Small-molecule ligands

Not all allosteric proteins are enzymes. In fact, probably the best-known and characterized allosteric protein is haemoglobin, which like an enzyme binds ligands (small molecules) to itself, for example, oxygen rather than a substrate. 

Competitive, non-competitive and allosteric effects all rely on weak binding between the enzyme and the various ligands (small molecules which attach to a bigger molecule). Such weak binding attractions are not covalent bonds, unlike the situation described below. 

Cell specific ligand (small molecules, peptide etc.)... 

The protein footprinting approach utilizes chemical modifications to generate a mass shift either on amino acid side chains or the protein amide backbone, followed by MS analysis. This approach can capture minor changes in protein solvent accessibilities that are induced by protein-ligand (ligand small molecule, protein, DNA, etc.) interactions or protein conformational changes. 

The PDB contains 20 254 experimentally determined 3D structures (November, 2002) of macromolecules (nucleic adds, proteins, and viruses). In addition, it contains data on complexes of proteins with small-molecule ligands. Besides information on the structure, e.g., sequence details (primary and secondary structure information, etc.), atomic coordinates, crystallization conditions, structure factors. 

GAs or other methods from evolutionary computation are applied in various fields of chemistry Its tasks include the geometry optimization of conformations of small molecules, the elaboration of models for the prediction of properties or biological activities, the design of molecules de novo, the analysis of the interaction of proteins and their ligands, or the selection of descriptors [18]. The last application is explained briefly in Section 9.7.6. 

The calculation of E] and X from computational methods is the focus here. Generally, the energetics of these quantities are separated into contributions from the inner and outer shells. For transfer between small molecules, the inner shell generally is defined as the entire solutes A and D, and the outer shell is generally defined as only the solvent. However, in a more practical approach for proteins, the inner shell is defined as only the redox site, which consists of the metal plus its ligands no further than atoms of the side chains that are directly coordinated to the metal, and the outer shell is defined as the rest of the protein plus the surrounding solvent. Thus... 

Fig. 1.3 Various small-molecule peptoid ligands derived from combinatorial libraries...

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