Force-field parameters of the Psi and Phi around glycosidic bonds to oxygen and sulfur atoms.
The Psi and Phi torsion angles around glycosidic bonds in a glycoside chain are the most important determinants of the conformation of a glycoside chain. We determined force-field parameters for Psi and Phi torsion angles around a glycosidic bond bridged by a sulfur atom, as well as a bond bridged by an oxygen atom as a preparation for the next study, i.e., molecular dynamics free energy calculations for protein-sugar and protein-inhibitor complexes. First, we extracted the Psi or Phi torsion energy component from a quantum mechanics (QM) total energy by subtracting all the molecular mechanics (MM) force-field components except for the Psi or Phi torsion angle. The Psi and Phi energy components extracted (hereafter called "the remaining energy components") were calculated for simple sugar models and plotted as functions of the Psi and Phi angles. The remaining energy component curves of Psi and Phi were well represented by the torsion force-field functions consisting of four and three cosine functions, respectively. To confirm the reliability of the force-field parameters and to confirm its compatibility with other force-fields, we calculated adiabatic potential curves as functions of Psi and Phi for the model glycosides by adopting the Psi and Phi force-field parameters obtained and by energetically optimizing other degrees of freedom. The MM potential energy curves obtained for Psi and Phi well represented the QM adiabatic curves and also these curves' differences with regard to the glycosidic oxygen and sulfur atoms. Our Psi and Phi force-fields of glycosidic oxygen gave MM potential energy curves that more closely represented the respective QM curves than did those of the recently developed GLYCAM force-field.
Saito
Minoru
M
Graduate School of Science and Technology, Hirosaki University, 3 Bunkyo-cho, Hirosaki, Aomori 036-8561, Japan. msaito@cc.hirosaki-u.ac.jp
Okazaki
Isao
I
D002241:Carbohydrates / Q000737:chemistry*; D008958:Models, Molecular; D008968:Molecular Conformation; D010100:Oxygen / Q000737:chemistry*; D013455:Sulfur / Q000737:chemistry*; D013816:Thermodynamics
D002241:Carbohydrates; D013455:Sulfur; D010100:Oxygen