Alternate Structural Conformations of Streptococcus pneumoniae Hyaluronan Lyase: Insights into Enzyme Flexibility and Underlying Molecular Mechanism of Action.

Streptococcus pneumoniae hyaluronan lyase is a surface enzyme of this Gram-positive bacterium. The enzyme degrades several biologically important, information-rich linear polymeric glycans: hyaluronan, unsulfated chondroitin, and some chondroitin sulfates. This degradation facilitates spreading of bacteria throughout the host tissues and presumably provides energy and a carbon source for pneumococcal cells. Its β-elimination catalytic mechanism is an acid/base process termed proton acceptance and donation leading to cleavage of β-1,4 linkages of the substrates. The degradation of hyaluronan occurs in two stages, initial endolytic cuts are followed by processive exolytic cleavage of one disaccharide at a time. In contrast, the degradation of chondroitins is purely endolytic. Structural studies together with flexibility analyses of two streptococcal enzymes, from S. pneumoniae and Streptococcus agalactiae, allowed for insights into this enzyme's molecular mechanism. Here, two new X-ray crystal structures of the pneumococcal enzyme in novel conformations are reported. These new conformations, complemented by molecular dynamics simulation results, directly confirm the predicted domain motions presumed to facilitate the processive degradative process. One of these new structures resembles the S. agalactiae enzyme conformation, and provides evidence of a uniform mechanistic/dynamic behavior of this protein across different bacteria

The centrosomal Deubiquitylase USP21 regulates Gli1 transcriptional activity and stability

USP21 is a centrosome-associated deubiquitylase (DUB) that has been implicated in the formation of primary cilia – crucial organelles for the regulation of the Hedgehog (Hh) signaling pathway in vertebrates. Here, we identify KCTD6 – a cullin-3 E3-ligase substrate adapter that has been previously linked to Hh signaling – as well as Gli1, the key transcription factor responsible for Hh signal amplification, as new interacting partners of USP21. We identify a cryptic structured protein interaction domain in KCTD6, which is predicted to have a similar fold to Smr domains. Importantly, we show that both depletion and overexpression of catalytically active USP21 suppress Gli1-dependent transcription. Gli proteins are negatively regulated through protein kinase A (PKA)-dependent phosphorylation. We provide evidence that USP21 recruits and stabilises Gli1 at the centrosome where it promotes its phosphorylation by PKA. By revealing an intriguing functional pairing between a spatially restricted deubiquitylase and a kinase, our study highlights the centrosome as an important hub for signal coordination

Monomorphic subtelomeric DNA in the filamentous fungus, Metarhizium anisopliae, contains a RecQ helicase-like gene.

In most filamentous fungi, telomere-associated sequences (TASs) are polymorphic, and the presence of restriction fragment length polymorphisms (RFLPs) may permit the number of chromosome ends to be estimated from the number of telomeric bands obtained by restriction digestion. Here, we describe strains of Metarhizium, Gliocladium and Paecilomyces species in which only one or a few telomeric bands of unequal intensity are detectable by Southern hybridization, indicating that interchromosomal TAS exchange occurs. We also studied an anomalous strain of Metarhizium anisopliae, which produces polymorphic telomeric bands larger than 8 kb upon digestion of genomic DNA with XhoI. In this case, the first XhoI site in from the chromosome end must lie beyond the presumed monomorphic region. Cloned telomeres from this strain comprise 18?26 TTAGGG repeats, followed at the internal end of the telomere tract by five repeats of the telomere-like sequence TAAACGCTGG. An 8.1-kb TAS clone also contains a gene for a RecQ-like helicase, designated TAH1, suggesting that this TAS is analogous to the Y elements in yeast and the subtelomeric helicase ORFs of Ustilago maydis (UTASRecQ) and Magnaporthe grisea (TLH1). The TAS in the anomalous strain of M. anisopliae, however, appears distinct from these in that it is found at most telomeres and its predicted protein product possesses a significantly longer N-terminal region in comparison to the M. grisea and U. maydis helicases. Hybridization analyses showed that TAH1 homologues are present in all other anomalous M. anisopliae strains studied, as well as in some other polymorphic strains, where the recQ-like gene also appears to be telomere-associated.Published online: 2 June 2005

