A neural network potential based on pairwise resolved atomic forces and energies

Molecular simulations have become a key tool in molecular and materials design. Machine learning (ML)-based potential energy functions offer the prospect of simulating complex molecular systems efficiently at quantum chemical accuracy. In previous work, we have introduced the ML-based PairF-Net approach to neural network potentials, that adopts a pairwise interatomic scheme to predicting forces within a molecular system. Here, we further develop the PairF-Net model to intrinsically incorporate energy conservation and couple the model to a molecular mechanical (MM) environment within the OpenMM package. The updated PairF-Net model yields energy and force predictions and dynamical distributions in good agreement with the rMD17 dataset of ten small organic molecules in the gas-phase. We further show that these in vacuo ML models of small molecules can be applied to force predictions in aqueous solution via hybrid ML/MM simulations. We present a new benchmark dataset for these ten molecules in solution, obtained from QM/MM simulations, which we denote as rMD17-aq (https://zenodo.org/records/10048644); and assess the ability of PairF-Net to reproduce the molecular energy, atomic forces and dynamical distributions of these solution conformations via ML/MM simulations.

Vaccination with structurally adapted fungal protein fibrils induces immunity to Parkinson's disease

The pathological misfolding and aggregation of soluble α-synuclein into toxic oligomers and insoluble amyloid fibrils causes Parkinson's disease, a progressive age-related neurodegenerative disease for which there is no cure. HET-s is a soluble fungal protein that can form assembled amyloid fibrils in its prion state. We engineered HET-s(218-298) to form four different fibrillar vaccine candidates, each displaying a specific conformational epitope present on the surface of α-synuclein fibrils. Vaccination with these four vaccine candidates prolonged the survival of immunized TgM83+/- mice challenged with α-synuclein fibrils by 8% when injected into the brain to model brain-first Parkinson's disease or by 21% and 22% when injected into the peritoneum or gut wall, respectively, to model body-first Parkinson's disease. Antibodies from fully immunized mice recognized α-synuclein fibrils and brain homogenates from patients with Parkinson's disease, dementia with Lewy bodies and multiple system atrophy. Conformation-specific vaccines that mimic epitopes present only on the surface of pathological fibrils but not on soluble monomers, hold great promise for protection against Parkinson's disease, related synucleinopathies and other amyloidogenic protein misfolding disorders.

Co/C Nanocomposites with Tunable Condensed States Induced by Conformation-Mediated Strategy for Electromagnetic Wave Absorption

The strategic regulation of condensed state structures in multicomponent nanomaterials has emerged as an effective approach for achieving controllable electromagnetic (EM) properties. Herein, a novel conformation-mediated strategy is proposed to manipulate the condensed states of Co and C, as well as their interaction. The conformation of polyvinylpyrrolidone molecules is adjusted using a gradient methanol/water ratio, whereby the coordination dynamic equilibrium effectively governs the deposition of metal-organic framework precursors. This process ultimately influences the combined impact of derived Co and C in the resulting Co/C nanocomposites post-pyrolysis. The experimental results show that the condensed state structure of Co/C nanocomposites transitions from agglomerate state → to biphasic compact state → to loose packing state. Benefiting from the tunable collaboration between interfacial polarization and defects polarization, and the appropriate electrical conductivity, the diphasic compact state of Co/C nanocomposites achieves an effective absorbing bandwidth of 7.12 GHz (2.1 mm) and minimum reflection loss of -32.8 dB. This study highlights the significance of condensed state manipulation in comprehensively regulating the EM wave absorption characteristics of carbon-based magnetic metal nanocomposites, encompassing factors such as conductivity loss, magnetic loss, defect polarization, and interface polarization.

Monitoring Anthracycline Cancer Drug-Nucleosome Interaction by NMR Using a Specific Isotope Labeling Approach for Nucleosomal DNA

Chromatinized DNA is targeted by proteins and small molecules to regulate chromatin function. For example, anthracycline cancer drugs evict nucleosomes in a mechanism that is still poorly understood. We here developed a flexible method for specific isotope labeling of nucleosomal DNA enabling NMR studies of such nucleosome interactions. We describe the synthesis of segmental one-strand 13C-thymidine labeled 601-DNA, the assignment of the methyl signals, and demonstrate its use to observe site-specific binding to the nucleosome by aclarubicin, an anthracycline cancer drug that intercalates into the DNA minor grooves. Our results highlight intrinsic conformational heterogeneity in the 601 DNA sequence and show that aclarubicin binds an exposed AT-rich region near the DNA end. Overall, our data point to a model where the drug invades the nucleosome from the terminal ends inward, eventually resulting in histone eviction and nucleosome disruption.

