Electronic Structure of Cytochrome P450

The optical properties of P450 have been investigated by means of polarized absorption spectroscopy of single crystals of camphor- bound P450CAM in the oxidized, reduced, and CO-reduced states, and iterative extended Ruckel (IEH) calculations. The heme chromophores are orientated such that transitions polarized in the heme plane (x,y-polarized) can be readily distinguished from transitions polarized perpendicular to the heme plane (z-polarized) . High spin oxidized P450 exhibits two broad z-polarized bands, at 567 and 323 nm. IEH calculations suggest that these bands arise from cysteine mercaptide sulfur-to-iron charge transfer transitions. High spin reduced P450 has no z-polarized bands. IEH calculations suggest that loss of these bands occurs because the cysteine sulfur is protonated to a mercaptan. Low spin CO-P450 has an intense x,y-polarized band at 363 nm. This transition, assigned as a mercaptide sulfur-to-porphyrin charge transfer transition, has the correct symmetry to mix with the Soret and may cause the anomalous red shift of the Soret

Electronic Structure of Cytochrome P450

The optical properties of P450 have been investigated by means of polarized absorption spectroscopy of single crystals of camphor- bound P450CAM in the oxidized, reduced, and CO-reduced states, and iterative extended Ruckel (IEH) calculations. The heme chromophores are orientated such that transitions polarized in the heme plane (x,y-polarized) can be readily distinguished from transitions polarized perpendicular to the heme plane (z-polarized) . High spin oxidized P450 exhibits two broad z-polarized bands, at 567 and 323 nm. IEH calculations suggest that these bands arise from cysteine mercaptide sulfur-to-iron charge transfer transitions. High spin reduced P450 has no z-polarized bands. IEH calculations suggest that loss of these bands occurs because the cysteine sulfur is protonated to a mercaptan. Low spin CO-P450 has an intense x,y-polarized band at 363 nm. This transition, assigned as a mercaptide sulfur-to-porphyrin charge transfer transition, has the correct symmetry to mix with the Soret and may cause the anomalous red shift of the Soret

EcoCyc: A comprehensive view of Escherichia coli biology

EcoCyc (http://EcoCyc.org) provides a comprehensive encyclopedia of Escherichia coli biology. EcoCyc integrates information about the genome, genes and gene products; the metabolic network; and the regulatory network of E. coli. Recent EcoCyc developments include a new initiative to represent and curate all types of E. coli regulatory processes such as attenuation and regulation by small RNAs. EcoCyc has started to curate Gene Ontology (GO) terms for E. coli and has made a dataset of E. coli GO terms available through the GO Web site. The curation and visualization of electron transfer processes has been significantly improved. Other software and Web site enhancements include the addition of tracks to the EcoCyc genome browser, in particular a type of track designed for the display of ChIP-chip datasets, and the development of a comparative genome browser. A new Genome Omics Viewer enables users to paint omics datasets onto the full E. coli genome for analysis. A new advanced query page guides users in interactively constructing complex database queries against EcoCyc. A Macintosh version of EcoCyc is now available. A series of Webinars is available to instruct users in the use of EcoCyc

EcoCyc: a comprehensive database of Escherichia coli biology

EcoCyc (http://EcoCyc.org) is a comprehensive model organism database for Escherichia coli K-12 MG1655. From the scientific literature, EcoCyc captures the functions of individual E. coli gene products; their regulation at the transcriptional, post-transcriptional and protein level; and their organization into operons, complexes and pathways. EcoCyc users can search and browse the information in multiple ways. Recent improvements to the EcoCyc Web interface include combined gene/protein pages and a Regulation Summary Diagram displaying a graphical overview of all known regulatory inputs to gene expression and protein activity. The graphical representation of signal transduction pathways has been updated, and the cellular and regulatory overviews were enhanced with new functionality. A specialized undergraduate teaching resource using EcoCyc is being developed

Systematic Analysis of Pleiotropy in C. elegans Early Embryogenesis

Pleiotropy refers to the phenomenon in which a single gene controls several distinct, and seemingly unrelated, phenotypic effects. We use C. elegans early embryogenesis as a model to conduct systematic studies of pleiotropy. We analyze high-throughput RNA interference (RNAi) data from C. elegans and identify “phenotypic signatures”, which are sets of cellular defects indicative of certain biological functions. By matching phenotypic profiles to our identified signatures, we assign genes with complex phenotypic profiles to multiple functional classes. Overall, we observe that pleiotropy occurs extensively among genes involved in early embryogenesis, and a small proportion of these genes are highly pleiotropic. We hypothesize that genes involved in early embryogenesis are organized into partially overlapping functional modules, and that pleiotropic genes represent “connectors” between these modules. In support of this hypothesis, we find that highly pleiotropic genes tend to reside in central positions in protein-protein interaction networks, suggesting that pleiotropic genes act as connecting points between different protein complexes or pathways

Systematic Analysis of Pleiotropy in C. elegans Early Embryogenesis

Pleiotropy refers to the phenomenon in which a single gene controls several distinct, and seemingly unrelated, phenotypic effects. We use C. elegans early embryogenesis as a model to conduct systematic studies of pleiotropy. We analyze high-throughput RNA interference (RNAi) data from C. elegans and identify “phenotypic signatures”, which are sets of cellular defects indicative of certain biological functions. By matching phenotypic profiles to our identified signatures, we assign genes with complex phenotypic profiles to multiple functional classes. Overall, we observe that pleiotropy occurs extensively among genes involved in early embryogenesis, and a small proportion of these genes are highly pleiotropic. We hypothesize that genes involved in early embryogenesis are organized into partially overlapping functional modules, and that pleiotropic genes represent “connectors” between these modules. In support of this hypothesis, we find that highly pleiotropic genes tend to reside in central positions in protein-protein interaction networks, suggesting that pleiotropic genes act as connecting points between different protein complexes or pathways

Rational Design of Temperature-Sensitive Alleles Using Computational Structure Prediction

Temperature-sensitive (ts) mutations are mutations that exhibit a mutant phenotype at high or low temperatures and a wild-type phenotype at normal temperature. Temperature-sensitive mutants are valuable tools for geneticists, particularly in the study of essential genes. However, finding ts mutations typically relies on generating and screening many thousands of mutations, which is an expensive and labor-intensive process. Here we describe an in silico method that uses Rosetta and machine learning techniques to predict a highly accurate “top 5” list of ts mutations given the structure of a protein of interest. Rosetta is a protein structure prediction and design code, used here to model and score how proteins accommodate point mutations with side-chain and backbone movements. We show that integrating Rosetta relax-derived features with sequence-based features results in accurate temperature-sensitive mutation predictions

Social science in a water observing system

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/95008/1/wrcr12336.pd

The genome sequence of E. coli W (ATCC 9637): comparative genome analysis and an improved genome-scale reconstruction of E. coli

Background: Escherichia coli is a model prokaryote, an important pathogen, and a key organism for industrial biotechnology. E. coli W (ATCC 9637), one of four strains designated as safe for laboratory purposes, has not been sequenced. E. coli W is a fast-growing strain and is the only safe strain that can utilize sucrose as a carbon source. Lifecycle analysis has demonstrated that sucrose from sugarcane is a preferred carbon source for industrial bioprocesses