Small angle X-ray scattering studies and modeling of Eudistylia vancouverii chlorocruorin and Macrobdella decora hemoglobin

Aggregation induced emission of a new naphthyridine-ethynyl-gold(i) complex as a potential tool for sensing guanosine nucleotides in aqueous media

A new organometallic alkynyl-gold(i) complex capable of exhibiting aggregation induced emission was designed and synthesized. The linear complex structure possesses a central Au(i) atom, bearing two axial ligands: (1) 1,3,5-triaza-7-phosphaadamantane and (2) 2-acetamido-7-ethynyl-1,8-naphthyridine. While the former accounts for its partial solubility in an aqueous environment, the latter acts as a receptor unit for binding guanosine nucleotides and derivatives via multiple hydrogen bonding interactions. At high concentrations, aggregation of the complex was observed by the formation of new absorption (λ_max∼ 400 nm) and emission bands (550-700 nm). Formation of aggregates of ca. 60 nm diameter was confirmed by Small Angle X-ray Scattering (SAXS). Disruption of the aggregates in the presence of guanosine derivatives resulted in a ratiometric signal with apparent association constants in the order of 10⁵ M^-1 and high sensitivity (around 63% signal change) which are, to the best of our knowledge, in line with the highest values recorded for nucleotide sensors based on hydrogen bonding and capable of working in water. Computational studies indicate the presence of additional hydrogen bonding interactions that account for the strong binding of the Au(i) complex to phosphorylated guanosine nucleotides.

Preparation and Antitumoral Activity of Au-Based Inorganic-Organometallic Nanocomposites

The synergy between gelator molecules and nanostructured materials is currently a novel matter of study. The possibility to carefully design the skeleton of the molecular entity as well as the nanostructure's morphological and chemical features offers the possibility to prepare a huge variety of nanocomposites with properties potentially different than just the sum of those of the individual building blocks. Here we describe the synthesis and characterization of nanocomposites made by the unconventional combination of phosphine-Au(I)-alkynyl-based organometallic gelating molecules and plasmonic Au nanoparticles. Our results indicate that the interaction between the two moieties leads to a significant degree of aggregation in both hydrophilic and hydrophobic media, either when using DAPTA or PTA-based organometallic molecules, with the formation of a sponge-like hybrid powder upon solvent evaporation. The biological activity of the nanocomposites was assessed, suggesting the existence of a synergetic effect evidenced by the higher cytotoxicity of the hybrid systems with respect to that of any of their isolated counterparts. These results represent a preliminary proof-of-concept for the exploitation of these novel nanocomposites in the biomedical field.

Supramolecular tripodal Au(i) assemblies in water. Interactions with a pyrene fluorescent probe

The synthesis of three gold(i) tripodal complexes derived from tripropargylamine and containing the water soluble phosphines PTA (1,3,5-triaza-7-phosphaadamantane), DAPTA (3,7-diacetyl-1,3,7-triaza-5-phosphabicyclo[3.3.1]nonane) and TPPTS (triphenylphosfine-3,3′,3′′-trisulfonic acid trisodium salt) is described here.

Crystallization and preliminary structural analysis of the giant haemoglobin from Glossoscolex paulistus at 3.2 Å

Glossoscolex paulistus is a free-living earthworm encountered in south-east Brazil. Its oxygen transport requirements are undertaken by a giant extracellular haemoglobin, or erythrocruorin (HbGp), which has an approximate molecular mass of 3.6 MDa and, by analogy with its homologue from Lumbricus terrestris (HbLt), is believed to be composed of a total of 180 polypeptide chains. In the present work the full 3.6 MDa particle in its cyanomet state was purified and crystallized using sodium citrate or PEG8000 as precipitant. The crystals contain one-quarter of the full particle in the asymmetric unit of the I222 cell and have parameters of a = 270.8 Å, b = 320.3 Å and c = 332.4 Å. Diffraction data were collected to 3.15 Å using synchrotron radiation on beamline X29A at the Brookhaven National Laboratory and represent the highest resolution data described to date for similar erythrocruorins. The structure was solved by molecular replacement using a search model corresponding to one-twelfth of its homologue from HbLt. This revealed that HbGp belongs to the type I class of erythrocruorins and provided an interpretable initial electron density map in which many features including the haem groups and disulfide bonds could be identified.

