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In eukaryotic cells, membrane proteins play a crucial role. They fall into three categories: intrinsic proteins, extrinsic proteins, and proteins that are essential to the human genome (30% of which is devoted to encoding them). Hydrophobic interactions inside the membrane serve to stabilize integral proteins, which span the lipid bilayer. This review investigates a number of computational and experimental methods used to study membrane proteins. It encompasses a variety of technologies, including electrophoresis, X-ray crystallography, cryogenic electron microscopy (cryo-EM), nuclear magnetic resonance spectroscopy (NMR), biophysical methods, computational methods, and artificial intelligence. The link between structure and function of membrane proteins has been better understood thanks to these approaches, which also hold great promise for future study in the field. The significance of fusing artificial intelligence with experimental data to improve our comprehension of membrane protein biology is also covered in this paper. This effort aims to shed light on the complexity of membrane protein biology by investigating a variety of experimental and computational methods. Overall, the goal of this review is to emphasize how crucial it is to understand the functions of membrane proteins in eukaryotic cells. It gives a general review of the numerous methods used to look into these crucial elements and highlights the demand for multidisciplinary approaches to advance our understanding. [ABSTRACT FROM AUTHOR]

Twenty novel Mn, Fe, and Cu complexes of ethylene cross-bridged tetraazamacrocycles with potentially copolymerizable allyl and benzyl pendant arms were synthesized and characterized. Multiple X-ray crystal structures demonstrate the cis-folded pseudo-octahedral geometry forced by the rigidifying ethylene cross-bridge and show that two cis coordination cites are available for interaction with substrate and oxidant. The Cu complexes were used to determine kinetic stability under harsh acidic and high-temperature conditions, which revealed that the cyclam-based ligands provide superior stabilization with half-lives of many minutes or even hours in 5 M HCl at 50–90 °C. Cyclic voltammetry studies of the Fe and Mn complexes reveal reversible redox processes indicating stabilization of Fe2+/Fe3+ and Mn2+/Mn3+/Mn4+ oxidation states, indicating the likelihood of catalytic oxidation for these complexes. Finally, dye-bleaching experiments with methylene blue, methyl orange, and rhodamine B demonstrate efficient catalytic decolorization and allow selection of the most successful monomeric catalysts for copolymerization to produce future heterogeneous water purification materials. [ABSTRACT FROM AUTHOR]

Toxic heavy metals are priority pollutants in wastewater, commonly present in dangerous concentrations in many places across the globe. Although in trace quantities copper is a heavy metal essential to human life, in excess it causes various diseases, whereby its removal from wastewater is a necessity. Among several reported materials, chitosan is a highly abundant, non-toxic, low-cost, biodegradable polymer, comprising free hydroxyl and amino groups, that has been directly applied as an adsorbent or chemically modified to increase its performance. Taking this into account, reduced chitosan derivatives (RCDs 1–4) were synthesised by chitosan modification with salicylaldehyde, followed by imine reduction, characterised by RMN, FTIR-ATR, TGA and SEM, and used to adsorb Cu(II) from water. A reduced chitosan (RCD3), with a moderate modification percentage (43%) and a high imine reduction percentage (98%), proved to be more efficient than the remainder RCDs and even chitosan, especially at low concentrations under the best adsorption conditions (pH 4, RS/L = 2.5 mg mL−1). RCD3 adsorption data were better described by the Langmuir–Freundlich isotherm and the pseudo-second-order kinetic models. The interaction mechanism was assessed by molecular dynamics simulations, showing that RCDs favour Cu(II) capture from water compared to chitosan, due to a greater Cu(II) interaction with the oxygen of the glucosamine ring and the neighbouring hydroxyl groups. [ABSTRACT FROM AUTHOR]

