Computational and NMR Conformational Analysis of Galactofuranoside Cycles Presented in Bacterial and Fungal Polysaccharide Antigens

Unlike pyranoside cycles which are generally characterized by strictly defined conformational preferences, furanosides are flexible and may adopt a wide range of available conformations. During our previous studies, conformational changes of galactofuranoside cycles upon total sulfation were described computationally, using a simple Hartree–Fock (HF) method, and principal conformers of the 5-membered galactose ring were revealed. However, in the case of more complex disaccharide structures, it was found that this method and the widely applied DFT-B3LYP produced results that deviated from experimental evidence. In this study, other DFT functionals (PBE0 and double hybrid B2PLYP) along with RI-MP2 are employed to study the conformational behavior of the galactofuranoside ring. Reinvestigation of galactofuranosides with a lactic acid substituent at O-3 revealed that changes in the orientation of lactic acid residue at O-3 might induce conformational changes of the furanoside cycle. Such findings are important for further modeling of carbohydrate–protein interaction.

Conformational Behavior, Topographical Features, and Antioxidant Activity of Partly De-Esterified Arabinoxylans

This study aimed to investigate the effect of arabinoxylans (AX) partial de-esterification with feruloyl esterase on the polysaccharide conformational behavior, topographical features, and antioxidant activity. After enzyme treatment, the ferulic acid (FA) content in AX was reduced from 7.30 to 5.48 µg FA/mg polysaccharide, and the molecule registered a small reduction in radius of gyration (RG), hydrodynamic radius (Rh), characteristic ratio (C∞), and persistence length (q). A slight decrease in α and a small increase in K constants in the Mark–Houwink–Sakurada equation for partially de-esterified AX (FAX) suggested a reduction in molecule structural rigidity and a more expanded coil conformation, respectively, in relation to AX. Fourier transform infrared spectroscopy spectra of AX and FAX presented a pattern characteristic for this polysaccharide. Atomic force microscopy topographic analysis of FAX showed a more regular surface without larger hollows in relation to AX. The antioxidant activity of FAX, compared to AX, was reduced by 30 and 41% using both 2,2′-azino-bis (3-ethylbenzothiazoline-6-sulphonic acid) (ABTS+) and 1,1-diphenyl-2-picryl-hydrazyl (DPPH) methods, respectively. These results suggest that feruloyl esterase treatment of AX could offer a strategy to tailor AX chains conformation, morphological features, and antioxidant activity, impacting the development of advanced biomaterials for biomedical and pharmaceutical applications.

High-throughput dissection of the thermodynamic and conformational properties of a ubiquitous class of RNA tertiary contact motifs

Despite RNA’s diverse secondary and tertiary structures and its complex conformational changes, nature utilizes a limited set of structural “motifs”—helices, junctions, and tertiary contact modules—to build diverse functional RNAs. Thus, in-depth descriptions of a relatively small universe of RNA motifs may lead to predictive models of RNA tertiary conformational landscapes. Motifs may have different properties depending on sequence and secondary structure, giving rise to subclasses that expand the universe of RNA building blocks. Yet we know very little about motif subclasses, given the challenges in mapping conformational properties in high throughput. Previously, we used “RNA on a massively parallel array” (RNA-MaP), a quantitative, high-throughput technique, to study thousands of helices and two-way junctions. Here, we adapt RNA-MaP to study the thermodynamic and conformational properties of tetraloop/tetraloop receptor (TL/TLR) tertiary contact motifs, analyzing 1,493 TLR sequences from different classes. Clustering analyses revealed variability in TL specificity, stability, and conformational behavior. Nevertheless, natural GAAA/11ntR TL/TLRs, while varying in tertiary stability by ∼2.5 kcal/mol, exhibited conserved TL specificity and conformational properties. Thus, RNAs may tune stability without altering the overall structure of these TL/TLRs. Furthermore, their stability correlated with natural frequency, suggesting thermodynamics as the dominant selection pressure. In contrast, other TL/TLRs displayed heterogenous conformational behavior and appear to not be under strong thermodynamic selection. Our results build toward a generalizable model of RNA-folding thermodynamics based on the properties of isolated motifs, and our characterized TL/TLR library can be used to engineer RNAs with predictable thermodynamic and conformational behavior.