Exploring the speed and performance of molecular replacement with AMPLE using QUARK ab initio protein models

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/110744/1/S1399004714025784.pd

Mildred Dresselhaus and Solid State Pedagogy at MIT

Mildred Dresselhaus is known for her influential research on the physics of carbon. Her wide‐ranging influence as a physics teacher, although well‐known to her students, has been less thoroughly examined. Exploring how Dresselhaus grew into her role teaching solid state physics at MIT reveals much about how that subfield evolved

Comparison between methods for creating DEMs of physical models

Within physical modelling, it is often necessary to create DEMs (digital elevation models) when testing the stability of rock structures or the filter layers and scour protection around foundations and other marine structures. These DEMs are used to detect changes in the position of the structure or surrounding protective material. Several methods are available to create these models, yet no one technique has been selected as an industry standard. A comparison between three widely used methods – terrestrial laser scanner (TLS), combined laser scanner (CLS) and structure from motion (SfM) – are presented within this paper. The CLS in underwater mode gave low measurement errors and can be deployed without having to drain the facility but requires a traverser system. An area of approximately 7 m by 4 m can be measured in half an hour. The TLS can survey a much larger area in the same time, but requires the facility to be drained. SfM is cheapest method, but struggles to create a full shape and more care must be taken. The CLS in underwater mode has been chosen for use in scour studies in the Fast Flow Facility, with high volumes of water but a relatively limited area

Subtropical Banana Information Kit. Agrilink, your growing guide to better farming guide

Each Agrilink kit has been designed to be both comprehensive and practical. As the kits are arranged to answer questions of increasing complexity, they are useful references for both new and experienced producers of specific crops. Agrilink integrates the technology of horticultural production with the management of horticultural enterprises. REPRINT INFORMATION - PLEASE READ! For updated information please call 13 25 23 or visit the website www.daf.qld.gov.au This publication has been reprinted as a digital book without any changes to the content published in 2004. We advise readers to take particular note of the areas most likely to be out-of-date and so requiring further research: see detailed information on first page of the kit. Even with these limitations we believe this information kit provides important and valuable information for intending and existing growers. This publication was last revised in 2004. The information is not current and the accuracy of the information cannot be guaranteed by the State of Queensland. This information has been made available to assist users to identify issues involved in the production of subtropical bananas. This information is not to be used or relied upon by users for any purpose which may expose the user or any other person to loss or damage. Users should conduct their own inquiries and rely on their own independent professional advice. While every care has been taken in preparing this publication, the State of Queensland accepts no responsibility for decisions or actions taken as a result of any data, information, statement or advice, expressed or implied, contained in this publication

Routine phasing of coiled-coil protein crystal structures with AMPLE

Coiled-coil protein folds are among the most abundant in nature. These folds consist of long wound α-helices and are architecturally simple, but paradoxically their crystallographic structures are notoriously difficult to solve with molecular-replacement techniques. The program AMPLE can solve crystal structures by molecular replacement using ab initio search models in the absence of an existent homologous protein structure. AMPLE has been benchmarked on a large and diverse test set of coiled-coil crystal structures and has been found to solve 80% of all cases. Successes included structures with chain lengths of up to 253 residues and resolutions down to 2.9 Å, considerably extending the limits on size and resolution that are typically tractable by ab initio methodologies. The structures of two macromolecular complexes, one including DNA, were also successfully solved using their coiled-coil components. It is demonstrated that both the ab initio modelling and the use of ensemble search models contribute to the success of AMPLE by comparison with phasing attempts using single structures or ideal polyalanine helices. These successes suggest that molecular replacement with AMPLE should be the method of choice for the crystallographic elucidation of a coiled-coil structure. Furthermore, AMPLE may be able to exploit the presence of a coiled coil in a complex to provide a convenient route for phasing

Molecular modeling and inhibitory activity of cowpea cystatin against bean bruchid pests.

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