Study of the influence of actin-binding proteins using linear analyses of cell deformability

The actin cytoskeleton plays a key role in the deformability of the cell and in mechanosensing. Here we analyze the contributions of three major actin cross-linking proteins, myosin II, a-actinin and filamin, to cell deformability, by using micropipette aspiration of Dictyostelium cells. We examine the applicability of three simple mechanical models: for small deformation, linear viscoelasticity and drop of liquid with a tense cortex; and for large deformation, a Newtonian viscous fluid. For these models, we have derived linearized equations and we provide a novel, straightforward methodology to analyze the experiments. This methodology allowed us to differentiate the effects of the cross-linking proteins in the different regimes of deformation. Our results confirm some previous observations and suggest important relations between the molecular characteristics of the actin-binding proteins and the cell behavior: the effect of myosin is explained in terms of the relation between the lifetime of the bond to actin and the resistive force; the presence of a-actinin obstructs the deformation of the cytoskeleton, presumably mainly due to the higher molecular stiffness and to the lower dissociation rate constants; and filamin contributes critically to the global connectivity of the network, possibly by rapidly turning over crosslinks during the remodeling of the cytoskeletal network, thanks to the higher rate constants, flexibility and larger size. The results suggest a sophisticated relationship between the expression levels of actinbinding proteins, deformability and mechanosensing.

Development of an electrochemical maltose biosensor

In this work, electrochemical maltose biosensors based on mutants of the maltose binding protein (MBP) are developed. A ruthenium II complex (Ru II ), which is covalently attached to MBP, serves as an electrochemical reporter of MBP conformational changes. Biosensors were made through direct attachment of Ru II complex modified MBP to gold electrode surfaces. The responses of some individual mutants were evaluated using square wave voltammetry. A maltose-dependent change in Faradic current and capacitance was observed. It is therefore demonstrated that biosensors using generically this family of bacterial periplasmic binding proteins (bPBP) can be made lending themselves to facile biorecognition element preparation and low cost electrochemical transduction.

A role of Toc33 in the protochlorophyllide-dependent plastid import pathway of NADPH:proto¬chlorophyllide oxidoreductase (POR) A

NADPH: protochlorophyllide oxido reductase (POR) A is a key enzyme of chlorophyll biosynthesis in angiosperms. It is nucleus-encoded, synthesized as a larger precursor in the cytosol and imported into the plastids in a substrate-dependent manner. Plastid envelope membrane proteins, called protochlorophyllide dependent translocon proteins, Ptcs, have been identified that interact with pPORA during import. Amongthem are a 16-kDa ortholog of the previously characterized outer envelope protein Oep16 (named Ptc16) and a33-kDa protein (Ptc33) related to the GTP-binding proteins Toc33 and Toc34 of Arabidopsis. In the present work, we studied the interactions and roles of Ptc16 and Ptc33 during pPORA import. Radio labeled Ptc16/Oep16 was synthesized from a corresponding cDNA and imported into isolated Arabidopsis plastids. Crosslinking experiments revealed that import of35S-Oep16/Ptc16 is stimulated by GTP.35S-Oep16/Ptc16forms larger complexes with Toc33 but not Toc34. Plastids of the ppi1 mutant of Arabidopsis lacking Toc33, were unable to import pPORA in darkness but imported the small subunit precursor of ribulose-1,5-bisphosphate carboxylase/oxygenase (pSSU), precursor ferredoxin (pFd) as well as pPORB which is a close relative of pPORA. In white light, partial suppressions of pSSU, pFd and pPORB import were observed. Our results unveil a hitherto unrecognized role of Toc33 in pPORA import and suggest photo oxidative membrane damage, induced by excess Pchlide accumulating in ppi1 chloroplasts because of the lack of pPORA import, to be the cause of the general drop of protein import.

Estructura de una red esencial de señalización que regula la homeostasis iónica en plantas

