Nuria Sánchez-Puig

Bioactive Peptides from Marine Organisms: A Short Overview

Marine organisms are an immense source of new biologically active compounds. These compounds are unique because the aqueous environment requires a high demand of specific and potent bioactive molecules. Diverse peptides with a wide range of biological activities have been discovered, including antimicrobial, antitumoral, and antiviral activities and toxins amongst others. These proteins have been isolated from different phyla such as Porifera, Cnidaria, Nemertina, Crustacea, Mollusca, Echinodermata and Craniata. Purification techniques used to isolate these peptides include classical chromatographic methods such as gel filtration, ionic exchange and reverse-phase HPLC. Multiple in vivo and in vitro bioassays are coupled to the purification process to search for the biological activity of interest. The growing interest to study marine natural products results from the discovery of novel pharmacological tools including potent anticancer drugs now in clinical trials. This review presents examples of interesting peptides obtained from different marine organisms that have medical relevance. It also presents some of the common methods used to isolate and characterize them.

Mutations in EFL1, an SBDS partner, are associated with infantile pancytopenia, exocrine pancreatic insufficiency and skeletal anomalies in a Shwachman-Diamond like syndrome

Background For the final step of the maturation of the ribosome, the nascent 40S and 60S subunits are exported from the nucleus to the cell cytoplasm. To prevent premature association of these ribosomal subunits, eukaryotic initiation factor 6 (eIF6) binds the 60S subunit within the nucleus. Its release in the cytoplasm requires the interaction of EFL1 and SDBS proteins. In Shwachman-Diamond syndrome (SDS), a defective SDBS protein prevents eIF6 eviction, inhibiting its recycle to the nucleus and subsequent formation of the active 80S ribosome. Objective This study aims to identify the molecular basis of an SDS-like disease, manifested by pancytopenia, exocrine pancreatic insufficiency and skeletal abnormalities in six patients from three unrelated families. Methods Whole exome analysis was used for mutation identification. Fluorescence microscopy studies assessed the localisation of Tif6-GFP, the yeast eIF6 homologue, in yeast WT and mutant cells. Human and yeast EFL1 proteins, WT and mutants, were expressed in Saccharomyces cerevisiae BCY123 strain, and circular dichroism and small-angle X-ray scattering were used to assess the folding and flexibility of these proteins. Green malachite colorimetric assay was performed to determine the GTPase activity of WT and Efl1 mutants. Results Four patients were homozygous for p.R1095Q variant and two patients were homozygous for p.M882K variant in EFL1. Residue R1095 and M882 are conserved across species. Neither the GTPase activity of the mutant proteins nor its activation by the SDBD protein or the 60S ribosomal subunit were affected. Complementation of efl1Δ yeast cells with the EFL1 mutants rescued the slow growth phenotype. Nonetheless, Tif6-GFP was relocalised to the cytoplasm in mutant yeast cells in contrast to its nuclear localisation in WT cells. Conclusions Mutations in EFL1 clinically manifest as SDS-like phenotype. Similar to the molecular pathology of SDS, mutant EFL1 proteins do not promote the release of cytoplasmic Tif6 from the 60S subunit, likely preventing the formation of mature ribosomes.

Controlling the morphology of silica–carbonate biomorphs using proteins involved in biomineralization

Silica–carbonate biomorphs are inorganic self-organized structures that mimic the morphology of living organisms. In this study, we present the effect that proteins involved in the in vivo biomineralization of silica and calcium carbonate have on the formation of silica–carbonate biomorphs. We tested four different sources of protein: (1) struthiocalcin-1, (2) the catalytic domain of silicatein-α of Tethya aurantia, (3) a protein extract obtained from the spicules of a vitreous sponge (Protosuberitis sp.), and (4) a protein extract obtained from the spines of the sea urchin Echinometra lucunter. In addition to the well-established role that pH plays in biomorph formation, all the proteins tested controlled the morphology of these aggregates. Biomorphs obtained in the presence of the catalytic domain of silicatein-α were similar in shape to those observed in the control though considerably smaller in size. Struthiocalcin-1 affected the availability of carbonate ions and completely inhibited the formation of biomorphs resulting only in worm-like aggregates. Finally, novel biomorphs with shapes such as twisting rods, sunflowers, and mitotic cells were obtained in the presence of protein extracts from the marine sponge spicules and sea urchin spines.

