Structural and functional characterization of USP47 reveals a hot spot for inhibitor design.

USP47 is widely involved in tumor development, metastasis, and other processes while performing a more regulatory role in inflammatory responses, myocardial infarction, and neuronal development. In this study, we investigate the functional and biochemical properties of USP47, whereby depleting USP47 inhibited cancer cell growth in a p53-dependent manner-a phenomenon that enhances during the simultaneous knockdown of USP7. Full-length USP47 shows higher deubiquitinase activity than the catalytic domain.

Rho family GTPase signaling through type II p21-activated kinases.

Signaling from the Rho family small GTPases controls a wide range of signaling outcomes. Key among the downstream effectors for many of the Rho GTPases are the p21-activated kinases, or PAK group. The PAK family comprises two types, the type I PAKs (PAK1, 2 and 3) and the type II PAKs (PAK4, 5 and 6), which have distinct structures and mechanisms of regulation.

Molecular basis for integrin adhesion receptor binding to p21-activated kinase 4 (PAK4).

Integrin adhesion receptors provide links between extracellular ligands and cytoplasmic signaling. Multiple kinases have been found to directly engage with integrin β tails, but the molecular basis for these interactions remain unknown. Here, we assess the interaction between the kinase domain of p21-activated kinase 4 (PAK4) and the cytoplasmic tail of integrin β5.

Allosteric MEK inhibitors act on BRAF/MEK complexes to block MEK activation.

The RAF/MEK/ERK pathway is central to the control of cell physiology, and its dysregulation is associated with many cancers. Accordingly, the proteins constituting this pathway, including MEK1/2 (MEK), have been subject to intense drug discovery and development efforts. Allosteric MEK inhibitors (MEKi) exert complex effects on RAF/MEK/ERK pathway signaling and are employed clinically in combination with BRAF inhibitors in malignant melanoma.

Recognition of physiological phosphorylation sites by p21-activated kinase 4.

Many serine/threonine protein kinases discriminate between serine and threonine substrates as a filter to control signaling output. Among these, the p21-activated kinase (PAK) group strongly favors phosphorylation of Ser over Thr residues. PAK4, a group II PAK, almost exclusively phosphorylates its substrates on serine residues.

CDC42 binds PAK4 via an extended GTPase-effector interface.

The p21-activated kinase (PAK) group of serine/threonine kinases are downstream effectors of RHO GTPases and play important roles in regulation of the actin cytoskeleton, cell growth, survival, polarity, and development. Here we probe the interaction of the type II PAK, PAK4, with RHO GTPases. Using solution scattering we find that the full-length PAK4 heterodimer with CDC42 adopts primarily a compact organization.

Structural basis for Ufm1 recognition by UfSP.

Ubiquitin and ubiquitin-like proteins (Ubls) are involved in a variety of cellular functions, and dysfunction of these proteins often leads to disease, thus requiring the precise molecular recognition of the partner. Here, we report a structural basis for the recognition of Ufm1 by the Ufm1-specific protease (UfSP), both from Caenorhabditis elegans. Ufm1 functions in endoplasmic reticulum homeostasis, cell cycle regulation, and dysfunctions of this protein can result in breast cancer and neurological disorders.

The crystal structure of pseudokinase PEAK1 (Sugen kinase 269) reveals an unusual catalytic cleft and a novel mode of kinase fold dimerization.

The pseudokinase group encompasses some 10% of protein kinases, but pseudokinases diverge from canonical kinases in key motifs. The two members of the small new kinase family 3 (NKF3) group are considered pseudokinases. These proteins, pseudopodium-enriched atypical kinase 1 (PEAK1, Sugen kinase 269, or SgK269) and pragmin (Sugen kinase 223 or SgK223), act as scaffolds in growth factor signaling pathways, and both contain a kinase fold with degraded kinase motifs at their C termini.

PAK4 crystal structures suggest unusual kinase conformational movements.

Unlabelled: In order for protein kinases to exchange nucleotide they must open and close their catalytic cleft. These motions are associated with rotations of the N-lobe, predominantly around the 'hinge region'. We conducted an analysis of 28 crystal structures of the serine-threonine kinase, p21-activated kinase 4 (PAK4), including three newly determined structures in complex with staurosporine, FRAX486, and fasudil (HA-1077).

Structural and biochemical characterization of FabK from Thermotoga maritima.

TM0800 from Thermotoga maritima is one of the hypothetical proteins with unknown function. The crystal structure determined at 2.3 Å resolution reveals a two domain structure: the N-terminal domain forming a barrel and the C-terminal forming a lid.

Acoustofluidic particle manipulation inside a sessile droplet: four distinct regimes of particle concentration.

In this study, we have investigated the motion of polystyrene microparticles inside a sessile droplet of water actuated by surface acoustic waves (SAWs), which produce an acoustic streaming flow (ASF) and impart an acoustic radiation force (ARF) on the particles. We have categorized four distinct regimes (R1-R4) of particle aggregation that depend on the particle diameter, the SAW frequency, the acoustic wave field (travelling or standing), the acoustic waves' attenuation length, and the droplet volume. The particles are concentrated at the centre of the droplet in the form of a bead (R1), around the periphery of the droplet in the form of a ring (R2), at the side of the droplet in the form of an isolated island (R3), and close to the centre of the droplet in the form of a smaller ring (R4).

