Large Supramolecular Structures Research Articles

Poly(amidoamine) and Poly(propyleneimine) Dendrimers Show Distinct Binding Behaviors with Sodium Dodecyl Sulfate: Insights from SAXS and NMR Analysis

We investigate the interactions of generation 3 (G3) poly(amidoamine) (PAMAM) and G3 poly(propylenimine) (PPI) dendrimers with sodium dodecyl sulfate (SDS) in aqueous solution. Size and structure of the dendrimer-SDS aggregates as a function of SDS/dendrimer molar ratio were revealed by SAXS and NMR. G3 PAMAM has a relatively open and dense-core structure, while G3 PPI with the same number of surface amine groups possesses a compact and uniform structure. Upon addition of SDS, much more SDS monomers were encapsulated in the interior of PPI rather than in PAMAM. More significant size increase in PAMAM-SDS aggregate is observed at low SDS concentrations, due to the binding of SDS on PAMAM surface and further assembly into larger supramolecular structures. Both noncooperative and cooperative binding of SDS on G3 PPI surface are observed, while only noncooperative binding is proposed on G3 PAMAM, due to its open surface and large surface group distance. The size of the PPI-SDS complex is larger than that of PAMAM-SDS at higher SDS concentrations. Within the investigated SDS concentrations, SDS exhibits much stronger interactions with G3 PPI than with G3 PAMAM. These results provide new insights into dendrimer-surfactant interactions and explain why PPI is much more cytotoxic than PAMAM.

Chlorosome antenna complexes from green photosynthetic bacteria

Chlorosomes are the distinguishing light-harvesting antenna complexes that are found in green photosynthetic bacteria. They contain bacteriochlorophyll (BChl) c, d, e in natural organisms, and recently through mutation, BChl f, as their principal light-harvesting pigments. In chlorosomes, these pigments self-assemble into large supramolecular structures that are enclosed inside a lipid monolayer to form an ellipsoid. The pigment assembly is dictated mostly by pigment-pigment interactions as opposed to protein-pigment interactions. On the bottom face of the chlorosome, the CsmA protein aggregates into a paracrystalline baseplate with BChl a, and serves as the interface to the next energy acceptor in the system. The exceptional light-harvesting ability at very low light conditions of chlorosomes has made them an attractive subject of study for both basic and applied science. This review, incorporating recent advancements, considers several important aspects of chlorosomes: pigment biosynthesis, organization of pigments and proteins, spectroscopic properties, and applications to bio-hybrid and bio-inspired devices.

Identification of a newSchistosoma mansoniSMYB1 partner: putative roles in RNA metabolism

SMYB1 is a Schistosoma mansoni protein highly similar to members of the Y-box binding protein family. Similar to other homologues, SMYB1 is able to bind double- and single-stranded DNA, as well as RNA molecules. The characterization of proteins involved in the regulation of gene expression in S. mansoni is of great importance for the understanding of molecular events that control morphological and physiological changes in this parasite. Here we demonstrate that SMYB1 is located in the cytoplasm of cells from different life-cycle stages of S. mansoni, suggesting that this protein is probably acting in mRNA metabolism in the cytoplasm and corroborating previous findings from our group that showed its ability to bind RNA. Protein-protein interactions are important events in all biological processes, since most proteins execute their functions through large supramolecular structures. Yeast two-hybrid screenings using SMYB1 as bait identified a partner in S. mansoni similar to the SmD3 protein of Drosophila melanogaster (SmRNP), which is important in the assembly of small nuclear ribonucleoprotein complexes. Also, pull-down assays were conducted using immobilized GST-SMYB1 proteins and confirmed the SMYB1-SmRNP interaction. The interaction of SMYB1 with a protein involved in mRNA processing suggests that it may act in processes such as turnover, transport and stabilization of RNA molecules.

