A role for the vesicle-associated tubulin binding protein ARL6 (BBS3) in flagellum extension in Trypanosoma brucei.

The small GTPase Arl6 is implicated in the ciliopathic human genetic disorder Bardet-Biedl syndrome, acting at primary cilia in recruitment of the octomeric BBSome complex, which is required for specific trafficking events to and from the cilium in eukaryotes. Here we describe functional characterisation of Arl6 in the flagellated model eukaryote Trypanosoma brucei, which requires motility for viability. Unlike human Arl6 which has a ciliary localisation, TbARL6 is associated with electron-dense vesicles throughout the cell body following co-translational modification by N-myristoylation.

Selective inhibitors of protozoan protein N-myristoyltransferases as starting points for tropical disease medicinal chemistry programs.

Inhibition of N-myristoyltransferase has been validated pre-clinically as a target for the treatment of fungal and trypanosome infections, using species-specific inhibitors. In order to identify inhibitors of protozoan NMTs, we chose to screen a diverse subset of the Pfizer corporate collection against Plasmodium falciparum and Leishmania donovani NMTs. Primary screening hits against either enzyme were tested for selectivity over both human NMT isoforms (Hs1 and Hs2) and for broad-spectrum anti-protozoan activity against the NMT from Trypanosoma brucei.

Discovery of Plasmodium vivax N-myristoyltransferase inhibitors: screening, synthesis, and structural characterization of their binding mode.

N-Myristoyltransferase (NMT) is a prospective drug target against parasitic protozoa. Herein we report the successful discovery of a series of Plasmodium vivax NMT inhibitors by high-throughput screening. A high-resolution crystal structure of the hit compound in complex with NMT was obtained, allowing understanding of its novel binding mode.

Active comparator-controlled, rater-blinded study of corticotropin-based immunotherapies for opsoclonus-myoclonus syndrome.

To test the efficacy and safety of corticotropin-based immunotherapies in pediatric opsoclonus-myoclonus syndrome, 74 children received corticotropin alone or with intravenous immunoglobulin (groups 1 and 2, active controls); or both with rituximab (group 3) or cyclophosphamide (group 4); or with rituximab plus chemotherapy (group 5) or steroid sparers (group 6). There was 65% improvement in motor severity score across groups (P < .0001), but treatment combinations were more effective than corticotropin alone (P = .

Key role of CXCL13/CXCR5 axis for cerebrospinal fluid B cell recruitment in pediatric OMS.

To study aberrant B cell trafficking into the CSF in opsoclonus-myoclonus syndrome (OMS), chemoattractants CXCL13 and CXCL12, and B cell frequency and CXCR5 expression, were evaluated. CSF CXCL13 concentration and the CSF/serum ratio were higher in untreated OMS than controls, related directly to OMS severity and inversely to OMS duration, and correlated with CSF B cell frequency and oligoclonal bands. CXCL12 showed the opposite pattern.

Multifunctional protein labeling via enzymatic N-terminal tagging and elaboration by click chemistry.

A protocol for selective and site-specific enzymatic labeling of proteins is described. The method exploits the protein co-/post-translational modification known as myristoylation, the transfer of myristic acid (a 14-carbon saturated fatty acid) to an N-terminal glycine catalyzed by the enzyme myristoyl-CoA:protein N-myristoyltransferase (NMT). Escherichia coli, having no endogenous NMT, is used for the coexpression of both the transferase and the target protein to be labeled, which participate in the in vivo N-terminal attachment of synthetically derived tagged analogs of myristic acid bearing a 'clickable' tag.

Application of activity-based protein profiling to the study of microbial pathogenesis.

Activity-based protein profiling (ABPP) is a powerful technology for the dissection of dynamic and complex enzyme interactions. The mechanisms involved in microbial pathogenesis are an example of just such a system, with a plethora of highly regulated enzymatic interactions between the infecting organism and its host. In this review we will discuss some of the cutting-edge applications of ABPP to the study of bacterial and parasitic pathogenesis and virulence, with an emphasis on Clostridium difficile, methicillin-resistant Staphylococcus aureus, quorum sensing, and malaria.

A fluorescence-based assay for N-myristoyltransferase activity.

N-myristoylation is the irreversible attachment of a C(14) fatty acid, myristic acid, to the N-terminal glycine of a protein via formation of an amide bond. This modification is catalyzed by myristoyl-coenzyme A (CoA):protein N-myristoyltransferase (NMT), an enzyme ubiquitous in eukaryotes that is up-regulated in several cancers. Here we report a sensitive fluorescence-based assay to study the enzymatic activity of human NMT1 and NMT2 based on detection of CoA by 7-diethylamino-3-(4-maleimido-phenyl)-4-methylcoumarin.

Protein multi-scale organization through graph partitioning and robustness analysis: application to the myosin-myosin light chain interaction.

Despite the recognized importance of the multi-scale spatio-temporal organization of proteins, most computational tools can only access a limited spectrum of time and spatial scales, thereby ignoring the effects on protein behavior of the intricate coupling between the different scales. Starting from a physico-chemical atomistic network of interactions that encodes the structure of the protein, we introduce a methodology based on multi-scale graph partitioning that can uncover partitions and levels of organization of proteins that span the whole range of scales, revealing biological features occurring at different levels of organization and tracking their effect across scales. Additionally, we introduce a measure of robustness to quantify the relevance of the partitions through the generation of biochemically-motivated surrogate random graph models.

Novel inhibitors of surface layer processing in Clostridium difficile.

