Biblioteca Digital

The 1,3-dioxin-4-one ring in the title compound, C(16)H(16)O(3), is in a half-boat conformation with the quaternary O-C(CH(3))(2)-O atom lying 0.546 (1) angstrom out of the plane defined by the remaining five atoms. The crystal structure is consolidated by C-H center dot center dot center dot O contacts that lead to supramolecular layers.; FAPESP[07/59404-2]; FAPESP[08/02531-5]; CNPq[472237/2008-0]; CNPq[300613/2007]; CNPq[307121/2006-0]; Coordenacao de Aperfeicoamento de Pessoal de Nivel Superior (CAPES)

The tetrahydropyrimidinone ring in the title compound, C(20)H(20)N(2)O(2), is in a half-boat conformation with the N-C-N C atom 0.580 (2) angstrom out of the plane defined by the remaining five atoms. In the crystal structure, molecules are connected into centrosymmetric dimers via N-H center dot center dot center dot O interactions. The dimeric aggregates are linked into supramolecular chains along the a axis via C-H center dot center dot center dot pi interactions.; FAPESP[07/59404-2]; FAPESP[08/02531-5]; CNPq[472237/2008-0]; CNPq[300613/2007]; CNPq[307121/2006-0]; Coordenacao de Aperfeicoamento de Pessoal de Nivel Superior (CAPES)

Two-dimensional crystalline bacterial surface layers (S-layers) are found in a broad range of bacteria and archaea as the outermost cell envelope component. The self-assembling properties of the S-layers permit them to recrystallize on solid substrates. Beyond their biological interest as S-layers, they are currently used in nanotechnology to build supramolecular structures. Here, the structure of S-layers and the interactions between them are studied through surface force techniques. Scanning force microscopy has been used to study the structure of recrystallized S-layers from Bacillus sphaericus on mica at different 1:1 electrolyte concentrations. They give evidence of the two-dimensional organization of the proteins and reveal small corrugations of the S-layers formed on mica. The lattice parameters of the S-layers were a = b = 14 nm, γ = 90° and did not depend on the electrolyte concentration. The interaction forces between recrystallized S-layers on mica were studied with the surface force apparatus as a function of electrolyte concentration. Force measurements show that electrostatic and steric interactions are dominant at long distances. When the S-layers are compressed they exhibit elastic behavior. No adhesion between recrystallized layers takes place. We report for the first time...

The three-dimensional structure of the 29-residue designed coiled coil having the amino acid sequence acetyl-E VEALEKK VAALESK VQALEKK VEALEHG-amide has been determined and refined to a crystallographic R-factor of 21.4% for all data from 10-A to 2.1-A resolution. This molecule is called coil-VaLd because it contains valine in the a heptad positions and leucine in the d heptad positions. In the trigonal crystal, three molecules, related by a crystallographic threefold axis, form a parallel three-helix bundle. The bundles are stacked head-to-tail to form a continuous coiled coil along the c-direction of the crystal. The contacts among the three helices within the coiled coil are mainly hydrophobic: four layers of valine residues alternate with four layers of leucine residues to form the core of the bundle. In contrast, mostly hydrophilic contacts mediate the interaction between trimers: here a total of two direct protein--protein hydrogen bonds are found. Based on the structure, we propose a scheme for designing crystals of peptides containing continuous two-, three-, and four-stranded coiled coils.

Acacia gum is a branched complex polysaccharide whose main chain consists of 1,3-linked β-D-galactopyranosyl units. Acacia gum is defined as a heteropolysaccharide since it contains ∼2% of a polypeptide. The major molecular fraction (F1) accounting for ∼88% of the total acacia gum mass is an arabinogalactan peptide with a weight-average molecular weight of 2.86 × 105 g/mol. The molecular structure of F1 is actually unknown. From small angle neutron scattering experiments in charge screening conditions, F1 appeared to be a dispersion of two-dimensional structures with a radius of gyration of ∼6.5 nm and an inner dense branched structure. Inverse Fourier transform of F1 scattering form factor revealed a disk-like morphology with a diameter of ∼20 nm and a thickness below 2 nm. Ab initio calculations on the pair distance distribution function produced a porous oblate ellipsoid particle with a central intricated “network”. Both transmission electron microscopy and atomic force microscopy confirm the thin disk model and structural dimensions. The model proposed is a breakthrough in the field of arabinogalactan-protein-type macromolecules. In particular, concerning the site of biosynthesis of these macromolecules, the structural dimensions found in this study would be in agreement with a phloem-mediated long-distance transport. In addition...

