Probing functional perfection in substructures of ribonuclease T1: double combinatorial random mutagenesis involving Asn43, Asn44, and Glu46 in the guanine binding loop

Structural and Functional Differences between Homologous Bacterial Ribonucleases

Small cationic guanyl-preferring ribonucleases (RNases) produced by the Bacillus species share a similar protein tertiary structure with a high degree of amino acid sequence conservation. However, they form dimers that differ in conformation and stability. Here, we have addressed the issues (1) whether the homologous RNases also have distinctions in catalytic activity towards different RNA substrates and interactions with the inhibitor protein barstar, and (2) whether these differences correlate with structural features of the proteins. Circular dichroism and dynamic light scattering assays revealed distinctions in the structures of homologous RNases. The activity levels of the RNases towards natural RNA substrates, as measured spectrometrically by acid-soluble hydrolysis products, were similar and decreased in the row high-polymeric RNA >>> transport RNA > double-stranded RNA. However, stopped flow kinetic studies on model RNA substrates containing the guanosine residue in a hairpin stem or a loop showed that the cleavage rates of these enzymes were different. Moreover, homologous RNases were inhibited by the barstar with diverse efficiency. Therefore, minor changes in structure elements of homologous proteins have a potential to significantly effect molecule stability and functional activities, such as catalysis or ligand binding.

Probing the effect of water-water interactions on enzyme activity with salt gradients: a case-study using ribonuclease t1

Water molecules interact with one another via hydrogen bonds. Experimental and theoretical evidence indicates that these hydrogen bonds occur in two modalities--high- and low-angle hydrogen bonding--and that the addition of various solutes to water affects only the number of water molecules participating in a specific type of hydrogen bond interactions, not the nature of the water-water interactions. In this work, we have investigated the effect of each of these hydrogen bonding types upon the activity of the enzyme ribonuclease t1. This was done through perturbation of the water hydrogen bonding distribution by using various salts. Our results indicate that various salts differ in their ability to reduce the enzymatic activity of ribonuclease t1, and this ability is well correlated with the ability of each salt to promote high-angle hydrogen bonding in water. By applying the two-phase model of liquid water (i.e., liquid water being modeled as an equilibrium existing between two phases, LD and HD water), we demonstrate that our results are compatible with the assumption that increasing the population of high-angle hydrogen bonds among water molecules stabilizes the more compact, less active conformations of the enzyme. This indicates that the structures that proteins adopt in water solution depend upon the nature of interactions between water molecules.

Low molecular weight chitosan is an efficient inhibitor of ribonucleases

RNase inhibitors are commonly used to block the RNase activity in manipulations with RNA-containing preparations. Recently RNase inhibitors, either synthetic or natural, have been intensively sought because they appeared to be promising for therapy of cancer and allergy. However, there is only a limited number of efficient RNase inhibitors. We have shown that a low molecular weight chitosan (M(r) approximately 6 kDa) inhibits activity of pancreatic RNase A and some bacterial RNases with inhibition constants in the range of 30-220 nM at pH 7.0 and ionic strength 0.14 M. The preferential contribution to the chitosan complex formation with RNases is due to establishment of 5-6 ion pairs. The results of this work show that polycations may efficiently inhibit ribonuclease activities.

Purine activity of RNase T1RV is further improved by substitution of Trp59 by tyrosine

Ribonuclease T1 is an enzyme that cleaves single-stranded RNA with high specificity after guanylyl residues. Although this enzyme is a very good characterized protein with respect to structure and enzymatic function, we were only recently successful in generating RNase T1-RV, a variant where the specificity was changed from guanine to purine. As this change of substrate specificity was made at the cost of activity, the aim was now to further improve the overall activity of the enzyme. Therefore, we have substituted the tryptophan in position 59 by tyrosine. This substitution led to an increase of enzymatic activity in comparison to variant RV to 425%. As the extent of this enhancement is unique so far we have crystallized and analyzed the structure of this variant in order to get more insights into the reasons for this. Here, we present the crystal structure of this so-called RNase T1-R2 at 2.1A resolution. The structure was determined by molecular replacement using the coordinates of the RV variant (PDB entry: 1Q9E). The data were refined to an R-factor of 18.7% and R(free) of 24%, respectively. The asymmetric unit contains three molecules and the crystal packing is very similar to that of variant RV.

Conserved asparagine residue 54 of alpha-sarcin plays a role in protein stability and enzyme activity

Asparagine 54 of alpha-sarcin is a conserved residue within the proteins of the ribotoxin family of microbial ribonucleases. It is located in loop 2 of the protein, which lacks repetitive secondary structure elements but exhibits a well-defined conformation. Five mutant variants at this residue have been produced and characterized. The spectroscopic characterization of these proteins indicates that the overall conformation is not changed upon mutation. Activity and denaturation assays show that Asn-54 largely contributes to protein stability, and its presence is a requirement for the highly specific inhibitory activity of these ribotoxins on ribosomes.

