SystemC^FL : a formalism for hardware/software co-design

SystemCFL is a formal language for hardware/software codesign. Principally, SystemCFL is the formalization of SyslemC based on classical process algebra ACP. The language is aimed to give formal specification of SystemC designs and perform formal analysis of SystemC processes. This paper, designed for the first-time user of SystemCFL, guides the reader through modeling, analyzing and verifying designs using SystemCFL. This paper illustrates the use of SysternCFL with two case studies taken from literature

A bimane‐based peptide staple for combined helical induction and fluorescent imaging

The thiol-selective fluorescent imaging agent, dibromobimane, has been repurposed to crosslink cysteine- and homocysteine- containing peptides, with the resulting bimane linker acting as both a structural constraint and a fluorescent tag. Macro- cyclisation was conducted on nine short peptides containing two cysteines and/or homocysteines, both on-resin and in buffered aqueous solution, to give macrocycles ranging in size from 16 (i,i +2) to 31 (i,i + 7) atoms. The structures were defined by CD, NMR structure calculations by using Xplor-NIH, NMR secondary shift and J HαNH analyses to reveal helical structure in the i,i + 4 (1, 2), and i,i + 3 (5) constrained peptides. Cellular- uptake studies were conducted with three of the macrocycles. Subsequent confocal imaging revealed punctate fluorescence within the cytosol indicative of peptides trapped in endocytic vesicles. These studies demonstrate that dibromobimane is an effective tool for defining secondary structure within short peptides, whilst simultaneously introducing a fluorescent tag suitable for common cell-based experiments.Aimee J. Horsfall, Kylie R. Dunning, Kelly L. Keeling, Denis B. Scanlon, Kate L. Wegener, Andrew D. Abel

Mycobacterium tuberculosis Dethiobiotin Synthetase Facilitates Nucleoside Triphosphate Promiscuity through Alternate Binding Modes

The penultimate step in the biosynthesis of biotin is the closure of the ureido heterocycle in a reaction requiring a nucleoside triphosphate (NTP). In Mycobacterium tuberculosis this reaction is catalyzed by dethiobiotin synthetase (MtDTBS). MtDTBS is unusual as it can employ multiple (NTPs), with a >100-fold preference for cytidine triphosphate (CTP). Here the molecular basis of NTP binding was investigated using a surface plasmon resonance-based ligand binding assay and X-ray crystallography. The biophysical and structural data revealed two discrete mechanisms by which MtDTBS binds NTPs: (i) A high affinity binding mode employed by CTP (KD 160 nM) that is characterized by a slow dissociation rate between enzyme and ligand (kd 5.3 × 10–2 s–1) and that is defined by an extended network of specific ligand–protein interactions involving both the cytidine and triphosphate moieties and (ii) a low affinity mode employed by the remaining NTPs (KD > 16.5 μM), that is characterized by weak interactions between protein and ligand. Previously intractable structures of MtDTBS in complex with ATP, GTP, UTP, and ITP were obtained to define the molecular basis of the low affinity ligand binding. Anchoring of the triphosphate moiety into the phosphate binding loop of MtDTBS allows the promiscuous utilization of multiple NTPs. Both high and low binding mechanisms showed conserved hydrogen bonding interactions involving the β-phosphate of NTPs and a high-affinity anion binding site within the phosphate binding loop. This study provides insights into enzymes that can likewise utilize multiple NTPs.Andrew P. Thompson, Wanisa Salaemae, Jordan L. Pederick, Andrew D. Abell, Grant W. Booker, John B. Bruning, Kate L. Wegener and Steven W. Polya

Biochemical characterisation of class III biotin protein ligases from Botrytis cinerea and Zymoseptoria tritici

