Chemical Biology Discussion Group: Special Year End Meeting
Tuesday, June 5, 2007
Presented by the Chemical Biology Discussion Group
Speakers: Homme Hellinga, Duke University; Minkui Luo, Albert Einstein College of Medicine; Carl Machutta, Stony Brook University; Barney Yoo, New York University; Alessandro Senes, University of Pennsylvania; Pamela Peralta-Yahya , Columbia University; Robert McGinty, The Rockefeller University
Recent years have seen an increasing level of dialogue between chemists and biologists, the lines of communication consolidated by the availability of recombinant biotechnology tools for manipulating the chemical structure of genes and the proteins they encode. This has led to an explosion of interdisciplinary activity at the chemistry-biology interface, now coined chemical biology. The goal of the Chemical Biology Discussion Group is to bring together chemists and biologists working in the New York area who are interested in hearing about the latest ideas in this rapidly growing field. This group will provide a forum for lively discussion and for establishing connections, and perhaps collaborations, between chemists armed with novel technologies and biologists receptive to using these approaches to solve their chosen biological problem.
Rational Design of Proteins with New Functions: Theory, Experiments, Applications
Homme Hellinga, PhD
Establishing a general method for engineering proteins with new functions at will is a major goal in protein chemistry. Not only will such a capability provide fundamental insights in the encoding of function in three-dimensional structure and mechanisms of biological adaptation at the molecular level, but it also holds great promise for developing new biotechnologies. We are developing, experimentally validating, and applying computational design approaches to engineer new functions in proteins.. We have engineered various members of the periplasmic binding protein (PBP) superfamily with radically altered ligand-binding specificity to function as reagentless biosensors for various ligands including TNT, nerve agent surrogates, and metabolites. The designed receptors also drive synthetic two-component signal transduction pathways in E. coli to control gene transcription in response to xenobiotics. We have introduced triose phosphate isomerase (TIM) activity into one of the PBPs. The resulting "novoTIM" complements E. coli TIM deletion mutants. Current research includes more complex enzyme reactions, protein-protein, and protein-DNA interactions.
Picomolar inhibitors as transition state probes of 5'-methylthioadenosine nucleosidases
Albert Einstein College of Medicine
Transition state structures of enzymatic reactions are informative for designing powerful inhibitors, because the binding energy for transition state analogues is proportional to the catalytic rate acceleration of the target enzymes. Enzymatic transition states can be distinguished by their affinity for related transition state analogues. 5'-Methylthioadenosine N-ribosyl transferases are involved in bacterial quorum sensing pathways and thus are promising targets for the design of anti-bacterial drugs. Seven 5'-methylthioadenosine N-ribosyl transferases were examined for their transition state characteristics by analyzing Ki values with a small array of representative transition state analogue inhibitors. Inhibitors designed to mimic early and late dissociative transition states show dissociation constants in the range of picomolar. Our approach indicates that the ratio of dissociation constants for mimics of early and late transition states are effective to distinguish between early and late dissociative transition states. In contrast, the dissociation constant values alone exhibited significant variation for these enzymes. The transition state structures of several of these enzymes have been solved by kinetic isotope effect studies and are consistent with the results obtained with the inhibitor array assay.
Coauthors: Jemy A. Gutierrez, Vipender Singh, Lei Li, Rosemary L. Brown, Gillian E. Norris, Gary B. Evans, Richard H. Furneaux, Peter C. Tyler, Gavin F. Painter, Dirk H. Lenz, and Vern L. Schramm
KasA Inhibition by Thiolactomycin; Mechanism