Despite numerous studies investigating histamine and its receptors, the impact of histamine protonation states on binding to the histamine H 1 -receptor (H 1 R) has remained elusive. Therefore, we assessed the influence of different histamine tautomers (τ -tautomer, π -tautomer) and charge states (mono- vs. dicationic) on the interaction with the ternary histamine-H 1 R-Gq complex. In atomistic molecular dynamics simulations, the τ -tautomer formed stable interactions with the receptor, while the π -tautomer induced a rotation of the histamine ring by 180° and formed only weaker hydrogen bonding interactions. This suggests that the τ -tautomer is more relevant for stabilization of the active ternary histamine-H 1 R-Gq complex. In addition to the two monocationic tautomers, the binding of dicationic histamine was investigated, whose interaction with the H 1 R had been observed in a previous experimental study. Our simulations showed that the dication is less compatible with the ternary histamine-H 1 R-Gq complex and rather induces an inactive conformation in the absence of the Gq protein. Our data thus indicate that the charge state of histamine critically affects its interactions with the H 1 R. Ultimately these findings might have implications for the future development of new ligands that stabilize distinct H 1 R activation states. [ABSTRACT FROM AUTHOR]

Tetraazamacrocycles, cyclic molecules with four nitrogen atoms, have long been known to produce highly stable transition metal complexes. Cross-bridging such molecules with two-carbon chains has been shown to enhance the stability of these complexes even further. This provides enough stability to use the resulting compounds in applications as diverse and demanding as aqueous, green oxidation catalysis all the way to drug molecules injected into humans. Although the stability of these compounds is believed to result from the increased rigidity and topological complexity imparted by the cross-bridge, there is insufficient experimental data to exclude other causes. In this study, standard organic and inorganic synthetic methods were used to produce unbridged dibenzyl tetraazamacrocycle complexes of Co, Ni, Cu, and Zn that are analogues of known cross-bridged tetraazamacrocycles and their transition metal complexes to allow direct comparison of molecules that are identical except for the cross-bridge. The syntheses of the known tetraazamacrocycles and the new transition metal complexes were successful with high yields and purity. Initial chemical characterization of the complexes was conducted by UV-Visible spectroscopy, while cyclic voltammetry showed more marked differences in electronic properties from bridged versions. Direct comparison studies of the unbridged and bridged compounds' kinetic stabilities, as demonstrated by decomposition using high acid concentration and elevated temperature, showed that the cyclen-based complex stability did not benefit from cross-bridging. This is likely due to poor complementarity with the Cu2+ ion while cyclam-based complexes benefited greatly. We conclude that ligand–metal complementarity must be maintained in order for the topological and rigidity constraints imparted by the cross-bridge to contribute significantly to complex robustness. [ABSTRACT FROM AUTHOR]

Interaction of β-D-glucopyranuronic acid (GlcA), N-acetyl-β-D-glucosamine (GlcNAc), N-acetyl-β-D-galactosamine (GalNAc) and two natural decameric glycosaminoglycans, hyaluronic acid (HA) and Chondroitin (Ch) with carboxylated carbon nanotubes, were studied using molecular dynamics simulations in a condensed phase. The force field used for carbohydrates was the GLYCAM-06j version, while functionalized carbon nanotubes (fCNT) were described using version two of the general amber force field. We found a series of significant differences in carbohydrate-fCNT adsorption strength depending on the monosaccharide molecule and protonation state of surface carboxyl groups. GlcNAc and GalNAc reveal a strong adsorption on fCNT with deprotonated carboxyl groups, and a slightly weaker adsorption on the fCNT with protonated carboxyl groups. On the contrary, GlcA weakly adsorbs on fCNT. The change in protonation state of surface carboxyl groups leads to the reversal orientation of GlcNAc and GalNAc in reference to the fCNT surface, while GlcA is not sensitive to that factor. Adsorption of decameric oligomers on the surface of fCNT weakens with the increasing number of monosaccharide units. Chondroitin adsorbs weaker than hyaluronic acid and incorporation of four Ch molecules leads to partial detachment of them from the fCNT surface. The glycan–fCNT interactions are strong enough to alter the conformation of carbohydrate backbone; the corresponding conformational changes act toward a more intensive contact of glycan with the fCNT surface. Structural and energetic features of the adsorption process suggest the CH-π interaction-driven mechanism. [ABSTRACT FROM AUTHOR]