Investigation of Cellulose-Based Materials Applied in Life Sciences Using Laser Light Scattering Methods

This review emphasizes the practical importance of laser light scattering methods for characterizing cellulose and its derivatives. The physicochemical parameters like molecular weights, the radius of gyration, hydrodynamic radius, and conformation will be considered when the reproducibility of polymer behavior in solution is necessary for the subsequent optimization of the property profile of a designed product. Since there are various sources of cellulose, and the methods of cellulose extraction and chemical modification have variable yields, materials with variable molecular weights, and size polydispersity will often result. Later, the molecular masses will influence other physicochemical properties of cellulosic materials, both in solution and solid state. Consequently, the most rigorous determination of these quantities is imperative. In this regard, the following are presented and discussed in this review: the theoretical foundations of the light scattering phenomenon, the evolution of the specific instrumentation and detectors, the development of the detector-coupling techniques which include a light scattering detector, and finally, the importance of the specific parameters of polymers in solution, resulting from the data analysis of light scattering signals. All these aspects are summarized according to the chemical classification of the materials: celluloses, esters of cellulose, co-esters of cellulose, alkyl esters of cellulose, ethers of cellulose, and other heterogeneous cellulose derivatives with applications in life sciences.

The impact of ultrasonic-assisted extraction on the in vitro hypoglycemic activity of peach gum polysaccharide in relation to its conformational conversion

BACKGROUND

Peach gum (PG) is an exudate of the peach tree (Prunus persica of the Rosaceae family), which consists primarily of polysaccharides with a large molecular weight and branching structure. Consequently, PG can only swell in water and does not dissolve easily, which severely limits its application. Current conventional extraction methods for PG polysaccharide (PGPS) are time consuming and inefficient. This study investigated the impact of ultrasonic-assisted extraction (UAE) on PGPS structure and conformation, and their relationship to hypoglycemic activity in vitro.

RESULTS

In comparison with conventional aqueous extraction, UAE enhanced PGPS yielded from 28.07-32.83% to 80.37-84.90% (w/w) in 2 h. It drastically decreased the molecular size and conformational parameters of PGPS, including weight-average molecular weight (Mw), number-average molecular weight (Mn), z-average radius of gyration (Rg), hydrodynamic radius (Rh) and instrinsic viscosity ([η]) values. Peach gum polysaccharide conformation converted extended molecules to flexible random coil chains or compact spheres with no obvious primary structure alteration. Furthermore, UAE altered the flow behavior of PGPS solution from that of a non-Newtonian fluid to that of a Newtonian fluid. As a result, PGPS treated with UAE displayed weaker inhibitory activity than untreated PGPS, mostly because UAE weakens the binding strength of PGPS to α-glucosidase. However, this negative effect of UAE on PGPS activity was compensated by the increased solubility of polysaccharide. This enabled PGPS to achieve a wider range of doses.

CONCLUSION

Ultrasonic-assisted extraction is capable of degrading PGPS efficiently while preserving its primary structure, resulting in a Newtonian fluid solution. The degraded PGPS conformations displayed a consistent correlation with their inhibitory effect on α-glucosidase activity. © 2024 Society of Chemical Industry.

