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. (c) 2009 Wiley Periodicals, Inc., J Comput Chem, 2009.