Cytosine-rich DNA sequences are able to fold into noncanonical structures, in which semi-protonated cytosine pairs develop extra hydrogen bonds, and these bonds are responsible for the overall stability of a structure called the i-motif. The i-motif can be formed in many regions of the genome, but the most representative is the telomeric region in which the CCCTAA sequences are repeated thousands of times. The ability to reverse folding/unfolding in response to pH change makes the above sequence and i-motif very promising components of nanomachines, extended DNA structures, and drug carriers. Molecular dynamics analysis of such structures is highly beneficial due to direct insights into the microscopic structure of the considered systems. We show that Amber force fields for DNA predict the stability of the i-motif over a long timescale; however, these force fields are not able to predict folding of the cytosine-rich sequences into the i-motif. The reason is the kinetic partitioning of the folding process, which makes the transitions between various intermediates too time-consuming in atomistic force field representation. Application of coarse-grained force fields usually highly accelerates complex structural transitions. We, however, found that three of the most popular coarse-grained force fields for DNA (oxDNA, 3SPN, and Martini) were not able to predict the stability of the i-motif structure. Obviously, they were not able to accelerate the folding of unfolded states into an i-motif. This observation must be strongly highlighted, and the need to develop suitable extensions of coarse-grained force fields for DNA is pointed out. However, it will take a great deal of effort to successfully solve these problems. [ABSTRACT FROM AUTHOR]

Expanded (x) and widened (y) deoxyribose nucleic acids (DNA) have an extra benzene ring incorporated either horizontally (xDNA) or vertically (yDNA) between a natural pyrimidine base and the deoxyribose, or between the 5- and 6-membered rings of a natural purine. Far-reaching applications for (x,y)DNA include nucleic acid probes and extending the natural genetic code. Since modified nucleobases must encode information that can be passed to the next generation in order to be a useful extension of the genetic code, the ability of translesion (bypass) polymerases to replicate modified bases is an active area of research. The common model bypass polymerase DNA polymerase IV (Dpo4) has been previously shown to successfully replicate and extend past a single modified nucleobase on a template DNA strand. In the current study, molecular dynamics (MD) simulations are used to evaluate the accommodation of expanded/widened nucleobases in the Dpo4 active site, providing the first structural information on the replication of (x,y)DNA. Our results indicate that the Dpo4 catalytic (palm) domain is not significantly impacted by the (x,y)DNA bases. Instead, the template strand is displaced to accommodate the increased C1'-C1' base-pair distance. The structural insights unveiled in the present work not only increase our fundamental understanding of Dpo4 replication, but also reveal the process by which Dpo4 replicates (x,y)DNA, and thereby will contribute to the optimization of high fidelity and efficient polymerases for the replication of modified nucleobases. [ABSTRACT FROM AUTHOR]

The thrombin binding aptamer (TBA) is a promising nucleic acid-based anticoagulant. We studied the effects of chemical modifications, such as dendrimer Trebler and NHS carboxy group, on TBA with respect to its structures and thrombin binding affinity. The two dendrimer modifications were incorporated into the TBA at the 5′ end and the NHS carboxy group was added into the thymine residues in the thrombin binding site of the TBA G-quadruplex (at T4, T13 and both T4/T13) using solid phase oligonucleotide synthesis. Circular dichroism (CD) spectroscopy confirmed that all of these modified TBA variants fold into a stable G-quadruplex. The binding affinity of TBA variants with thrombin was measured by surface plasmon resonance (SPR). The binding patterns and equilibrium dissociation constants (KD) of the modified TBAs are very similar to that of the native TBA. Molecular dynamics simulations studies indicate that the additional interactions or stability enhancement introduced by the modifications are minimized either by the disruption of TBA–thrombin interactions or destabilization elsewhere in the aptamer, providing a rational explanation for our experimental data. Overall, this study identifies potential positions on the TBA that can be modified without adversely affecting its structure and thrombin binding preference, which could be useful in the design and development of more functional TBA analogues. [ABSTRACT FROM AUTHOR]

We explore the structure of two ionic liquids based on the choline cation and the monoanion of the maleic acid. We consider two isomers of the anion (H-maleate, the cis-isomer and H-fumarate, the trans-isomer) having different physical chemical properties. H-maleate assumes a closed structure and forms a strong intramolecular hydrogen bond whereas H-fumarate has an open structure. X-ray diffraction, infrared and Raman spectroscopy and molecular dynamics have been used to provide a reliable picture of the interactions which characterize the structure of the fluids. All calculations indicate that the choline cation prefers to connect mainly to the carboxylate group through OH⋯O interactions in both the compounds and orient the charged head N(CH3)3+ toward the negative portion of the anion. However, the different structure of the two anions affects the distribution of the ionic components in the fluid. The trans conformation of H-fumarate allows further interactions between anions through COOH and CO2− groups whereas intramolecular hydrogen bonding in H-maleate prevents this association. Our theoretical findings have been validated by comparing them with experimental X-ray data and infrared and Raman spectra. [ABSTRACT FROM AUTHOR]

