Rodrigo V. Portugal

Active Glutaminase C Self-assembles into a Supratetrameric Oligomer That Can Be Disrupted by an Allosteric Inhibitor

Background: GAC supplies for increased metabolic needs of tumors because of exclusive localization and kinetic properties. Results: Higher than tetramer oligomers are the active form in in vitro and in cellular assays. Bis-2-(5-phenylacetamido-1,3,4-thiadiazol-2-yl)ethyl sulfide disrupts oligomers. Conclusion: A novel molecular mechanism for GAC activation is proposed. Significance: The data affect the development of therapies targeting GAC in tumors, with emphasis on allosteric inhibitors. The phosphate-dependent transition between enzymatically inert dimers into catalytically capable tetramers has long been the accepted mechanism for the glutaminase activation. Here, we demonstrate that activated glutaminase C (GAC) self-assembles into a helical, fiber-like double-stranded oligomer and propose a molecular model consisting of seven tetramer copies per turn per strand interacting via the N-terminal domains. The loop 321LRFNKL326 is projected as the major regulating element for self-assembly and enzyme activation. Furthermore, the previously identified in vivo lysine acetylation (Lys311 in humans, Lys316 in mouse) is here proposed as an important down-regulator of superoligomer assembly and protein activation. Bis-2-(5-phenylacetamido-1,3,4-thiadiazol-2-yl)ethyl sulfide, a known glutaminase inhibitor, completely disrupted the higher order oligomer, explaining its allosteric mechanism of inhibition via tetramer stabilization. A direct correlation between the tendency to self-assemble and the activity levels of the three mammalian glutaminase isozymes was established, with GAC being the most active enzyme while forming the longest structures. Lastly, the ectopic expression of a fiber-prone superactive GAC mutant in MDA-MB 231 cancer cells provided considerable proliferative advantages to transformed cells. These findings yield unique implications for the development of GAC-oriented therapeutics targeting tumor metabolism.

Association between cationic liposomes and low molecular weight hyaluronic acid.

This work presents a study of the association between low molecular weight hyaluronic acid (16 kDa HA) and cationic liposomes composed of egg phosphatidylcholine (EPC), 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine (DOPE), and 1,2-dioleoyl-3-trimethylammonium-propane (DOTAP). The cationic liposome/HA complexes were evaluated to determine their mesoscopic structure, average size, zeta potential, and morphology as a function of the amount of HA in the system. Small angle X-ray scattering results revealed that neighboring cationic liposomes either stick together after a partial coating of low concentration HA or disperse completely in excess of HA, but they never assemble as multilamellar vesicles. Cryo-transmission electron microscopy images confirm the existence of unilamellar vesicles and large aggregates of unilamellar vesicles for HA fractions up to 80% (w/w). High concentrations of HA (> 20% w/w) proved to be efficient for coating extruded liposomes, leading to particle complexes with sizes in the nanoscale range and a negative zeta potential.

A posteriori correction of camera characteristics from large image data sets

Large datasets are emerging in many fields of image processing including: electron microscopy, light microscopy, medical X-ray imaging, astronomy, etc. Novel computer-controlled instrumentation facilitates the collection of very large datasets containing thousands of individual digital images. In single-particle cryogenic electron microscopy (“cryo-EM”), for example, large datasets are required for achieving quasi-atomic resolution structures of biological complexes. Based on the collected data alone, large datasets allow us to precisely determine the statistical properties of the imaging sensor on a pixel-by-pixel basis, independent of any “a priori” normalization routinely applied to the raw image data during collection (“flat field correction”). Our straightforward “a posteriori” correction yields clean linear images as can be verified by Fourier Ring Correlation (FRC), illustrating the statistical independence of the corrected images over all spatial frequencies. The image sensor characteristics can also be measured continuously and used for correcting upcoming images.

Assembly stoichiometry of bacterial selenocysteine synthase and SelC (tRNAsec)

In bacteria selenocysteyl–tRNAsec (SelC) is synthesized by selenocysteine synthase (SelA). Here we show by fluorescence anisotropy binding assays and electron microscopical symmetry analysis that the SelA–tRNAsec binding stoichiometry is of one tRNAsec molecule per SelA monomer (1:1) rather than the 1:2 value proposed previously. Negative stain transmission electron microscopy revealed a D5 pointgroup symmetry for the SelA–tRNAsec assembly both with and without tRNAsec bound. Furthermore, SelA can associate forming a supramolecular complex of stacked decamer rings, which does not occur in the presence of tRNAsec. We discuss the structure–function relationships of these assemblies and their regulatory role in bacterial selenocysteyl–tRNAsec synthesis.

On the denaturation mechanisms of the ligand binding domain of thyroid hormone receptors

The ligand binding domain (LBD) of nuclear hormone receptors adopts a very compact, mostly alpha-helical structure that binds specific ligands with very high affinity. We use circular dichroism spectroscopy and high-temperature molecular dynamics simulations to investigate unfolding of the LBDs of thyroid hormone receptors (TRs). A molecular description of the denaturation mechanisms is obtained by molecular dynamics simulations of the TRalpha and TRbeta LBDs in the absence and in the presence of the natural ligand Triac. The simulations show that the thermal unfolding of the LBD starts with the loss of native contacts and secondary structure elements, while the structure remains essentially compact, resembling a molten globule state. This differs from most protein denaturation simulations reported to date and suggests that the folding mechanism may start with the hydrophobic collapse of the TR LBDs. Our results reveal that the stabilities of the LBDs of the TRalpha and TRbeta subtypes are affected to different degrees by the binding of the isoform selective ligand Triac and that ligand binding confers protection against thermal denaturation and unfolding in a subtype specific manner. Our simulations indicate two mechanisms by which the ligand stabilizes the LBD: (1) by enhancing the interactions between H8 and H11, and the interaction of the region between H1 and the Omega-loop with the core of the LBD, and (2) by shielding the hydrophobic H6 from hydration.

