Keywords: Amyloid formation; Conformational analysis; Glycosylation; Molecular dynamics simulations; Partial charge; Sialic acid
Protein glycosylation is one of the most important forms of post-translational processing associated with numerous biological functions in life.1 Carbohydrates fulfill many common as well as extremely important functions in nature.2 Many reports claim that glycosylation changes structure, activity, and physical stability of proteins.2–4 Particularly for O-glycosylation, considerable evidence has been accumulated regarding cellular processes and human diseases.5,6 The conformational changes of protein structure are often related to neurodegenerative disorders such as Parkinson’s or Alzheimer’s disease.7,8 Site-specific O-glycosylation of tau protein is reported to be responsible for regulating protein aggregation.9 The O-glycosylation cycling also modulates tauopathy, amyloid β-peptide, and polyglutamine expansion in transgenic models.10 Molecular details played by glycosylation are complicated by the subtle nature of variations in the glycan structu...
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...ate gradient method to prepare the initial structure for MD simulations.
1.2 MD simulation and data analysis
The MD simulations were carried out using a sander module of Amber 12 program to trace the dynamic nature of each peptide with ff03 and GLYCAM force field. An implicit water model was used to treat the solvation effects with the modified Generalized Born/Surface Area (GB/SA) model developed by Onufriev and coworkers.16 Each peptide system was gradually heated to 298 K for 50 ps and equilibrated for 1 ns at the same temperature. A production MD run was performed for 200 ns with a time step of 1.0 fs, and the trajectory was collected for every 50 ps. A constant temperature of 298 K was regulated using a Langevin dynamics mode with 5.0 ps of collision frequency. The final MD trajectories were analyzed and processed using a ‘ptraj’ facility of the Amber program.
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