Search Results (4)

In this paper we present a detailed study of bonded knots and their related structures, integrating recent developments into a single framework. Bonded knots are classical knots endowed with embedded bonding arcs modeling physical or chemical bonds. We consider bonded knots in three categories (long, standard, and tight) according to the type of bonds, and in two categories, topological vertex and rigid vertex, according to the allowed isotopy moves, and we define invariants for each category. We then develop the theory of bonded braids, the algebraic counterpart of bonded knots. We define the bonded braid monoid, with its generators and relations, and formulate the analogues of the Alexander and Markov theorems for bonded braids in the form of L-equivalence for bonded braids. Next, we introduce enhanced bonded knots and braids, incorporating two types of bonds (attracting and repelling) corresponding to different interactions. We define the enhanced bonded braid group and show how the bonded braid monoid embeds into this group. These models capture the topology of chains with inter and intra-chain bonds and suggest new invariants for classifying biological macromolecules. Full article

Various reaction mechanisms for the catalytic degradation of formaldehyde (HCHO) remain to be debated. Density functional theory (DFT) was applied to investigate whether the catalytic oxidation of HCHO on pristine Co₃O₄ (110) surface follows the Mars-van Krevelen (MvK) mechanism or the Langmuir–Hinshelwood (L-H) mechanism. Firstly, HCHO and O₂ co-adsorb on the surface and two H atoms from HCHO are peculiarly prone to transfer to O₂, forming CO and HOOH. For the MvK mechanism, CO₂ is generated through CO grabbing a lattice oxygen. Meanwhile, the O–O bond of HOOH is broken into two OH groups. One OH fills the oxygen vacancy and its H atom moves to another OH group for H₂O formation. For the L-H mechanism, CO directly obtains one OH group to generate COOH. Subsequently, the H atom of COOH transfers to another OH group along with CO₂ and H₂O generation. Both two mechanisms exhibit a similar maximum activation barrier. The lattice oxygen in the MvK mechanism and the surface-absorbed OH group in the L-H mechanism are the key reactive oxygen species. The small difference in energetic span further suggests that the catalytic cycle through the two mechanisms is feasible. This theoretical study provides new insight into the catalytic reaction path of HCHO oxidation on pristine Co₃O₄ surface. Full article

Down regulation of the major histocompatibility class (MHC) I pathway plays an important role in tumour development, and can be achieved by suppression of HLA expression or mutations in the MHC peptide-binding pocket. The peptide-loading complex (PLC) loads peptides on the MHC-I molecule in a dynamic multi-step assembly process. The effects of cancer variants on ERp57 and tapasin components from the MHC-I pathway is less known, and they could have an impact on antigen presentation. Applying computational approaches, we analysed whether the ERp57-tapasin binding might be altered by missense mutations. The variants H408R(ERp57) and P96L, D100A, G183R(tapasin) at the protein–protein interface improved protein stability (ΔΔG) during the initial screen of 14 different variants. The H408R(ERp57) and P96L(tapasin) variants, located close to disulphide bonds, were further studied by molecular dynamics (MD). Identifying intramolecular a-a’ domain interactions, MD revealed open and closed conformations of ERp57 in the presence and absence of tapasin. In wild-type and mutant ERp57-tapasin complexes, residues Val97, Ser98, Tyr100, Trp405, Gly407(ERp57) and Asn94, Cys95, Arg97, Asp100(tapasin) formed common H-bond interactions. Moreover, comparing the H-bond networks for P96L and H408R with each other, suggests that P96L(tapasin) improved ERp57-tapasin binding more than the H408R(ERp57) mutant. During MD, the C-terminus domain (that binds MHC-I) in tapasin from the ERp57(H408R)-tapasin complex moved away from the PLC, whereas in the ERp57-tapasin(P96L) system was oppositely displaced. These findings can have implications for the function of PLC and, ultimately, for the presentation of MHC-I peptide complex on the tumour cell surface. Full article

Features of solute-solvent intermolecular interaction establishing hydrogen bonds were studied in view of proton sharing in the O---H⁺–O moiety that is the prerequisite for proton moving through water. Liquid microcrystals are expected to be formed due to the protons moving through water confined in their precursors. Among the different oxygen-containing organic solvents well-dissolved in water, tetrahydrofuran (THF) has been found the most suitable since it forms a molecular complex with carbon dioxide dissolved in water producing the ions H⁺ and (HCO₃)⁻. This three-component complex exhibits in infrared spectra vibrational bands characterizing the complex and the proton sharing in the O---H⁺–O moiety. Assemblies consisting of mono- protonated meso-tetraphenylporphine (TPP) dimers self-organized into submicroscopic particles in solution and water with 0.86 mol·L⁻¹ THF have been investigated by infrared spectroscopy, SEM, and AFM in thin layers. Earlier found tight water covering the submicroscopic particles is proved to exhibit an ordered and non-ordered local areas on the surface. Molecular characteristics estimated for the three-component complex involving THF suggest that the complex together with the TPP dimers partakes in the crystallization process providing protons moving through water. Full article