The design and synthesis of a new family of multiferrocene complexes with enhanced control of structure and stoichimetry via coordination-driven self-assembly is described. Insight into the structure and electronic properties of all supramolecules was obtained by electrochemical studies. The collective results provide an enhanced understanding of the influence of structural factors on the electrochemistry of multifunctional electroactive supramolecular architectures.

Self-compartmentalizing proteases orchestrate protein turnover through an original architecture characterized by a central catalytic chamber. Here we report the first structure of an archaeal member of a new self-compartmentalizing protease family forming a cubic-shaped octamer with D4 symmetry and referred to as CubicO. We solved the structure of the Pyrococcus abyssi Pab87 protein at 2.2 Å resolution using the anomalous signal of the high-phasing-power lanthanide derivative Lu-HPDO3A. A 20 Å wide channel runs through this supramolecular assembly of 0.4 MDa, giving access to a 60 Å wide central chamber holding the eight active sites. Surprisingly, activity assays revealed that Pab87 degrades specifically d-amino acid containing peptides, which have never been observed in archaea. Genomic context of the Pab87 gene showed that it is surrounded by genes involved in the amino acid/peptide transport or metabolism. We propose that CubicO proteases are involved in the processing of d-peptides from environmental origins.

The composite and versatile structure of the cytoskeleton confers complex mechanical properties on cells. Actin filaments sustain the cell membrane and their dynamics insure cell shape changes. For example, the lamellipodium moves by actin polymerization, a mechanism that has been studied using simplified experimental systems. Much less is known about the actin cortex, a shell-like structure underneath the membrane that contracts for cell movement. We have designed an experimental system that mimicks the cell cortex by allowing actin polymerization to nucleate and assemble at the inner membrane of a liposome. Actin shell growth can be triggered inside the liposome, which offers a useful system for a controlled study. The observed actin shell thickness and estimated mesh size of the actin structure are in good agreement with cellular data. Such a system paves the way for a thorough characterization of cortical dynamics and mechanics.

Since the early studies on the resolution and reconstitution of the oxidative phosphorylation system from animal mitochondria, coupling factor B was recognized as an essential component of the machinery responsible for energy-driven ATP synthesis. At the phenomenological level, factor B was agreed to lie at the interface of energy transfer between the respiratory chain and the ATP synthase complex. However, biochemical characterization of the factor B polypeptide has proved difficult. It was not until 1990 that the N-terminal amino acid sequence of bovine mitochondrial factor B was reported, which followed, a decade later, by the report describing the amino acid sequence of full-length human factor B and its functional characterization. The present review summarizes the recent advances in structure-functional studies of factor B, including its recently determined crystal structure at 0.96 Å resolution. Ectopic expression of human factor B in cultured animal cells has unexpectedly revealed its role in shaping mitochondrial morphology. The supramolecular assembly of ATP synthase as dimer ribbons at highly curved apices of the mitochondrial cristae was recently suggested to optimize ATP synthesis under proton-limited conditions. We propose that the binding of the ATP synthase dimers with factor B tetramers could be a means to enhance the efficiency of the terminal step of oxidative phosphorylation in animal mitochondria.