Solid-State NMR-Based Approaches for Supramolecular Structure Elucidation

Supramolecular chemistry provides structural and conformational information about complexes formed from multiple molecules. While the molecule is held together by strong intramolecular contacts like covalent bonds, supramolecular structures can be further stabilized by weaker or transient intermolecular interactions. These interactions can confer a great diversity and sensitivity to exogenous factors like temperature, pressure, or ionic strength to multimolecular arrangements. Solid-state nuclear magnetic resonance (ssNMR) can provide atomic-scale structural and dynamical information in highly disordered or heterogeneous biological systems, even in complex environments such as cellular membranes or whole cells. In these systems, the molecule of interest no longer exists as a separate unit, but it entangles with its surroundings in a dynamic interplay. Researchers have long accounted for the complexity of these intermolecular arrangements through a rather phenomenological description. But now the focus is shifting toward a detailed understanding of supramolecular structure at atomic resolution, constantly expanding our understanding of the stunning influence of the environment. In this Account, we discuss how ssNMR can help to dissect the remarkable interplay between intra- and intermolecular interactions. We describe biochemical and spectroscopic strategies that tailor ssNMR spectroscopic methods to the challenge of supramolecular structure investigation. In particular, we consider protein-protein interactions or the protein-membrane topology, and we review recent applications of these techniques. Furthermore, we summarize methods for integrating ssNMR information with other experimental techniques or computational methods, and we offer perspectives on how this overall information allows us to target increasingly large and intricate supramolecular structures of biomolecules. Advancements in ssNMR methodology and instrumentation, including the incorporation of signal enhancement methods such as dynamic nuclear polarization will further increase the potential of ssNMR spectroscopy, and together with additional developments in the field of NMR-hybrid strategies, ssNMR may become an ideal tool to study the heterogeneous, dynamic, and often transient nature of molecular interactions in complex biological systems.

Missing pieces in protein deposition and mobilization inside legume seed storage vacuoles: calcium and magnesium ions

AbstractDuring the maturation of dicotyledonous seeds, organic carbon, nitrogen and sulphur are stored in protein storage vacuoles (PSVs) as storage globulins. Several studies point to the coexistence of storage proteins with proteases responsible for their degradation inside PSVs. Different mechanisms have been proposed to explain why there is no proteolysis during this period. Protein aggregation to form large supramolecular structures resistant to proteolytic attack could be the reason. However, during germination, and particularly following its completion, the globulin aggregates must undergo disintegration to allow protease attack for protein reserve mobilization. Based on the well-described concentration-dependent ability of Ca2+ and Mg2+ to promote in vitro aggregation and disaggregation of globulins, we explored a possible role for these alkaline earth cations in globulin packaging and mobilization. Ca2+ and Mg2+ measurements in purified PSVs [6.37 μmol and 43.9 μmol g− 1 dry weight (DW) of cotyledons, respectively] showed the presence of these two alkaline earth cations within this compartment. To our knowledge, this is the first time that Ca2+ and Mg2+ have been quantified in purified PSVs from Lupinus albus seeds. Considering the importance of these two alkaline earth cations inside PSVs, which represent 14.6% and 60.7% of the total seed Mg2+and Ca2+, respectively, globulin aggregation and disaggregation profiles were assayed using experimental conditions closer to those that are physiologically present (proportion of Ca2+ and Mg2+, and acidic pH). Based on: (1) the high in vivo abundance of Ca2+ and Mg2+ inside PSVs; and (2) globulin aggregation and disaggregation profiles, together with structural and physiological evidence already reported in the literature, an important physiological role for Ca2+ and Mg2+ in globulin packaging and mobilization inside PSVs is suggested.

Herringbone and Helical Self-Assembly of π-Conjugated Molecules in the Solid State through CH/π Hydrogen Bonds

Self-organization of organic molecules through weak noncovalent forces such as CH/π interactions and creation of large hierarchical supramolecular structures in the solid state are at the very early stage of research. The present study reports direct evidence for CH/π interaction driven hierarchical self-assembly in π-conjugated molecules based on custom-designed oligophenylenevinylenes (OPVs) whose structures differ only in the number of carbon atoms in the tails. Single-crystal X-ray structures were resolved for these OPV synthons and the existence of long-range multiple-arm CH/π interactions was revealed in the crystal lattices. Alignment of these π-conjugated OPVs in the solid state was found to be crucial in producing either right-handed herringbone packing in the crystal or left-handed helices in the liquid-crystalline mesophase. Pitch- and roll-angle displacements of OPV chromophores were determined to trace the effect of the molecular inclination on the ordering of hierarchical structures. Furthermore, circular dichroism studies on the OPVs were carried out in the aligned helical structures to prove the existence of molecular self-assembly. Thus, the present strategy opens up new approaches in supramolecular chemistry based on weak CH/π hydrogen bonding, more specifically in π-conjugated materials.