Efficient transmission of human prion diseases to a glycan-free prion protein-expressing host

It is increasingly evident that the association of glycans with the prion protein (PrP), a major post-translational modification, significantly impacts the pathogenesis of prion diseases. A recent bioassay study has provided evidence that the presence of PrP glycans decreases spongiform degeneration and disease-related PrP (PrPD) deposition in a murine model. We challenged (PRNPN181Q/197Q) transgenic (Tg) mice expressing glycan-free human PrP (TgGlyc-), with isolates from sporadic Creutzfeldt-Jakob disease subtype MM2 (sCJDMM2), sporadic fatal insomnia and familial fatal insomnia, three human prion diseases that are distinct but share histotypic and PrPD features. TgGlyc- mice accurately replicated the basic histotypic features associated with the three diseases but the transmission was characterized by high attack rates, shortened incubation periods and a greatly increased severity of the histopathology, including the presence of up to 40 times higher quantities of PrPD that formed prominent deposits. Although the engineered protease-resistant PrPD shared at least some features of the secondary structure and the presence of the anchorless PrPD variant with the wild-type PrPD, it exhibited different density gradient profiles of the PrPD aggregates and a higher stability index. The severity of the histopathological features including PrP deposition appeared to be related to the incubation period duration. These findings are clearly consistent with the protective role of the PrP glycans but also emphasize the complexity of the conformational changes that impact PrPD following glycan knockout. Future studies will determine whether these features apply broadly to other human prion diseases or are PrPD-type dependent.

Central Ring Puckering Enhances the Stokes Shift of Xanthene Dyes

Small-molecule dyes are generally designed based on well-understood electronic effects. However, steric hindrance can promote excited-state geometric relaxation, increasing the difference between the positions of absorption and emission bands (the Stokes shift). Accordingly, we hypothesized that sterically induced central ring puckering in xanthene dyes could be used to systematically increase their Stokes shift. Through a combined experimental/quantum-chemical approach, we screened a group of (9-acylimino)-pyronin dyes with a perturbed central ring geometry. Our results showed that an atom with sp3 hybridization in position 10 of (9-acylimino)-pyronins induces central ring puckering and facilitates excited-state geometric relaxation, thereby markedly enhancing their Stokes shifts (by up to ~2000 cm-1). Thus, we prepared fluorescent (9-acylimino)-pyronin pH sensors, which showed a Stokes shift disparity between acid and base forms of up to ~8700 cm-1. Moreover, the concept of ring puckering-enhanced Stokes shift can be applied to a wide range of xanthene analogues found in the literature. Therefore, central ring puckering may be reliably used as a strategy for enhancing Stokes shifts in the rational design of dyes.

Upregulation of outer membrane porin gene ompC contributed to enhancement of azithromycin susceptibility in multidrug-resistant Escherichia coli

The outer membrane (OM) in gram-negative bacteria contains proteins that regulate the passive or active uptake of small molecules for growth and cell function, as well as mediate the emergence of antibiotic resistance. This study aims to explore the potential mechanisms for restoring bacteria to azithromycin susceptibility based on transcriptome analysis of bacterial membrane-related genes. Transcriptome sequencing was performed by treating multidrug-resistant Escherichia coli T28R with azithromycin or in combination with colistin and confirmed by reverse transcription-quantitative PCR (RT-qPCR). Azithromycin enzyme-linked immunosorbent assay (ELISA) test, ompC gene overexpression, and molecular docking were utilized to conduct the confirmatory research of the potential mechanisms. We found that colistin combined with azithromycin led to 48 differentially expressed genes, compared to azithromycin alone, such as downregulation of tolA, eptB, lpxP, and opgE and upregulation of ompC gene. Interestingly, the addition of colistin to azithromycin differentially downregulated the mph(A) gene mediating azithromycin resistance, facilitating the intracellular accumulation of azithromycin. Also, overexpression of the ompC elevated azithromycin susceptibility, and colistin contributed to further suppression of the Mph(A) activity in the presence of azithromycin. These findings suggested that colistin firstly enhanced the permeability of bacterial OM, causing intracellular drug accumulation, and then had a repressive effect on the Mph(A) activity along with azithromycin. Our study provides a novel perspective that the improvement of azithromycin susceptibility is related not only to the downregulation of the mph(A) gene and conformational remodeling of the Mph(A) protein but also the upregulation of the membrane porin gene ompC.IMPORTANCEUsually, active efflux via efflux pumps is an important mechanism of antimicrobial resistance, such as the AcrAB-TolC complex and MdtEF. Also, bacterial porins exhibited a substantial fraction of the total number of outer membrane proteins in Enterobacteriaceae, which are involved in mediating the development of the resistance. We found that the upregulation or overexpression of the ompC gene contributed to the enhancement of resistant bacteria to azithromycin susceptibility, probably due to the augment of drug uptakes caused and the opportunity of Mph(A) function suppressed by azithromycin with colistin. Under the combination of colistin and azithromycin treatment, OmpC exhibited an increased selectivity for cationic molecules and played a key role in the restoral of the antibiotic susceptibility. Investigations on the regulation of porin expression that mediated drug resistance would be important in clinical isolates treated with antibiotics.