Biotin protein ligase (BPL) is an essential enzyme in all kingdoms of life, making it a potential target for novel anti-infective agents. Whilst bacteria and archaea have simple BPL structures (class I and II), the homologues from certain eukaryotes such as mammals, insects and yeast (class III) have evolved a more complex structure with a large extension on the N-terminus of the protein in addition to the conserved catalytic domain. The absence of atomic resolution structures of any class III BPL hinders structural and functional analysis of these enzymes. Here, two new class III BPLs from agriculturally important moulds Botrytis cinerea and Zymoseptoria tritici were characterised alongside the homologue from the prototypical yeast Saccharomyces cerevisiae. Circular dichroism and ion mobility-mass spectrometry analysis revealed conservation of the overall tertiary and secondary structures of all three BPLs, corresponding with the high sequence similarity. Subtle structural differences were implied by the different thermal stabilities of the enzymes and their varied Michaelis constants for their interactions with ligands biotin, MgATP, and biotin-accepting substrates from different species. The three BPLs displayed different preferences for fungal versus bacterial protein substrates, providing further evidence that class III BPLs have a 'substrate validation' activity for selecting only appropriate proteins for biotinylation. Selective, potent inhibition of these three BPLs was demonstrated despite sequence and structural homology. This highlights the potential for targeting BPL for novel, selective antifungal therapies against B. cinerea, Z. tritici and other fungal species.Louise M. Sternicki, Stephanie Nguyen, Kamila J. Pacholarz, Perdita Barran, Nicole R. Pendini, Grant W. Booker, Yoann Huet, Rachel Baltz, Kate L. Wegener, Tara L. Pukala, Steven W. Polya

Inhibition of Mycobacterium tuberculosis dethiobiotin synthase (MtDTBS): toward next-generation antituberculosis agents

Mycobacterium tuberculosis dethiobiotin synthase (MtDTBS) is a crucial enzyme involved in the biosynthesis of biotin in the causative agent of tuberculosis, M. tuberculosis. Here, we report a binder of MtDTBS, cyclopentylacetic acid 2 (K(D) = 3.4 ± 0.4 mM), identified viain silico screening. X-ray crystallography showed that 2 binds in the 7,8-diaminopelargonic acid (DAPA) pocket of MtDTBS. Appending an acidic group to the para-position of the aromatic ring of the scaffold revealed compounds 4c and 4d as more potent binders, with K(D) = 19 ± 5 and 17 ± 1 μM, respectively. Further optimization identified tetrazole 7a as a particularly potent binder (K(D) = 57 ± 5 nM) and inhibitor (Ki = 5 ± 1 μM) of MtDTBS. Our findings highlight the first reported inhibitors of MtDTBS and serve as a platform for the further development of potent inhibitors and novel therapeutics for the treatment of tuberculosis.Nicholas C. Schumann, Kwang Jun Lee, Andrew P. Thompson, Wanisa Salaemae, Jordan L. Pederick, Thomas Avery, Birgit I. Gaiser, James Hodgkinson-Bean, Grant W. Booker, Steven W. Polyak, John B. Bruning, Kate L. Wegener, and Andrew D. Abel

Proposed diagnostic criteria and nosology of acute transverse myelitis

Acute transverse myelitis (ATM) is a focal inflammatory disorder of the spinal cord, resulting in motor, sensory, and autonomic dysfunction. A set of uniform diagnostic criteria and nosology for ATM is proposed to avoid the confusion that inevitably results when investigators use differing criteria. This will ensure a common language of classification, reduce diagnostic confusion, and lay the groundwork necessary for multicenter clinical trials. In addition, a framework is suggested for evaluation of individuals presenting with signs and symptoms of ATM. Best treatment often depends on a timely and accurate diagnosis. Because acute transverse myelopathies are relatively rare, delayed and incomplete work-ups often occur. Rapid and precise diagnosis will ensure not only that compressive lesions are detected and treated but also that idiopathic ATM is distinguished from ATM secondary to a known underlying disease. Identification of etiologies may suggest medical treatment, whereas no clearly established medical treatment currently exists for idiopathic ATM. Establishment of a diagnostic algorithm will likely lead to improved care, although it is recognized that the entire evaluation may not be performed for each patient