Protein structure patterns

Colovos, C. and Yeates, T. O. (1993) Verification of protein structures patterns of nonbonded atomic interactions. Protein Sci. 2, 1511-1519. 

An outstanding summary of protein structural patterns and principles the author originated the very useful ribbon representations of protein structure. 

Varieties of Globular Protein Structure Patterns of Folding (Figure 6.16, Figure 6.17, Figure 6.18, Figure 6.19)... 

Richardson, J.S., Richardson, D.C. Principles and patterns of protein conformation. In Prediction of Protein Structure and the Principles of Protein Conformation (ed. Fasman, G.D.), pp. 1-98. New York Plenum, 1989. 

Levitt, M., Chothia, C. Structural patterns in globular proteins. Nature 261 552-558, 1976. 

A very narrow window produces monochromatic radiation that is still several orders of magnitude more intense than the beam from conventional rotating anode x-ray sources. Sucb beams allow crystallographers to record diffraction patterns from very small crystals of the order of 50 micrometers or smaller. In addition, the diffraction pattern extends to higher resolution and consequently more accurate structural details are obtained as described later in this chapter. The availability and use of such beams have increased enormously in recent years and have greatly facilitated the x-ray determination of protein structures. 

Despite the unity in secondary structural patterns, little is known about the three-dimensional, or tertiary, structure of rRNAs. Even less is known about the quaternary interactions that occur when ribosomal proteins combine with rRNAs and when the ensuing ribonucleoprotein complexes, the small and large subunits, come together to form the complete ribosome. Furthermore, assignments of functional roles to rRNA molecules are still tentative and approximate. (We return to these topics in Chapter 33.)... 

Multiple isomorphous replacement allows the ab initio determination of the phases for a new protein structure. Diffraction data are collected for crystals soaked with different heavy atoms. The scattering from these atoms dominates the diffraction pattern, and a direct calculation of the relative position of the heavy atoms is possible by a direct method known as the Patterson synthesis. If a number of heavy atom derivatives are available, and... 

An important step is to validate the structure, that is, to compare features of the structure to features in known protein structures. This includes localized fit to density, hydrogen bonding patterns, divergence from standard geometry, and much more [12]. Such calculations can highlight where the model requires further improvement. 

Kabsch, W., and C. Sander. 1983. Dictionary of Protein Secondary Structure Pattern Recognition of Hydrogen-Bonded and Geometrical Features. Biopol. 22,2577-2637. 

Once the protein interaction pattern is translated from Cartesian coordinates into distances from the reactive center of the enzyme and the structure of the ligand has been described with similar fingerprints, both sets of descriptors can be compared [25]. The hydrophobic complementarity, the complementarity of charges and H-bonds for the protein and the substrates are all computed using Carbo similarity indices [26]. The prediction of the site of metabolism (either in CYP or in UGT) is based on the hypothesis that the distance between the reactive center on the protein (iron atom in the heme group or the phosphorous atom in UDP) and the interaction points in the protein cavity (GRID-MIF) should correlate to the distance between the reactive center of the molecule (i.e. positions of hydrogen atoms and heteroatoms) and the position of the different atom types in the molecule [27]. 

X-ray data suggest that the peptide linkage is planar in either small molecules or proteins themselves215-220. The planarity of the peptide linkage results into interesting structural patterns encountered in polypeptide molecules. Two important conformations of peptides are the a-helix and fully extended conformations221. Examination of the fully extended form of a polypeptide immediately reveals that this conformation enjoys considerable stabilization from the factors we have been discussing. 

Prosite is perhaps the best known of the domain databases (Hofmann et al., 1999). The Prosite database is a good source of high quality annotation for protein domain families. Prosite documentation includes a section on the functional meaning of a match to the entry and a list of example members of the family. Prosite documentation also includes literature references and cross links to other databases such as the PDB collection of protein structures (Bernstein et al., 1977). For each Prosite document, there is a Prosite pattern, profile, or both to detect the domain family. The profiles are the most sensitive detection method in Prosite. The Prosite profiles provide Zscores for matches allowing statistical evaluation of the match to a new protein. Profiles are now available for many of the common protein domains. Prosite profiles use the generalized profile software (Bucher et al., 1996). 

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