X-ray solution scattering (SAXS) combined with crystallography and computation: defining accurate macromolecular structures, conformations and assemblies in solution

Crystallography supplies unparalleled detail on structural information critical for mechanistic analyses; however, it is restricted to describing low energy conformations of macromolecules within crystal lattices. Small angle X-ray scattering (SAXS) offers complementary information about macromolecular folding, unfolding, aggregation, extended conformations, flexibly linked domains, shape, conformation, and assembly state in solution, albeit at the lower resolution range of about 50 A to 10 A resolution, but without the size limitations inherent in NMR and electron microscopy studies. Together these techniques can allow multi-scale modeling to create complete and accurate images of macromolecules for modeling allosteric mechanisms, supramolecular complexes, and dynamic molecular machines acting in diverse processes ranging from eukaryotic DNA replication, recombination and repair to microbial membrane secretion and assembly systems. This review addresses both theoretical and practical concepts, concerns and considerations for using these techniques in conjunction with computational methods to productively combine solution scattering data with high-resolution structures. Detailed aspects of SAXS experimental results are considered with a focus on data interpretation tools suitable to model protein and nucleic acid macromolecular structures, including membrane protein, RNA, DNA, and protein-nucleic acid complexes. The methods discussed provide the basis to examine molecular interactions in solution and to study macromolecular flexibility and conformational changes that have become increasingly relevant for accurate understanding, simulation, and prediction of mechanisms in structural cell biology and nanotechnology.

Modeling complex biological macromolecules: reduction of multibead models

The shape of simple and complex biological macromolecules can be approximated by bead modeling procedures. Such approaches are required, for example, for the analysis of the scattering and hydrodynamic behavior of the models under analysis and the prediction of their molecular properties. Using the atomic coordinates of proteins for modeling inevitably leads to models composed of a multitude of beads. In particular, for hydrodynamic modeling, a drastic reduction of the bead number may become unavoidable to enable computation. A systematic investigation of different approaches and computation modes shows that the 'running mean', 'cubic grid,' and 'hexagonal grid' approaches are successful, provided that the extent of reduction does not exceed a factor of 100 and the grid approaches use beads of unequal size and the beads are located at the centers of gravity. Further precautions to be taken include usage of appropriate interaction tensors for overlapping beads of unequal size and appropriate volume corrections when calculating intrinsic viscosities. The applied procedures were tested with the small protein lysozyme in a case study and were then applied to the huge capsid of the phage fr and its trimeric building block. The appearance of the models and the agreement of molecular properties and distance distribution functions of unreduced and reduced models can be used as evaluation criteria.

Conformational analysis of the leukocyte-specific EF-hand protein p65/L-plastin by X-ray scattering in solution

p65/L-Plastin is a leukocyte-specific EF-hand protein which plays a vital role in organizing the actin cytoskeleton. Since its overall structural information has been largely unknown, we employed the X-ray scattering technique to elucidate the structure. Kratky plots of p65/L-plastin showed one peak, indicating that the protein takes compact globular conformations. The radii of gyration (Rg) of the monomer p65/L-plastin estimated from Guinier plots were 27.5 +/- 0.5 A and 28.6 A in the absence and presence of Ca(2+), respectively. The distance distribution function P(r) gave single peaks at 31.5-32.3 A and 33 A in the absence and presence of Ca(2+), respectively. These indicate that p65/L-plastin becomes somewhat larger in the presence of Ca(2+). The molecular shape of p65/L-plastin reconstructed from X-ray scattering data using the DAMMIN program has provided the first view of the overall structure of full-length plastin/fimbrin family proteins: a compact horseshoe-like shape with a small projection, which also exhibits Ca(2+) -induced conformational changes.