title: Histidine-mediated pH-sensitive regulation of M-ficolin:GlcNAc binding activity in innate immunity examined by molecular dynamics simulations.
abstract: BACKGROUND
  M-ficolin, a pathogen recognition molecule in the innate immune system, binds sugar residues including N-acetyl-D-glucosamine (GlcNAc), which is displayed on invading microbes and on apoptotic cells. The cis and trans Asp282-Cys283 peptide bond in the M-ficolin, which was found to occur at neutral and acidic pH in crystal structures, has been suggested to represent binding and non-binding activity, respectively. A detailed understanding of the pH-dependent conformational changes in M-ficolin and pH-mediated discrimination mechanism of GlcNAc-binding activity are crucial to both immune-surveillance and clearance of apoptotic cells.
  
  
  RESULTS
  By immunodetection analysis, we found that the pH-sensitive binding of GlcNAc is regulated by a conformational equilibrium between the active and inactive states of M-ficolin. We performed constant pH molecular dynamics (MD) simulation at a series of pH values to explore the pH effect on the cis-trans isomerization of the Asp282-Cys283 peptide bond in the M-ficolin fibrinogen-like domain (FBG). Analysis of the hydrogen bond occupancy of wild type FBG compared with three His mutants (H251A, H284A and H297A) corroborates that His284 is indispensible for pH-dependent binding. H251A formed new but weaker hydrogen bonds with GlcNAc. His297, unlike the other two His mutants, is more dependent on the solution pH and also contributes to cis-trans isomerization of the Asp282-Cys283 peptide bond in weak basic solution.
  
  
  CONCLUSIONS
  Constant pH MD simulation indicated that the cis active isomer of Asp282-Cys283 peptide bond was predominant around neutral pH while the trans bond gradually prevailed towards acidic environment. The protonation of His284 was found to be associated with the trans-to-cis isomerization of Asp282-Cys283 peptide bond which dominantly regulates the GlcNAc binding. Our MD simulation approach provides an insight into the pH-sensitive proteins and hence, ligand binding activity.
authors.affiliation: Computational and Systems Biology, Singapore-MIT Alliance, Singapore, Singapore.
authors.forename: Lifeng
authors.initials: L
authors.lastname: Yang
authors.forename: Jing
authors.initials: J
authors.lastname: Zhang
authors.forename: Bow
authors.initials: B
authors.lastname: Ho
authors.forename: Jeak Ling
authors.initials: JL
authors.lastname: Ding
mesh_terms: D000117:Acetylglucosamine / Q000378:metabolism*; D006639:Histidine / Q000378:metabolism*; D006860:Hydrogen Bonding; D006863:Hydrogen-Ion Concentration; D007113:Immunity, Innate / Q000276:immunology*; D007536:Isomerism; D037102:Lectins / Q000737:chemistry* / Q000378:metabolism*; D056004:Molecular Dynamics Simulation; D050505:Mutant Proteins / Q000737:chemistry / Q000378:metabolism; D010455:Peptides / Q000378:metabolism; D011485:Protein Binding; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary; D011522:Protons; D012997:Solvents; D000097604:Ficolins
chemical_list: D000117:Acetylglucosamine; D006639:Histidine; D037102:Lectins; D050505:Mutant Proteins; D010455:Peptides; D011522:Protons; D012997:Solvents; D000097604:Ficolins