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Extra resources for Thermodynamics - Interaction Studies - Solids, Liquids and Gases
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Information about ps-to-ns time scale molecular motions can be readily obtained from the MD simulation trajectory and analysed either through diagonalisation of the covariance matrix of displacements of atomic Cartesian coordinates - quasi-harmonic analysis, Schlitter's approach (7,8), analysed through principal component analysis (PCA), or quantified NMR-like via generalised order parameters. Entropy changes can be estimated from the MD trajectory through Yang and Kay's relationship (9). The order parameter analysis has the advantage of being able to calculate order parameters by-vector, thus providing site-specific information on flexibility and hence intrinsic entropic contribution.
8. Conformational changes between apo-ABP (light blue) and galactose-ABP complex. The apo protein is much more 'open' than the complex. Large conformational changes are observed in the hinge region (coloured red), and the reorientation of N-domain (yellow) and C-domain (dark blue) towards each other is quite pronounced. Bound galactose is coloured cyan and displayed as VDW spheres. Side chains of several residues involved in direct interactions with ABP are showed and coloured dark cyan. 34 Thermodynamics – Interaction Studies – Solids, Liquids and Gases Full sets of 15N relaxation measurements were made for ABP in its apo form and in complex with D-galactose, L-arabinose and D-fucose.
5 Molecular dynamics (MD) simulations MD simulations were used to examine the solvation of the binding pocket of MUP and HBP. , 2006). Even if water molecules were artificially “forced in” at the beginning of the MD simulation, they did not remain inside the pocket. This observation contributed to the explanation of the unexpected thermodynamic signature of the ligand binding to MUP, measured by ITC. An average of five to six water molecules is observed in the binding pocket of HBP over the simulation time in the absence of ligand.