The synthesis and spectral characterization of novel diorganotin complexes with 3-hydroxypyridine-2-carbaldehyde thiosemicarbazone, H2L(1), [SnMe2(L)] (2), [SnBu2(L)] (3), and [SnPh2(L)] (4) are reported. The single-crystal X-ray structure of complex [SnPh2(L)(DMSO)] (5) shows that the ligand is doubly deprotonated and is coordinated as tridentate ligand. The six coordination number is completed by two carbon atoms of phenyl groups. There are two similar monomers 5a (Sn1) and 5b (Sn51) in the asymmetric unit. The monomers 5a and 5b are linked through intermolecular hydrogen bonds of N–H–O and C–H–S type. C–H → π, intermolecular interactions, intra- and intermolecular hydrogen bonds stabilize this structure and leads to aggregation and a supramolecular assembly. The IR and NMR (1H, 13C and 119Sn) spectroscopic data of the complexes are reported. The in vitro cytotoxic activity has been evaluated against the cells of three human cancer cell lines: MCF-7 (human breast cancer cell line), T-24 (bladder cancer cell line), A-549 (nonsmall cell lung carcinoma) and a mouse L-929 (a fibroblast-like cell line cloned from strain L). Compounds 1, 3, and 4 were found active against all four cell lines. Selectivity was observed for complexes 3 and 4 which were found especially active against MCF-7 and T-24 cancer cell lines.

The native state of a protein is usually associated with a compact globular conformation possessing a rigid and highly ordered structure. At the turn of the last century certain studies arose which concluded that many proteins cannot, in principle, form a rigid globular structure in an aqueous environment, but they are still able to fulfill their specific functions — i.e., they are native. The existence of the disordered regions allows these proteins to interact with their numerous binding partners. Such interactions are often accompanied by the formation of complexes that possess a more ordered structure than the original components. The functional diversity of these proteins, combined with the variability of signals related to the various intra-and intercellular processes handled by these proteins and their capability to produce multi-variant and multi-directional responses allow them to form a unique regulatory net in a cell. The abundance of disordered proteins inside the cell is precisely controlled at the synthesis and clearance levels as well as via interaction with specific binding partners and posttranslational modifications. Another recently recognized biologically active state of proteins is the functional amyloid. The formation of such functional amyloids is tightly controlled and therefore differs from the uncontrolled formation of pathogenic amyloids which are associated with the pathogenesis of several conformational diseases...

Structural analyses of heterologously expressed mammalian membrane proteins remain a great challenge given that microgram to milligram amounts of correctly folded and highly purified proteins are required. Here, we present a novel method for the expression and affinity purification of recombinant mammalian and in particular human transport proteins in Xenopus laevis frog oocytes. The method was validated for four human and one murine transporter. Negative stain transmission electron microscopy (TEM) and single particle analysis (SPA) of two of these transporters, i.e., the potassium-chloride cotransporter 4 (KCC4) and the aquaporin-1 (AQP1) water channel, revealed the expected quaternary structures within homogeneous preparations, and thus correct protein folding and assembly. This is the first time a cation-chloride cotransporter (SLC12) family member is isolated, and its shape, dimensions, low-resolution structure and oligomeric state determined by TEM, i.e., by a direct method. Finally, we were able to grow 2D crystals of human AQP1. The ability of AQP1 to crystallize was a strong indicator for the structural integrity of the purified recombinant protein. This approach will open the way for the structure determination of many human membrane transporters taking full advantage of the Xenopus laevis oocyte expression system that generally yields robust functional expression.

Nature presents various protein fibers that bridge the nanometer to micrometer regimes. These structures provide inspiration for the de novo design of biomimetic assemblies, both to address difficulties in studying and understanding natural systems, and to provide routes to new biomaterials with potential applications in nanotechnology and medicine. We have designed a self-assembling fiber system, the SAFs, in which two small α-helical peptides are programmed to form a dimeric coiled coil and assemble in a controlled manner. The resulting fibers are tens of nm wide and tens of μm long, and, therefore, comprise millions of peptides to give gigadalton supramolecular structures. Here, we describe the structure of the SAFs determined to approximately 8 Å resolution using cryotransmission electron microscopy. Individual micrographs show clear ultrastructure that allowed direct interpretation of the packing of individual α-helices within the fibers, and the construction of a 3D electron density map. Furthermore, a model was derived using the cryotransmission electron microscopy data and side chains taken from a 2.3 Å X-ray crystal structure of a peptide building block incapable of forming fibers. This was validated using single-particle analysis techniques...