Addressing the Challenge of Changing the Specificity of RNase T1 with Rational and Evolutionary Approaches

Although ribonuclease T1 (RNase T1) is one of the best-characterized proteins with respect to structure and enzymatic action, numerous attempts at altering the specificity of the enzyme to cleave single-stranded RNA at the 3'-side of adenylic instead of guanylic residues by rational approaches have failed so far. Recently we generated and characterized the RNase T1 variant RV with a 7200-fold increase in adenylyl-3',5'-cytidine (ApC)/guanylyl-3',5'-cytidine (GpC) preference, with the guanine-binding loop changed from 41-KYNNYE-46 (wt) to 41-EFRNWN-46. Now we have introduced the asparagine residue at position 46 of the wild-type enzyme as a single-point mutation in variant E46N and in combination with the Y45W exchange also occurring in RV. Both variants show an improved ApC/GpC preference with a 1450-fold increase for E46N and a 2100-fold increase for Y45W/E46N in comparison to wild-type activity. We also addressed the challenge of altering enzyme specificity with an evolutionary approach. We have randomly introduced point mutations into the RNase T1 wild-type gene and into the gene of the variant RV with different mutation rates. Altogether we have screened about 100,000 individual clones for activity on RNase indicator plates; 533 of these clones were active. A significant change in substrate specificity towards an ApC preference could not be observed for any of these active variants; this demonstrated the magnitude of the challenge to alter the specificity of this evolutionary perfected enzyme.

Identification of substrate binding sites in enzymes by computational solvent mapping

Enzyme structures determined in organic solvents show that most organic molecules cluster in the active site, delineating the binding pocket. We have developed algorithms to perform solvent mapping computationally, rather than experimentally, by placing molecular probes (small molecules or functional groups) on a protein surface, and finding the regions with the most favorable binding free energy. The method then finds the consensus site that binds the highest number of different probes. The probe-protein interactions at this site are compared to the intermolecular interactions seen in the known complexes of the enzyme with various ligands (substrate analogs, products, and inhibitors). We have mapped thermolysin, for which experimental mapping results are also available, and six further enzymes that have no experimental mapping data, but whose binding sites are well characterized. With the exception of haloalkane dehalogenase, which binds very small substrates in a narrow channel, the consensus site found by the mapping is always a major subsite of the substrate-binding site. Furthermore, the probes at this location form hydrogen bonds and non-bonded interactions with the same residues that interact with the specific ligands of the enzyme. Thus, once the structure of an enzyme is known, computational solvent mapping can provide detailed and reliable information on its substrate-binding site. Calculations on ligand-bound and apo structures of enzymes show that the mapping results are not very sensitive to moderate variations in the protein coordinates.

Leucine 145 of the ribotoxin alpha-sarcin plays a key role for determining the specificity of the ribosome-inactivating activity of the protein

Secreted fungal RNases, represented by RNase T1, constitute a family of structurally related proteins that includes ribotoxins such as alpha-sarcin. The active site residues of RNase T1 are conserved in all fungal RNases, except for Phe 100 that is not present in the ribotoxins, in which Leu 145 occupies the equivalent position. The mutant Leu145Phe of alpha-sarcin has been recombinantly produced and characterized by spectroscopic methods (circular dichroism, fluorescence spectroscopy, and NMR). These analyses have revealed that the mutant protein retained the overall conformation of the wild-type alpha-sarcin. According to the analyses performed, Leu 145 was shown to be essential to preserve the electrostatic environment of the active site that is required to maintain the anomalous low pKa value reported for the catalytic His 137 of alpha-sarcin. Enzymatic characterization of the mutant protein has revealed that Leu 145 is crucial for the specific activity of alpha-sarcin on ribosomes.

Kinetic studies of guanine recognition and a phosphate group subsite on ribonuclease T1 using substitution mutants at Glu46 and Lys41

pH-Dependent kinetic studies were performed with ribonuclease T1 (RNase T1) and its Glu46Ser, Lys41Met, and Lys41Thr mutants with GpC and polyinosinic acid (PolyI) as substrates. Plots of pH versus log(k(cat)/K(M)) for both substrates had ascending slopes that were significantly greater for RNase T1 compared with Glu46Ser-RNase T1, which indicated that the gamma-carboxyl group of conserved Glu46 must be deprotonated (anionic) for maximal interaction with N1H and N2H of the guanine moiety of GpC or the N1H of the hypoxanthine moiety of PolyI. The involvement of the epsilon -ammonium group of nonconserved Lys41 at the 2p subsite (i.e., for an RNA phosphate group two nucleotide positions 5'-upstream from the active site) was supported by comparisons of Lys41Met-RNase T1 and Lys41Thr-RNase T1 with wild-type. These mutants shared identical catalytic properties (i.e., k(cat) and K(M)) with wild-type using GpC as a substrate. However, k(cat)/K(M) for both were identical with each other but lower than those for wild-type when PolyI was the substrate (PolyI has a phosphate group that could interact at a putative 2p site). The pH dependence of this latter difference can be interpreted as reflecting the loss of the 2p subsite interaction with the wild-type enzyme upon deprotonation of the epsilon -ammonium group of Lys41. Subsite interactions for ribonucleases are shown to mainly increase k(cat) and result in an attenuated pH dependence of k(cat)/K(M).