Prediction of function in protein superfamilies

Assignment of function for enzymes encoded in sequenced genomes is a challenging task. Predictions of enzyme function can be made using clues from superfamily assignment, structure, genome context, phylogenetic conservation, and virtual screening to identify potential ligands. Ultimately, confident assignment of function requires experimental verification as well as an understanding of the physiological role of an enzyme in the context of the metabolic network

Identification and localization of a stable sulfenic acid in peroxide-treated tetrachlorohydroquinone dehalogenase using electrospray mass spectrometry

Background: Tetrachlorohydroquinone dehalogenase catalyzes the reductive dehalogenation of tetrachlorohydroquinone to trichlorohydroquinone and then to 2,6-dichlorohydroquinone. This enzyme undergoes oxidative damage during purification which causes it to form aberrant products. The damage is reversible by treatment with dithiothreitol. Possible types of oxidative damage include an inappropriate disulfide bond, a cysteine sulfenic acid, or a methionine sulfoxide.Results: Using electrospray liquid chromatography / mass spectrometry, we have demonstrated that oxidation of tetrachlorohydroquinone dehalogenase with H2O2 results in formation of a sulfenic acid at Cys13. Further oxidation to a sulfinic acid was also observed.Conclusions: Oxidation of Cys13 to a sulfenic acid prevents the normal reductive dehalogenation reaction from being completed. This finding is consistent with previous work which suggested that Cys13 acts as a nucleophile during the conversion of tetrachlorohydroquinone to trichlorohydroquinone. The technique described for identification and localization of the cysteine sulfenic acid should be applicable to a wide variety of biological systems

MotifCluster: an interactive online tool for clustering and visualizing sequences using shared motifs

MotifCluster finds related motifs in a set of sequences and clusters the sequences into families using the motifs they contain

Three serendipitous pathways in E. coli can bypass a block in pyridoxal-5′-phosphate synthesis

Overexpression of seven different genes restores growth of a ΔpdxB strain of E. coli, which cannot make pyridoxal phosphate (PLP), on M9/glucose.None of the enzymes encoded by these genes has a promiscuous 4-phosphoerythronate dehydrogenase activity that can replace the activity of PdxB.Overexpression of these genes restores PLP synthesis by three different serendipitous pathways that feed into the normal PLP synthesis pathway downstream of the blocked step.Reactions in one of these pathways are catalyzed by low-level activities of enzymes of unknown function and a promiscuous activity of an enzyme that normally has a role in another pathway; one reaction appears to be non-enzymatic

The Whole Genome Sequence of Sphingobium chlorophenolicum L-1: Insights into the Evolution of the Pentachlorophenol Degradation Pathway

Sphingobium chlorophenolicum Strain L-1 can mineralize the toxic pesticide pentachlorophenol (PCP). We have sequenced the genome of S. chlorophenolicum Strain L-1. The genome consists of a primary chromosome that encodes most of the genes for core processes, a secondary chromosome that encodes primarily genes that appear to be involved in environmental adaptation, and a small plasmid. The genes responsible for degradation of PCP are found on chromosome 2. We have compared the genomes of S. chlorophenolicum Strain L-1 and Sphingobium japonicum, a closely related Sphingomonad that degrades lindane. Our analysis suggests that the genes encoding the first three enzymes in the PCP degradation pathway were acquired via two different horizontal gene transfer events, and the genes encoding the final two enzymes in the pathway were acquired from the most recent common ancestor of these two bacteria