Sensing PEGylated Peptide Conformations Using a Protein Nanopore

Membrane pores are exploited for the stochastic sensing of various analytes, and here, we use electrical recordings to explore the interaction of PEGylated peptides of different sizes with a protein pore, CymA. This wide-diameter natural pore comprises densely filled charged residues, facilitating electrophoretic binding of polyethylene glycol (PEG) tagged with a nonaarginine peptide. The small PEG 200 peptide conjugates produced monodisperse blockages and exhibited voltage-dependent translocation across the pores. Notably, the larger PEG 1000 and 2000 peptide conjugates yielded heterogeneous blockages, indicating a multitude of PEG conformations hindering their translocation through the pore. Furthermore, a much larger PEG 5000 peptide occludes the pore entrance, resulting in complete closure. The competitive binding of different PEGylated peptides with the same pore produced specific blockage signals reflecting their identity, size, and conformation. Our proposed model of sensing distinct polypeptide conformations corresponds to disordered protein unfolding, suggesting that this pore can find applications in proteomics.

Prioritization of Appearance over Health and Temperament Is Detrimental to the Welfare of Purebred Dogs and Cats

Fashions in the appearance of purebred dogs and cats are encouraged by celebrity culture, social media, and online impulse buying. The popularity of characteristics perceived as cute, quirky, and anthropomorphic has driven increasingly exaggerated breed features appealing to aesthetics rather than health. 'Hypertypes' of some breeds have emerged that take a breed's distinctive appearance to extremes beyond the intended interpretation of breed standards. This has severe, direct and indirect health and welfare consequences. Extreme conformations are associated with chronic health conditions including brachycephalic obstructive airway disorder, ocular, dental, skin, and musculoskeletal disorders. Puppy and kitten farms and illegal traders that meet the demand for hypertypes are associated with poor husbandry that neglects the physical, behavioral, and mental health of parents and offspring. A multidimensional approach involving collaboration between breeders, geneticists, owners, veterinarians, kennel clubs, cat fanciers' associations, animal charities, the academic and research communities, commercial enterprises, and governments is needed to safeguard breeds and tackle these challenges. There are many ongoing initiatives by national kennel clubs and global partnerships to educate pet owners and support responsible pet ownership and sustainable breeding. The resounding message is that health, temperament, and well-being must be prioritized over appearance.

Glucans from Armillaria luteo-virens: Structural Characterization and In Vivo Immunomodulatory Investigation under Different Administration Routes

Polysaccharides fromArmillaria luteo-virens (ALP) were investigated for structural characterization and immunomodulatory activities. Three fractions (ALP-1, ALP-2, and ALP-3) were obtained with the yield of 2.4, 3.7, and 3.0 wt %, respectively. ALP-1 was proposed as a β-(1 → 3)(1 → 6)-glucan with a triple-helix conformation; ALP-2 and ALP-3 were both identified as α-(1 → 4)(1 → 6)-glucan differing in their Mw and branching degree with a spherical conformation. The in vitro digestibility experiment and in vivo experiments using cyclophosphamide (CY)-treated mice demonstrated that intraperitoneal injection of α-glucan (1 mg·kg-1·day-1) and intragastric gavage of β-glucan (10 mg·kg-1·day-1) both effectively restored the decrease in body weight, immune organ indexes, immune cell activities, serum immune marker levels, colonic short-chain fatty acids (SCFA) levels, and Bacteroidetes/Firmicutes ratio in immunosuppression mice. This study provides novel insights into the immunomodulatory activity of α- and β-glucans under different administration routes, thereby promoting their application in both food and pharmaceutical areas.

