Protein, proteins pockets

The latter would normally require a high pH and the contribution of the enzyme is therefore presumed to be the provision of a suitable environment, within the protein pocket, which allows the dissociation of the coordinated H,0 to occur in a medium of pH 7 which would otherwise be much too low. 

This indicates how favorable it is to take the ligand out of solution and into the protein binding pocket. 

In natural systems dimerization reactions are prevented by the location of the haeme group in a sterically protected protein pocket, which prevents another haeme group approaching and attacking the original haeme. Analogously, protonation reactions are limited by the fact that the haeme group lies in a hydrophobic pocket. 

Geometry-based approach from a geometrical point of view, a cavity is a concave empty space that can be described using 2D (surface) or 3D shape descriptors (19-21). We consider three regions in the protein environment the protein bulk, the bulk solvent and the cavity space. The protein bulk is the space filled by the protein atoms. The bulk solvent is the space outside the protein which differentiates from the space inside the protein which defines the cavity where the drug-like molecule is supposed to bind. The identification of protein pockets by numerical methods suppose the capacity to discriminate first the protein bulk from the rest... 

Panjkovich A, Daura X (2010) Assessing the structural conservation of protein pockets to study functional and allosteric sites implications for drug discovery. BMC Struct Biol 10 9-33... 

Morris RRJ, Najmanovich RRJ, Kahraman A et al (2005) Real spherical harmonic expansion coefficients as 3D shape descriptors for protein binding pocket and ligand comparisons. Bioinformatics (Oxford, England) 21 2347-2355... 

Liang J, Edelsbrimner H, Woodward C (1998) Anatomy of protein pockets and cavities measmement of binding site geometry and implications for ligand design. Protein Sci 7 1884-1897... 

Petrek M, Otyepka M, Bands P et al (2006) CAVER a new tool to explore routes from protein clefts, pockets and cavities. BMC Bioinformatics 7 316-325... 

Brady GP, Stouten PE (2000) Fast prediction and visualization of protein binding pockets with PASS. J Comput Aided Mol Des 14 383-401... 

Metz A, Pfleger C, Kopitz H et al (2011) Hot spots and transient pockets predicting the determinants of smaU-molecule binding to a protein-protein interface. J Chem Inf Model 52 120-133... 

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