diaz@aecom.YU.EDU (Dizzy Dan Diaz) (11/09/87)
The following briefly summarizes some of the highlights of the recent PROTEIN DOMAINS symposium held 2-3 November at the Waksman Institute for Microbiology at Rutgers University. FIRST DAY Alan A.R. Fersht Imperial College of Science & Technology, London UK "Protein Engineering of Enzyme Structure and Activity" Fersht spoke on his work with Bacillus stearothermophilus Tyr tRNA synthetase. An interesting enzyme because although it is composed of two identical subunits (a homodimer), only one of the two active sites appears to be catalytic under physiological conditions. This is called "half the sites" activity and is apparently observed in some other homodimers. The crystal structure of the enzyme reveals that one domain is so mobile that the structure has not been determined. This is strong evidence against the criticism of many that crystals are totally static structures and can therefore tell us little about solution structures. Adenylate is H-bonded by 8 sidechains of the enzyme, as demonstrated by crystal structure and site-directed mutagenesis, that beloved new baby of structural biochemists. Fersht stated very directly that the adenylate is not distorted by the enzyme, and that in general he does not believe in enzyme distortion of substrates. He was also very emphatic about using mutagenesis only after one has the crystal structure, a view I considered narrow. Adrian Goldman Waksman Institute, Rutgers University "Deconstruction: The Relationship of Protein Folding to Literary Theory" The protein folding problem has asked "given a sequence, what will its structure be?" Deconstruction asks "given a structure, what will be its sequence?" The structures of a number of alpha, beta barrel structures were compared in an effort to see whether the sequences followed the patterns of the structures. Muconate lactinizing enzyme (MLE) was compared to triose phosphate isomerase (some call me TIM) and pyruvate kinase (why are phosphorylating enzymes called kinases?). Goldman concluded that because the structural similarities have no underlying sequence similarities, there is no homology. He concluded that these very similar structures have arisen as a result of convergent evolution. Don Wiley Harvard University "A 3D Structure for Influenza Virus-Cell Receptor Interaction" Influenza virus hemagglutinin is a very pretty trimer about 135 A tall. It apparently binds sialic acid in the membranes of the cellular host. The sialic acid binding pocket lies in a crater, and is composed of amino acids conserved in over 50 strains of virus. The amino acids surrounding the crater are quite variable; mutating at a very rapid rate. It is these mutating aas that are recognized by neutralizing antibodies. Their rapid rate of mutation makes antibodies for one flu strain ineffective against others. John Rosenberg University of Pittsburgh "Structure and Recognition Mechanism of the EcoRI Endonuclease" I think most of us have seen the pretty pictures of the EcoRI homodimer surrounding a DNA duplex containing the cannonical recognition sequence, published in Nature. A recent TIBS review is also fun to read. EcoRI binds to and hydrolyzes DNA of its cannonical sequence 10^7 times more than non-cannonical sequence. Despite its low Vmax, therefore, its incredible Km makes it as good as any of the "lightning" enzymes. Specificity is the result of the number of H-bonds between enzymic sidechains and major groove nucleotide bases. Crystals are enzymatically active, as shown by the hydrolysis of co-crystallized DNA when Mg++ is diffused into co-crystals. This is more evidence that protein crystals are not static. Rosenberg has annoyed some by not releasing the coordinates of the EcoRI structure to the PDB at Brookhaven. If Dan Davison had his way, people like Rosenberg wouldn't get any funding unless they released the coordinates of their structures (right Dan?). I don't know if it would work, but just discussing the possibility would likely scare people like Rosenberg, Alex Rich and others. -- dn/dx Dept Molecular Biology diaz@aecom.yu.edu Dan Diaz Albert Finkelstein College of Medicine