Periodate oxidized CTP (oCTP) was used to investigate the importance of lysine residues in the CTP binding site of the cytidine 5′-monophosphate N-acetylneuraminic acid (CMP-NeuAc) synthetase (EC 2.7.7.43) from Haemophilus ducreyi. The reaction of oCTP with the enzyme follows pseudo-first-order saturation kinetics, giving a maximum rate of inactivation of 0.6 min−1 and a KI of 6.0 mM at pH 7.1. Mass spectrometric analysis of the modified enzyme provided data that was consistent with β-elimination of triphosphate after the reaction of oCTP with the enzyme. A fully reduced enzyme-oCTP conjugate, retaining the triphosphate moiety, was obtained by inclusion of NaBH3CN in the reaction solution. The β-elimination product of oCTP reacted several times more rapidly with the enzyme compared to equivalent concentrations of oCTP. This compound also formed a stable reduced morpholino adduct with CMP-NeuAc synthetase when the reaction was conducted in the presence of NaBH3CN, and was found to be a useful lysine modifying reagent. The substrate CTP was capable of protecting the enzyme to a large degree from inactivation by oCTP and its β-elimination product. Lys19, a residue conserved in CMP-NeuAc synthetases, was identified as being labeled with the β-elimination product of oCTP.

GRASS (Graphical Representation and Analysis of Structures Server), a new web-based server, is described. GRASS exploits many of the features of the GRASP program and is designed to provide interactive molecular graphics and quantitative analysis tools with a simple interface over the World-Wide Web. Using GRASS, it is now possible to view many surface features of biological macromolecules on either standard workstations used in macromolecular analysis or personal computers. The result is a World-Wide Web-based, platform-independent, easily used tool for macromolecular visualization and structure analysis.

Using techniques from optimization theory, we have developed a computer program that approximates a desired probability distribution for amino acids by imposing a probability distribution on the four nucleotides in each of the three codon positions. These base probabilities allow for the generation of biased codons for use in mutational studies and in the design of biologically encoded libraries. The dependencies between codons in the genetic code often makes the exact generation of the desired probability distribution for amino acids impossible. Compromises are often necessary. The program, therefore, not only solves for the “optimal” approximation to the desired distribution (where the definition of “optimal” is influenced by several types of parameters entered by the user), but also solves for a number of “sub-optimal” solutions that are classified into families of similar solutions. A representative of each family is presented to the program user, who can then choose the type of approximation that is best for the intended application. The Combinatorial Codons program is available for use over the web from http://www.wi.mit.edu/kim/computing.html.

A novel superfamily designated MAPEG (Membrane Associated Proteins in Eicosanoid and Glutathione metabolism), including members of widespread origin with diversified biological functions is defined according to enzymatic activities, sequence motifs, and structural properties. Two of the members are crucial for leukotriene biosynthesis, and three are cytoprotective exhibiting glutathione S-transferase and peroxidase activities. Expression of the most recently recognized member is strongly induced by p53, and may therefore play a role in apoptosis or cancer development. In spite of the different biological functions, all six proteins demonstrate common structural characteristics typical of membrane proteins. In addition, homologues are identified in plants, fungi, and bacteria, demonstrating this superfamily to be generally occurring.

This Handbook of Proteolytic Enzymes is a massive undertaking by Alan Barrett, Neil Rawlings, and Fred Woessner, the book's three editors. Not only was the multi-author Handbook designed and edited by them, but also they have made significant contributions in writing major sections of the book. The Handbook consists of 1666 pages, 569 chapters organized into four major catalytic peptidase classes: serine (threonine), cysteine, aspartic, and metallopeptidases. An additional category deals with presently unclassified peptidases. Within each of the above mechanistic categories, the peptidases are grouped into clans and families, the members of which derive from a common evolutionary ancestor. The members of a family have statistically significant similarities in the amino acid sequences of the peptidase portion of the molecules. That the individual families of a clan are derived from a common evolutionary ancestor is usually not detectable at the level of amino acid sequence. This classification scheme was the brain-child of Rawlings and Barrett (1993) and has gained wide acceptance as the major system to unify the previously rather arbitrary nomenclature of proteolytic enzymes.

In a recent press release, the British MRC announced a historic day in scientific history, the completion of the Ceanorhebtitis elegans genome. This first genetic blueprint of an animal adds more than 19,000 genes to the several hundred thousand already available. The sequence databases are regarded as a treasure store. Genome data mining shows signs of triggering a gold rush.