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M Saqi

Publications and source records attributed to M Saqi.

4 recordsLinked to original sources

Delineation of the arginine- and tetrahydrobiopterin-binding sites of neuronal nitric oxide synthase.

Nitric oxide synthase (EC 1.14.13.39) catalyses the conversion of arginine, NADPH and oxygen to nitric oxide and citrulline, using haem, (6R)-5,6,7,8-tetrahydro-l-biopterin (tetrahydrobiopterin), calmodulin, FAD and FMN as cofactors. The enzyme consists of a central calmodulin-binding sequence flanked on the N-terminal side by a haem-binding region that contains the arginine and tetrahydrobiopterin sites and on the C-terminal side by a region homologous with NADPH:cytochrome P-450 reductase. By using domain boundaries defined by limited proteolysis of full-length enzyme, recombinant haem-binding regions of rat brain neuronal nitric oxide synthase were expressed and purified. Two proteins were made in high yield: one, corresponding to residues 221-724, contained bound haem and tetrahydrobiopterin and was able to bind Nomega-nitro-l-arginine (nitroarginine) or arginine; the other, containing residues 350-724, contained bound haem but was unable to bind tetrahydrobiopterin, nitroarginine or arginine. These results showed that rat brain neuronal nitric oxide synthase contains a critical determinant for arginine/tetrahydrobiopterin binding between residues 221 and 350. Limited proteolysis with chymotrypsin of the former protein resulted in a new species with an N-terminal residue 275 that retained the ability to bind nitroarginine, further defining the critical region for arginine binding as being between 275 and 350. Comparison of the sequences of nitric oxide synthase and the tetrahydrobiopterin-requiring amino acid hydroxylases revealed a similarity in the region between residues 470 and 600, suggesting that this might represent the core region of the pterin-binding site. The stoichiometries of binding of substrate and cofactors to the recombinant domains were not more than 0.5 mol/mol of monomer, suggesting that there might be a single high-affinity site per dimer.

Amino Acid Sequence↗

PdbAlign, PdbDist and DistAlign: tools to aid in relating sequence variability to structure.

Many sequence analysis problems involve consideration of a multiple sequence alignment where the 3-dimensional structure of one (or more) of the aligned sequences is known. In such cases, it is useful to map the sequence variability onto the atomic co-ordinates of known structure. If the structure also includes a bound ligand (or the location of the active site is known), each column position in the multiple sequence alignment may be annotated with its 'distance' from the binding site. These annotations, together with a measure of sequence variability, provide additional insights into drug specificity, for example among viral mutants. This paper describes several useful programs that automate this analysis.

Amino Acid Sequence↗

An analysis of structural instances of low complexity sequence segments.

Amino acid sequence databases contain many low complexity, compositionally biased sequence segments. However, only a limited number of relatively short instances of these segments occur in proteins of known structure. An analysis is presented of structural instances of these low complexity sequence segments in the Brookhaven Protein Data Bank with regard to preferences for sequence composition, secondary structural conformation and the local atomic environment. The complexity varies almost linearly with segment length, reflecting the absence of very long, low complexity segments in the structural database. The low complexity segments identified are not disordered and have temperature factors which are generally the same as the rest of the protein. It is observed that these segments are predominantly exposed and either helical or coiled, in excess of what would be expected by chance. Secondary structure prediction methods perform well in correctly predicting those low complexity segments which are helical but poorly in correctly predicting segments that are strands.

Amino Acid Sequence↗