By Matesanz, R.; Pera, B.; Díaz, J.F
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Additional resources for Thermodynamics as a Tool for the Optimization of Drug Binding, Thermodynamics - Interaction Studies - Solids, Liquids and Gases
Sample text
Chemical shifts for galactose binding to ABP. Changes in backbone amide chemical shifts are plotted against protein residue number. Fig. 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.
Conformational) during the simulation. , 2009 and references therein). MD methods rely on quality of the force field (parameters, inclusion of non-additive effects, etc), description of solvent effects, adequate sampling, and quality of initial structures used for the simulations. The quality of the results relies also on the duration of the simulation. There are limits on the time scales at which the system of interest can be considered. Simulation runs are fairly short: typically nanoseconds to microseconds, rarely extending to miliseconds, if super-fast computers are employed.
26 Thermodynamics – Interaction Studies – Solids, Liquids and Gases QM methods are also used in molecular docking. The application of QM methods to molecular docking was pioneered by Raha and Merz (2004), who developed a semiempirical QM-based scoring function and studied ion-mediated ligand binding processes. Their conclusion was that quantum chemical description is required for metal-containing systems, mainly because of poorly-defined atom types of metal atoms in most of the force field parameters, which cannot describe the interactions between a small molecule ligand and a metal ion in the active site of the protein.