Flexibility binding site

J. Apostolakis, A. Pluckthun, and A. Caflisch. Docking small ligands in flexible binding sites. Journal of Computational Chemistry, 19 21-37, 1998. 

The tertiary structure of a protein is the folding pattern of the secondary structural elements into a three-dimensional conformation, as shown for the LDH domain in Figure 7.8. As illustrated with examples below, this three-dimensional structure is designed to serve all aspects of the protein s function. It creates specific and flexible binding sites for ligands (the compound that binds), illustrated with actin and myoglobin. The tertiary structure also maintains residues on the surface appropriate for the protein s cellular location, polar residues for cytosolic proteins, and hydrophobic residues for transmembrane proteins (illustrated with the P2-adrenergic receptor). 

Prodock The program docks flexible hgands to a flexible binding site (representing the structure 16... 

IV, ] Ruppert and A N Jain 1996. Hammerhead Fast, Fully Automated Docking of Flexible ands to Protein Binding Sites. Chemistry and Biology 3 449-462. 

Huxley suggested that crossbridges can move out in this way and bind to actin because S-2 of HMM acted as a flexible link between LMM in the thick filament backbone and S-1. This was based on the observation that heavy meromyosin could be digested by chymotrypsin into two further subffagments (Lowey et al., 1966), S-1 and S-2, as described above, and that S-1 contained the ATPase and actin binding sites, whereas S-2 did not moreover, S-2 did not self-aggregate, as did the rod or LMM portion of myosin. 

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