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E Marcotte

Publications and source records attributed to E Marcotte.

5 recordsLinked to original sources
PubMed2001

Exploiting big biology: integrating large-scale biological data for function inference.

The amount of data produced by molecular biologists is growing at an exponential rate. Some of the fastest growing sets of data are measurements of gene expression, comparable in quantity only to gene sequences and the vast biological literature. Both gene expression data and sequence data offer hints as to the functions of thousands of newly discovered genes, but neither give complete answers. Therefore, much effort is being focused on integrating these large data sets and combining them with all available functional data to draw inferences about the functions of uncharacterised genes. This review discusses the most pertinent functional data for genome-wide functional inference and describes several methods by which these disparate data types are being integrated.

Data Collection↗
PubMed1997

Kinetic analysis of barley chitinase.

The endochitinase from barley is the archetypal enzyme for a large class of plant-derived antifungal chitinases. The X-ray structure was solved previously in our laboratory and a mechanism of action proposed based on structural considerations. In this manuscript we report the use of a defined soluble substrate, 4-methylumbelliferyl beta-N,N',N"-triacetylchitotrioside, to characterize kinetic parameters of the enzyme. The pH profile shows that activity is controlled by a base with a pKa of 3.9 (Glu 89) and an acid with a pKa of 6.9 (Glu 67). The Km using the synthetic substrate is 33 microM, and the k(cat) is 0.33 min(-1), while the Km for (GlcNAc)4 is 3 microM and k(cat) is 35 min(-1). Binding constants were measured for beta-linked oligomers of N-acetylglucosamine. The monomer does not bind and dissociation constants for the dimer, trimer, and tetramer are 43, 19, and 6 microM, respectively. Analysis of kinetic and dissociation constants proves the mechanism of barley chitinase is consistent with a Bi-Bi kinetic model for hydrolysis, with (GlcNAc)4 and water as substrates and (GlcNAc)2 as products. Substrate cleavage patterns show that (GlcNAc)6 is cleaved in half to (GlcNAc)3 as well as into (GlcNAc)4 and (GlcNAc)2 with almost equal efficiency. NMR analysis of cleavage products confirms that the enzyme proceeds with anomeric inversion of products.

Acetylglucosamine↗
PubMed1994

Control of cellular morphogenesis by the Ip12/Bem2 GTPase-activating protein: possible role of protein phosphorylation.

The IPL2 gene is known to be required for normal polarized cell growth in the budding yeast Saccharomyces cerevisiae. We now show that IPL2 is identical to the previously identified BEM2 gene. bem2 mutants are defective in bud site selection at 26 degrees C and localized cell surface growth and organization of the actin cytoskeleton at 37 degrees C. BEM2 encodes a protein with a COOH-terminal domain homologous to sequences found in several GTPase-activating proteins, including human Bcr. The GTPase-activating protein-domain from the Bem2 protein (Bem2p) or human Bcr can functionally substitute for Bem2p. The Rho1 and Rho2 GTPases are the likely in vivo targets of Bem2p because bem2 mutant phenotypes can be partially suppressed by increasing the gene dosage of RHO1 or RHO2. CDC55 encodes the putative regulatory B subunit of protein phosphatase 2A, and mutations in BEM2 have previously been identified as suppressors of the cdc55-1 mutation. We show here that mutations in the previously identified GRR1 gene can suppress bem2 mutations. grr1 and cdc55 mutants are both elongated in shape and cold-sensitive for growth, and cells lacking both GRR1 and CDC55 exhibit a synthetic lethal phenotype. bem2 mutant phenotypes also can be suppressed by the SSD1-vl (also known as SRK1) mutation, which was shown previously to suppress mutations in the protein phosphatase-encoding SIT4 gene. Cells lacking both BEM2 and SIT4 exhibit a synthetic lethal phenotype even in the presence of the SSD1-v1 suppressor. These genetic interactions together suggest that protein phosphorylation and dephosphorylation play an important role in the BEM2-mediated process of polarized cell growth.

Amino Acid Sequence↗
PubMed1993

Crystallization of a chitosanase from Streptomyces N174.

Chitosanases are produced by many soil fungi and bacteria to degrade chitosan present in fungal cell walls. Here, we report the crystallization of a 29,500 dalton protein with chitosan endo-hydrolase activity isolated from Streptomyces N174. The crystals were grown by vapor diffusion. They are mechanically strong and diffract to at least 1.9 A resolution. The crystals belong to the monoclinic space group P2(1) with unit cell parameters a = 56.4 A, b = 59.6 A, c = 86.1 A and beta = 96.6 degrees. Cell parameters and crystal density are consistent with two chitosanase molecules per asymmetric unit.

Crystallization↗