Aptamers are functional nucleic acids that bind to a range of targets (small molecules, proteins or cells) with a high affinity and specificity. Chemically-modified aptamers are of interest because the incorporation of novel nucleobase components can enhance aptamer binding to target proteins, while fluorescent base analogues permit the design of functional aptasensors that signal target binding. However, since optimally modified nucleoside designs have yet to be identified, information about how to fine tune aptamer stability and target binding affinity is required. The present work uses molecular dynamics (MD) simulations to investigate modifications to the prototypical thrombin-binding aptamer (TBA), which is a 15-mer DNA sequence that folds into a G-quadruplex structure connected by two TT loops and one TGT loop. Specifically, we modeled a previously synthesized thymine (T) analog, namely 5-furyl-2′-deoxyuridine (5FurU), into each of the six aptamer locations occupied by a thymine base in the TT or TGT loops of unbound and thrombin bound TBA. This modification and aptamer combination were chosen as a proof-of-principle because previous experimental studies have shown that TBA displays emissive sensitivity to target binding based on the local environment polarity at different 5FurU modification sites. Our simulations reveal that the chemically-modified base imparts noticeable structural changes to the aptamer without affecting the global conformation. Depending on the modification site, 5FurU performance is altered due to changes in the local environment, including the modification site structural dynamics, degree of solvent exposure, stacking with neighboring bases, and interactions with thrombin. Most importantly, these changes directly correlate with the experimentally-observed differences in the stability, binding affinity and emissive response of the modified aptamers. Therefore, the computational protocols implemented in the present work can be used in subsequent studies in a predictive way to aid the fine tuning of aptamer target recognition for use as biosensors (aptasensors) and/or therapeutics. [ABSTRACT FROM AUTHOR]

The interest in diphenyl ditelluride (Ph2Te2) is related to its strict analogy to diphenyl diselenide (Ph2Se2), whose capacity to reduce organic peroxides is largely exploited in catalysis and green chemistry. Since the latter is also a promising candidate as an antioxidant drug and mimic of the ubiquitous enzyme glutathione peroxidase (GPx), the use of organotellurides in medicinal chemistry is gaining importance, despite the fact that tellurium has no recognized biological role and its toxicity must be cautiously pondered. Both Ph2Se2 and Ph2Te2 exhibit significant conformational freedom due to the softness of the inter-chalcogen and carbon–chalcogen bonds, preventing the existence of a unique structure in solution. Therefore, the accurate calculation of the NMR chemical shifts of these flexible molecules is not trivial. In this study, a detailed structural analysis of Ph2Te2 is carried out using a computational approach combining classical molecular dynamics and relativistic density functional theory methods. The goal is to establish how structural changes affect the electronic structure of diphenyl ditelluride, particularly the 125Te chemical shift. [ABSTRACT FROM AUTHOR]

Peptaibols are a special class of fungal peptides with an acetylated N-terminus and a C-terminal 1,2-amino alcohol along with non-standard amino acid residues. New peptaibols named tripleurins were recently identified from a strain of the filamentous fungal species Trichoderma pleuroti, which is known to cause green mould disease on cultivated oyster mushrooms. To understand the mode of action of these peptaibols, the three-dimensional structure of tripleurin (TPN) XIIc, an 18-mer peptide, was elucidated using an enhanced sampling method, accelerated MD, in water and chloroform solvents. Non-standard residues were parameterized by the Restrained Electrostatic Potential (RESP) charge fitting method. The dihedral distribution indicated towards a right-handed helical formation for TPN XIIc in both solvents. Dihedral angle based principal component analysis revealed a propensity for a slightly bent, helical folded conformation in water solvent, while two distinct conformations were revealed in chloroform: One that folds into highly bent helical structure that resembles a beta-hairpin and another with an almost straight peptide backbone appearing as a rare energy barrier crossing event. The hinge-like movement of the terminals was also observed and is speculated to be functionally relevant. The convergence and efficient sampling is addressed using Cartesian PCA and Kullback-Leibler divergence methods. [ABSTRACT FROM AUTHOR]