Abelardo Silva

The refined structure of beef liver catalase at 2·5 Å resolution

The crystal structure of beef liver catalase [Murthy, Reid, Sicignano, Tanaka & Rossmann (1981). J. Mol. Biol. 152, 465-499] has now been refined by a restrained parameter least-squares method [Konnert & Hendrickson (1980). Acta Cryst. A36, 344-350] with respect to 2.5 A data. Some extra density was discovered during the refinement process. This was interpreted in terms of a bound NADP molecule [Kirkman & Gaetani (1984). Proc. Natl Acad. Sci. USA, 81, 4343-4348; Fita & Rossmann (1985). Proc. Natl Acad. Sci. USA, 82, 1604-1608]. When the noncrystallographic symmetry was imposed as a constraint, the R factor was reduced to 21.2%. However, refinement of the two crystallographic independent subunits gave a final R factor of 19.1%. The refined coordinates have been re-analyzed for main-chain and side-chain hydrogen bonding, charge distribution, secondary structural element interactions, subunit contacts and molecular packing. The fractional accessibility and the temperature-factor variation are also discussed. The oligomerization process is considered in terms of the unusual quaternary structure. The organization of the heme channel and its relation to the enzymes catalytic properties have been discussed elsewhere [Fita & Rossmann (1985). J. Mol. Biol. 185, 21-37].

Refined structure of southern bean mosaic virus at 2.9 Å resolution

The T = 3 capsid of southern bean mosaic virus is analyzed in detail. The beta-sheets of the beta-barrel folding motif that form the subunits show a high degree of twist, generated by several beta-bulges. Only 34 water molecules were identified in association with the three quasi-equivalent subunits, most of them on the external viral surface. Subunit contacts related by quasi-3-fold axes are similar, are dominated by polar interactions and have almost identical calcium binding sites. There is no metal ion on the quasi-3-fold axis, as previously reported. Subunits related by quasi-2-fold and icosahedral 2-fold axes have different contacts but nevertheless display almost identical interactions between the antiparallel helices alpha A. A dipole-dipole type interaction between these helices may produce an energetically stable hinge that allows two types of dimers in a T = 3 assembly. The temperature factor distribution, the hydrogen-bonding pattern, and the contacts across the icosahedral 2-fold axes suggest that one of the dimer types is present in the intact virion and probably also in solution; the other is produced only during capsid assembly. Interactions along the 5-fold axes are mainly polar and possibly form an ion channel. The beta-sheet structures of the three subunits can be superimposed with considerable precision. Significant relative distortions between quasi-equivalent subunits occur mainly in helices and loops. The two dimeric forms and the subunit distortions are the consequence of the non-equivalent subunit environments in the capsid.

Enamino-oxindole HIV protease inhibitors

We have designed and synthesized a series of HIV protease inhibitors (PIs) with enamino-oxindole substituents optimized to interact with the S2 subsite of the HIV protease binding pocket. Several of these inhibitors have sub-nanomolar K(i) and antiviral IC(50) in the low nM range against WT HIV and against a panel of multi-drug resistant (MDR) strains.