Roadmap on Li-ion battery manufacturing research

Growth in the Li-ion battery market continues to accelerate, driven primarily by the increasing need for economic energy storage for electric vehicles. Electrode manufacture by slurry casting is the first main step in cell production but much of the manufacturing optimisation is based on trial and error, know-how and individual expertise. Advancing manufacturing science that underpins Li-ion battery electrode production is critical to adding to the electrode manufacturing value chain. Overcoming the current barriers in electrode manufacturing requires advances in materials, manufacturing technology, in-line process metrology and data analytics, and can enable improvements in cell performance, quality, safety and process sustainability. In this roadmap we explore the research opportunities to improve each stage of the electrode manufacturing process, from materials synthesis through to electrode calendering. We highlight the role of new process technology, such as dry processing, and advanced electrode design supported through electrode level, physics-based modelling. Progress in data driven models of electrode manufacturing processes is also considered. We conclude there is a growing need for innovations in process metrology to aid fundamental understanding and to enable feedback control, an opportunity for electrode design to reduce trial and error, and an urgent imperative to improve the sustainability of manufacture

Roadmap on Li-ion battery manufacturing research

Growth in the Li-ion battery market continues to accelerate, driven primarily by the increasing need for economic energy storage for electric vehicles. Electrode manufacture by slurry casting is the first main step in cell production but much of the manufacturing optimisation is based on trial and error, know-how and individual expertise. Advancing manufacturing science that underpins Li-ion battery electrode production is critical to adding to the electrode manufacturing value chain. Overcoming the current barriers in electrode manufacturing requires advances in materials, manufacturing technology, in-line process metrology and data analytics, and can enable improvements in cell performance, quality, safety and process sustainability. In this roadmap we explore the research opportunities to improve each stage of the electrode manufacturing process, from materials synthesis through to electrode calendering. We highlight the role of new process technology, such as dry processing, and advanced electrode design supported through electrode level, physics-based modelling. Progress in data driven models of electrode manufacturing processes is also considered. We conclude there is a growing need for innovations in process metrology to aid fundamental understanding and to enable feedback control, an opportunity for electrode design to reduce trial and error, and an urgent imperative to improve the sustainability of manufacture

Roadmap on Li-ion battery manufacturing research

Growth in the Li-ion battery market continues to accelerate, driven by increasing need for economic energy storage in the electric vehicle market. Electrode manufacture is the first main step in production and in an industry dominated by slurry casting, much of the manufacturing process is based on trial and error, know-how and individual expertise. Advancing manufacturing science that underpins Li-ion battery electrode production is critical to adding value to the electrode manufacturing value chain. Overcome the current barriers in the electrode manufacturing requires advances in material innovation, manufacturing technology, in-line process metrology and data analytics to improve cell performance, quality, safety and process sustainability. In this roadmap we present where fundamental research can impact advances in each stage of the electrode manufacturing process from materials synthesis to electrode calendering. We also highlight the role of new process technology such as dry processing and advanced electrode design supported through electrode level, physics-based modelling. To compliment this, the progresses in data driven models of full manufacturing processes is reviewed. For all the processes we describe, there is a growing need process metrology, not only to aid fundamental understanding but also to enable true feedback control of the manufacturing process. It is our hope this roadmap will contribute to this rapidly growing space and provide guidance and inspiration to academia and industry

Roadmap on Li-ion battery manufacturing research

Growth in the Li-ion battery market continues to accelerate, driven by increasing need for economic energy storage in the electric vehicle market. Electrode manufacture is the first main step in production and in an industry dominated by slurry casting, much of the manufacturing process is based on trial and error, know-how and individual expertise. Advancing manufacturing science that underpins Li-ion battery electrode production is critical to adding value to the electrode manufacturing value chain. Overcome the current barriers in the electrode manufacturing requires advances in material innovation, manufacturing technology, in-line process metrology and data analytics to improve cell performance, quality, safety and process sustainability. In this roadmap we present where fundamental research can impact advances in each stage of the electrode manufacturing process from materials synthesis to electrode calendering. We also highlight the role of new process technology such as dry processing and advanced electrode design supported through electrode level, physics-based modelling. To compliment this, the progresses in data driven models of full manufacturing processes is reviewed. For all the processes we describe, there is a growing need process metrology, not only to aid fundamental understanding but also to enable true feedback control of the manufacturing process. It is our hope this roadmap will contribute to this rapidly growing space and provide guidance and inspiration to academia and industry