Alanines free energy calculations

Fig. 6 Schematic representation of the yeast ODCase active site, depicting the effects on transition state binding affinity of replacing individual active site residues with alanine. Free energy contributions (AAG) of individual interactions were calculated from the decrease in catalytic efficiency (/Ccat/ m) produced upon mutation to alanine. The sum of individual mutations totals more than 45 kcal/mol of binding free energy...

Fig. 4.5. Free energy profile of alanine dipeptide as a function of

As an example, this approach was applied to the calculation of the PMF for alanine dipeptide as a function of the two torsion angles

resulting free energy surface is shown in Fig. 4.5. Bilinear Qi elements were used to approximate the free energy. Control points were chosen such that there are four of them around each data point. This was done in order to increase the smoothness and quality of the reconstructed free energy. The position of the Q i nodes and control points is shown in Fig. 4.6. 

Fig. 4.11. Free energy profile for Deca-L-alanine calculated using the ABF. The inset shows the number of samples as a function of ...

Calculate the free energy of formation of L-alanine at 25°C for the reaction ... 

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