Combination of multiple computational methods revealing specific sub-sectional recognition and hydrogen-bond dependent transportation of CKII peptide fragment in O-GlcNAc transferase

Graphical abstract
Highlights • Mechanism of CKII peptide recognition, transportation and binding in OGT is obtained. • Peptide delivery is strong exothermic, highly dependent on hydrogen bond network. • Typical ‘spread’ & ‘V’ conformation change noticed for peptide accompanies stable OGT. • Specific subsection of peptide has diverse performance in its recognition and delivery. • Multiple methods combination may be used in other bio-system with flexible substrate.
O-linked β-N-acetyl-D-glucosamine (O-GlcNAc) transferase (OGT) is an essential enzyme in many cellular physiological catalytic reactions that regulates protein O-GlcNAcylation. Aberrant O-GlcNAcylation is related to insulin resistance, diabetic complications, cancer and neurodegenerative diseases. Understanding the peptide delivery in OGT is significant in comprehending enzymatic catalytic process, target-protein recognition and pathogenic mechanism. Herein extensive molecular dynamics (MD) simulations combined with various techniques are utilized to study the recognizing and binding mechanism of peptide fragment extracted from casein kinase II by OGT from atomic level. The residues of His496, His558, Thr633, Lys634, and Pro897 are demonstrated to play a dominant role in the peptide stabilization via hydrogen bonds and σ-π interaction, whose van der Waals and non-polar solvent effects provide the main driving force. In addition, two channels are identified. The delivery mode, mechanism together with thermodynamic and dynamic characterizations for the most favorable channel are determined. The peptide is more inclined to be recognized by OGT through the cavity comprised of residues 799–812, 893–899, and 865–871, and Tyr13-terminal is prior recognized to Met26-terminal. The transportation process is accompanied with conformation changes between the “spread” and “V” shapes. The whole process is strong exothermic that is highly dependent on the variation of hydrogen bond interactions between peptide and OGT as well as the performance of different subsections of peptide. Besides that, multiple computational methods combinations may contribute meaningfully to calculation of similar bio-systems with long and flexible substrate.