Uttamkumar Samanta

Environment of tryptophan side chains in proteins.

Although relatively rare, the tryptophan residue (Trp), with its large hydrophobic surface, has a unique role in the folded structure and the binding site of many proteins, and its fluorescence properties make it very useful in studying the structures and dynamics of protein molecules in solution. An analysis has been made of its environment and the geometry of its interaction with neighbors using 719 Trp residues in 180 different protein structures. The distribution of the number of partners interacting with the Trp aromatic ring shows a peak at 6 (considering protein residues only) and 8 (including water and substrate molecules also). The means of the solvent‐accessible surface areas of the ring show an exponential decrease with the increase in the number of partners; this relationship can be used to assess the efficiency of packing of residues around Trp. Various residues exhibit different propensities of binding the Trp side chain. The aromatic residues, Met and Pro have high values, whereas the smaller and polar‐chain residues have weaker propensities. Most of the interactions are with residues far away in sequence, indicating the importance of Trp in stabilizing the tertiary structure. Of all the ring atoms NE1 shows the highest number of interactions, both along the edge (hydrogen bonding) as well as along the face. Various weak but specific interactions, engendering stability to the protein structure, have been identified. Proteins 2000;38:288–300.

Packing of aromatic rings against tryptophan residues in proteins

The geometry of the interaction of the aromatic side chains of phenylalanine (Phe), tyrosine (Tyr), tryptophan (Trp) and histidine (His) with the indole ring of Trp has been analyzed using the structures in the Protein Data Bank in order to understand the dependence of the packing behaviour on the size and chemical nature of the aromatic rings. The Phe ring prefers to interact either perpendicularly, with its edge pointing towards the Trp face, or in an offset-stacked arrangement. The edge-to-face motif is typical of a Trp-Trp pair. While parallel stacking is the dominant feature of Trp-His interaction, Tyr packs in a more uniform manner around Trp with a higher than expected occurrence at the edge and a few cases of possible OH-pi interaction.

Insight into the role of a unique SSEHA motif in the activity and stability of Helicobacter pylori arginase

Arginase is a binuclear Mn2+‐metalloenzyme of urea cycle that hydrolyzes arginine to ornithine and urea. Unlike other arginases, the Helicobacter pylori enzyme is selective for Co2+ and has all conserved motifs except 88SSEHA92 (instead of GGDHS). To examine the role of this motif in the activity and stability, steady‐state kinetics, mutational analysis, thermal denaturation, and homology modeling were carried out. With a series of single and double mutants, we show that mutations of Ser88 and Ala92 to its analogous residues in other arginases individually enhance the catalytic activity. This is supported by the modeling studies, where the motif plays a role in alteration at the active site structure compared to other arginases. Mutational analysis further shows that both Glu90 and His91 are important for the activity, as their mutations lead to significant decrease in the catalytic efficiency but they appear to act in two different ways; Glu90 has a more catalytic role as its mutant displays binding of the two metal ions per monomer of the protein, but His91 plays a critical role in retaining the metal ion at the active site as its mutation exhibits a loss of one metal ion. Thermal denaturation studies demonstrated that Ser88 and His91 both play crucial roles in the stability of the protein as their mutants showed a decrease in the Tm by ∼10–11°. Unlike wild type, the metal ions have larger role in providing the stability to the mutant proteins. Thus, our data demonstrate that the motif not only plays an important role in the activity but also critical in the stability of the protein.

Silver(I) oxide–silver halide mediated alcoholysis of O-benzoyl-myo-inositol 1,3,5-orthoformates: intramolecular assistance by the sulfonyl group

Silver(I) oxide–silver halide mediated alcoholyses of racemic 2,4-di-O-benzoyl-myo-inositol 1,3,5-orthoformate, and its 6-O-methyl and 6-O-sulfonylated derivatives, under identical conditions have been compared. While only the 4-O-benzoyl group undergoes solvolysis in the former two, to yield the corresponding 2-O-benzoyl-myo-inositol 1,3,5-orthoformate, both the 4-O- as well as the 2-O-benzoyl groups undergo solvolysis in the latter, to yield racemic 6-O-sulfonyl-myo-inositol 1,3,5-orthoformates. These results show that solvolysis of the 2-O-benzoyl group in sulfonates is a consequence of intramolecular assistance by the sulfonyl group. Catalytic efficiency of the silver halides in bringing about solvolysis of the benzoates decreased in the order AgI > AgBr > AgCl. A reaction mechanism involving silver–inositol derivative chelates has been proposed.

2-O-Benzoyl-myo-inositol-1, 3, 5-orthoformate

Protected myo-inositol derivatives are important precursors in the synthesis of phosphorylated myo-inositol derivatives which play a significant role in the cellular signal transduction. The structure of the title compound, C14H14O7, which was prepared from myo-inositol, has been determined by X-ray crystallography. Several types of hydrogen-bonding interactions are involved in the packing of the molecule in the crystal.