Structural Studies Providing Insights into Production and Conformational Behavior of Amyloid-β Peptide Associated with Alzheimer’s Disease Development

Alzheimer’s disease is the most common type of neurodegenerative disease in the world. Genetic evidence strongly suggests that aberrant generation, aggregation, and/or clearance of neurotoxic amyloid-β peptides (Aβ) triggers the disease. Aβ accumulates at the points of contact of neurons in ordered cords and fibrils, forming the so-called senile plaques. Aβ isoforms of different lengths are found in healthy human brains regardless of age and appear to play a role in signaling pathways in the brain and to have neuroprotective properties at low concentrations. In recent years, different substances have been developed targeting Aβ production, aggregation, interaction with other molecules, and clearance, including peptide-based drugs. Aβ is a product of sequential cleavage of the membrane glycoprotein APP (amyloid precursor protein) by β- and γ-secretases. A number of familial mutations causing an early onset of the disease have been identified in the APP, especially in its transmembrane domain. The mutations are reported to influence the production, oligomerization, and conformational behavior of Aβ peptides. This review highlights the results of structural studies of the main proteins involved in Alzheimer’s disease pathogenesis and the molecular mechanisms by which perspective therapeutic substances can affect Aβ production and nucleation.

Protein O-Fucosyltransferase 1 Undergoes Interdomain Flexibility in Solution

Protein O-fucosyltransferase 1 (PoFUT1) is a GT-B fold enzyme that fucosylates proteins containing EGF-like repeats. GT-B glycosyltransferases have shown a remarkable grade of plasticity adopting closed and open conformations as a way of tuning their catalytic cycle, a feature that has not been observed for PoFUT1. Here, we analyzed Caenorhabditis elegans PoFUT1 (CePoFUT1) conformational behavior in solution by atomic force microscopy (AFM) and single-molecule fluorescence resonance energy transfer (SMF-FRET). Our results show that this enzyme is very flexible and adopts mainly compact conformations and to a lesser extend a highly dynamic population that oscillates between compact and highly extended conformations. Overall, our experiments illustrate the inherent complexity of CePoFUT1 dynamics, which might play a role during its catalytic cycle.

INFLUENCEOFCROSSLINKINGAGENTON ELECTROCHEMICAL AND CONFORMATIONAL BEHAVIOR OF MOLECULARLY IMPRINTED POLYMERS BASED ON METHACRYLIC ACID AND 4-VINYLPYRIDINE IN AN AQUEOUS MEDIUM

Molecularly imprinted polymers (MIPs) based on methacrylic acid (MAA) and 4-vinylpyridine (4VP) of two types have been synthesized (the difference in types is based on the use of ethylene glycol dimethacrylate (EGDMA) and diethylene glycol dimethacrylate (DEGDMA) as a crosslinking agent). Salts of cerium, praseodymium, neodymium, samarium, and europium were used as templates for the synthesis. Control samples of Molecularly imprinted polymers were also synthesized (samples synthesized in exactly the same way, but without the templates).Electrochemical and conformational behavior of the synthesized structures in an aqueous medium was studied. Molecularly imprinted polymers are weakly exposed to swelling and ionization due to tight crosslinking, while it should be noted that a high degree of crosslinking leads to high mechanical strength of macromolecular structures.Comparison of the measured parameters (electrical conductivity, pH) of molecularly imprinted polymers containing a template with control samples of MIP indicate the presence of cavities complementary to the template (rare-earth metal ion) used in their synthesis. In the presence of MIP synthesized in the presence of EGDMA (MIP-1) higher values of electrical conductivity and pH are observed as compared to MIP synthesized in the presence of DEGDMA (MIP-2) due to less tight crosslinking.