Substrate-Assisted Catalysis Unifies Two Families of Chitinolytic Enzymes

Hen egg-white lysozyme has long been the paradigm for enzymatic glycosyl hydrolysis with retention of configuration, with a protonated carboxylic acid and a deprotonated carboxylate participating in general acid-base catalysis. In marked contrast, the retaining chitin degrading enzymes from glycosyl hydrolase families 18 and 20 all have a single glutamic acid as the catalytic acid but lack a nucleophile on the enzyme. Both families have a catalytic (βα)8-barrel domain in common. X-ray structures of three different chitinolytic enzymes complexed with substrates or inhibitors identify a retaining mechanism involving a protein acid and the carbonyl oxygen atom of the substrate’s C2 N-acetyl group as the nucleophile. These studies unambiguously demonstrate the distortion of the sugar ring toward a sofa conformation, long postulated as being close to that of the transition state in glycosyl hydrolysis.

An ATP-binding cassette-type cysteine transporter in Campylobacter jejuni inferred from the structure of an extracytoplasmic solute receptor protein

Campylobacter jejuni is a Gram-negative food-borne pathogen associated with gastroenteritis in humans as well as cases of the autoimmune disease Guillain Barre syndrome. C. jejuni is asaccharolytic because it lacks an active glycolytic pathway for the use of sugars as a carbon source. This suggests an increased reliance on amino acids as nutrients and indeed the genome sequence of this organism indicates the presence of a number of amino acid uptake systems. Cj0982, also known as CjaA, is a putative extracytoplasmic solute receptor for one such uptake system as well as a major surface antigen and vaccine candidate. The crystal structure of Cj0982 reveals a two-domain protein with density in the enclosed cavity between the domains that clearly defines the presence of a bound cysteine ligand. Fluorescence titration experiments were used to demonstrate that Cj0982 binds cysteine tightly and specifically with a K-d of similar to 10(-7) M consistent with a role as a receptor for a high- affinity transporter. These data imply that Cj0982 is the binding protein component of an ABC-type cysteine transporter system and that cysteine uptake is important in the physiology of C. jejuni

Structure and mechanism of acetolactate decarboxylase

Acetolactate decarboxylase catalyzes the conversion of both enantiomers of acetolactate to the (R)-enantiomer of acetoin, via a mechanism that has been shown to involve a prior rearrangement of the non-natural (R)-enantiomer substrate to the natural (S)-enantiomer. In this paper, a series of crystal structures of ALDC complex with designed transition state mimics are reported. These structures, coupled with inhibition studies and site-directed mutagenesis provide an improved understanding of the molecular processes involved in the stereoselective decarboxylation/protonation events. A mechanism for the transformation of each enantiomer of acetolactate is proposed

Analogy making and the structure of implied volatility skew

An analogy based option pricing model is put forward. If option prices are determined in accordance with the analogy model, and the Black Scholes model is used to back-out implied volatility, then the implied volatility skew arises, which flattens as time to expiry increases. The analogy based stochastic volatility and the analogy based jump diffusion models are also put forward. The analogy based stochastic volatility model generates the skew even when there is no correlation between the stock price and volatility processes, whereas, the analogy based jump diffusion model does not require asymmetric jumps for generating the skew

Mechanisms of redundancy and specificity of the Aspergillus fumigatus Crh transglycosylases

Transglycosylases strengthen the fungal cell wall by forming a rigid network of crosslinks. Here, Fang et al. show that the five Crh transglycosylases of Aspergillus fumigatus are dispensable for cell wall integrity in vitro, and solve the crystal structure of Crh5 in complex with chitooligosaccharides

Mechanism of USP7/HAUSP activation by its C-terminal ubiquitin-like domain and allosteric regulation by GMP-synthetase.

The ubiquitin-specific protease USP7/HAUSP regulates p53 and MDM2 levels, and cellular localization of FOXO4 and PTEN, and hence is critically important for their role in cellular processes. Here we show how the 64 kDa C-terminal region of USP7 can positively regulate deubiquitinating activity. We present the crystal structure of this USP7/HAUSP ubiquitin-like domain (HUBL) comprised of five ubiquitin-like (Ubl) domains organized in 2-1-2 Ubl units. The last di-Ubl unit, HUBL-45, is sufficient to activate USP7, through binding to a “switching” loop in the catalytic domain, which promotes ubiquitin binding and increases activity 100-fold. This activation can be enhanced allosterically by the metabolic enzyme GMPS. It binds to the first three Ubl domains (HUBL-123) and hyperactivates USP7 by stabilization of the HUBL-45-dependent active stat

