Protein crystallography constraints

Most experimental structures are solved by X-ray crystallographic methods. The standard procedure for the determination of the 3-D arrangement of atoms involves the raw diffraction data (the intensities of the reflected X-ray beams or structure factors) and the refinement by a theoretical model based on an atomic model of the molecule in the case of proteins, this is the primary structure. The introduction of constraints is necessary for most diffraction experiments, in particular in the area of protein crystallography. Only with these can a chemically reasonable structure with the positions of all atoms in the molecule be obtained [288]. 

Biological fibers, such as can be formed by DNA and fibrous proteins, may contain crystallites of highly ordered molecules whose structure can in principle be solved to atomic resolution by x-ray crystallography. In practice, however, these crystallites are rarely as ordered as true crystals, and in order to locate individual atoms it is necessary to introduce stereochemical constraints in the x-ray analysis so that the structure can be refined by molecular modeling. 

Distance geometry provides sets of 3-D structures of a protein or nucleic acid that fulfill the constraints. The combination of distance geometry, for generation of molecular starting points, with molecular dynamics computations can yield 3-D models of small proteins with precision equal to X-ray crystallography. This combination of NMR, molecular mechanics, and molecular dynamics can be used to provide a three-dimensional protein structure in a situation where the protein cannot be crystallized or the crystals are not appropriate for X-ray crystallography. 

Properties of proteins such as solubility and chromatographic behavior depend on the residues that are accessible to the solvent. The nonpolar residues buried in the interior of the molecules should not directly affect these properties. Therefore, the surface hydrophobicity may be the more relevant parameter. Of course, the ideal model depicted by the polarity ratio is never attained. Because of the steric constraints and the inevitable adjacency of polar and nonpolar residues in the amino acid sequence, a proportion of nonpolar residues will be found at or close to the periphery of molecules. For proteins whose structures have been determined (e.g., by x-ray crystallography), it is possible to calculate the surface hydrophobicity. Some values are recorded in Table 9.1. Because of their heterogeneity, cereal proteins are not easily amenable to structure determination, so their surface hydrophobicities have not been calculated. 

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