PAK6 targets to cell-cell adhesions through its N-terminus in a Cdc42-dependent manner to drive epithelial colony escape.

The six serine/threonine kinases in the p21-activated kinase (PAK) family are important regulators of cell adhesion, motility and survival. PAK6, which is overexpressed in prostate cancer, was recently reported to localize to cell-cell adhesions and to drive epithelial cell colony escape. Here we report that PAK6 targeting to cell-cell adhesions occurs through its N-terminus, requiring both its Cdc42/Rac interactive binding (CRIB) domain and an adjacent polybasic region for maximal targeting efficiency.

Generation of Dynamic Free-Form Temperature Gradients in a Disposable Microchip.

Temperature gradients (TGs) provide an effective approach to controlling solvated molecules and creating spatiotemporally varying thermal stimuli for biochemical research. Methods developed to date for generating TGs can only create a limited set of static temperature profiles. This article describes a method for establishing dynamic free-form TGs in polydimethylsiloxane (PDMS) as well as in gases and liquids in contact with the PDMS.

Dynamic manipulation of particles via transformative optofluidic waveguides.

Optofluidics is one of the most remarkable areas in the field of microfluidic research. Particle manipulation with optofluidic platforms has become central to optical chromatography, biotechnology, and μ-total analysis systems. Optical manipulation of particles depends on their sizes and refractive indices (n), which occasionally leads to undesirable separation consequences when their optical mobilities are identical.

Acoustothermal heating of polydimethylsiloxane microfluidic system.

We report an observation of rapid (exceeding 2,000 K/s) heating of polydimethylsiloxane (PDMS), one of the most popular microchannel materials, under cyclic loadings at high (~MHz) frequencies. A microheater was developed based on the finding. The heating mechanism utilized vibration damping in PDMS induced by sound waves that were generated and precisely controlled using a conventional surface acoustic wave (SAW) microfluidic system.

Signaling, Regulation, and Specificity of the Type II p21-activated Kinases.

The p21-activated kinases (PAKs) are a family of six serine/threonine kinases that act as key effectors of RHO family GTPases in mammalian cells. PAKs are subdivided into two groups: type I PAKs (PAK1, PAK2, and PAK3) and type II PAKs (PAK4, PAK5, and PAK6). Although these groups are involved in common signaling pathways, recent work indicates that the two groups have distinct modes of regulation and have both unique and common substrates.

Structure of the ABL2/ARG kinase in complex with dasatinib.

ABL2/ARG (ABL-related gene) belongs to the ABL (Abelson tyrosine-protein kinase) family of tyrosine kinases. ARG plays important roles in cell morphogenesis, motility, growth and survival, and many of these biological roles overlap with the cellular functions of the ABL kinase. Chronic myeloid leukemia (CML) is associated with constitutive ABL kinase activation resulting from fusion between parts of the breakpoint cluster region (BCR) and ABL1 genes.

Microchannel anechoic corner for size-selective separation and medium exchange via traveling surface acoustic waves.

We demonstrate a miniaturized acoustofluidic device composed of a pair of slanted interdigitated transducers (SIDTs) and a polydimethylsiloxane microchannel for achieving size-selective separation and exchange of medium around polystyrene particles in a continuous, label-free, and contactless fashion. The SIDTs, deposited parallel to each other, produce tunable traveling surface acoustic waves (TSAWs) at desired locations, which, in turn, yield an anechoic corner inside the microchannel that is used to selectively deflect particles of choice from their streamlines. The TSAWs with frequency fR originating from the right SIDT and propagating left toward the microchannel normal to the fluid flow direction, laterally deflect larger particles with diameter d1 from the hydrodynamically focused sample fluid that carries other particles as well with diameters d2 and d3, such that d1 > d2 > d3.

Submicron separation of microspheres via travelling surface acoustic waves.

Submicron separation is the segregation of particles having a diameter difference of less than one micrometre. We present an acoustofluidic particle separator with submicron separation resolution to study the continuous, label-free, and contactless separation of polystyrene (PS) particles based on their acoustofluidic parameters such as size, density, compressibility and shape. In this work, the submicron separation of PS microspheres, having a marginal size difference, is achieved inside a polydimethylsiloxane (PDMS) microfluidic channel via travelling surface acoustic waves (TSAWs).

Identification of a major determinant for serine-threonine kinase phosphoacceptor specificity.

Eukaryotic protein kinases are generally classified as being either tyrosine or serine-threonine specific. Though not evident from inspection of their primary sequences, many serine-threonine kinases display a significant preference for serine or threonine as the phosphoacceptor residue. Here we show that a residue located in the kinase activation segment, which we term the "DFG+1" residue, acts as a major determinant for serine-threonine phosphorylation site specificity.