The structure of the unusually long (∼100 amino-acid residues) N-terminal domain of the light-harvesting protein CP29 of plants is not defined in the crystal structure of this membrane protein. We studied the N-terminus using two electron paramagnetic resonance (EPR) approaches: the rotational diffusion of spin labels at 55 residues with continuous-wave EPR, and three sets of distances with a pulsed EPR method. The N-terminus is relatively structured. Five regions that differ considerably in their dynamics are identified. Two regions have low rotational diffusion, one of which shows α-helical character suggesting contact with the protein surface. This immobile part is flanked by two highly dynamic, unstructured regions (loops) that cover residues 10–22 and 82–91. These loops may be important for the interaction with other light-harvesting proteins. The region around residue 4 also has low rotational diffusion, presumably because it attaches noncovalently to the protein. This section is close to a phosphorylation site (Thr-6) in related proteins, such as those encoded by the Lhcb4.2 gene. Phosphorylation might influence the interaction with other antenna complexes, thereby regulating the supramolecular organization in the thylakoid membrane.

The slightly yellow-coloured title complex, [Zn(C18H16N4O4)(H2O)]n, crystallizes with one mol­ecule in the asymmetric unit. The structure clearly shows the mer-η4 O,O,N,N-binding mode of the N,N′-bis-(2-cyano-ethyl­propeno­yl)-1,2-di­amido­benzene ligand stabilizing the Zn centre of a distorted octa­hedral environment. The fifth coordination site in one apical position is held by a coordinating solvent water mol­ecule whereas the complete octa­hedral coordination sphere is completed by coordination of one N atom from a CN group of a neighbouring mol­ecule, leading to the final polymeric structure consisting of zigzag staggered chains in parallel orientation along the c-axis direction. Between the coord­in­ated water solvent molecule and the N atoms of uncoord­in­ated cyano-groups of neighboured units, two H-bridge bonds are formed. One of these H-bridge bonds is of inter- whereas the other of intra-strand nature, leading to a two-dimensional network parallel to (110) stabilizing the supramolecular structure. Six Zn—O or Zn—N bonds are found with lengths ranging from 2.061 (1) to 2.185 (1) Å and bond angles about the Zn atom are clustered in the ranges 79.83 (4)–104.21 (4) and 167.05 (4)–170.28 (4)°.

Poly-L-glutamic acid (PLGA) often serves as a model in studies on amyloid fibrils and conformational transitions in proteins, and as a precursor for synthetic biomaterials. Aggregation of PLGA chains and formation of amyloid-like fibrils was shown to continue on higher levels of superstructural self-assembly coinciding with the appearance of so-called β2-sheet conformation manifesting in dramatic redshift of infrared amide I′ band below 1600 cm−1. This spectral hallmark has been attributed to network of bifurcated hydrogen bonds coupling C = O and N-D (N-H) groups of the main chains to glutamate side chains. However, other authors reported that, under essentially identical conditions, PLGA forms the conventional in terms of infrared characteristics β1-sheet structure (exciton-split amide I′ band with peaks at ca. 1616 and 1683 cm−1). Here we attempt to shed light on this discrepancy by studying the effect of increasing concentration of intentionally induced defects in PLGA on the tendency to form β1/β2-type aggregates using infrared spectroscopy. We have employed carbodiimide-mediated covalent modification of Glu side chains with n-butylamine (NBA), as well as electrostatics-driven inclusion of polylysine chains, as two different ways to trigger structural defects in PLGA. Our study depicts a clear correlation between concentration of defects in PLGA and increasing tendency to depart from the β2-structure toward the one less demanding in terms of chemical uniformity of side chains: β1-structure. The varying predisposition to form β1- or β2-type aggregates assessed by infrared absorption was compared with the degree of morphological order observed in electron microscopy images. Our results are discussed in the context of latent covalent defects in homopolypeptides (especially with side chains capable of hydrogen-bonding) that could obscure their actual propensities to adopt different conformations...

