taylor EJ. The structural characterization of a prophage-encoded extracellular DNase from Streptococcus pyogenes. Nucleic Acids Res 2011; 40:928-38. [PMID: 21948797 PMCID: PMC3258162 DOI: 10.1093/nar/gkr789] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The pathogenic bacterium Group A Streptococcus pyogenes produces several extracellular DNases that have been shown to facilitate invasive infection by evading the human host immune system. DNases degrade the chromatin in neutrophil extracellular traps, enabling the bacterium to evade neutrophil capture. Spd1 is a type I, nonspecific ββα/metal-dependent nuclease from Streptococcus pyogenes, which is encoded by the SF370.1 prophage and is likely to be expressed as a result of prophage induction. We present here the X-ray structure of this DNase in the wild-type and Asn145Ala mutant form. Through structural and sequence alignments as well as mutagenesis studies, we have identified the key residues His121, Asn145 and Glu164, which are crucial for Spd1 nucleolytic activity and shown the active site constellation. Our wild-type structure alludes to the possibility of a catalytically blocked dimeric form of the protein. We have investigated the multimeric nature of Spd1 using size-exclusion chromatography with multi-angle light scattering (SEC-MALLS) in the presence and absence of the divalent metal ion Mg(2+), which suggests that Spd1 exists in a monomeric form in solution.
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Affiliation(s)
- Justyna E Korczynska
- Department of Chemistry, Structural Biology Laboratory, The University of York, YO10 5YW, UK
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17
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Moon AF, Midon M, Meiss G, Pingoud A, London RE, Pedersen LC. Structural insights into catalytic and substrate binding mechanisms of the strategic EndA nuclease from Streptococcus pneumoniae. Nucleic Acids Res 2010; 39:2943-53. [PMID: 21113026 PMCID: PMC3074123 DOI: 10.1093/nar/gkq1152] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
EndA is a sequence non-specific endonuclease that serves as a virulence factor during Streptococcus pneumoniae infection. Expression of EndA provides a strategy for evasion of the host's neutrophil extracellular traps, digesting the DNA scaffold structure and allowing further invasion by S. pneumoniae. To define mechanisms of catalysis and substrate binding, we solved the structure of EndA at 1.75 Å resolution. The EndA structure reveals a DRGH (Asp-Arg-Gly-His) motif-containing ββα-metal finger catalytic core augmented by an interesting ‘finger-loop’ interruption of the active site α-helix. Subsequently, we delineated DNA binding versus catalytic functionality using structure-based alanine substitution mutagenesis. Three mutants, H154A, Q186A and Q192A, exhibited decreased nuclease activity that appears to be independent of substrate binding. Glu205 was found to be crucial for catalysis, while residues Arg127/Lys128 and Arg209/Lys210 contribute to substrate binding. The results presented here provide the molecular foundation for development of specific antibiotic inhibitors for EndA.
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Affiliation(s)
- Andrea F Moon
- Laboratory of Structural Biology, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina 27709, USA
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18
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Abstract
Nucleases cleave the phosphodiester bonds of nucleic acids and may be endo or exo, DNase or RNase, topoisomerases, recombinases, ribozymes, or RNA splicing enzymes. In this review, I survey nuclease activities with known structures and catalytic machinery and classify them by reaction mechanism and metal-ion dependence and by their biological function ranging from DNA replication, recombination, repair, RNA maturation, processing, interference, to defense, nutrient regeneration or cell death. Several general principles emerge from this analysis. There is little correlation between catalytic mechanism and biological function. A single catalytic mechanism can be adapted in a variety of reactions and biological pathways. Conversely, a single biological process can often be accomplished by multiple tertiary and quaternary folds and by more than one catalytic mechanism. Two-metal-ion-dependent nucleases comprise the largest number of different tertiary folds and mediate the most diverse set of biological functions. Metal-ion-dependent cleavage is exclusively associated with exonucleases producing mononucleotides and endonucleases that cleave double- or single-stranded substrates in helical and base-stacked conformations. All metal-ion-independent RNases generate 2',3'-cyclic phosphate products, and all metal-ion-independent DNases form phospho-protein intermediates. I also find several previously unnoted relationships between different nucleases and shared catalytic configurations.
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Midon M, Schäfer P, Pingoud A, Ghosh M, Moon AF, Cuneo MJ, London RE, Meiss G. Mutational and biochemical analysis of the DNA-entry nuclease EndA from Streptococcus pneumoniae. Nucleic Acids Res 2010; 39:623-34. [PMID: 20846957 PMCID: PMC3025545 DOI: 10.1093/nar/gkq802] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
EndA is a membrane-attached surface-exposed DNA-entry nuclease previously known to be required for genetic transformation of Streptococcus pneumoniae. More recent studies have shown that the enzyme also plays an important role during the establishment of invasive infections by degrading extracellular chromatin in the form of neutrophil extracellular traps (NETs), enabling streptococci to overcome the innate immune system in mammals. As a virulence factor, EndA has become an interesting target for future drug design. Here we present the first mutational and biochemical analysis of recombinant forms of EndA produced either in a cell-free expression system or in Escherichia coli. We identify His160 and Asn191 to be essential for catalysis and Asn182 to be required for stability of EndA. The role of His160 as the putative general base in the catalytic mechanism is supported by chemical rescue of the H160A variant of EndA with imidazole added in excess. Our study paves the way for the identification and development of protein or low-molecular-weight inhibitors for EndA in future high-throughput screening assays.
