Molecular Modeling\nof Glycosylated Catalytic Domain\nof Human Carbonic Anhydrase IX

Glycans exhibit significant structural diversity due\nto the flexibility\nof glycosidic bonds linking their constituent monosaccharides and\nthe formation of numerous hydrogen bonds. The present work searches\na simulated ensemble of glycan chain conformations attached to the\ncatalytic domain of N-glycosylated human carbonic anhydrase IX (HCA\nIX-c) to identify conformations pointed away or back-folded toward\nthe protein surface guided by different amino acid residues. A series\nof classical molecular dynamics (MD) simulation studies for a total\nof 30 μs followed by accelerated MD simulations for a total\nof 2 μs have been performed using two different force fields\nto capture varying degrees of fluctuations of both glycan chain and\nHCA IX. From the underlying free energy profile and kinetics derived\nusing hidden Markov state model, several stable glycan orientations\nare identified that extend away from the protein surface and convert\namong each other with rate constants of the order 10<sup>7</sup>–10<sup>10</sup> <sub>S</sub><sup>–1</sup>. Most importantly, we have\nidentified a <i>rare</i> glycan conformation which reaches\nclose to a catalytically important amino acid residue, Glu-106. We\nfurther enlist the protein residues that couple such less frequent\nevent of the glycan chain back-folding toward the surface of the protein.