computer modeling in molecular biology.pdf

236 Oliver S. Smarttermediates marked “A” and “B” were identified further PEM runs started to connectthem. Small artefacts in the low energy regions of the path were accepted. Acomparison between the overall route (Figure 8-7c) and the initial unsmoothed PEMpath (Figure 8-7 b) shows an important feature of the PEM technique. The initialpath is very much shorter than the final result. By initially concentrating on findinga path through the transition state rather than the overall intrinsic reaction coordinate,the method reduces the size of any problem enormously.The overall optimal route found which links the eoc and pC1 forms found here(Figure 8-7c) differs markedly from the results previously found. As well as havinga markedly smaller peak energy the route goes through a new low energy intermediate(marked “B”). This form has a slightly lower energy than pC1 and differsin the position of atoms 01 and H2 as shown in Figure 8-5.Table 8-3 compares the relative potential energies of important positions foundin this study and previously. The estimate of the energy barrier to the rearrangementof the substrate’s coordination to the metal ion has been reduced to 7.2 kcal/mol.Comparison with the Arrhenius activation for the enzyme reaction of 14.6 kcal/mol[59] adds weight to the identification that the transition is unlikely to be rate-determining[32].The potential energy function used to date to simulate the rearrangement takesa rather inconsistent approach mixing the empirically derived Amber potentialenergy function with the Mg2+ representation of Dietz et al. [58] derived by quantummechanical calculation. Aquist [60] has derived a consistent set of van der Waalsradii and well depth for the alkali and alkali earth ions using a fit to the free energyof solvation for the ion. Energy minimization and PEM was used to repeat thesimulation of the conformational transition between the eoc and pC1 forms usingthe Aqvist parameters for Mg2+ rather than the representation of Dietz et al. [58].Table 8-3. Conformational rearrangement of substrate in D-xylose isomerase: potentialenergiesa of important forms.PC1 3.1PC24.8New intermediate -Lowest Peak 11.0Barrier 03 * 02‘ 7.9Old results b,d New resultsd New parameters(3.1)(4.8)2.79.97.2Potential energy in kcal/mol (1 cal = 4.184 J), relative to the eoc model.Calculated by the reaction co-ordinate methods presented by Smart, Akins & Blow [32].The potential energy barrier for a conformational rearrangement between substrate withatoms 03 and 04 co-ordinate to metal ion [l] and an 02/04 co-ordinate form.Values calculated in the first two columns use the parametrization of problem as presentedby Smart, Akins & Blow [32], whereas new parameters use Mg2+ representation due toAqvist [60].1.35.03.28.37.0