The nature of the allosteric interactions of ribonuclease and its ligands

Positional preferences in flavonoids for inhibition of ribonuclease A: Where "OH" where?

Flavonoids are a class of polyphenols that possess diverse properties. The structure-activity relationship of certain flavonoids and resveratrol with ribonuclease A (RNase A) has been investigated. The selected flavonoids have a similar skeleton and the positional preferences of the phenolic moieties toward inhibition of the catalytic activity of RNase A have been studied. The results obtained for RNase A inhibition by flavonoids suggest that the planarity of the molecules is necessary for effective inhibitory potency. Agarose gel electrophoresis and precipitation assay experiments along with kinetic studies reveal K_i values for the various flavonoids in the micromolar range. Minor secondary structural changes of RNase A were observed after interaction with the flavonoids. An insight into the specific amino acid involvement in the binding of the substrate using docking studies is also presented. The dipole moment of the flavonoids that depends on the orientation of the hydroxyl groups in the molecule bears direct correlation with the inhibitory potency against RNase A. The direct association of this molecular property with enzyme inhibition can be exploited for the design and development of inhibitors of proteins.

Protein Carbamylation: Chemistry, Pathophysiological Involvement, and Biomarkers

Protein carbamylation refers to a nonenzymatic modification, which consists in the binding of isocyanic acid on protein functional groups. This reaction is responsible for the alteration in structural and functional properties of proteins, which participate in their molecular aging. Protein molecular aging is now considered a molecular substratum for the development of chronic and inflammatory diseases, including atherosclerosis, chronic kidney disease, or rheumatoid arthritis. As a consequence, carbamylation-derived products have been proposed as interesting biomarkers in various pathological contexts and appropriate analytical methods have been developed for their quantification in biological fluids. The purpose of this review is (i) to describe the biochemical bases of the carbamylation reaction, (ii) to explain how it contributes to protein molecular aging, (iii) to provide evidence of its involvement in aging and chronic diseases, and (iv) to list the available biomarkers of carbamylation process and the related analytical methods.

The structural and functional studies of His119 and His12 in RNase A via chemical modification

The histidyl residues of bovine pancreatic ribonuclease A (RNase A) play a crucial role in enzymatic activity. Diethylpyrocarbonate (DEPC) is a potent inhibitor of RNase A, and its precise sites of action on the imidazole rings of the four histidyl residues of RNase A are not clearly defined. We have used a multidisciplinary approach including enzyme assay, calculation of accessible surface area (ASA), isoelectric pH gradient technique, fluorescence investigations, circular dichroism spectroscopy, differential scanning calorimetry, and 1H NMR analysis to study the sites of DEPC interaction with the imidazole rings of the four histidyl residues. Our results demonstrate that among the histidyl residues of RNase A, His48 is not accessible to react with DEPC. However, the sequential carbethoxylation of the imidazole rings of His119, His105, and His12 occurs on the nitrogen atoms of Ndelta, Nepsilon, and Nepsilon, respectively. Carbethoxylation of His119 was followed by conversion of the A conformation to the B conformation in the active site. However, the carbethoxylation of His12 was accompanied by a second spatial rotation of the corresponding imidazole ring in the active site to adopt a new conformation. These conformation changes are accompanied by subsequent decrements in the thermal stability of the protein. Therefore, these findings reinforce the important structural roles of the spatial positions for His119 and His12 in the active site of RNase A.

Nonenzymatic deamidation of asparaginyl and glutaminyl residues in proteins

Some asparagine and glutamine residues in proteins undergo deamidation to aspartate and glutamate with rates that depend upon the sequence and higher-order structure of the protein. Functional groups within the protein can catalyze this reaction, acting as general acids, bases, or stabilizers of the transition state. Information from specific proteins that deamidate and analysis of protein sequence and structure data bases suggest that asparagine and glutamine lability has been a selective pressure in the evolution of protein sequence and folding. Asparagine and glutamine deamidation can affect protein structure and function in natural and engineered mutant sequences, and may play a role in the regulation of protein folding, protein breakdown, and aging.

Preparation of allosteric ribonuclease

A method for the preparation of allosteric ribonuclease from bovine pancreas is described. The effects of freeze-drying ribonuclease from acid and alkaline solutions on plots of velocity versus substrate concentration for the hydrolysis of 2':3'-cyclic CMP are examined. Comparison of these plots with the plots obtained with severeal commercial enzyme preparations indicates that the conformation of the enzyme is dependent on the method of preparation. Aging experiments demonstrate that further conformational changes occur at different rates, depending on the methods of storage. Results suggest that the allosteric behaviour of ribonuclease has not always been observed with commercial preparations, owing to variations in methods of preparation and storage of the enzyme.