Neoglycolipids Micelle-like Structures as a Basis for Drug Delivery Systems

Targeted drug delivery is one of the most promising tasks of nanomedicine, as this is a real way to increase the effectiveness of therapeutic effects against many diseases. In this regard, the development of new inexpensive highly effective stimulating and non-immunogenic drug delivery systems (DDS) is of great importance. In this work new molecular candidates were proposed and studied for the creation of such systems based on the use of new compounds, neoglycolipids. It is shown that these compounds are capable of self-association in aqueous solutions and can serve as potential carriers of drug compounds with targeted delivery determined by their terminal groups (in particular, glycans). The processes of their associates formation and features of their structure are investigated. The results show that these selforganizing nanoscale systems can be used as a basis for developing new drug delivery systems. Keywords: neoglycolipids, micelle-like structures, small-angle X-ray scattering, molecular dynamics simulatio

Application of PCR-based approaches for evaluation of cell-free DNA fragmentation in colorectal cancer

Cell-free DNA (cfDNA) testing is the core of most liquid biopsy assays. In particular, cfDNA fragmentation features could facilitate non-invasive cancer detection due to their interconnection with tumor-specific epigenetic alterations. However, the final cfDNA fragmentation profile in a purified sample is the result of a complex interplay between informative biological and artificial technical factors. In this work, we use ddPCR to study cfDNA lengths in colorectal cancer patients and observe shorter and more variable cfDNA fragments in accessible chromatin loci compared to the densely packed pericentromeric region. We also report a convenient qPCR system suitable for screening cfDNA samples for artificial high molecular weight DNA contamination

Objective Criteria for Estimation of Initial Parameters for the Modeling of Micelle and Liposome Structures from Small-Angle X-ray Scattering Data

The structures of hydrophobic membrane proteins are studied using matrices, which serve as models of cell membranes and are formed by the appropriate amphiphilic molecules, e.g., by surfactant or lipid molecules. To study the structure of a protein incorporated into an artificial membrane, first of all it is necessary to determine the structure of the membrane. The ELLLIP and ELLMIC algorithms were previously developed to address this issue by small-angle X-ray scattering. These algorithms allow the construction of models of ellipsoidal vesicles based on the atomic structure of a lipid or surfactant monomer. However, the results of modeling depend, to a large extent, on the subjective assessment of the initial values of the structural parameters of the matrices and may be wrong due to the ambiguity in the solution of such problems. Here, we present an independent approach to the determination of the initial sizes of model membranes for their subsequent structural modeling, which is based on the analysis of the pair-distance distribution functions derived directly from the small-angle X-ray scattering curve

Small-Angle X-ray Scattering Study of Changes in the Quaternary Structure of Nucleotide-Regulated Pyrophosphatase from Desulfitobacterium hafniense upon Ligand Binding in Solution

The regulation of nucleotide-regulated inorganic pyrophosphatases at a molecular level has been extensively studied in order to establish the mechanism of signal transduction between the active and regulatory sites of these enzymes. However, this issue cannot be ultimately addressed because of the lack of reliable structural data on the full-length protein and its interactions with ligands. The low-resolution structure of nucleotide-regulated pyrophosphatase from Desulfitobacterium hafniense was determined for the first time by small-angle X-ray scattering. The structural changes in the full-length enzyme upon binding of adenosine monophosphate and diadenosine tetraphosphate were revealed. In dilute solutions the protein was found to exist as a stable homotetramer, the structure of which depends on the nature of the bound ligand. The structural data are important for an understanding of the molecular basis for regulation of this family of enzymes

The Ambiguity Issue in Solving Inverse Problems of Small-Angle Scattering: A Consistent Approach Using an Insulin Receptor-Related Receptor as an Example. Methods for Interpreting SAXS Data

The construction of three-dimensional models of protein macromolecules is a serious challenge due to the possible ambiguity of solving the inverse problem of reconstructing a three-dimensional structure from a one-dimensional small-angle scattering profile. The target function of this task can have several local minima, which leads to the dependence of the solution on the initial values of the model parameters and on the method of finding the global minimum. The problem of creating structural models is also complicated by averaging the scattering pattern over all orientations of particles in space and by the size and shape distribution of scattering objects in the case of polydispersity and/or polymorphism. In this study, the issue of ambiguity in solving inverse problems and restoring the three-dimensional structure of a protein is considered using the structure of the ectodomain of an insulin receptor-related receptor (ectoIRR) in solution as an example. The paper presents a consistent approach to solving this problem, starting from the determination of general structural parameters and ab initio reconstruction of shape to modeling by rigid bodies (using molecular tectonics), hybrid methods, and analysis of scattering profiles by singular vector decomposition

Effect of Buffer Composition on Conformational Flexibility of N-Terminal Fragments of Dps and the Nature of Interactions with DNA. Small-Angle X-Ray Scattering Study

The DNA-binding protein Dps plays a key role in the formation of Dps–DNA crystalline arrays in living bacterial cells, which allows bacteria to survive under stress conditions and under the influence of various adverse factors. Such genome-protective mechanisms can lead to the emergence of bacterial resistance to antibiotics and other drugs. Elucidation of the fundamental biochemical, genetic, and structural basis of the resistance is of primary importance for the development of strategies for combating and preventing bacterial resistance, as well as the elaboration of innovative therapeutic approaches. Conformational characteristics of Dps and its N-terminal fragments responsible for the nature of interactions of this protein with DNA in solution were studied by small-angle scattering

Characterization of Tobacco Mosaic Virus Virions and Repolymerized Coat Protein Aggregates in Solution by Small-Angle X-Ray Scattering

The structure of tobacco mosaic virus (TMV) virions and stacked disk aggregates of TMV coat protein (CP) in solution was analyzed by synchrotron-based small-angle X-ray scattering (SAXS) and negative contrast transmission electron microscopy (TEM). TMV CP aggregates had a unique stability but did not have helical symmetry. According to the TEM data, they were stacked disks associated into transversely striated rod-shaped structures 300 to 800 Å long. According to modeling based on the crystallographic model of the 4-layer TMV CP aggregate (PDB: 1EI7), the stacked disks represented hollow cylinders. The calculated SAXS pattern for the disks was compared to the experimental one over the entire measured range. The best correlation with the SAXS data was found for the model with the repeating central pair of discs; the SAXS curves for the stacked disks were virtually identical irrespectively of the protein isolation method. The positions of maxima on the scatter curves could be used as characteristic features of the studied samples; some of the peaks were assigned to the existing elements of the quaternary structure (periodicity of aggregate structure, virion helix pitch). Low-resolution structural data for the repolymerized TMV CP aggregates in solution under conditions similar to natural were produced for the first time. Analysis of such nano-size objects is essential for their application in biomedicine and biotechnology