Gregory K. Farber

The evolution of α/β barrel enzymes

There is provided a dispensing spout in a carton box adapted to accomodate powdery materials like detergents which is simple in construction and easy not only to open by pushing with the finger but also to keep closed after it has been cut out.

The structure and evolution of alpha/beta barrel proteins.

Roughly 10% of all known enzyme structures have an α/β barrel domain. The members of this large family of proteins catalyze very different types of reactions. Such diversity of function has made this family a target for protein engineering. The evolutionary history of this family has been the subject of vigorous debate. In this paper, arguments are made to support the divergence of all members of this family from a common ancestor. Because of the lack of strong sequence homology, the ancestral molecule must be very old. A hypothesis concerning the relationship between chemical mechanism and evolutionary history is discussed. Evidence is presented to suggest that convergent molecular evolution occurs when there is only one energetically reasonable pathway for a chemical reaction.—Reardon, D., Farber, G. K. The structure and evolution of α/β barrel proteins. FASEB J. 9, 497–503 (1995)

An α/β-barrel full of evolutionary trouble

The eight-stranded α/β-barrel (TIM barrel) is by far the most common shape for an enzyme: roughly one out of 10 enzymes have this domain. Three different evolutionary pathways have been proposed for this group of proteins. Recent work still cannot differentiate between the proposed pathways.

Long duration growth of protein crystals in microgravity aboard the MIR space station

Abstract A series of protein crystallization experiments using hen egg white lysozyme and D-amino transferase were flown on the Soviet space station MIR from December, 1989, to February, 1990. The total duration of the crystal growth phase of the experiment was 56 days. These experiments were designed to evaluate MIR as a platform for protein crystallization; the temperature, radiation, and other environmental parameters of the space station were found to be satisfactory for such experiments. The size and diffraction characteristics of the crystals grown in microgravity are superior to crystals grown on earth using identical methods and hardware. In a second independent comparison with crystals grown on earth by standard laboratory techniques, the observed improvement in the size, lattice order, and diffraction quality of microgravity crystals is small, but measurable, for these two specific proteins. In addition, crystals grown in microgravity sometimes exhibit different crystal morphologies compared to crystals grown on earth under identical conditions. This effect provides a second reason to consider microgravity as a variable in protein crystal growth.

A dimeric two-component receiver domain inhibits the sigma54-dependent ATPase in DctD.

We report the crystal structure of a fragment of Sinorhizobium meliloti DctD, a bacterial enhancer binding protein, at 1.7 Å. The fragment contains the proteins two‐component receiver module and adjacent linker, which in the native protein joins the receiver domain to a σ54‐dependent ATPase domain. The structure reveals a novel dimerization surface, which sequence analysis indicates is common to 4.5% of the known two‐component receiver domains. Genetic, biochemical, and structural data for amino acid substitution variants indicate that the dimer is necessary to inhibit the basal activity of the ATPase domain. The dimerization element is thus needed to maintain the “off” state, and changes within it may signal activation. Analytical ultracentrifugation data for the phosphorylated fragment of DctD appear to rule out the simple model that signaling is mediated via monomerization of the receiver domain.

Distributions of structural features contributing to thermostability in mesophilic and thermophilic α/β barrel glycosyl hydrolases

Analysis of the structural basis for thermostability in proteins has come mainly from pairwise comparisons of mesophilic and thermophilic structures and has often yielded conflicting results. Interpretation of these results would be enhanced by knowing the normal range of features found for mesophilic proteins. In order to provide the average and distribution values of structural features among similar mesophilic proteins, we compared the amino acid composition, solvent accessible surface area, hydrogen bonds, number of ion pairs, and thermal factors of 22 structures of alpha/beta barrel glycosyl hydrolases. These distributions are then compared to values from seven alpha/beta barrel glycosyl hydrolases from thermophilic organisms. We find that the distribution of each structural feature is broad within the mesophilic proteins and illustrates the difficulty of making pairwise comparisons of mesophiles to thermophiles where differences for individual proteins may be within the normal range for the group. In comparing mesophiles to thermophiles as a group, we find that thermophilic structures have fewer glycines in a particular region of the structure and higher thermal factors at room temperature. These results suggest the basis for thermostability may be related to protein motion rather than to static features of protein structure.

New approaches to rational drug design

Rational drug design has emerged as a powerful technique. In this review, three new developments in rational drug design are explored. These developments include new methods to find binding sites for small molecules on the surface of a protein, the suggestion that the protein environment may change the shape of a protein sufficiently to alter drug design, and the use of data emerging from structural genomics in drug design. Although these are three new and distinct areas, the insights derived from these studies suggest a reason for the observation that similar drugs do not always bind to a protein in the same manner.

NMR assignments for the aldopentoses

Abstract The 1 H and 13 C NMR assignments for the simple aldopentopyranoses in 2 H 2 O were made using high field 2D NMR spectroscopy. The furanose forms of ribose were also tentatively assigned. The 2D techniques used to assign the resonances include the HMQC, HMBC, 2QF-COSY, TOCSY, 2Q, and INADEQUATE experiments. Selective 1D TOCSY experiments were also necessary to assign the crowded proton spectrum of ribose.

Design of apparatus and experiments to determine the effect of microgravity on the crystallization of biological macromolecules using the MIR spacestation

Abstract We have designed apparatus and an experimental protocol for crystallization of biological macromolecules aboard the MIR spacestation. Techniques to be employed include vapor diffusion, boundary layer diffusion, and batch crystallization methods over periods of time from six weeks to 3 months. Photography of the specimens before and after return to earth will complement characterization of ground- and space-grown specimens by X-ray crystallography.

Laue Crystallography: It's show time

New crystallographic techniques make it possible to observe directly all of the intermediates in an enzymatic reaction. Such a series of structures can be combined to create a detailed movie of enzymatic catalysis.