Histidine-mediated pH-sensitive regulation of M-ficolin:GlcNAc binding activity in innate immunity examined by molecular dynamics simulations |
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Authors: | Yang Lifeng Zhang Jing Ho Bow Ding Jeak Ling |
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Institution: | Computational and Systems Biology, Singapore-MIT Alliance, Singapore, Singapore. |
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Abstract: | BackgroundM-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.Methodology/Principal FindingsBy 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/SignificanceConstant 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. |
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