Structural basis for specificity of retroviral proteases

The Rous sarcoma virus (RSV) protease S9 variant has been engineered to exhibit high affinity for HIV-1 protease substrates and inhibitors in order to verify the residues deduced to be critical for the specificity differences. The variant has 9 substitutions (S38T, I42D, I44V, M73V, A100L, V104T, R105P, G106V, and S107N) of structurally equivalent residues from HIV-1 protease. Unlike the wild-type enzyme, RSV S9 protease hydrolyzes peptides representing the HIV-1 protease polyprotein cleavage sites. The crystal structure of RSV S9 protease with the inhibitor, Arg-Val-Leu-r-Phe-Glu-Ala-Nle-NH2, a reduced peptide analogue of the HIV-1 CA-p2 cleavage site, has been refined to an R factor of 0.175 at 2.4-A resolution. The structure shows flap residues that were not visible in the previous crystal structure of unliganded wild-type enzyme. Flap residues 64-76 are structurally similar to residues 47-59 of HIV-1 protease. However, residues 61-63 form unique loops at the base of the flaps. Mutational analysis indicates that these loop residues are essential for catalytic activity. Side chains of flap residues His 65 and Gln 63' make hydrogen bond interactions with the inhibitor P3 amide and P4' carbonyl oxygen, respectively. Other interactions of RSV S9 protease with the CA-p2 analogue are very similar to those observed in the crystal structure of HIV-1 protease with the same inhibitor. This is the first crystal structure of an avian retroviral protease in complex with an inhibitor, and it verifies our knowledge of the molecular basis for specificity differences between RSV and HIV-1 proteases.     

Abnormal duodenal bile composition in patients with acalculous chronic cholecystitis

The purpose of this study was to evaluate the effects of the calcification inhibitors FeCl3 and sodium dodecyl sulfate (SDS) on the morphology of glutaraldehyde-crosslinked type I collagen sponges and on their serum conditioning. Scanning electron microscopy (SEM) showed that the morphology of the sponges, already modified by glutaraldehyde crosslinking, underwent further changes after treatment of the hydrogels with inhibitors. Coral-like structures were found to branch from the bulk of the material especially in the case of SDS-treated samples. The composition and morphology of the conditioning layers was characterized after 48 h incubation in serum by SDS-polyacrylamide gel electrophoresis-immunoblot of the adsorbed proteins, by energy-dispersive X-ray analysis of the elements (EDX), and by SEM of the conditioned surfaces. All the samples showed the adsorption of proteins with molecular weights ranging from 10 to 203 kD. However, the peculiar adsorption of an approximately 10-kD band (complement C3 fragment) and of fibronectin were detected in the case of glutaraldehyde-crosslinked collagen. On the other hand, glutaraldehyde-crosslinked collagen treated with 0.1M FeCl3 showed the remarkable adsorption of a 29-kD band. The glutaraldehyde-crosslinked hydrogels showed the massive precipitation of crystals on their exposed surfaces, whereas a disordered network structure surrounding the collagen fibrils was found in the case of the samples pretreated with inhibitors. A predominant precipitation of sodium and chloride was detected in all the sponges, although the ratio between the peaks changed from from one hydrogel to another. The results reported in this article clearly indicate that the treatments with SDS and FeCl3 change the surface conditioning of collagen sponges, suggesting a possible role of deposited serum solutes in affecting mineralization processes on bioprosthesis.     

Crystal structure of TNF-alpha mutant R31D with greater affinity for receptor R1 compared with R2

Crystal structures have been determined of recombinant human tumor necrosis factor-alpha (TNF-alpha) and its R31D mutant that preferentially binds to TNF receptor R1 with more than seven times the relative affinity of binding to receptor R2. Crystals of the wild-type TNF were of space group P4(1)2(1)2 and had unit cell dimensions of a = b = 94.7 and c = 117.4 A. Refinement of the structure gave an R-factor of 22.3% at 2.5 A resolution. The crystals of TNF R31D mutant diffracted to 2.3 A resolution, and were of identical space group to the wild type with unit cell dimensions of a = b = 95.4 and c = 116.2 A, and the structure was refined to an R-factor of 21.8%. The trimer structures of the wild-type and mutant TNF were similar with a root mean square (r.m.s.) deviation of 0.56 A for Calpha atoms; however, the subunits within each trimer were more variable with an average r.m.s. deviation of 1.00 A on Calpha atoms for pairwise comparison of subunits. Model complexes of TNF with receptors R1 and R2 have been used to predict TNF-receptor interactions. Arg31 in all three subunits of wild-type TNF is predicted to form an ionic interaction with the equivalent glutamic acid in both receptors R1 and R2. Asp31 of the TNF R31D mutant is predicted to interact differently with the two receptors. The side chain of Asp31 in two subunits of the TNF mutant is predicted to form hydrogen bond interactions with Ser59 or Cys70 of R1, while it has no predicted interactions with R2. The loss of three strong ionic interactions of Arg31 and the electrostatic repulsion of Asp31 with Glu in the receptors is consistent with the reduced binding of the R31D mutant to both receptors relative to wild-type TNF. The replacement of these ionic interactions by two weaker hydrogen bond interactions between Asp31 of the R31D mutant and R1, compared with no interactions with R2, is in agreement with the observed preferential binding of the R31D mutant to R1 over R2. Analysis of the structure and function of receptor-discriminating mutants of TNF will help understand the biological role of TNF and facilitate its use as an antitumor agent.