The hexameric lattice of an immature retroviral particle consists of Gag polyprotein, which is the precursor of all viral structural proteins. Lentiviral and alpharetroviral Gag proteins contain a peptide sequence called the spacer peptide (SP), which is localized between the capsid (CA) and nucleocapsid (NC) domains. SP plays a critical role in intermolecular interactions during the assembly of immature particles of several retroviruses. Published models of supramolecular structures of immature particles suggest that in lentiviruses and alpharetroviruses, SP adopts a rod-like six-helix bundle organization. In contrast, Mason-Pfizer monkey virus (M-PMV), a betaretrovirus that assembles in the cytoplasm, does not contain a distinct SP sequence, and the CA-NC connecting region is not organized into a clear rod-like structure. Nevertheless, the CA-NC junction comprises a sequence critical for assembly of immature M-PMV particles. In the present work, we characterized this region, called the SP-like domain, in detail. We provide biochemical data confirming the critical role of the M-PMV SP-like domain in immature particle assembly, release, processing, and infectivity. Circular dichroism spectroscopy revealed that, in contrast to the SP regions of other retroviruses...

Thèse numérisée par la Division de la gestion de documents et des archives de l'Université de Montréal

The fibrillation propensity of the multidomain protein human serum albumin (HSA) was analyzed under different solution conditions. The aggregation kinetics, protein conformational changes upon self-assembly, and structure of the different intermediates on the fibrillation pathway were determined by means of thioflavin T (ThT) fluorescence and Congo Red absorbance; far- and near-ultraviolet circular dichroism; tryptophan fluorescence; Fourier transform infrared spectroscopy; x-ray diffraction; and transmission electron, scanning electron, atomic force, and microscopies. HSA fibrillation extends over several days of incubation without the presence of a lag phase, except for HSA samples incubated at acidic pH and room temperature in the absence of electrolyte. The absence of a lag phase occurs if the initial aggregation is a downhill process that does not require a highly organized and unstable nucleus. The fibrillation process is accompanied by a progressive increase in the β-sheet (up to 26%) and unordered conformation at the expense of α-helical conformation, as revealed by ThT fluorescence and circular dichroism and Fourier transform infrared spectroscopies, but changes in the secondary structure contents depend on solution conditions. These changes also involve the presence of different structural intermediates in the aggregation pathway...

mu-Benzene-1,2,4,5-tetracarboxylato-kappa O-2(1):O-4) bis[aquabis(2,2-methylpropane-1,3-diamine-kappa N-2,N') nickel(II)] methanol disolvate tetrahydrate, [Ni-2(C10H2O8)(C5H14N2)(4)(H2O)(2)]center dot 2CH(4)O center dot 4H(2)O, (I), is dinuclear, with elemental units built up around an inversion centre halving the benzene-1,2,4,5-tetracarboxylate (btc) anion, which bridges two symmetry-related Ni-II cations. The octahedral Ni polyhedron is completed by two chelating 2,2-methylpropane-1,3-diamine (dmpda) groups and a terminal aqua ligand. Two methanol and four water solvent molecules are involved in a number of N-H center dot center dot center dot O and O-H center dot center dot center dot O hydrogen bonds which define a strongly bound two-dimensional supramolecular structure. The structure of catena-poly[[[bis(2,2-methylpropane-1,3-diamine-kappa N-2,N') nickel(II)]-mu-pyridine-2,5-dicarboxylato-kappa O-3(5): N,O-2[(2,2-methylpropane-1,3-diamine-kappa N-2,N') nickel(II)]-mu-pyridine-2,5-dicarboxylato-kappa N-3,O-2:O-5] octahydrate], {[Ni-2(C7H3NO4) 2(C5H14N2)(3)]center dot 8H(2)O}(n), (II), is polymeric, forming twisted chains around three independent Ni centres, two of which lie on inversion centres and the third in a general position. There are three chelating dmpda ligands (one disordered over two equally populated positions)...