Orphan nuclear receptor NGFI‐B forms dimers with nonclassical interface

The orphan receptor nerve growth factor‐induced B (NGFI‐B) is a member of the nuclear receptors subfamily 4A (Nr4a). NGFI‐B was shown to be capable of binding both as a monomer to an extended half‐site containing a single AAAGGTCA motif and also as a homodimer to a widely separated everted repeat, as opposed to a large number of nuclear receptors that recognize and bind specific DNA sequences predominantly as homo‐ and/or heterodimers. To unveil the structural organization of NGFI‐B in solution, we determined the quaternary structure of the NGFI‐B LBD by a combination of ab initio procedures from small‐angle X‐ray scattering (SAXS) data and hydrogen–deuterium exchange followed by mass spectrometry. Here we report that the protein forms dimers in solution with a radius of gyration of 2.9 nm and maximum dimension of 9.0 nm. We also show that the NGFI‐B LBD dimer is V‐shaped, with the opening angle significantly larger than that of classical dimers exemplified by estrogen receptor (ER) or retinoid X receptor (RXR). Surprisingly, NGFI‐B dimers formation does not occur via the classical nuclear receptor dimerization interface exemplified by ER and RXR, but instead, involves an extended surface area composed of the loop between helices 3 and 4 and C‐terminal fraction of the helix 3. Remarkably, the NGFI‐B dimer interface is similar to the dimerization interface earlier revealed for glucocorticoid nuclear receptor (GR), which might be relevant to the recognition of cognate DNA response elements by NGFI‐B and to antagonism of NGFI‐B–dependent transcription exercised by GR in cells.

Ultra-small solid archaeolipid nanoparticles for active targeting to macrophages of the inflamed mucosa

AIM Develop nanoparticulate agents for oral targeted delivery of dexamethasone (Dex) to macrophages of inflamed mucosa. MATERIALS & METHODS Solid archaeolipid nanoparticles (SAN-Dex) (compritol/Halorubrum tebenquichense polar archaeolipids/soybean phosphatidylcholine/Tween-80 4; 0.9; 0.3; 3% w/w) loaded with Dex were prepared. Their mucopenetration, stability under digestion and in vitro anti-inflammatory activity, were determined. RESULTS Ultra-small SAN-Dex strongly reduced the levels of TNF-α, IL-6 and IL-12 on J774A1 cells stimulated with lipopolysaccharides as compared with free Dex or loaded in ordinary solid lipid nanoparticles-Dex. After in vitro digestion, the anti-inflammatory activity of SAN-Dex was retained, while that of solid lipid nanoparticles-Dex was lost. CONCLUSION Because of their structural and pharmacodynamic features, SAN-Dex may be suitable for oral targeted delivery to inflamed mucosa.

Single-particle cryo-EM using alignment by classification (ABC) : the structure of Lumbricus terrestris haemoglobin

An efficient and fast pipeline is presented for obtaining near-atomic resolution structures from large single-particle cryo-EM data sets. The approach is virtually reference-free and is therefore less prone to the perils of reference bias.

A sumatriptan coarse-grained model to explore different environments: interplay with experimental techniques

In this work, we developed a coarse-grained model of sumatriptan suitable for extensive molecular dynamics simulations. First, we confirmed the interfacial distribution of this drug in bilayers through cryogenic transmission electron microscopy and small-angle X-ray scattering techniques, as was predicted by our previous atomistic simulations. Based on these simulations, we developed a coarse-grained model for sumatriptan able to reproduce its overall molecular behavior, captured by atomistic simulations and experiments. We then tested the sumatriptan model in a micellar environment along with experimental characterization of sumatriptan-loaded micelles. The simulation results showed good agreement with photon correlation spectroscopy and electrophoretic mobility experiments performed in this work. The particle size of the obtained micelles was comparable with the simulated ones; meanwhile, zeta-potential results suggest adsorption of the drug on the micellar surface. This model is a step forward in the search for a suitable drug-delivery system for sumatriptan.

Topical vaccination with super-stable ready to use nanovesicles

Ultradeformable archaeosomes (UDA) are nanovesicles made of total polar archaeolipids (TPA) from the archaea Halorubrum tebenquichense, soybean phosphatidylcholine and sodium cholate (3:3:1w/w). Fresh dispersions of UDA including different type of antigens are acknowledged as efficient topical vaccination agents. UDA dispersions however, if manufactured for pharmaceutical use, have to maintain colloidal stability upon liposomicidal processes such as sterilization and lyophilization (SLRUDA), needed to extend shelf life during storage. The remaining capacity of SLRUDA to act as adjuvants was therefore tested here for the first time. Another unexplored issue addressed here, is the outcome of replacing classical antigen inclusion into nanovesicles by their physical mixture. Our results showed that UDA behaved as super-stable nanovesicles because of its high endurance during heat sterilization and storage for 5 months at 40°C. The archaeolipid content of UDA however, was insufficient to protect it against lyophilization, which demanded the addition of 2.5% v/v glycerol plus 0.07% w/v glucose. No significant differences were found between serum anti-ovalbumin (OVA) IgG titers induced by fresh or SLRUDA upon topical application of 4 weekly doses at 600μg lipids/75μg OVA to Balb/c mice. Finally, SLRUDA mixed with OVA elicited the same Th2 biased plus a non-specific cell mediated response than OVA encapsulated within UDA. Concluding, we showed that TPA is key component of super-stable nanovesicles that confers resistance to heat sterilization and to storage under cold-free conditions. The finding of SLRUDA as ready-to-use topical adjuvant would lead to simpler manufacture processing and cheaper products. .