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Wade, J. Clark, P. J. Goodford J. Med. Chem. 1993, 36, 140–147. 7 R. C. Wade, P. J. Goodford J. Med. Chem. 1993, 36, 148–156. 8 M. von Itzstein et al. Nature (London) 1993, 363, 418–423. 9 P. J. Goodford J. Chemometrics 1996, 10, 107–117. 10 T. Langer Quant. -Act. Relat. 1996, 15, 469–474. 11 A. Berglund; M. C. De Rosa, S. Wold J. Comput-Aided. Mol. Design 1997, 11, 601–612. 12 P. J. ), 1998, 215–226. 27 2 Calculation and Application of Molecular Interaction Fields Rebecca C. 1 Introduction Molecular interaction fields (MIFs) can be calculated for any molecule of known three-dimensional (3D) structure.
However, the GRID program does allow for probe-induced switching between histidine tautomers. g. for metalloproteins. Well ordered water molecules may also be considered part of the target. GRID also permits the possibility for a water-bridged target–probe interaction to be considered without a priori defining the position of the water molecule. The remaining solvent molecules are treated as a continuum that modulates the interaction energy between probe and target and may also have an entropic effect on the probe–target interaction.
One must conclude that hydrophobic interactions may stabilise the multilayer TRP–ARG sandwich of gp130, in spite of the different character of these two amino acids, and in spite of the entropic penalty mentioned above. However the gp130 crystals themselves came from a solution which contained glycerol molecules and sulfate ions, and both of these components were trapped in the crystals where they may have helped to stabilise the observed protein structure. It would not be altogether surprising if some alternative conformation or conformations of gp130 may also occur in vivo, if those somewhat unphysiological substances are not present in the human body in sufficient concentrations to stabilise the structure as observed.