Homology determination

The overall distribution of the components determined is shown in Table II. Items reported for each class of components include total amount, the number of homologous series (in Z number), and individual carbon-number homologs determined in that class and their ranges (in carbon number). 

The algorithm was demonstrated on NMR data from a 76- residue protein, human ubiquitin, matched to four structures, including one mutant (homolog), determined either by X-ray crystallography or NMR experiments (without RDCs). NVR achieves an average assignment accuracy of over 99%. ... 

Sequences have been determined for plasminogen and bovine Factor XII, and they are not homologous with the other serine proteases. The amino-terminal sequence of Factor XII is homologous, however, with the active site of several naturally occurring protease inhibitors (11). 

Figure 9 Relative accuracy of comparative models. Upper left panel, comparison of homologous structures that share 40% sequence identity. Upper right panel, conformations of ileal lipid-binding protein that satisfy the NMR restraints set equally well. Lower left panel, comparison of two independently determined X-ray structures of interleukin 1(3. Lower right panel, comparison of the X-ray and NMR structures of erabutoxin. The figure was prepared using the program MOLSCRIPT [236].

MI Sutcliffe, CM Dobson, RE Oswald. Solution structure of neuronal bungarotoxm determined by two-dimensional NMR spectroscopy Calculation of tertiary structure using systematic homologous model building, dynamical simulated annealing, and restrained molecular dynamics. Biochemistry 31 2962-2970, 1992. 

The lac repressor monomer, a chain of 360 amino acids, associates into a functionally active homotetramer. It is the classic member of a large family of bacterial repressors with homologous amino acid sequences. PurR, which functions as the master regulator of purine biosynthesis, is another member of this family. In contrast to the lac repressor, the functional state of PurR is a dimer. The crystal structures of these two members of the Lac I family, in their complexes with DNA fragments, are known. The structure of the tetrameric lac repressor-DNA complex was determined by the group of Mitchell Lewis, University of Pennsylvania, Philadelphia, and the dimeric PurR-DNA complex by the group of Richard Brennan, Oregon Health Sciences University, Portland. 

The position of the keto group of A-homo-5a-cholestan-3-one (5b) was determined by Nelson and Schut by an unambiguous synthesis of ketone (5b) involving bis-homologation of 2,3-seco-5a-cholestane-2,3-dioic acid (8) using the Arndt-Eistert sequence [(9) (11)]. 

The HIV-l protease is a remarkable viral imitation of mammalian aspartic proteases It is a dimer of identical subunits that mimics the two-lobed monomeric structure of pepsin and other aspartic proteases. The HIV-l protease subunits are 99-residue polypeptides that are homologous with the individual domains of the monomeric proteases. Structures determined by X-ray diffraction studies reveal that the active site of HIV-l protease is formed at the interface of the homodimer and consists of two aspartate residues, designated Asp and Asp one contributed by each subunit (Figure 16.29). In the homodimer, the active site is covered by two identical flaps, one from each subunit, in contrast to the monomeric aspartic proteases, which possess only a single active-site flap. 

Gas-phase basity and proton affinity values for 3,4,6,7,8,9-hexahydro-2/f-pyrido[l,2-n]pyrimidine were determined and they were compared to other super bases, including its lower and higher piperidine ring homologs (94JP0725, 01JPO25). 

Bruhl found that the increase of CHj in all the homologous series of fatty compounds corresponds to a difierence of 4 57 in the molecular refraction for the red hydrogen line. By deducting n times this value from the molecular refraction cf an aldehyde or ketone of the formula C H2 0, he found 2 328 to be the value for intra-radical oxygen. Similarly the values of other groupings have been determined which may be summarised as follows —... 

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