Molecular interactions of UvrB protein and DNA from Helicobacter pylori: Insight into a molecular modeling approach

Helicobacter pylori (H. pylori) persevere in the human stomach, an environment in which they encounter many DNA-damaging conditions, including gastric acidity. The pathogenicity of H. pylori is enhanced by its well-developed DNA repair mechanism, thought of as 'machinery,' such as nucleotide excision repair (NER). NER involves multi-enzymatic excinuclease proteins (UvrABC endonuclease), which repair damaged DNA in a sequential manner. UvrB is the central component in prokaryotic NER, essential for damage recognition. Therefore, molecular modeling studies of UvrB protein from H. pylori are carried out with homology modeling and molecular dynamics (MD) simulations. The results reveal that the predicted structure is bound to a DNA hairpin with 3-bp stem, an 11-nucleotide loop, and 3-nt 3' overhang. In addition, a mutation of the Y96A variant indicates reduction in the binding affinity for DNA. Free-energy calculations demonstrate the stability of the complex and help identify key residues in various interactions based on residue decomposition analysis. Stability comparative studies between wild type and mutant protein-DNA complexes indicate that the former is relatively more stable than the mutant form. This predicted model could also be useful in designing new inhibitors for UvrB protein, as well as preventing the pathogenesis of H. pylori.

[1]  D. Berg,et al.  Emergence of recombinant strains of Helicobacter pylori during human infection , 1999, Molecular microbiology.

[2]  K Schulten,et al.  VMD: visual molecular dynamics. , 1996, Journal of molecular graphics.

[3]  G. Moolenaar,et al.  Role of ATP hydrolysis by UvrA and UvrB during nucleotide excision repair. , 2001, Research in microbiology.

[4]  F. Rossi,et al.  The biological and structural characterization of Mycobacterium tuberculosis UvrA provides novel insights into its mechanism of action , 2011, Nucleic acids research.

[5]  S. Broyde,et al.  Exploring damage recognition models in prokaryotic nucleotide excision repair with a benzo[a]pyrene-derived lesion in UvrB. , 2009, Biochemistry.

[6]  R. Maier,et al.  Dual Roles of Helicobacter pylori NapA in Inducing and Combating Oxidative Stress , 2006, Infection and Immunity.

[7]  M. Sippl.  Recognition of errors in three‐dimensional structures of proteins , 1993, Proteins.

[8]  Mario Plebani,et al.  Pathogenesis of Helicobacter pylori Infection , 2010, Helicobacter.

[9]  S. Jamal,et al.  Hydrophobic Interactions Are a Key to MDM2 Inhibition by Polyphenols as Revealed by Molecular Dynamics Simulations and MM/PBSA Free Energy Calculations , 2016, PloS one.

[10]  J. Hearst,et al.  Active Site of (A)BC Excinuclease AND MUTANTS OF UvrB REVEAL A DIRECT ROLE IN 3’ AND AN INDIRECT ROLE IN , 2001 .

[11]  B. Van Houten,et al.  Nucleotide excision repair in Escherichia coli , 1990, Microbiological reviews.

[12]  C. Wyman,et al.  The presence of two UvrB subunits in the UvrAB complex ensures damage detection in both DNA strands , 2002, The EMBO journal.

[13]  C. Bagnéris,et al.  Crystal structure of the UvrB dimer: insights into the nature and functioning of the UvrAB damage engagement and UvrB–DNA complexes , 2012, Nucleic acids research.

[14]  Conrad C. Huang,et al.  UCSF Chimera—A visualization system for exploratory research and analysis , 2004, J. Comput. Chem..

[15]  M. Parrinello,et al.  Canonical sampling through velocity rescaling. , 2007, The Journal of chemical physics.

[16]  B. Van Houten,et al.  The β-Hairpin Motif of UvrB Is Essential for DNA Binding, Damage Processing, and UvrC-mediated Incisions* , 2002, The Journal of Biological Chemistry.

[17]  Crystal structure of the DNA nucleotide excision repair enzyme UvrB from Thermus thermophilus. , 1999, Proceedings of the National Academy of Sciences of the United States of America.

[18]  A. Sancar,et al.  Active site of (A)BC excinuclease. I. Evidence for 5' incision by UvrC through a catalytic site involving Asp399, Asp438, Asp466, and His538 residues. , 1992, The Journal of biological chemistry.

[19]  M. Yamada,et al.  Genetic Analysis of Repair and Damage Tolerance Mechanisms for DNA-Protein Cross-Links in Escherichia coli , 2009, Journal of bacteriology.

[20]  Rohit Bavi,et al.  Exploration of Novel Inhibitors for Bruton’s Tyrosine Kinase by 3D QSAR Modeling and Molecular Dynamics Simulation , 2016, PloS one.

[21]  M. Tang,et al.  Two Forms of UvrC Protein with Different Double-stranded DNA Binding Affinities* , 2001, The Journal of Biological Chemistry.

[22]  Adebanke F. Fagbemi,et al.  Regulation of endonuclease activity in human nucleotide excision repair. , 2011, DNA repair.

[23]  A. Sancar,et al.  A novel repair enzyme: UVRABC excision nuclease of Escherichia coli cuts a DNA strand on both sides of the damaged region , 1983, Cell.

