Protein Similarity

In one case the shape of the ligands was used (FLAP LB, see legend on Fig. 4.6) as a constraint and in another case the shape of the receptor (FLAP SB, see legend on Fig. 4.6). Exactly the same procedure was applied in Catalyst [29] for comparison. 

Proteins can also be compared, with or without using information from ligands that bind to them. From the protein site points FLAP identifies the pharmacophores that are in common on-the-fly. Then complementarities between the proteins are evaluated maximizing the site-point features and the shape complementary between protein cavities. The resultant matches are then written out to a file. 

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Lipman, D ] and W R Pearson 1985. Rapid and Sensitive Protein Similarity Searches. Science 227 1435-1441. 

The methacrylic backbone structure makes the spherical Toyopearl particles rigid, which in turn allows linear pressure flow curves up to nearly 120 psi (<10 bar), as seen in Fig. 4.45. Toyopearl HW resins are highly resistant to chemical and microbial attack and are stable over a wide pH range (pH 2-12 for operation, and from pH 1 to 13 for routine cleaning and sanitization). Toyopearl HW resins are compatible with solvents such as methanol, ethanol, acetone, isopropanol, -propanol, and chloroform. Toyopearl HW media have been used with harsh denaturants such as guanidine chloride, sodium dodecyl sulfate, and urea with no loss of efficiency or resolution (40). Studies in which Toyopearl HW media were exposed to 50% trifluoroacetic acid at 40°C for 4 weeks revealed no change in the retention of various proteins. Similarly, the repeated exposure of Toyopearl HW-55S to 0.1 N NaOH did not change retention times or efficiencies for marker compounds (41). 

Comparative Aspects of Rieske Proteins Similarity and Diversity... 

Lipman DJ, Pearson WR. Rapid and sensitive protein similarity searches. Science 1985 227 1435-41. 

Proteins similar to importins, referred to as ex-portins, are involved in export of many macromolecules from the nucleus. Cargo molecules for export carry nuclear export signals (NESs). Ran proteins are involved in this process also, and it is now established that the processes of import and export share a number of common feamres. 

Various other protein hormones circulate in the blood but are not usually designated as plasma proteins. Similarly, ferritin is also found in plasma in small amounts, but it too is not usually characterized as a plasma protein. 

POTTER s M, FERTILE J and BERBER-JIMENEZ M D (1996) Soy protein concentrate and isolated soy protein similarly lower blood serum cholesterol hut differently affect thyroid hormones in hamsters. J Nutr. 126 (8) 2007-11. 

Some work has been completed on reaction of proteins with nitrite followed by hydrolysis and analysis for amino acids It has been shown that 3-nitrotyrosine and 3,4-dihydroxyphenylalanine are formed from bovine serum albumin when nitrosation occurs under conditions similar to those found in the human stomach (36), Direct demonstration that nitrite reacts with protein has been made by using NaN02 with bovine serum albumin (pH 5.5, 20 C and 200 ppm nitrite). A 60% loss of the originally added nitrite was observed in one week and nearly half of the nitrite (labelled %) could be recovered from the protein. Similar work with myosin revealed that 10-20% of the incorporated label was present as 3-nitrotyro-sine (J7). 

Most of the molecules introduced in this chapter are hydrophobic. Even those molecules that have been functionalized to improve water-solubility (for example, CCVJ and CCVJ triethyleneglycol ester 43, Fig. 14) contain large hydrophobic structures. In aqueous solutions that contain proteins or other macromolecules with hydrophobic regions, molecular rotors are attracted to these pockets and bind to the proteins. Noncovalent attraction to hydrophobic pockets is associated with restricted intramolecular rotation and consequently increased quantum yield. In this respect, molecular rotors are superior protein probes, because they do not only indicate the presence of proteins (similar to antibody-conjugated fluorescent markers), but they also report a constricted environment and can therefore be used to probe protein structure and assembly. 

Secondary structural predictions about NPAs, and direct biophysical measurements, have demonstrated that the NPAs are rich in a-helix, with no p-structure either predicted from secondary structure prediction algorithms, or detected by circular dichroism (Kennedy et al, 1995b). In this they are the antithesis of the similarly sized cLBPs and lipocalins. The predictions are that each individual NPA unit protein will fold into four main regions of helix, and it has been speculated that the tertiary structure is as a four-bundle helix protein, similar to other invertebrate carrier proteins (Sheriff et al., 1987). 

All the described properties of such a s-fraction of poly(NVCl-co-NVIAz) synthesized at the temperature above the PST of the reacting system allowed us to draw the conclusion that the chains of this type had the comonomer sequence, which at the temperatures above the conformation transition facilitated the formation of polymer particles, where H-blocks are in the interior shielded by the P-blocks against additional intermolecular association. Such a behaviour of this copolymer in aqueous media is close to that of oligomeric proteins similar to casein [46] possessing a rather hydrophobic core surrounded by the polar segments. 

Oxidative stress and inflammation are elevated in hemodialysis patients, which, at least partly, might be initiated by intravenous iron administration. Thus, Tovbin et al. [377] showed that the administration of iron saccharide to hemodialysis patients increased the blood level of oxidized proteins. Similarly, an increase in the levels of free ( nontransferrin-bound or labile ) iron has been shown in the plasma of hemodialysis patients [378] including patients after intravenous iron saccharate infusion [379]. 

In favorable systems, the coherent movement of neuro-filaments and microtubule proteins provides strong evidence for the structural hypothesis. Striking evidence was provided by pulse-labeling experiments in which NF proteins moved over periods of weeks as a bell-shaped wave with little or no trailing of NF protein. Similarly, coordinated transport of tubulin and MAPs makes sense only if MTs are being moved, since MAPs do not interact with unpolymerized tubulin [31]. 

Peroxidases are heme iron-containing proteins similar in structure to that of cytochromes P450. The major difference is that peroxidases have histidine as the axial ligand instead of cysteine, and there are also other polar amino acids close to the heme iron that help to catalyze the peroxidase function of the enzyme (41). The result is that the peroxidases very rapidly catalyze the reduction of hydroperoxides to alcohols (or water in the case of... 

Wu, Y.C., and Horvitz, H.R., 1998, The C. elegans cell corpse engulfinent gene ced-7 encodes a protein similar to ABC transporters, Cell 93 951-960. 

The above observations provide a clear demonstration that cosolvents in selected ranges of concentration create reversible perturbations of protein similar to those induced by other modifiers. The reversibility of the cosolvent effect is a prerequisite to cosolvent use and will depend on the concentration of cosolvent, which in turn will vary markedly with the type of solvent used. For instance, polyols can be used at concentrations up to 8 Af while methanol at 3 M causes the appearance of a new absorption band (410 nm) and, after further increases in concentration, an irreversible conversion of cytochrome P-450 into P-420. Other aliphatic alcohols cause denaturation at much lower concentrations. 

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