Catalytic Ring Expanding Difluorination: An Enantioselective Platform to Access β,β-Difluorinated Carbocycles

Cyclic β,β-difluoro-carbonyl compounds have a venerable history as drug discovery leads, but limitations in the synthesis arsenal continue to impede chemical space exploration. This challenge is particularly acute in the arena of fluorinated medium rings where installing the difluoromethylene unit subtly alters the ring conformation by expanding the internal angle (∠C-CF2-C>∠C-CH2-C): this provides a handle to modulate physicochemistry (e.g. pKa). To reconcile this disparity, a highly modular ring expansion has been devised that leverages simple α,β-unsaturated esters and amides, and processes them to one-carbon homologated rings with concomitant geminal difluorination (6 to 10 membered rings, up to 95 % yield). This process is a rare example of the formal difluorination of an internal alkene and is enabled by sequential I(III)-enabled O-activation. Validation of enantioselective catalysis in the generation of unprecedented medium ring scaffolds is reported (up to 93 : 7 e.r.) together with X-ray structural analyses and product derivatization.

3D imaging and body measurement of riding horses using four scanners simultaneously

Although there have been advances in the technology for measuring horse body size with stereoscopic three-dimensional (3D) scanners, previously reported methods with a single scanner still face a significant challenge: the time necessary for scanning is too long for the horses to remain stationary. This study attempted to scan the horse simultaneously from four directions using four scanners in order to complete the scans in a short amount of time and then combine the images from the four scans on a computer into one whole image of each horse. This study also compared body measurements from the combined 3D images with those taken from conventional manual measurements. Nine riding horses were used to construct stereoscopic composite images, and the following 10 measurements were taken: height at the withers, back, and croup; chest depth; width of the chest (WCh), croup, and waist; girth circumference, cannon circumference (CaC), and body length. The same 10 measurements were taken by conventional manual methods. Relative errors ranged from -1.89% to 7.05%. The correlation coefficient between manual and 3D measurements was significant for all body measurements (P<0.01) except for WCh and CaC. A simple regression analysis of all body measurements revealed a strong correlation (P<0.001, R2=0.9994, root-mean-square error=1.612). Simultaneous scanning with four devices from four directions reduced the scanning time from 60 sec with one device to 15 sec. This made it possible to perform non-contact body measurements even on incompletely trained horses who could not remain stationary for long periods of time.

Comparative Conformational Analysis of Acyclic Sugar Alcohols Ribitol, Xylitol and d-Arabitol by Solution NMR and Molecular Dynamics Simulations

Ribitol (C5H12O5) is an acyclic sugar alcohol that was recently identified in O-mannose glycan on mammalian α-dystroglycan. The conformation and dynamics of acyclic sugar alcohols such as ribitol are dependent on the stereochemistry of the hydroxyl groups; however, the dynamics are not fully understood. To gain insights into the conformation and dynamics of sugar alcohols, we carried out comparative analyses of ribitol, d-arabitol and xylitol by a crystal structure database search, solution NMR analysis and molecular dynamics (MD) simulations. The crystal structures of the sugar alcohols showed a limited number of conformations, suggesting that only certain stable conformations are prevalent among all possible conformations. The three-bond scholar coupling constants and exchange rates of hydroxyl protons were measured to obtain information on the backbone torsion angle and possible hydrogen bonding of each hydroxyl group. The 100 ns MD simulations indicate that the ribitol backbone has frequent conformational transitions with torsion angles between 180∘ and ±60∘, while d-arabitol and xylitol showed fewer conformational transitions. Taking our experimental and computational data together, it can be concluded that ribitol is more flexible than d-arabitol or xylitol, and the flexibility is at least in part defined by the configuration of the OH groups, which may form intramolecular hydrogen bonds.

O-Antigen decorations in Salmonella enterica play a key role in eliciting functional immune responses against heterologous serovars in animal models

Introduction

Different serovars of Salmonella enterica cause systemic diseases in humans including enteric fever, caused by S. Typhi and S. Paratyphi A, and invasive nontyphoidal salmonellosis (iNTS), caused mainly by S. Typhimurium and S. Enteritidis. No vaccines are yet available against paratyphoid fever and iNTS but different strategies, based on the immunodominant O-Antigen component of the lipopolysaccharide, are currently being tested. The O-Antigens of S. enterica serovars share structural features including the backbone comprising mannose, rhamnose and galactose as well as further modifications such as O-acetylation and glucosylation. The importance of these O-Antigen decorations for the induced immunogenicity and cross-reactivity has been poorly characterized.

