Structural homology, identification

Zheng, W., and Doniach, S. (2002). Protein structure prediction constrained by solution X-ray scattering data and structural homology identification. J. Mol. Biol. 316, 173-187. 

The routes to the proof of structure and identification of species of PAF and related homologs and analogs can be classified into two methodological approaches. The first one can provide limited, but meaningful, data and can be accomplished in any laboratory equipped with basic chemical and biochemical capability, and the second one centers on the use of highly sophisticated (and expensive) instrumentation. These will be referred to simply as Approach 1 and Approach II, respectively. 

As a corollary to the notion that enzyme superfamilies comprise members that share a common catalytic mechanism, but not necessarily sequence or structural homology, recent studies have shown that directed ABPP probes, which typically target a large set of mechanistically related enzymes (e.g., SHs, metalloproteases), can also facilitate the identification of unannotated members of enzyme superfamilies [55, 56]. 

The use of 5-IAF-labeled lamins of vertebrates and invertebrates for microinjection into cells of distantly related metazoa and protozoa species (Schmidt et al., 1995) could aid in identification of lamin binding partners in the nuclear envelopes of these species. Binding of the labeled lamin to the nuclear envelope would suggest the presence of a protein, or proteins, that exhibit sufficient structural homologies to, or are capable of binding, such microinjected proteins. 

Knowledge of the amino acid sequence of a protein is paramount to an understanding of biological events and the molecular basis of its biological activity, and to predicting its three-dimensional structure. The identification of the exact molecular form of a protein is also important from the viewpoint of human health. An aberration in a protein structure can lead to a particular disease. Furthermore, a disease can canse an aberration in a protein structure. In addition, the amino acid sequence of a protein is useful to unravel evolutionary events. All proteins from a common ancestor have greater sequence homology. 

Detailed characterization of opioid receptors began in 1992 with the identification and cloning of the OPl (delta) receptor, followed by subsequent identification and cloning of OP2 (kappa) and OP3 (mu) receptors. All of these receptors are G-coupled proteins that have seven transmembrane domains and share 60% of structural homology. In 1994, a new receptor subtype was identified and was originally given the name opioid receptor like-1 (ORL-1). This subtype has typical opioid receptor characteristics, such as a G-coupled... 

The scope and mechanism of carboxylic acid homologation is examined here in relation to the structure of the carboxylic acid substrate, the concentrations and composition of the ruthenium catalyst precursor and iodide promoter, synthesis gas ratios, as well as 13C labelling studies and the spectral identification of ruthenium iodocarbonyl intermediates. 

---