Structural communication between the GTPase Sec4p and its activator Sec2p: Determinants of GEF activity and early deformations to nucleotide release

Ras GTPases are molecular switches that cycle between OFF and ON states depending on the bound nucleotide (i.e. GDP-bound and GTP-bound, respectively). The Rab GTPase, Sec4p, plays regulatory roles in multiple steps of intracellular vesicle trafficking. Nucleotide release is catalyzed by the Guanine Nucleotide Exchange Factor (GEF) Sec2p. Here, the integration of structural information with molecular dynamics (MD) simulations addressed a number of questions concerning the intrinsic and stimulated dynamics of Sec2p and Sec4p as well as the chain of structural deformations leading to GEF-assisted activation of the Rab GTPase. Sec2p holds an intrinsic ability to adopt the conformation found in the crystallographic complexes with Sec4p, thus suggesting that the latter selects and shifts the conformational equilibrium towards a pre-existing bound-like conformation of Sec2p. The anchoring of Sec4p to a suitable conformation of Sec2p favors the Sec2p-assisted pulling on itself of the α1/switch 1 (SWI) loop and of SWI, which loose any contact with GDP. Those deformations of Sec4p would occur earlier. Formation of the final Sec2p-Sec4p hydrophobic interface, accomplishes later. Disruption of the nucleotide cage would cause firstly loss of interactions with the guanine ring and secondly loss of interactions with the phosphates. The ease in sampling the energy landscape and adopting a bound-like conformation likely favors the catalyzing ability of GEFs for Ras GTPases

Network and atomistic simulations unveil the structural determinants of mutations linked to retinal diseases

A number of incurable retinal diseases causing vision impairments derive from alterations in visual phototransduction. Unraveling the structural determinants of even monogenic retinal diseases would require network-centered approaches combined with atomistic simulations. The transducin G38D mutant associated with the Nougaret Congenital Night Blindness (NCNB) was thoroughly investigated by both mathematical modeling of visual phototransduction and atomistic simulations on the major targets of the mutational effect. Mathematical modeling, in line with electrophysiological recordings, indicates reduction of phosphodiesterase 6 (PDE) recognition and activation as the main determinants of the pathological phenotype. Sub-microsecond molecular dynamics (MD) simulations coupled with Functional Mode Analysis improve the resolution of information, showing that such impairment is likely due to disruption of the PDEgamma binding cavity in transducin. Protein Structure Network analyses additionally suggest that the observed slight reduction of theRGS9-catalyzed GTPase activity of transducin depends on perturbed communication between RGS9 and GTP binding site. These findings provide insights into the structural fundamentals of abnormal functioning of visual phototransduction caused by a missense mutation in one component of the signaling network. This combination of network-centered modeling with atomistic simulations represents a paradigm for future studies aimed at thoroughly deciphering the structural determinants of genetic retinal diseases. Analogous approaches are suitable to unveil the mechanism of information transfer in any signaling network either in physiological or pathological conditions

The response of the algae Fucus virsoides (Fucales, Ochrophyta) to Roundup® solution exposure: A metabolomics approach

8noGlyphosate, as a broad-spectrum herbicide, is frequently detected in water and several studies have investigated its effects on several freshwater aquatic organisms. Yet, only few investigations have been performed on marine macroalgae. Here, we studied both the metabolomics responses and the effect on primary production in the endemic brown algae Fucus virsoides exposed to different concentration (0, 0.5, 1.5 and 2.5 mg L−1) of a commercial glyphosate-based herbicide, namely Roundup®. Our results show that Roundup® significantly reduced quantum yield of photosynthesis (Fv/Fm) and caused alteration in the metabolomic profiles of exposed thalli compared to controls. Together with the decrease in the aromatic amino acids (phenylalanine and tyrosine), an increase in shikimate content was detected. The branched-amino acids differently varied according to levels of herbicide exposure, as well as observed for the content of choline, formate, glucose, malonate and fumarate. Our results suggest that marine primary producers could be largely affected by the agricultural land use, this asking for further studies addressing the ecosystem-level effects of glyphosate-based herbicides in coastal waters.partially_openopenFelline, Serena; Del Coco, Laura; Kaleb, Sara; Guarnieri, Giuseppe; Fraschetti, Simonetta; Terlizzi, Antonio; Fanizzi, Francesco Paolo; Falace, AnnalisaFelline, Serena; Del Coco, Laura; Kaleb, Sara; Guarnieri, Giuseppe; Fraschetti, Simonetta; Terlizzi, Antonio; Fanizzi, Francesco Paolo; Falace, Annalis

Preliminary observations of caulerpin accumulation from the invasive Caulerpa cylindracea in native Mediterranean fish species

Recent studies have shown that the Mediterranean white sea bream Diplodus sargus includes the invasive green alga Caulerpa cylindracea in its diet, with consequent metabolic and enzymatic alterations. As a result of this novel alimentary habit, the bioactive algal red pigment caulerpin has been detected in its tissues. However, this may not be an isolated case: other fish species have also been reported to feed on C. cylindracea, although the possible accumulation of caulerpin in their tissues has not yet been investigated. In this report, we analysed stomach contents and caulerpin levels in the native sparid species Spondyliosoma cantharus, Sarpa salpa, and Diplodus vulgaris, and in the scarid Sparisoma cretense, along with the Lessepsian siganid Siganus luridus. C. cylindracea was found in the stomachs of all but one fish species, the exception being S. cretense, in which prey items could not be determined due to the high degree of digestion. Chemical analysis of fish tissues revealed that only S. cantharus and S. salpa accumulated caulerpin, while no traces of the compound were detected in the other species. Despite intense research efforts on natural products obtained from C. cylindracea, a complete picture of the impacts caused by fish including this alga in their diet has not been elucidated. The identification of caulerpin in other Mediterranean native fish suggests a need for further research in order to assess the possible transfer of such molecules to humans through seafood consumption