Clostridium difficile, a leading cause of hospital-acquired bacterial infection, is coated in a dense surface layer (S-layer) that is thought to provide both physicochemical protection and a scaffold for host-pathogen interactions. The key structural components of the S-layer are two proteins derived from a polypeptide precursor, SlpA, via proteolytic cleavage by the protease Cwp84. Here, we report the design, synthesis and in vivo characterization of a panel of protease inhibitors and activity-based probes (ABPs) designed to target S-layer processing in live C.

Cerebrospinal fluid oligoclonal bands in childhood opsoclonus-myoclonus.

Oligoclonal bands in cerebrospinal fluid reflect local B-cell responses associated with various neuroinflammatory disorders. In opsoclonus-myoclonus syndrome, cerebrospinal fluid B-cell expansion was demonstrated, but no studies of oligoclonal bands are available. In a prospective case-control study of 132 children (103 with opsoclonus-myoclonus, 29 neurologic control subjects), cerebrospinal fluid oligoclonal bands, measured by isoelectric focusing with immunofixation, were observed in 35% with opsoclonus-myoclonus and none of the control subjects, with the highest frequency in severe cases (56%).

Ofatumumab for a rituximab-allergic child with chronic-relapsing paraneoplastic opsoclonus-myoclonus.

Ofatumumab is a fully human anti-CD20 monoclonal antibody in phase II-III trials for various autoimmune and lymphoreticular diseases. We used it to treat a rituximab-allergic child with severe, chronic-relapsing, opsoclonus-myoclonus syndrome (OMS), characterized by persistent cerebrospinal fluid (CSF) B-cell expansion and T-cell dysregulation. He had relapsed despite chemotherapy, plasma exchange with immunoadsorption, and resection of ganglioneuroblastoma, detected 3 years after OMS onset.

Roles of cysteine proteases Cwp84 and Cwp13 in biogenesis of the cell wall of Clostridium difficile.

Clostridium difficile expresses a number of cell wall proteins, including the abundant high-molecular-weight and low-molecular-weight S-layer proteins (SLPs). These proteins are generated by posttranslational cleavage of the precursor SlpA by the cysteine protease Cwp84. We compared the phenotypes of C.

Activity-based profiling for drug discovery.

Activity-based protein profiling (ABPP) is emerging as a game-changing tool for drug discovery, target validation, and basic biology. In this issue, Chang et al. (2011) report the ABPP-facilitated discovery of JW480, a highly selective potent and orally bioavailable inhibitor of monoalkylglycerol ether hydrolase KIAA1363 that dramatically impairs in vivo growth of human prostate cancer cell lines.

Bioorthogonal chemical tagging of protein cholesterylation in living cells.

We report the first chemical probe for bioorthogonal chemical tagging of post-translationally cholesterylated proteins with an azide in living cells. This enables rapid multiplexed fluorescence detection and affinity labelling of protein cholesterylation, as exemplified by Sonic hedgehog protein, opening up new approaches for the de novo identification of cholesterylated proteins.

Chemokine/cytokine profiling after rituximab: reciprocal expression of BCA-1/CXCL13 and BAFF in childhood OMS.

The aim of the study was to test the hypothesis that B-cell repopulation following rituximab (anti-CD20) therapy is orchestrated by chemokines and non-chemokine cytokines. Twenty-five children with opsoclonus-myoclonus syndrome (OMS) received rituximab with or without conventional agents. A comprehensive panel of 40 chemokines and other cytokines were measured in serum by ELISA and multiplexed fluorescent bead-based immunoassay.

Activity-based probes: discovering new biology and new drug targets.

The development and application of chemical technologies enabling direct analysis of enzyme activity in living systems has undergone explosive growth in recent years. Activity-based protein profiling (ABPP) is a key constituent of this broad field, and is among the most powerful and mature chemical proteomic technologies. This tutorial review introduces the essential features of ABPP and the design and application of activity-based probes (ABPs) from drug target elucidation and in vivo visualisation of enzyme activity to comprehensive profiling of the catalytic content of living systems, and the discovery of new biological pathways.

Comparing experimental and computational alanine scanning techniques for probing a prototypical protein-protein interaction.

The central role of protein-protein interactions in a wide range of cellular processes makes them a target for research and drug discovery. A variety of methods, both experimental and theoretical, exist for probing protein interfaces for residues that affect activity and binding affinity. Using as an example a protein-protein complex between trypsin and a nine-residue synthetic peptide, we experimentally assay-binding affinities for a variety of mutants and determine their relative free energy of binding, ΔΔG, to rank the importance of interface residues to binding.

Membrane enhanced peptide synthesis.

This communication reports a new technology platform that advantageously combines organic solvent nanofiltration (a newly emerging technology capable of molecular separations in organic solvents) with solution phase peptide synthesis-Membrane Enhanced Peptide Synthesis (MEPS).

Interaction and dynamics of the Plasmodium falciparum MTIP-MyoA complex, a key component of the invasion motor in the malaria parasite.

The myosin tail domain interacting protein-myosin A (MTIP-MyoA) protein complex is an essential element of the motor driving invasion of red blood cells by the Plasmodium species that cause malaria. Here we report the key determinants of binding at the MTIP/MyoA interface, and the first structural study on the complex in solution using protein NMR.

Getting a chemical handle on protein post-translational modification.

This article highlights the emerging field of chemical proteomics, a powerful technology for the study of post- and co-translational modification of proteins. Genome mapping and the study of protein post-translational modifications have revealed the astounding chemical complexity present in the proteome of even the simplest organisms. The identification and characterisation of the modifications present on specific proteins in such complex mixtures has become a central challenge for post-genomic functional studies in cell and systems biology.