Surface amino acid residues

It is known that CYP1A2 preferentially binds molecules with a relatively planar moiety, with heterocyclic aromatic amines, xanthines and quinolones. It is also likely that surface amino acid residues are responsible for the recognition of and the selectivity towards specific ligands [11]. 

Elaboration of LRET mechanism by resolving the parameters that determine specific rates of LRET has stimulated pulse radiolysis studies in proteins. Examples include generation of metastable electron donor and acceptor complexes in (1) native and mutant proteins, (2) proteins with the directed single-site specific mutations, (3) native and mutant multisite redox proteins, (4) proteins with the site specific modification with transition metal complexes covalently attached to a specific surface amino acid residues. 

The molecular basis for quasi-equivalent packing was revealed by the very first structure determination to high resolution of a spherical virus, tomato bushy stunt virus. The structure of this T = 3 virus was determined to 2.9 A resolution in 1978 by Stephen Harrison and co-workers at Harvard University. The virus shell contains 180 chemically identical polypeptide chains, each of 386 amino acid residues. Each polypeptide chain folds into distinct modules an internal domain R that is disordered in the structure, a region (a) that connects R with the S domain that forms the viral shell, and, finally, a domain P that projects out from the surface. The S and P domains are joined by a hinge region (Figure 16.8). 

In 1975, the fabrication of a chiral electrode by permanent attachment of amino acid residues to pendant groups on a graphite surface was reported At the same time, stimulated by the development of bonded phases on silica and aluminia surfaces the first example of derivatized metal surfaces for use as chemically modified electrodes was presented. A silanization technique was used for covalently binding redox species to hydroxy groups of SnOj or Pt surfaces. Before that time, some successful attemps to create electrode surfaces with deliberate chemical properties made use of specific adsorption techniques... 

The aldehyde oxidoreductase from Desulfovibrio gigas shows 52% sequence identity with xanthine oxidase (199, 212) and is, so far, the single representative of the xanthine oxidase family. The 3D structure of MOP was analyzed at 1.8 A resolution in several states oxidized, reduced, desulfo and sulfo forms, and alcohol-bound (200), which has allowed more precise definition of the metal coordination site and contributed to the understanding of its role in catalysis. The overall structure, composed of a single polypeptide of 907 amino acid residues, is organized into four domains two N-terminus smaller domains, which bind the two types of [2Fe-2S] centers and two much larger domains, which harbor the molybdopterin cofactor, deeply buried in the molecule (Fig. 10). The pterin cofactor is present as a cytosine dinucleotide (MCD) and is 15 A away from the molecular surface,... 

The characteristic coiled-coil motifs found in proteins share an (abcdefg) heptad repeat of polar and nonpolar amino acid residues (Fig. 1). In this motif, positions a, d, e, and g are responsible for directing the dimer interface, whereas positions b, c, and f are exposed on the surfaces of coiled-coil assemblies. Positions a and d are usually occupied by hydrophobic residues responsible for interhelical hydrophobic interactions. Tailoring positions a, d, e, and g facilitates responsiveness to environmental conditions. Two or more a-helix peptides can self-assemble with one another and exclude hydrophobic regions from the aqueous environment [74]. Seven-helix coiled-coil geometries have also been demonstrated [75]. 

Loss of the native conformation of a protein generally exposes hydrophobic amino acid residues that are normally buried on the inside of the self-associated structure and are shielded from the aqueous environment. This leads to association between the exposed hydrophobic residues of neighboring proteins (aggregation) or between these exposed residues and hydrophobic surfaces that the protein may encounter either in the manufacturing process or in the primary package. 

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