Methods

These immunological aspects were investigated in this study using Generalized Modules for Membrane Antigens (GMMA) as delivery systems for the different O-Antigen variants. This platform allowed the rapid generation and in vivo testing of defined and controlled polysaccharide structures through genetic manipulation of the O-Antigen biosynthetic genes.

Results

Results from mice and rabbit immunization experiments highlighted the important role played by secondary O-Antigen decorations in the induced immunogenicity. Moreover, molecular modeling of O-Antigen conformations corroborated the likelihood of cross-protection between S. enterica serovars.

Discussion

Such results, if confirmed in humans, could have a great impact on the design of a simplified vaccine composition able to maximize functional immune responses against clinically relevant Salmonella enterica serovars.

The Binding Properties of Antibodies to Z-DNA in the Sera of Normal Healthy Subjects

Antibodies to DNA are a diverse set of antibodies that bind sites on DNA, a polymeric macromolecule that displays various conformations. In a previous study, we showed that sera of normal healthy subjects (NHS) contain IgG antibodies to Z-DNA, a left-handed helix with a zig-zig backbone. Recent studies have demonstrated the presence of Z-DNA in bacterial biofilms, suggesting a source of this conformation to induce responses. To characterize further antibodies to Z-DNA, we used an ELISA assay with brominated poly(dGdC) as a source of Z-DNA and determined the isotype of these antibodies and their binding properties. Results of these studies indicate that NHS sera contain IgM and IgA as well as IgG anti-Z-DNA antibodies. As shown by the effects of ionic strength in association and dissociation assays, the anti-Z-DNA antibodies bind primarily by electrostatic interactions; this type of binding differs from that of induced anti-Z-DNA antibodies from immunized animals which bind by non-ionic interactions. Furthermore, urea caused dissociation of NHS anti-Z-DNA at molar concentrations much lower than those for the induced antibodies. These studies also showed IgA anti-Z-DNA antibodies in fecal water. Together, these studies demonstrate that antibodies to Z-DNA occur commonly in normal immunity and may arise as a response to Z-DNA of bacterial origin.

Synergistic Effects of High-Intensity Ultrasound Combined with L-Lysine for the Treatment of Porcine Myofibrillar Protein Regarding Solubility and Flavour Adsorption Capacity

This study aimed to investigate the synergistic effects of high-intensity ultrasound (0, 5, 10, 15, and 20 min) in combination with L-lysine (15 mM) on improving the solubility and flavour adsorption capacity of myofibrillar proteins (MPs) in low-ion-strength media. The results revealed that the ultrasound treatment for 20 min or the addition of L-lysine (15 mM) significantly improved protein solubility (p < 0.05), with L-lysine (15 mM) showing a more pronounced effect (p < 0.05). The combination of ultrasound treatment and L-lysine further increased solubility, and the MPs treated with ultrasound at 20 min exhibited the best dispersion stability in water, which corresponded to the lowest turbidity, highest absolute zeta potential value, and thermal stability (p < 0.05). Based on the reactive and total sulfhydryl contents, Fourier transform infrared spectroscopy, and fluorescence spectroscopy analysis, the ultrasound treatment combined with L-lysine (15 mM) promoted the unfolding and depolymerization of MPs, resulting in a larger exposure of SH groups on the surface, aromatic amino acids in a polar environment, and a transition of protein conformation from α-helix to β-turn. Moreover, the combined treatment also increased the hydrophobic bonding sites, hydrogen-bonding sites, and electrostatic effects, thereby enhancing the adsorption capacity of MPs to bind kenone compounds. The findings from this study provide a theoretical basis for the production and flavour improvement of low-salt MP beverages and the utilisation of meat protein.