[24]  H. Gohlke,et al.  Free Energy Calculations by the Molecular Mechanics Poisson−Boltzmann Surface Area Method , 2012, Molecular informatics.

[25]  J. Hearst,et al.  Post-incision steps of nucleotide excision repair in Escherichia coli. Disassembly of the UvrBC-DNA complex by helicase II and DNA polymerase I. , 1992, The Journal of biological chemistry.

[26]  C. Kisker,et al.  Structural basis for DNA recognition and processing by UvrB , 2006, Nature Structural &Molecular Biology.

[27]  B. Van Houten,et al.  Initiation of repair of DNA-polypeptide cross-links by the UvrABC nuclease. , 2005, Biochemistry.

[28]  Samuel Genheden,et al.  How to obtain statistically converged MM/GBSA results , 2009, J. Comput. Chem..

[29]  VINCENT ZOETE,et al.  SwissParam: A fast force field generation tool for small organic molecules , 2011, J. Comput. Chem..

[30]  D S Moss,et al.  Main-chain bond lengths and bond angles in protein structures. , 1993, Journal of molecular biology.

[31]  B. Van Houten,et al.  Effect of DNA polymerase I and DNA helicase II on the turnover rate of UvrABC excision nuclease. , 1985, Proceedings of the National Academy of Sciences of the United States of America.

[32]  P. Kollman,et al.  Settle: An analytical version of the SHAKE and RATTLE algorithm for rigid water models , 1992 .

[33]  J. Hoeijmakers,et al.  Architecture of nucleotide excision repair complexes: DNA is wrapped by UvrB before and after damage recognition , 2001, The EMBO journal.

[34]  M. Machius,et al.  The nucleotide excision repair protein UvrB, a helicase-like enzyme with a catch. , 2000, Mutation research.

[35]  E. Myers,et al.  Basic local alignment search tool. , 1990, Journal of molecular biology.

[36]  Keun Woo Lee,et al.  Novel chemical scaffolds of the tumor marker AKR1B10 inhibitors discovered by 3D QSAR pharmacophore modeling , 2015, Acta Pharmacologica Sinica.

[37]  Jack Snoeyink,et al.  Nucleic Acids Research Advance Access published April 22, 2007 MolProbity: all-atom contacts and structure validation for proteins and nucleic acids , 2007 .

[38]  P. Kaźmierczak,et al.  DNA damage and repair in Helicobacter pylori-infected gastric mucosa cells. , 2005, Mutation research.

[39]  P. Kollman,et al.  Calculating structures and free energies of complex molecules: combining molecular mechanics and continuum models. , 2000, Accounts of chemical research.

[40]  R. Visse,et al.  Catalytic Sites for 3′ and 5′ Incision of Escherichia coli Nucleotide Excision Repair Are Both Located in UvrC* , 2000, The Journal of Biological Chemistry.

[41]  Osamu Miyashita,et al.  Crystal molecular dynamics simulations to speed up MM/PB(GB)SA evaluation of binding free energies of di‐mannose deoxy analogs with P51G‐m4‐Cyanovirin‐N , 2011, J. Comput. Chem..

[42]  D. van der Spoel,et al.  GROMACS: A message-passing parallel molecular dynamics implementation , 1995 .

[43]  C. Goodwin,et al.  Restriction endonuclease analysis of the genome of Campylobacter pylori with a rapid extraction method: evidence for considerable genomic variation. , 1988, The Journal of infectious diseases.

[44]  Julio Collado-Vides,et al.  TFmodeller: comparative modelling of protein-DNA complexes , 2007, Bioinform..

[45]  T. Darden,et al.  Particle mesh Ewald: An N⋅log(N) method for Ewald sums in large systems , 1993 .

[46]  E. Kuipers,et al.  Pathogenesis of Helicobacter pylori Infection , 2006, Clinical Microbiology Reviews.

[47]  S. Thompson,et al.  Molecular characterization of the Helicobacter pylori uvr B gene. , 1998, Gene.

[48]  P. Caron,et al.  Involvement of helicase II (uvrD gene product) and DNA polymerase I in excision mediated by the uvrABC protein complex. , 1985, Proceedings of the National Academy of Sciences of the United States of America.

[49]  L. Theriot,et al.  Three loci in Escherichia coli K-12 that control the excision of pyrimidine dimers and certain other mutagen products from DNA. , 1966, Genetics.

[50]  Tingjun Hou,et al.  Assessing the Performance of the MM/PBSA and MM/GBSA Methods. 1. The Accuracy of Binding Free Energy Calculations Based on Molecular Dynamics Simulations , 2011, J. Chem. Inf. Model..

[51]  M. Parrinello,et al.  Polymorphic transitions in single crystals: A new molecular dynamics method , 1981 .

[52]  B. Van Houten,et al.  DNA tandem lesion repair by strand displacement synthesis and nucleotide excision repair. , 2008, Biochemistry.

[53]  Berk Hess,et al.  LINCS: A linear constraint solver for molecular simulations , 1997, J. Comput. Chem..

[54]  B. Van Houten,et al.  Identification of Residues within UvrB That Are Important for Efficient DNA Binding and Damage Processing* , 2004, Journal of Biological Chemistry.

[55]  G. N. Ramachandran,et al.  Stereochemistry of polypeptide chain configurations. , 1963, Journal of molecular biology.