SAXS, DLS, and MD studies of the Rg/Rh ratio for swollen and collapsed dendrimers.

The radius of gyration, Rg, and the hydrodynamic radius, Rh, are the main experimental parameters that characterize the size of linear and branched macromolecules. In the case of dendrimers in solution, the ratio Rg/Rh, depending on the global conformation, varies from 1 (for a Gaussian soft sphere) to 3/5 (for a hard sphere). However, for high-generation dendrimers, this ratio may be less than the limiting value for a hard sphere.

Microfluidically Assisted Synthesis of Calcium Carbonate Submicron Particles with Improved Loading Properties.

The development of advanced methods for the synthesis of nano- and microparticles in the field of biomedicine is of high interest due to a range of reasons. The current synthesis methods may have limitations in terms of efficiency, scalability, and uniformity of the particles. Here, we investigate the synthesis of submicron calcium carbonate using a microfluidic chip with a T-shaped oil supply for droplet-based synthesis to facilitate control over the formation of submicron calcium carbonate particles.

Selection of Aptamers for Use as Molecular Probes in AFM Detection of Proteins.

Currently, there is great interest in the development of highly sensitive bioanalytical systems for diagnosing diseases at an early stage, when pathological biomarkers are present in biological fluids at low concentrations and there are no clinical manifestations. A promising direction is the use of molecular detectors-highly sensitive devices that detect signals from single biomacromolecules. A typical detector in this class is the atomic force microscope (AFM).

Microfluidic Vaterite Synthesis: Approaching the Nanoscale Particles.

The challenge of continuous CaCO particle synthesis is addressed using microfluidic technology. A custom microfluidic chip was used to synthesize CaCO nanoparticles in vaterite form. Our focus revolved around exploring one-phase and two-phase synthesis methods tailored for the crystallization of these nanoparticles.

Small-angle x-ray scattering investigation of the integration of free fatty acids in polysorbate 20 micelles.

A critical quality attribute for liquid formulations is the absence of visible particles. Such particles may form upon polysorbate hydrolysis resulting in release of free fatty acids into solution followed by precipitation. Strategies to avoid this effect are of major interest for the pharmaceutical industry.

Development of DNA aptamers for visualization of glial brain tumors and detection of circulating tumor cells.

Here, we present DNA aptamers capable of specific binding to glial tumor cells , , and for visualization diagnostics of central nervous system tumors. We selected the aptamers binding specifically to the postoperative human glial primary tumors and not to the healthy brain cells and meningioma, using a modified process of systematic evolution of ligands by exponential enrichment to cells; sequenced and analyzed ssDNA pools using bioinformatic tools and identified the best aptamers by their binding abilities; determined three-dimensional structures of lead aptamers (Gli-55 and Gli-233) with small-angle X-ray scattering and molecular modeling; isolated and identified molecular target proteins of the aptamers by mass spectrometry; the potential binding sites of Gli-233 to the target protein and the role of post-translational modifications were verified by molecular dynamics simulations. The anti-glioma aptamers Gli-233 and Gli-55 were used to detect circulating tumor cells in liquid biopsies.

NMR structure of emfourin, a novel protein metalloprotease inhibitor: Insights into the mechanism of action.

Emfourin (M4in) is a protein metalloprotease inhibitor recently discovered in the bacterium Serratia proteamaculans and the prototype of a new family of protein protease inhibitors with an unknown mechanism of action. Protealysin-like proteases (PLPs) of the thermolysin family are natural targets of emfourin-like inhibitors widespread in bacteria and known in archaea. The available data indicate the involvement of PLPs in interbacterial interaction as well as bacterial interaction with other organisms and likely in pathogenesis.

Local Flexibility of a New Single-Ring Chaperonin Encoded by Bacteriophage AR9 .

Chaperonins, a family of molecular chaperones, assist protein folding in all domains of life. They are classified into two groups: bacterial variants and those present in endosymbiotic organelles of eukaryotes belong to group I, while group II includes chaperonins from the cytosol of archaea and eukaryotes. Recently, chaperonins of a prospective new group were discovered in giant bacteriophages; however, structures have been determined for only two of them.

Untangling the Conformational Plasticity of V66M Human proBDNF Polymorphism as a Modifier of Psychiatric Disorder Susceptibility.

The human genetic variant BDNF (V66M) represents the first example of neurotrophin family member that has been linked to psychiatric disorders. In order to elucidate structural differences that account for the effects in cognitive function, this hproBDNF polymorph was expressed, refolded, purified, and compared directly to the WT variant for the first time for differences in their 3D structures by DSF, limited proteolysis, FT-IR, and SAXS measurements in solution. Our complementary studies revealed a deep impact of V66M polymorphism on hproBDNF conformations in solution.

The Cytoplasmic Tail of Influenza A Virus Hemagglutinin and Membrane Lipid Composition Change the Mode of M1 Protein Association with the Lipid Bilayer.

Influenza A virus envelope contains lipid molecules of the host cell and three integral viral proteins: major hemagglutinin, neuraminidase, and minor M2 protein. Membrane-associated M1 matrix protein is thought to interact with the lipid bilayer and cytoplasmic domains of integral viral proteins to form infectious virus progeny. We used small-angle X-ray scattering (SAXS) and complementary techniques to analyze the interactions of different components of the viral envelope with M1 matrix protein.

The USR domain of USF1 mediates NF-Y interactions and cooperative DNA binding.

The trimeric CCAAT-binding NF-Y is a "pioneer" Transcription Factor -TF- known to cooperate with neighboring TFs to regulate gene expression. Genome-wide analyses detected a precise stereo-alignment -10/12 bp- of CCAAT with E-box elements and corresponding colocalization of NF-Y with basic-Helix-Loop-Helix (bHLH) TFs. We dissected here NF-Y interactions with USF1 and MAX.