Las plantas son organismos sésiles que han desarrollado la capacidad para detectar variaciones sutiles en su ambiente y producir respuestas adaptativas mediante rutas de señalización. Los estímulos causados por el estrés biótico y abiótico son numerosos y dependiendo del tiempo de exposición y su intensidad, pueden reducir la tasa de crecimiento de las plantas y la producción. Los cambios en la concentración del calcio citosólico libre constituyen una de las primeras reacciones intracelulares a las situaciones de estrés abiótico. En esta situación, el calcio actúa como segundo mensajero y las variaciones en su concentración son descodificadas por proteínas de unión a calcio. Las más conocidas son las manos-EF y los dominios C2. Los dominios C2 han sido descritos como dominios de unión a lípidos dependientes de calcio. Estos dominios se consideran proteínas periféricas solubles en agua que se asocian de manera reversible a los lípidos de la membrana mediante una o dos regiones funcionales: el sitio de unión a calcio y el sitio polibásico. A pesar de que se conoce la estructura molecular de algunos dominios C2, se desconocen aspectos relacionados como las reglas que dirigen su forma de interaccionar con los diferentes fosfolípidos y proteínas, la posición que ocupan en la bicapa lipídica y su papel en la transmisión de señales. En esta tesis se ha estudiado una proteína de Arabidopsis thaliana (At3g17980) representativa de una nueva familia de proteínas con dominios C2, que consiste únicamente de un dominio C2. Esta proteína, llamada AtC2.1, ha sido clonada en el vector pETM11, expresada en E. coli y purificada a homogeneidad en dos pasos cromatográficos. Se obtuvieron cristales de AtC2.1 de buena calidad mediante técnicas de difusión de vapor. La proteína fue co-cristalizada con calcio, fosfocolina (POC) y el fosfolípido 1,2-dihexanoil-sn-glicero-3-fosfo-L-serina (PSF). Se recogieron ocho conjuntos de datos de difracción de rayos X empleando radiación sincrotrón. Los cristales difractaron hasta 1.6 Å de resolución. Siete de ellos pertenecían al grupo ortorrómbico P212121, con las dimensiones de la celdilla unidad a = 35.3, b = 88.9, c = 110.6 Å, y un cristal pertenecía al grupo espacial monoclínico C2, con a = 124.84, b = 35.27, c = 92.32 Å y = 121.70º. La estructura se resolvió mediante la técnica MR-SAD utilizando el cinc como dispersor anómalo. La estructura cristalina mostró que la molécula forma un dímero en el que cada protómero se pliega como un dominio C2 típico, con la topología tipo II y presenta una inserción de 43 aminoácidos que la diferencia de los dominios C2 conocidos. El mapa de densidad electrónica mostró dos átomos de calcio por protómero. Se resolvieron las estructuras de AtC2.1 en complejo con POC o PSF. En ambos complejos, el análisis cristalográfico detectó máximos de densidad electrónica en la región correspondiente al sitio polibásico formado por las hebras 2, 3 5 y el lazo 3. Éstos se interpretaron correctamente como dos moléculas de POC y un átomo de cinc, en un complejo, y como la cabeza polar del PSF en el otro. AtC2.1 define un sitio de interacción con lípidos dependiente de cinc. En conclusión, en este trabajo se presenta la estructura tridimensional de AtC2.1, miembro representativo de una familia de proteínas de Arabidopsis thaliana, identificadas como proteínas que interaccionan con los receptores de ABA. Estas proteínas están constituidas únicamente por un dominio C2. El análisis conjunto de los datos biofísicos y cristalográficos muestra que AtC2.1 es un sensor de calcio que une lípidos usando dos sitios funcionales. Estos datos sugieren un mecanismo de inserción en membrana dependiente de calcio que trae consigo la disociación de la estructura dimérica y, por consiguiente, un cambio en las propiedades de superficie de la molécula. Este mecanismo proporciona las bases del reconocimiento y transporte de los receptores de ABA y/o otras moléculas a la membrana celular. Plants are sessile organisms that have developed the capacity to detect slight variations of their environment. They are able to perceive biotic and abiotic stress signals and to transduce them by signaling pathways in order to trigger adaptative responses. Stress factors are numerous and, depending on their exposition time and their concentration, can reduce plant growth rate, limiting the productivity of crop plants. Changes in the cytosolic free calcium concentration are observed as one of the earliest intracellular reactions to abiotic stress signals. Calcium plays a key role as a second messenger, and calcium concentration signatures, called calcium signals, are decodified by calcium binding proteins. The main calcium binding structures are the EF-hand motif and the C2 domains. C2 domain is a calcium dependent lipid-binding domain of approximately 130 amino acids. C2 domain displays two functional regions: the Ca-binding region and the polybasic cluster. Both of them can interact with the membrane phospholipids. Despite the number of C2 domain 3D structures currently available, questions about how they interact with the different target phospholipids, their precise spatial position in the lipid bilayer, interactions with other proteins and their role in transmitting signals downstream, have not yet been explored. In this work we have studied an uncharacterized protein from Arabidopsis thaliana (At3g17980) consisting of only a single C2 domain, as member of a new protein C2-domain family. This protein called AtC2.1 was cloned into the pETM11 vector and expressed in E. coli, allowing the purification to homogeneity in two chromatographic steps. Good quality diffracting crystals were obtained using vapor-diffusion techniques. Crystals were co-crystalized with calcium; phosphocholine (POC) and/or the phospholipid 1,2-dihexanoyl-sn-glycero-3-phospho-L-serine (PSF). Eight data set were collected with synchrotron radiation. Crystals diffracted up to 1.6 Å resolution and seven of them belong to the orthorhombic space group P212121, with unit-cell parameters a = 35.3, b = 88.9, c = 110.6 Å. Another crystal was monoclinic, space group C2, with a = 124.84, b = 35.27, c = 92.32 Å and = 121.70º. The structural model was solved by MR-SAD using Zn2+ as anomalous scatterer. The crystal structure shows that the molecule is a dimer. Each monomer was folded as a canonical C2 domain with the topology II with a 43 residues insertion. The electron density map reveals two calcium ions per molecule. Structures of AtC2.1, complexed with POC and PSF, have been solved. Well-defined extra electron densities were found, in both complexes, within the concave surface formed by strands 2, 3, 5 and loop 3 of AtC2.1. These densities were clearly explained by the presence of the two POC molecules, one zinc atom and head groups of PSF, occupying the cavity of the polybasic site. AtC2.1 defines a new metal dependent lipid-binding site into the polybasic site. In conclusion, in this thesis it is presented the molecular structure of AtC2.1, a representative member of a family of Arabidopsis thaliana C2 domain proteins, of unknown function, but identified as a molecular interacting unit of the ABA receptors. The joint analyses of the biophysical and crystallographic data show that AtC2.1 is a calcium sensor that binds lipids in two sites and suggest a model of calcium-dependent membrane insertion mechanism that will involve either dimer dissociation or a strong rearrangement of the dimeric structure. This mechanism may be the basis for the recognition and delivery of ABA receptors or other protein molecules to cell membranes.