Highly efficient and exact method for parallelization of grid-based algorithms and its implementation in DelPhi.

The Gauss-Seidel (GS) method is a standard iterative numerical method widely used to solve a system of equations and, in general, is more efficient comparing to other iterative methods, such as the Jacobi method. However, standard implementation of the GS method restricts its utilization in parallel computing due to its requirement of using updated neighboring values (i.e., in current iteration) as soon as they are available. Here, we report an efficient and exact (not requiring assumptions) method to parallelize iterations and to reduce the computational time as a linear/nearly linear function of the number of processes or computing units. In contrast to other existing solutions, our method does not require any assumptions and is equally applicable for solving linear and nonlinear equations. This approach is implemented in the DelPhi program, which is a finite difference Poisson-Boltzmann equation solver to model electrostatics in molecular biology. This development makes the iterative procedure on obtaining the electrostatic potential distribution in the parallelized DelPhi several folds faster than that in the serial code. Further, we demonstrate the advantages of the new parallelized DelPhi by computing the electrostatic potential and the corresponding energies of large supramolecular structures.

The blueprint of the type-3 injectisome

Type-3 secretion systems are sophisticated syringe-like nanomachines present in many animal and plant Gram-negative pathogens. They are capable of translocating an arsenal of specific bacterial toxins (effector proteins) from the prokaryotic cytoplasm across the three biological membranes directly into the eukaryotic cytosol, some of which modulate host cell mechanisms for the benefit of the pathogen. They populate a particular biological niche, which is maintained by specific, pathogen-dependent effectors. In contrast, the needle complex, which is the central component of this specialized protein delivery machine, is structurally well-conserved. It is a large supramolecular cylindrical structure composed of multiple copies of a relatively small subset of proteins, is embedded in the bacterial membranes and protrudes from the pathogen's surface with a needle filament. A central channel traverses the entire needle complex, and serves as a hollow conduit for proteins destined to travel this secretion pathway. In the past few years, there has been a tremendous increase in an understanding on both the structural and the mechanistic level. This review will thus focus on new insights of this remarkable molecular machine.

New Parallelized DelPhi: Fast and Efficient Poisson-Boltzmann Solver to Calculate Electrostatics of Large Supramolecular Structures

Electrostatic potential in systems comprised of biological macromolecules and water phase is described by a 2nd order elliptic partial differential equation, known as the Poisson-Boltzmann equation (PBE). DelPhi is a PBE solver (http://compbio.clemson.edu/delphi.php) which adopts finite difference method to solve this equation numerically and has been widely recognized in the biological community due to its efficiency and accuracy. In this work, we introduce an efficient parallel computing technique via the unique implementation of Gauss-Seidel iteration method in DelPhi. The implementation allows for dynamics partitioning of the multiprocessing jobs by decision making algorithm which takes into account the available computing resources associated with a particular computer cluster. Further we demonstrate the advantages of the new parallelized DelPhi by computing the electrostatic potential and the corresponding energies of large supramolecular structures and molecular motors. The work is supported by NIH, NIGMS, grant number 1R01GM093937-01.

