Protein structure analysis 214 Subject

The structural analysis of membrane-associated peptides comprises two steps (a) the elucidation of the three-dimensional fold of the peptide and (b) the determination of the membrane-peptide interface. We will use our results gained for the 36 amino acid residue neuropeptide Y (NPY) [83] to demonstrate the approaches that can be used. NPY regulates important pharmacological functions such as blood pressure, food intake or memory retention and hence has been subject of many investigations (for a review see Ref. [84]). It targets the so-called Y receptors that belong to the class of seven transmembrane receptors coupled to G-proteins (GPCRs). 

Careful analysis of electron-density maps usually reveals many ordered water molecules on the surface of crystalline proteins (Plate 4). Additional disordered water is presumed to occupy regions of low density between the ordered particles. The quantity of water varies among proteins and even among different crystal forms of the same protein. The number of detectable ordered water molecules averages about one per amino-acid residue in the protein. Both the ordered and disordered water are essential to crystal integrity, and drying destroys the crystal structure. For this reason, protein crystals are subjected to X-ray analysis in a very humid atmosphere or in a solution that will not dissolve them, such as the mother liquor. 

It is possible at present to identify two main levels at which molecular similarity is of importance in proteins. First, detection of large-scale similarities between different protein structures, i.e. similarities in the way that the linear polypeptide sequence is folded up to form a three-dimensional structure. This is the subject of the remainder of Sect. 4. Second, comparative analysis of local aspects of protein structure, for example the examination of specific binding sites, or of the environments of particular sidechains. These methods are described in Sect. 5. 

In systems where the correlation holds, physical chemists can analyze the energetics of association and perform computer simulations of the recognition process based on this analysis. While still far from satisfactory, structure-based theoretical approaches to macromolecular recognition— another subject of our chapter—represent an active field of research with an important future in the postgenomic era. In a matter of years, large-scale efforts in protein structure determination are expected to provide... 

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