However, packing effects also explain the large structural similarity observed for the different ligand-bound and unbound structures, although such a structural similarity does not permit to rationalize the effect of deletion of the N-terminal residues on the binding affinities of certain ligands nor the pH sensitivity of NP7.
Since the crystallography of certain ligands (e. g. biglycans, hyaluronans and heparin sulphates, ssRNA) [ 44, 68] remains unknown and the precise positions of corresponding binding sites are still missing, our data provide important avenues towards understanding which codons might be candidates for ligand binding residues.
Riboswitches, RNA elements with the ability to control the translation of a coupled open reading frame upon binding specifically to certain ligands, are another class of parts that can be used to control metabolism (Famulok et al. 2007).
In a receptor with only a single potential binding site, the presence of repulsion for certain ligands might preclude them binding with high affinity at all and thus give selectivity for only those ligands where repulsion is absent.
In addition, the thermostabilization procedure had a significant impact on specific ligand affinities of the receptor and abolished or reduced the binding of certain antagonists.
RGD-containing peptides are able to inhibit the binding of ligands to certain β3 integrins, such as αIIbβ3 and αvβ3, both of which are involved in neointimal hyperplasia.
Monoclonal antibodies raised against β3 integrin are able to inhibit the binding of ligands to certain β3 integrins such as αIIbβ3 (glycoprotein IIb/IIIa complex) and αvβ3 (vitronectin receptor) and as such are inhibitors of platelet aggregation and smooth muscle cell (SMC) migration, both of which are involved in neointimal hyperplasia.
In one type of method, certain ligand-binding polypeptide tags were fused with target proteins in recombinant fusion proteins to achieve non-covalent binding of a fluorescent ligand [2], a labeled polypeptide ligand [3], or other small molecule ligands [4] [6].
One possible negative implication of considering only local features could be that local features are not sufficient to account for ligand binding quality of certain regions of protein surface since some ligand positions could be fixed by few relatively distant non-covalent bonds.
The binding of multiple ligands to individual receptors has previously been described [ 39]; however, certain interactions appear to be more important than others.