Atomic-resolution dynamics on the surface of amyloid-β protofibrils probed by solution NMR

Exchange dynamics between molecules free in solution and bound to the surface of a large supramolecular structure, a polymer, a membrane or solid support are important in many phenomena in biology and material science. Here we present a novel and generally applicable solution NMR technique, known as Dark-state Exchange Saturation Transfer (DEST), to probe such exchange phenomena with atomic resolution. This is illustrated by the exchange reaction between amyloid β (Aβ) monomers and polydisperse, NMR invisible ('dark') protofibrils, a process of significant interest since the accumulation of toxic, aggregated forms of Aβ, from small oligomers to very large assemblies, have been implicated in the etiology of Alzheimer's disease1–6. The 15N-DEST experiment imprints with single residue resolution dynamic information on the protofibril-bound species in the form of 15N transverse relaxation rates (15N-R2) and exchange kinetics between monomers and protofibrils onto the easily observed two-dimensional 1H-15N correlation spectrum of the monomer. The exchanging species on the protofibril surface comprise an ensemble of sparsely-populated states where each residue is either tethered to (via other residues) or in direct contact with the surface. The first eight residues exist predominantly in a mobile tethered state`, while the largely hydrophobic central region and part of the C-terminal hydrophobic region are in direct contact with the protofibril surface for a significant proportion of the time. The C-terminal residues of both Aβ40 and Aβ42 display lower affinity for the protofibril surface indicating that they are likely to be surface exposed rather than buried as in structures of Aβ fibrils7–10, and may therefore comprise the critical nucleus for fibril formation11,12. The values, however, are significantly larger for the C-terminal residues of Aβ42 than Aβ40 which may explain the former’s higher propensity for rapid aggregation and fibril formation13,14.

Influence of solvent on the thermal stability and organization of self-assembling fibrillar networks in methyl-4,6- O-( p-nitrobenzylidene)-α- d-glucopyranoside gels

Sugar based low-molecular-mass organogelator (LMOG) methyl-4,6- O-( p-nitrobenzylidene)-α- d-glucopyranoside, is a unique gelator because its small and weakly-interacting molecules can form large supramolecular structures in nonpolar, but also in polar, solvents and cause their gelation. The self-assembling properties of the gelator were studied in selected nonpolar and polar solvents. It was shown that the driving forces for both types of solvent are the intermolecular hydrogen bond interaction. The effect of the nature of the solvent on the thermal stability of the gels and on the three-dimensional network organization was determined. Different solvent parameters, such as dielectric constant, one-component solubility parameter, the polarity parameter and the Kamlet–Taft parameters were considered to quantify solvent effects on the gelation. Some correlation between these parameters and the gel stability, microstructure and the enthalpy of the phase transition were established. The effort to correlate the Kamlet–Taft parameters to the thermal stability and gelation ability is also possible but applies only to the studied gelator.

Cardiolipin Affects the Supramolecular Organization of ATP Synthase in Mitochondria

F 1F 0 ATP synthase forms dimers that tend to assemble into large supramolecular structures. We show that the presence of cardiolipin is critical for the degree of oligomerization and the degree of order in these ATP synthase assemblies. This conclusion was drawn from the statistical analysis of cryoelectron tomograms of cristae vesicles isolated from Drosophila flight-muscle mitochondria, which are very rich in ATP synthase. Our study included a wild-type control, a cardiolipin synthase mutant with nearly complete loss of cardiolipin, and a tafazzin mutant with reduced cardiolipin levels. In the wild-type, the high-curvature edge of crista vesicles was densely populated with ATP synthase molecules that were typically organized in one or two rows of dimers. In both mutants, the density of ATP synthase was reduced at the high-curvature zone despite unchanged expression levels. Compared to the wild-type, dimer rows were less extended in the mutants and there was more scatter in the orientation of dimers. These data suggest that cardiolipin promotes the ribbonlike assembly of ATP synthase dimers and thus affects lateral organization and morphology of the crista membrane.