Computed interactions of berenil with restricted foldamers of c-MYC DNA G-quadruplexes

G-quadruplexes (G4s) are secondary four-stranded DNA helical structures made up of guanine-rich nucleic acids that can assemble in the promoter regions of multiple genes under the appropriate conditions. Stabilization of G4 structures by small molecules can regulate transcription in non-telomeric regions, including in proto-oncogenes and promoter regions, contributing to anti-proliferative and anti-tumor activities. Because G4s are detectable in cancer cells but not in normal cells, they make excellent drug discovery targets. Diminazene, DMZ (or berenil), has been shown to be an efficient G-quadruplex binder. Due to the stability of the folding topology, G-quadruplex structures are frequently found in the promotor regions of oncogenes and may play a regulatory role in gene activation. Using molecular docking and molecular dynamics simulations on several different binding poses, we have studied DMZ binding toward multiple G4 topologies of the c-MYC G-quadruplex. DMZ binds preferentially to G4s that have extended loops and flanking bases. This preference arises from its interactions with the loops and the flanking nucleotides, which were not found in the structure lacking extended regions. The binding to the G4s with no extended regions instead occurred mostly through end stacking. All binding sites for DMZ were confirmed by 100 ns molecular dynamics simulations and through binding enthalpies calculated using the MM-PBSA method. The primary driving forces were electrostatic, as the cationic DMZ interacts with the anionic phosphate backbone, and through van der Waals interactions, which primarily contributed in end stacking interactions.Communicated by Ramaswamy H. Sarma.

Glycan Shape, Motions, and Interactions Explored by NMR Spectroscopy

Glycans in the form of oligosaccharides, polysaccharides, and glycoconjugates are ubiquitous in nature, and their structures range from linear assemblies to highly branched and decorated constructs. Solution state NMR spectroscopy facilitates elucidation of preferred conformations and shapes of the saccharides, motions, and dynamic aspects related to processes over time as well as the study of transient interactions with proteins. Identification of intermolecular networks at the atomic level of detail in recognition events by carbohydrate-binding proteins known as lectins, unraveling interactions with antibodies, and revealing substrate scope and action of glycosyl transferases employed for synthesis of oligo- and polysaccharides may efficiently be analyzed by NMR spectroscopy. By utilizing NMR active nuclei present in glycans and derivatives thereof, including isotopically enriched compounds, highly detailed information can be obtained by the experiments. Subsequent analysis may be aided by quantum chemical calculations of NMR parameters, machine learning-based methodologies and artificial intelligence. Interpretation of the results from NMR experiments can be complemented by extensive molecular dynamics simulations to obtain three-dimensional dynamic models, thereby clarifying molecular recognition processes involving the glycans.

Water Exchange from the Buried Binding Sites of Cytochrome P450 Enzymes 1A2, 2D6, and 3A4 Correlates with Conformational Fluctuations

Human cytochrome P450 enzymes (CYPs) are critical for the metabolism of small-molecule pharmaceuticals (drugs). As such, the prediction of drug metabolism by and drug inhibition of CYP activity is an important component of the drug discovery and design process. Relative to the availability of a wide range of experimental atomic-resolution CYP structures, the development of structure-based CYP activity models has been limited. To better characterize the role of CYP conformational fluctuations in CYP activity, we perform multiple microsecond-scale all-atom explicit-solvent molecular dynamics (MD) simulations on three CYP isoforms, 1A2, 2D6, and 3A4, which together account for the majority of CYP-mediated drug metabolism. The MD simulations employ a variety of positional restraints, ranging from keeping all CYP atoms close to their experimentally determined coordinates to allowing full flexibility. We find that, with full flexibility, large fluctuations in the CYP binding sites correlate with efficient water exchange from these buried binding sites. This is especially true for 1A2, which, when restrained to its crystallographic conformation, is unable to exchange water between the binding site and bulk solvent. These findings imply that, in addition to crystal structures, a representative ensemble of conformational states ought to be included when developing structure-based CYP activity models.

Identification of Conformational Variants for Bradykinin Biomarker Peptides from a Biofluid Using a Nanopore and Machine Learning