: expanded functionality and new tools for small-angle scattering data analysis.

The software suite encompasses a number of programs for the processing, visualization, analysis and modelling of small-angle scattering data, with a focus on the data measured from biological macromolecules. Here, new developments in the package are described. They include , for simulating isotropic 2D scattering patterns; , to perform operations on 2D images and masks; , a method for variance estimation of structural invariants through parametric resampling; , which computes the pair distance distribution function by a direct Fourier transform of the scattering data; , to compute the scattering data from a pair distance distribution function, allowing comparison with the experimental data; a new module in for Bayesian consensus-based concentration-independent molecular weight estimation; , an shape analysis method that optimizes the search model directly against the scattering data; , an application to set up the initial search volume for multiphase modelling of membrane proteins; , to perform quasi-atomistic modelling of liposomes with elliptical shapes; , which models conformational changes in nucleic acid structures through normal mode analysis in torsion angle space; , which reconstructs the shape of an unknown intermediate in an evolving system; and and , for modelling multilamellar and asymmetric lipid vesicles, respectively.

The protealysin operon encodes emfourin, a prototype of a novel family of protein metalloprotease inhibitors.

Protealysin is a Serratia proteamaculans metalloproteinase of the M4 peptidase family and the prototype of a large group of protealysin-like proteases (PLPs). PLPs are likely involved in bacterial interaction with plants and animals as well as in bacterial pathogenesis. We demonstrated that the PLP genes in bacteria colocalize with the genes of putative conserved proteins.

Capturing the Conformational Ensemble of the Mixed Folded Polyglutamine Protein Ataxin-3.

Ataxin-3 is a deubiquitinase involved in protein quality control and other essential cellular functions. It preferentially interacts with polyubiquitin chains of four or more units attached to proteins delivered to the ubiquitin-proteasome system. Ataxin-3 is composed of an N-terminal Josephin domain and a flexible C terminus that contains two or three ubiquitin-interacting motifs (UIMs) and a polyglutamine tract, which, when expanded beyond a threshold, leads to protein aggregation and misfolding and causes spinocerebellar ataxia type 3.

Synthesis and physico-chemical properties of poly(-vinyl pyrrolidone)-based hydrogels with titania nanoparticles.

Poly(-vinyl pyrrolidone) (PVP)-based hydrogels with titania nanoparticles (TN) were synthesized by the sol-gel method for the first time and were characterized in different states (native, freeze-dried, air-dried to constant weight and ground to powder, or swollen to constant weight in HO or DO) by various methods such as wide-angle and small-angle X-ray and neutron scattering, neutron spin-echo (NSE) spectroscopy, and scanning electron microscopy. The static (static polymer-polymer correlation length (mesh size), associates of cross-links and PVP microchains) and dynamic (polymer chain relaxation rate, hydrodynamic polymer-polymer correlation length) structural elements were determined. The incorporation of titania nanoparticles into PVP hydrogel slightly increases the size of structural inhomogeneities (an increase in the static and dynamic polymer-polymer correlation length, the formation of associates of cross-links and PVP chains).

Author Correction: Octa-repeat domain of the mammalian prion protein mRNA forms stable A-helical hairpin structure rather than G-quadruplexes.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Towards a solution of the inverse X-ray diffraction tomography challenge: theory and iterative algorithm for recovering the 3D displacement field function of Coulomb-type point defects in a crystal.

The theoretical framework and a joint quasi-Newton-Levenberg-Marquardt-simulated annealing (qNLMSA) algorithm are established to treat an inverse X-ray diffraction tomography (XRDT) problem for recovering the 3D displacement field function f(r - r) = h · u(r - r) due to a Coulomb-type point defect (Ctpd) located at a point r within a crystal [h is the diffraction vector and u(r - r) is the displacement vector]. The joint qNLMSA algorithm operates in a special sequence to optimize the XRDT target function {\cal F}\{ {\cal P} \} in a χ sense in order to recover the function f(r - r) [{\cal P} is the parameter vector that characterizes the 3D function f(r - r) in the algorithm search]. A theoretical framework based on the analytical solution of the Takagi-Taupin equations in the semi-kinematical approach is elaborated.

Dodecamers derived from the crystal structure were found in the pre-crystallization solution of the transaminase from the thermophilic bacterium by small-angle X-ray scattering.

The pre-crystallization solution of the transaminase from (TaTT) has been studied by small-angle X-ray scattering (SAXS). Regular changes in the oligomeric composition of the protein were observed after the addition of the precipitant. Comparison of the observed oligomers with the crystal structure of TaTT (PDB ID 6GKR) shows that dodecamers may act as building blocks in the growth of transaminase single crystals.

Octa-repeat domain of the mammalian prion protein mRNA forms stable A-helical hairpin structure rather than G-quadruplexes.

Misfolding and aggregation of prion protein (PrP) causes neurodegenerative diseases like Creutzfeldt-Jakob disease (CJD) and scrapie. Besides the consensus that spontaneous conversion of normal cellular PrP into misfolded and aggregating PrP is the central event in prion disease, an alternative hypothesis suggests the generation of pathological PrP by rare translational frameshifting events in the octa-repeat domain of the PrP mRNA. Ribosomal frameshifting most commonly relies on a slippery site and an adjacent stable RNA structure to stall translating ribosome.

Pre-crystallization phase formation of thermolysin hexamers in solution close to crystallization conditions.

Communicated by Ramaswamy H. Sarma.