αS1-casein, which is essential for efficient ER-to-Golgi casein transport, is also present in a tightly membrane-associated form

BackgroundCaseins, the main milk proteins, aggregate in the secretory pathway of mammary epithelial cells into large supramolecular structures, casein micelles. The role of individual caseins in this process and the mesostructure of the casein micelle are poorly known.ResultsIn this study, we investigate primary steps of casein micelle formation in rough endoplasmic reticulum-derived vesicles prepared from rat or goat mammary tissues. The majority of both αS1- and β-casein which are cysteine-containing casein was dimeric in the endoplasmic reticulum. Saponin permeabilisation of microsomal membranes in physico-chemical conditions believed to conserve casein interactions demonstrated that rat immature β-casein is weakly aggregated in the endoplasmic reticulum. In striking contrast, a large proportion of immature αS1-casein was recovered in permeabilised microsomes when incubated in conservative conditions. Furthermore, a substantial amount of αS1-casein remained associated with microsomal or post-ER membranes after saponin permeabilisation in non-conservative conditions or carbonate extraction at pH11, all in the presence of DTT. Finally, we show that protein dimerisation via disulfide bond is involved in the interaction of αS1-casein with membranes.ConclusionsThese experiments reveal for the first time the existence of a membrane-associated form of αS1-casein in the endoplasmic reticulum and in more distal compartments of the secretory pathway of mammary epithelial cells. Our data suggest that αS1-casein, which is required for efficient export of the other caseins from the endoplasmic reticulum, plays a key role in early steps of casein micelle biogenesis and casein transport in the secretory pathway.

Hierarchical Self-Assembly on Silicon

A set of modular components was designed, synthesized, and combined to yield an innovative, robust, and reliable methodology for the self-assembly of large supramolecular structures on silicon wafers. Specific host-guest and H-bonding motifs were embedded in a single molecule by exploiting the remarkable complexing properties of tetraphosphonate cavitands toward methylammonium and methylpyridinium salts and the outstanding homo- and hetero-dimerization capability of the ureidopyrimidone moiety. An assembly/disassembly sequence in solution was devised to assess the orthogonality and reversibility of H-bonding and host-guest interactions. The entire process was fully tested and characterized in solution and then successfully transferred to the solid state. The selected binding motifs resulted to be fully compatible in the assembly mode and individually addressable in the disassembly mode. The complete orthogonality of the two interactions allows the molecular level control of each step of the solid-state assembly and the predictable response to precise external stimuli. Complementary surface analysis techniques, such as atomic force microscopy (AFM), ellipsometry, and fluorescence, provided the univocal characterization of the realized structures in the solid state.

Tetraspanins and intercellular interactions.

The superfamily of tetraspanins comprises a group of polypeptides with four transmembrane domains that form large supramolecular structures in the plasma membrane through their associations to multiple integral membrane proteins. They are involved in homo- and heterotypic intercellular interactions in different processes such as hematopoiesis, lymphocyte activation, cancer metastasis, and fertilization. Intercellularly located tetraspanins regulate the juxtacrine activity of growth factors, cell fusion, and myelin formation. On the other hand, in motile cells they relocalize from cell-cell junctions to actin-based structures such as filopodia or growth cones and regulate cell motility in wound healing and angiogenesis processes.

Inter- and intramolecular contacts in a membrane protein/surfactant complex observed by heteronuclear dipole-to-dipole cross-relaxation

Heteronuclear dipole-to-dipole cross-relaxation has been applied to exploring intermolecular interactions and intramolecular spatial proximities in a large supramolecular structure comprised of a β-barrel membrane protein, OmpX, in complex with a polymeric surfactant, amphipol A8-35. The experiments, performed in either the laboratory or the rotating frame, reveal the existence of intermolecular contacts between aromatic amino acids and specific groups of the polymer, in addition to intra-protein dipolar interactions, some of them involving carbonyl carbons. This study opens the perspective of collecting by NMR spectroscopy a new kind of through-space structural information involving aromatic and carbonyl 13C atoms of large proteins.