An electrically assisted device for protein crystallization in a vapor‐diffusion setup

A new easy-to-use device has been designed and implemented for electric field-induced protein crystallization in a vapor-diffusion configuration. The device not only controls crystal nucleation by means of the electrical current, but also favors crystal growth owing to its vapor-diffusion setup. Crystallization was conducted in the presence of an internal electric field and direct current. The proteins investigated were lysozyme, as model protein, and 2TEL-lysozyme (a synthetic protein consisting of two tandem alpha helix motifs connected to a lysozyme moiety). Lysozyme crystals that grew attached to the cathode were larger than those grown attached to the anode or in the absence of an electric current. On the other hand, crystals of 2TEL-lysozyme qualitatively showed a better X-ray diffraction pattern when grown in the presence of an electric current.

Guanine nucleotide exchange in the ribosomal GTPase EFL1 is modulated by the protein mutated in the Shwachman–Diamond Syndrome

Ribosome biogenesis in eukaryotes is a complex process that requires the participation of several accessory proteins that are not part of the mature particle. Efl1 is a yeast GTPase required for the cytoplasmic maturation of the 60S ribosomal subunit. Together with Sdo1, the yeast ortholog of the protein mutated in the Shwachman-Diamond Syndrome (SBDS), Efl1 releases the anti-association factor Tif6 from the surface of the 60S subunit allowing the assembly of mature ribosomes. We characterized the structural content and folding stability of the Saccharomyces cerevisiae and human EFL1 GTPases, as well as their enzymatic properties alone and in the presence of Sdo1 and SBDS, respectively. The human and S. cerevisiae EFL1 GTPases are composed of a mixture of α-helices and β-sheets. Despite being orthologs, the yeast protein elicited a non-two state thermal unfolding behavior while the human EFL1 was highly resistant to thermal denaturation. Steady-state kinetic analyses indicated slow GTP hydrolysis for both EFL1 GTPases, with kcat values of 0.4 and 0.3min(-1) and Km for GTP of 110 and 180μM respectively. In the presence of the effector proteins, their kcat values remained unaltered while the Km decreased twofold suggesting that Sdo1 and SBDS act as nucleotide exchange factors.

A purified Palythoa venom fraction delays sodium current inactivation in sympathetic neurons.

Palythoa caribaeorum is a zoanthid (Phylum Cnidaria, class Anthozoa) commonly found in shallow waters of coral reefs along the Mexican Atlantic coast. Little is known on the pharmacological and biochemical properties of the venom components of this animal group. Toxin peptides from other cnidarian venoms, like sea anemones, target sodium and potassium voltage-gated channels. In this study, we tested the activity of a low molecular weight fraction from the venom of P. caribaeorum on voltage-gated sodium channels of the superior cervical ganglion (SCG) neurons of the rat. Our results showed that this fraction delays tetrodotoxin (TTX)-sensitive sodium channel inactivation indicated by a reversible 2-fold increase of the current at the decay. A peptide responsible for this activity was isolated and characterized. Its sequence showed that it does not resemble any previously reported toxin. Together, these results evidence the presence of neurotoxins in P. caribaeorum that act on sodium channels.

Optical properties of two fluorene derived BODIPY molecular rotors as fluorescent ratiometric viscosity probes