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Affiliation(s)
- Marika Midon
- Institute of Biochemistry, Justus-Liebig-University Giessen, Giessen, Germany
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20
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Loll B, Gebhardt M, Wahle E, Meinhart A. Crystal structure of the EndoG/EndoGI complex: mechanism of EndoG inhibition. Nucleic Acids Res 2010; 37:7312-20. [PMID: 19783821 PMCID: PMC2790893 DOI: 10.1093/nar/gkp770] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
EndoG is a ubiquitous nuclease that is translocated into the nucleus during apoptosis to participate in DNA degradation. The enzyme cleaves double- and single-stranded DNA and RNA. Related nucleases are found in eukaryotes and prokaryotes, which have evolved sophisticated mechanisms for genome protection against self-antagonizing nuclease activity. Common mechanisms of inhibition are secretion, sequestration into a separate cellular compartment or by binding to protein inhibitors. Although EndoG is silenced by compartmentalization into the mitochondrial intermembrane space, a nucleus-localized protein inhibitor protects cellular polynucleotides from degradation by stray EndoG under non-apoptotic conditions in Drosophila. Here, we report the first three-dimensional structure of EndoG in complex with its inhibitor EndoGI. Although the mechanism of inhibition is reminiscent of bacterial protein inhibitors, EndoGI has evolved independently from a generic protein-protein interaction module. EndoGI is a two-domain protein that binds the active sites of two monomers of EndoG, with EndoG being sandwiched between EndoGI. Since the amino acid sequences of eukaryotic EndoG homologues are highly conserved, this model is valid for eukaryotic dimeric EndoG in general. The structure indicates that the two active sites of EndoG occupy the most remote spatial position possible at the molecular surface and a concerted substrate processing is unlikely.
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Affiliation(s)
- Bernhard Loll
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany
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Nucleases encoded by the integrated elements CJIE2 and CJIE4 inhibit natural transformation of Campylobacter jejuni. J Bacteriol 2009; 192:936-41. [PMID: 20023031 DOI: 10.1128/jb.00867-09] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The species Campylobacter jejuni is naturally competent for DNA uptake; nevertheless, nonnaturally transformable strains do exist. For a subset of strains we previously showed that a periplasmic DNase, encoded by dns, inhibits natural transformation in C. jejuni. In the present study, genetic factors coding for DNase activity in the absence of dns were identified. DNA arrays indicated that nonnaturally transformable dns-negative strains contain putative DNA/RNA nonspecific endonucleases encoded by CJE0566 and CJE1441 of strain RM1221. These genes are located on C. jejuni integrated elements 2 and 4. Expression of CJE0566 and CJE1441 from strain RM1221 and a homologous gene from strain 07479 in DNase-negative Escherichia coli and C. jejuni strains indicated that these genes code for DNases. Genetic transfer of the genes to a naturally transformable C. jejuni strain resulted in a decreased efficiency of natural transformation. Modeling suggests that the C. jejuni DNases belong to the Serratia nuclease family. Overall, the data indicate that the acquisition of prophage-encoded DNA/RNA nonspecific endonucleases inhibits the natural transformability of C. jejuni through hydrolysis of DNA.
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Temme C, Weissbach R, Lilie H, Wilson C, Meinhart A, Meyer S, Golbik R, Schierhorn A, Wahle E. The Drosophila melanogaster Gene cg4930 Encodes a High Affinity Inhibitor for Endonuclease G. J Biol Chem 2009; 284:8337-48. [PMID: 19129189 DOI: 10.1074/jbc.m808319200] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Endonuclease G (EndoG) is a mitochondrial enzyme believed to be released during apoptosis to participate in the degradation of nuclear DNA. This paper describes a Drosophila protein, EndoGI, which inhibits EndoG specifically. EndoG and EndoGI associate with subpicomolar affinity, forming a 2:1 complex in which dimeric EndoG is bound by two tandemly repeated homologous domains of monomeric EndoGI. Binding appears to involve the active site of EndoG. EndoGI is present in the cell nucleus at micromolar concentrations. Upon induction of apoptosis, levels of the inhibitor appear to be reduced, and it is relocalized to the cytoplasm. EndoGI, encoded by the predicted open reading frame cg4930, is expressed throughout Drosophila development. Flies homozygous for a hypomorphic EndoGI mutation have a strongly reduced viability, which is modulated by genetic background and diet. We propose that EndoGI protects the cell against low levels of EndoG outside mitochondria.
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Affiliation(s)
- Claudia Temme
- Institute of Biochemistry and Biotechnology, Martin-Luther-University Halle-Wittenberg, Kurt-Mothes-Strasse 3, 06120 Halle, Germany
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