Organocuprate Conjugate Addition: Structural Features of Diastereomeric and Supramolecular π-Intermediates

In the reaction pathway of conjugate additions with organocuprate reagents, Cu(I) pi-complexes and Cu(III) sigma-complexes have been identified as central, NMR-detectable intermediate species. However, no experimental evidence for the structures of pi-intermediates with extensive chiral enones or the principal aggregation level and aggregate structure of pi-complexes in diethyl ether has been available so far. Furthermore, the structural characteristics of pi-complexes which are essential for their high reactivities and diastereoselectivities have not yet been rationalized experimentally. Therefore, the pi-intermediates of 4,4a,5,6,7,8-hexahydro-4a-methyl-naphthalen-2(3H)-one and Me2CuLi or Me2CuLi x LiX (X = I, CN) in diethyl ether are investigated in detail. For the first time, the formation of two intermediate cuprate enone pi-complexes on both sides of the double bond is observed. In addition, the conformation of the enone adopted in the major beta-face pi-complex rationalizes the exclusive syn addition observed in the synthetic product. For the investigation of the aggregation level and structure, a NMR screening of pi-complexes with Me2CuLi x LiX (X = I, CN) and three achiral enones is performed, which simplifies the spectra by the generation of enantiotopic pi-complexes. Thus, NMR diffusion experiments on cuprate intermediates and the detection of scalar couplings across copper without isotope labeling are possible for the first time. Extensive NMR studies, including those of cyclohexanone complexes, show that, in principle, salt-free dimethylcuprate is able to complex the carbonyl group. However, in the presence of salt, the carbonyl-complexing aggregates are composed of salt and cuprate moieties. These mixed aggregates cause the formation of large supramolecular pi-intermediate structures which control their reactivity. The pi-complexing cuprate units show a bent geometry as a general structural feature that is unaffected by the presence or kind of salt and the type of enone. Thus, the high diastereoselectivity and the reactivity of organocuprate 1,4-addition reactions are for the first time rationalized on the basis of structural characteristics of selected pi-intermediates.

Cell-free protein synthesis of perdeuterated proteins for NMR studies

Cell-free protein synthesis protocols for uniformly deuterated proteins typically yield low, non-uniform deuteration levels. This paper introduces an E. coli cell-extract, D-S30, which enables efficient production of proteins with high deuteration levels for all non-labile hydrogen atom positions. Potential applications of the new protocol may include production of proteins with selective isotope-labeling of selected amino acid residues on a perdeuterated background for studies of enzyme active sites or for ligand screening in drug discovery projects, as well as the synthesis of perdeuterated polypeptides for NMR spectroscopy with large supra-molecular structures. As an illustration, it is demonstrated that the 800-kDa chaperonine GroEL synthesized with the D-S30 cell-free system had a uniform deuteration level of about 95% and assembled into its biologically active oligomeric form.

Slow Relaxation Mode in Mixtures of Water and Organic Molecules: Supramolecular Structures or Nanobubbles?

Aqueous solutions of tetrahydrofuran, ethanol, urea, and alpha-cyclodextrin were studied by a combination of static and dynamic laser light scattering (LLS). In textbooks, these small organic molecules are soluble in water so that there should be no observable large structures or density fluctuation in either static or dynamic LLS. However, a slow mode has been consistently observed in these aqueous solutions in dynamic LLS. Such a slow mode was previously attributed to some large complexes or supramolecular structures formed between water and these small organic molecules. Our current study reveals that it is actually due to the existence of small bubbles ( approximately 100 nm in diameter) formed inside these solutions. Our direct evidence comes from the fact that it can be removed by repeated filtration and regenerated by air injection. Our results also indicate that the formation of such nanobubbles in small organic molecule aqueous solutions is a universal phenomenon. Such formed nanobubbles are rather stable. The measurement of isothermal compressibility confirms the existence of a low density microphase, presumably nanobubbles, in these aqueous solutions. Using a proposed structural model, that is, each bubble is stabilized by small organic molecules adsorbed at the gas/water interface, we have, for the first time, estimated the pressure inside these nanobubbles.

A visual approach to proteomics

Cryo-electron tomography is an emerging imaging technique that has unique potential for molecular cell biology. At the present resolution of 4-5 nm, large supramolecular structures can be studied in unperturbed cellular environments and, in the future, it will become possible to map molecular landscapes inside cells in a more comprehensive manner. 'Visual proteomics' aims to complement and extend mass-spectrometry-based inventories, and to provide a quantitative description of the macromolecular interactions that underlie cellular functions.