Identification of thaumatin-like protein and aspartyl protease as new major allergens in lettuce (Lactuca sativa)

Scope: Today, about 2–8% of the population of Western countries exhibits some type of food allergy whose impact ranges from localized symptoms confined to the oral mucosa to severe anaphylactic reactions. Consumed worldwide, lettuce is a Compositae family vegetable that can elicit allergic reactions. To date, however, only one lipid transfer protein has been described in allergic reaction to lettuce. The aim of this study was to identify potential new allergens involved in lettuce allergy. Methods and results: Sera from 42 Spanish lettuce-allergic patients were obtained from pa-tients recruited at the outpatient clinic. IgE-binding proteins were detected by SDS-PAGE and immunoblotting. Molecular characterization of IgE-binding bands was performed by MS. Thaumatin was purified using the Agilent 3100 OFFGEL system. The IgE-binding bands recognized in the sera of more than 50% of patients were identified as lipid transfer protein (9 kDa), a thaumatin-like protein (26 kDa), and an aspartyl protease (35 and 45 kDa). ELISA inhibition studies were performed to confirm the IgE reactivity of the purified allergen. Conclusion: Two new major lettuce allergens—a thaumatin-like protein and an aspartyl protease—have been identified and characterized. These allergens may be used to improve both diagnosis and treatment of lettuce-allergic patients.

Molecular physiology of nickel and cobalt homeostasis in Rhizobium leguminosarum.

Transition metals such as Fe, Cu, Mn, Ni, or Co are essential nutrients, as they are constitutive elements of a significant fraction of cell proteins. Such metals are present in the active site of many enzymes, and also participate as structural elements in different proteins. From a chemical point of view, metals have a defined order of affinity for binding, designated as the Irving-Williams series (Irving and Williams, 1948) Mg2+ menor que Mn2+ menor que Fe2+ menor que Co2+ menor que Ni2+ menor que Cu2+mayor queZn2+ Since cells contain a high number of different proteins harbouring different metal ions, a simplistic model in which proteins are synthesized and metals imported into a ?cytoplasmic soup? cannot explain the final product that we find in the cell. Instead we need to envisage a complex model in which specific ligands are present in definite amounts to leave the right amounts of available metals and protein binding sites, so specific pairs can bind appropriately. A critical control on the amount of ligands and metal present is exerted through specific metal-responsive regulators able to induce the synthesis of the right amount of ligands (essentially metal binding proteins), import and efflux proteins. These systems are adapted to establish the metal-protein equilibria compatible with the formation of the right metalloprotein complexes. Understanding this complex network of interactions is central to the understanding of metal metabolism for the synthesis of metalloenzymes, a key topic in the Rhizobium-legume symbiosis. In the case of the Rhizobium leguminosarum bv viciae (Rlv) UPM791 -Pisum sativum symbiotic system, the concentration of nickel in the plant nutrient solution is a limiting factor for hydrogenase expression, and provision of high amounts of this element to the plant nutrient solution is required to ensure optimal levels of enzyme synthesis (Brito et al., 1994).

Computational study of ligand binding in lipid transfer proteins: Structures, interfaces, and free energies of protein-lipid complexes

Plant nonspecific lipid transfer proteins (nsLTPs) bind a wide variety of lipids, which allows them to perform disparate functions. Recent reports on their multifunctionality in plant growth processes have posed new questions on the versatile binding abilities of these proteins. The lack of binding specificity has been customarily explained in qualitative terms on the basis of a supposed structural flexibility and nonspecificity of hydrophobic protein-ligand interactions. We present here a computational study of protein-ligand complexes formed between five nsLTPs and seven lipids bound in two different ways in every receptor protein. After optimizing geometries inmolecular dynamics calculations, we computed Poisson- Boltzmann electrostatic potentials, solvation energies, properties of the protein-ligand interfaces, and estimates of binding free energies of the resulting complexes. Our results provide the first quantitative information on the ligand abilities of nsLTPs, shed new light into protein-lipid interactions, and reveal new features which supplement commonly held assumptions on their lack of binding specificity.