BODIPY-derived molecular fluorescent rotors are one of the most useful families of fluorescent probes for the quantitative measurement of microviscosity. Here, we report the photophysical properties of two molecular rotors as ratiometric viscosity sensors, meso-(4-(9H-fluoren-2-yl)ethynyl)phenyl-4,4-difluoro-4-bora-3a,4a-diaza-s-indacene (1) and meso-(5-(9H-fluoren-2-yl)ethynyl)thiophen-2-yl-4,4-difluoro-4-bora-3a,4a-diaza-s-indacene (2) having two independent chromophores; one (fluorene) is not influenced by viscosity and is used to determine concentration properties, and the other chromophore (BODIPY) acts as a molecular rotor. The fluorescence ratiometric calibration against microviscosity for the most sensitive probe (1), was obtained in a wide linear dynamic range. The sensitivity of the spectroscopic observables for 1 and 2 towards solvent viscosity and the typical analytical interfering solvent polarity and polarizability parameters were investigated by means of two different solvent scales, namely Lippert–Mataga and Catalan, finding consistent results. Quantum chemical calculations were conducted to analyze the probe mechanism in terms of Natural Transition Orbitals (NTOs) and the spatial extent of charge transfer excitations.

Predicting Protein Crystallizability and Nucleation

The outcome of protein crystallization attempts is often uncertain due to inherent features of the protein or to the crystallization process that are not fully under control of the experimentalist. The aim of this contribution is to propose user-friendly tools that can increase the success rate of a protein crytallization project. Different bioinformatic approaches to predict the crystallization feasibility (before any crystallization attempts are undertaken) are discussed and a novel approach to assess the nucleation process of a given protein is proposed. Practical examples illustrate these two points.

Defective Guanine Nucleotide Exchange in the Elongation Factor-like 1 (EFL1) GTPase by Mutations in the Shwachman-Diamond Syndrome Protein.

Background: EFL1 and the protein mutated in the Shwachman-Diamond syndrome (SBDS) participate in the maturation of the 60S ribosomal subunit. Results: SBDS increases the dissociation constant of EFL1 for GDP 60-fold. SBDS S143L disease mutation disrupts the interaction with EFL1. Conclusion: SBDS favors GDP dissociation from EFL1 and disease mutations abolishe this function. Significance: SBDS disease mutations prevent the nucleotide exchange regulation on EFL1. Ribosome biogenesis is orchestrated by the action of several accessory factors that provide time and directionality to the process. One such accessory factor is the GTPase EFL1 involved in the cytoplasmic maturation of the ribosomal 60S subunit. EFL1 and SBDS, the protein mutated in the Shwachman-Diamond syndrome (SBDS), release the anti-association factor eIF6 from the surface of the ribosomal subunit 60S. Here we report a kinetic analysis of fluorescent guanine nucleotides binding to EFL1 alone and in the presence of SBDS using fluorescence stopped-flow spectroscopy. Binding kinetics of EFL1 to both GDP and GTP suggests a two-step mechanism with an initial binding event followed by a conformational change of the complex. Furthermore, the same behavior was observed in the presence of the SBDS protein irrespective of the guanine nucleotide evaluated. The affinity of EFL1 for GTP is 10-fold lower than that calculated for GDP. Association of EFL1 to SBDS did not modify the affinity for GTP but dramatically decreased that for GDP by increasing the dissociation rate of the nucleotide. Thus, SBDS acts as a guanine nucleotide exchange factor (GEF) for EFL1 promoting its activation by the release of GDP. Finally, fluorescence anisotropy measurements showed that the S143L mutation present in the Shwachman-Diamond syndrome altered a surface epitope for EFL1 and largely decreased the affinity for it. These results suggest that loss of interaction between these proteins due to mutations in the disease consequently prevents the nucleotide exchange regulation the SBDS exerts on EFL1.

SdsA polymorph isolation and improvement of their crystal quality using nonconventional crystallization techniques

SdsA, a sodium dodecyl sulfate hydrolase, from Pseudomonas aeruginosa was crystallized in three different crystal polymorphs and their three-dimensional structure was determined. The different polymorphs present different crystal packing habits. One of the polymorphs suggests the existence of a tetramer, an oligomeric state not observed previously, while the crystal packing of the remaining two polymorphs obstructs the active site entrance but stabilizes flexible regions of the protein. Nonconventional crystallization methods that minimize convection, such as counterdiffusion in polyvinyl alcohol gel coupled with the influence of a 500 MHz (10.2 T) magnetic field, were necessary to isolate the poorest diffracting polymorph and increase its internal order to determine its structure by X-ray diffraction. The results obtained show the effectiveness of nonconventional crystallographic methods to isolate different crystal polymorphs.