Comparative structural and functional analysis of Bunyavirus and Arenavirus cap-snatching Endonucleases

Segmented negative strand RNA viruses of the arena-, bunya- and orthomyxovirus families uniquely carry out viral mRNA transcription by the cap-snatching mechanism. This involves cleavage of host mRNAs close to their capped 5′ end by an endonuclease (EN) domain located in the N-terminal region of the viral polymerase. We present the structure of the cap-snatching EN of Hantaan virus, a bunyavirus belonging to hantavirus genus. Hantaan EN has an active site configuration, including a metal co-ordinating histidine, and nuclease activity similar to the previously reported La Crosse virus and Influenza virus ENs (orthobunyavirus and orthomyxovirus respectively), but is more active in cleaving a double stranded RNA substrate. In contrast, Lassa arenavirus EN has only acidic metal co-ordinating residues. We present three high resolution structures of Lassa virus EN with different bound ion configurations and show in comparative biophysical and biochemical experiments with Hantaan, La Crosse and influenza ENs that the isolated Lassa EN is essentially inactive. The results are discussed in the light of EN activation mechanisms revealed by recent structures of full-length influenza virus polymerase

wARP

wARP is a procedure that substantially improves crystallographic phases (and subsequently electron-density maps) as an additional step after density-modification methods such as solvent flattening and averaging. The initial phase set is used to create a number of dummy atom models which are subjected to least-squares or maximum-likelihood refinement and iterative model updating in an automated refinement procedure (ARP). Averaging of the phase sets calculated from the refined output models and weighting of structure factors by their similarity to an average vector results in a phase set that improves and extends the initial phases substantially. An important requirement is that the native data have a maximum resolution beyond \sim2.4 Å. The wARP procedure shortens the time-consuming step of model building in crystallographic structure determination and helps to prevent the introduction of errors

Remote sensing techniques as a tool for detecting water outflows. The case study of Cephalonia Island. p.1519

Η  ποσότητα  του  νερού,  που  εκφορτίζεται  στη  θάλασσα  και  τους  ωκεανούς, παρουσιάζει μια αργή αλλά σταθερή αύξηση τα τελευταία χρόνια, που σηματοδοτεί μια πιθανή  επιτάχυνση  του  κύκλου  του  νερού  λόγω  των  κλιματικών  αλλαγών. Ο εντοπισμός  των  εκροών  του  υπόγειου  νερού  και  η  εκμετάλλευσή  τους  είναι  πολύ σημαντική  για  την  ορθολογική  διαχείριση  των  υδάτων  μια  περιοχής.  Οι  τεχνικές τηλεπισκόπησης έχουν αποδειχθεί ένα πολύτιμο εργαλείο για τον εντοπισμό και την ταυτοποίηση των υποθαλάσσιων εκφορτίσεων μέσω των πηγών SGD . Στην παρούσα εργασία γίνεται εφαρμογή των μεθόδων αυτών στο νησί της Κεφαλονιάς στο Ιόνιο. Μια ζώνη επίδρασης 6 χιλιομέτρων γύρω από το νησί μελετήθηκε χρησιμοποιώντας εικόνες Landsat.   Υποθαλάσσιες   εκφορτίσεις   εντοπίστηκαν   με   μεθόδους τηλεπισκόπησης και τα αποτελέσματα αξιολογήθηκαν σε συνδυασμό με την τεκτονική και τις υδρογεωλογικές συνθήκες του νησιού. Μια ποσοτική ανάλυση της θερμοκρασία στα  όρια  επίδρασης  των  6 km  πραγματοποιήθηκε.  Οι  θερμικές  ανωμαλίες  που εμφανίζονται στη ζώνη αυτή διερευνήθηκαν.The amount of water flowing into the seas and oceans has slowly but steadily increased in recent years, signifying a possible speeding up of the water cycle due to climate change. The detection of the water outflows and the exploitation of them are very important to the rational water management. Remote sensing techniques has been  proven  a  valuable  tool  for  the  detection  and  identification  of  submarine groundwater discharge-SGD (Submarine Groundwater Discharge). In this study   the island of Cephalonia in Ionian sea, Greece is considered as a case study. A  6 Km  sea   buffer zone around the island is studied using Landsat images. Submarine groundwater discharge has been detected through remote sensing methods and the results have been combined with the tectonism and hydrogeological conditions of the island. A quantitative analysis of temperature in the    buffer zone was   carried out. The   sea thermal anomalies in the same zone were also investigated.