On the Mathematical Constitution and Explanation of Physical Facts

The mathematical nature of modern physics suggests that mathematics is bound to play some role in explaining physical reality. Yet, there is an ongoing controversy about the prospects of mathematical explanations of physical facts and their nature. A common view has it that mathematics provides a rich and indispensable language for representing physical reality but that, ontologically, physical facts are not mathematical and, accordingly, mathematical facts cannot really explain physical facts. In what follows, I challenge this common view. I argue that, in addition to its representational role, in modern physics mathematics is constitutive of the physical. Granted the mathematical constitution of the physical, I propose an account of explanation in which mathematical frameworks, structures, and facts explain physical facts. In this account, mathematical explanations of physical facts are either species of physical explanations of physical facts in which the mathematical constitution of some physical facts in the explanans are highlighted, or simply explanations in which the mathematical constitution of physical facts are highlighted. In highlighting the mathematical constitution of physical facts, mathematical explanations of physical facts deepen and increase the scope of the understanding of the explained physical facts. I argue that, unlike other accounts of mathematical explanations of physical facts, the proposed account is not subject to the objection that mathematics only represents the physical facts that actually do the explanation. I conclude by briefly considering the implications that the mathematical constitution of the physical has for the question of the unreasonable effectiveness of the use of mathematics in physics

psnGPCRdb: The Structure-network Database of G Protein Coupled Receptors

G protein coupled receptors (GPCRs) are critical eukaryotic signal transduction gatekeepers and represent the largest protein superfamily in the human proteome, with more than 800 members. They share seven transmembrane helices organized in an up-down bundle architecture. GPCR-mediated signaling pathways have been linked to numerous human diseases, and GPCRs are the targets of approximately 35% of all drugs currently on the market. Structure network analysis, a graph theory-based approach, represents a cutting-edge tool to deeply understand GPCR function, which strongly relies on communication between the extracellular and intracellular poles of their structure. psnGPCRdb stores the structure networks (i.e., linked nodes, hubs, communities and communication pathways) computed on all updated GPCR structures in the Protein Data Bank, in their isolated states or in complex with extracellular and/or intracellular molecules. The structure communication signatures of a sub-family or family of GPCRs as well as of their small-molecule activators or inhibitors are stored as consensus networks. The database stores also all meaningful structure network-based comparisons (i.e., difference networks) of functionally different states (i.e., inactive or active) of a given receptor sub-type, or of consensus networks representative of a receptor sub-type, type, sub-family or family. Single or consensus GPCR networks hold also information on amino acid conservation. The database allows to graphically analyze 3D structure networks together with interactive data-tables. Ligand-centric networks can be analyzed as well. psnGPCRdb is unique and represents a powerful resource to unravel GPCR function with important implications in cell signaling and drug design. psnGPCRdb is freely available at: http://webpsn.hpc.unimo.it/psngpcr.php

Short-term physiological and biometrical responses of Lepidium sativum seedlings exposed to PET-made microplastics and acid rain

Plastics enter in terrestrial natural system primarily by agricultural purposes, while acid rain is the result of anthropogenic activities. The synergistic effects of microplastics and acid rain on plant growth are not known. In this study, different sizes of polyethylene terephthalate (PET) and acid rain are tested on Lepidium sativum, in two separate experimental sets. In the first one we treated plants only with PET, in the second one we used PET and acid rain together. In both experimentations we analyzed: i) plant biometrical parameters (shoot height, leaf number, percentage inhibition of seed germination, fresh biomass), and ii) oxidative stress responses (hydrogen peroxide; ascorbic acid and glutathione). Results carried out from our experiments highlighted that different sizes of polyethylene terephthalate are able to affect plant growth and physiological responses, with or without acid rain supplied during acute toxicity (6 days). Short description: This study showed that different sizes of PET microplastics affect physiological and biometrical responses of Lepidum sativum seedlings, with or without acid rain; roots and leaves responded differently

Network and atomistic simulations unveil the structural determinants of mutations linked to retinal diseases.

A number of incurable retinal diseases causing vision impairments derive from alterations in visual phototransduction. Unraveling the structural determinants of even monogenic retinal diseases would require network-centered approaches combined with atomistic simulations. The transducin G38D mutant associated with the Nougaret Congenital Night Blindness (NCNB) was thoroughly investigated by both mathematical modeling of visual phototransduction and atomistic simulations on the major targets of the mutational effect. Mathematical modeling, in line with electrophysiological recordings, indicates reduction of phosphodiesterase 6 (PDE) recognition and activation as the main determinants of the pathological phenotype. Sub-microsecond molecular dynamics (MD) simulations coupled with Functional Mode Analysis improve the resolution of information, showing that such impairment is likely due to disruption of the PDE\u3b3 binding cavity in transducin. Protein Structure Network analyses additionally suggest that the observed slight reduction of theRGS9-catalyzed GTPase activity of transducin depends on perturbed communication between RGS9 and GTP binding site. These findings provide insights into the structural fundamentals of abnormal functioning of visual phototransduction caused by a missense mutation in one component of the signaling network. This combination of network-centered modeling with atomistic simulations represents a paradigm for future studies aimed at thoroughly deciphering the structural determinants of genetic retinal diseases. Analogous approaches are suitable to unveil the mechanism of information transfer in any signaling network either in physiological or pathological conditions

Ernia di Spigelio.

Cod. CNR P 0013506