There is a current need to develop methods for the sensitive detection of peptide biomarkers in complex mixtures of molecules, such as biofluids, to enable early disease detection. Moreover, to our knowledge, there is currently no detection method capable of identifying the different conformations of a peptide biomarker differing by a single amino acid. Single-molecule nanopore sensing promises to provide this level of resolution. In order to be able to identify these differences in a biofluid such as serum, it is necessary to carefully characterize electrical parameters to obtain specific signatures of each biomarker population observed. We are interested here in a family of peptide biomarkers, kinins such as bradykinin and des-Arg9 bradykinin, that are involved in many disabling pathologies (allergy, asthma, angioedema, sepsis, or cancer). We show the proof of concept for direct identification of these biomarkers in serum at the single-molecule level using a protein nanopore. Each peptide exhibits two unique electrical signatures attributed to specific conformations in bulk. The same signatures are found in serum, allowing their discrimination and identification in a complex mixture such as biofluid. To extend the utility of our experimental results, we developed a principal component analysis approach to define the most relevant electrical parameters for their identification. Finally, we used semisupervised classification to assign each event type to a specific biomarker at physiological serum concentration. In the future, single-molecule scale analysis of peptide biomarkers using a powerful nanopore coupled with machine learning will facilitate the identification and quantification of other clinically relevant biomarkers from biofluids.

Discovery of internal rotation and conformers of 1,2-dichloroethane: the dawn of the concept of conformation

In 1932, Mizushima and Higasi reported the dependence of the dipole moments of 1,2-dichloroethane on both temperature and solvent in the Proceedings of the Imperial Academy, Japan. This report was followed by their first proposal of the existence of conformers that exchanged by internal rotation about a C-C single bond based on experimental data. Their monumental work marked the beginning of the essential concept of conformation in modern stereochemistry. Their proposal was later confirmed by the direct observation of the anti and gauche conformers of 1,2-dichloroethane by Raman spectroscopy, and further supported by other experimental and theoretical methods. The relative stabilities of the anti and gauche conformers of 1,2-dichloroethane and other 1,2-disubstituted ethanes were discussed in terms of steric, electrostatic, and stereoelectronic effects based on analysis of calculated data. Those studies influenced the development of subsequent research in organic chemistry, such as the conformational analysis of cyclohexane derivatives and the isolation of chiral gauche conformers.

Different EGF-induced receptor dimer conformations for signaling and internalization

The structural basis of the activation and internalization of EGF receptors (EGFR) is still a matter of debate despite the importance of this target in cancer treatment. Whether agonists induce dimer formation or act on preformed dimers remains discussed. Here, we provide direct evidence that EGF-induced EGFR dimer formation as best illustrated by the very large increase in FRET between snap-tagged EGFR subunits induced by agonists. We confirm that Erlotinib-related TK (tyrosine kinase) inhibitors also induce dimer formation despite the inactive state of the binding domain. Surprisingly, TK inhibitors do not inhibit EGF-induced EGFR internalization despite their ability to fully block EGFR signaling. Only Erlotinib-related TK inhibitors promoting asymmetric dimers could slow down this process while the lapatinib-related ones have almost no effect. These results reveal that the conformation of the intracellular TK dimer, rather than the known EGFR signaling, is critical for EGFR internalization. These results also illustrate clear differences in the mode of action of TK inhibitors on the EGFR and open novel possibilities to control EGFR signaling for cancer treatment.

DNA-Modulated and Mechanoresponsive Excitonic Couplings Reveal Chiroptical Correlation of Conformation, Tension, and Dynamics of DNA Self-Assembly

Study of the conformational and mechanical behaviors of biomolecular assemblies is vital to the rational design and realization of artificial molecular architectures with biologically relevant functionality. Here, we revealed DNA-modulated and mechanoresponsive excitonic couplings between organic chromophores and verified strong correlations between the excitonic chiroptical responses and the conformational and mechanical states of DNA self-assemblies irrespective of fluorescence background interference. Besides, the excitonic chiroptical effect allowed sensitive monitoring of DNA self-assembled nanostructures due to small molecule bindings or DNA strand displacement reactions. Moreover, we developed a new chiroptical reporter, a DNA-templated dimer of an achiral cyanine5 and an intrinsically chiral BODIPY, that exhibited unique multiple-split spectral line shape of exciton-coupled circular dichroism, largely separated response wavelengths, and enhanced anisotropy dissymmetry factor (g-factor). These results shed light on a promising chiroptical spectroscopic tool for studying biomolecular recognition and binding, conformation dynamics, and soft mechanics in general.

Conformer aggregates exhibit dual wavelength emissions on chiral binaphthyl-based triphenylethylenes and acetone detection

The study on structure-property relationship has been a significant focus in the field of organic molecular luminescence. In the present work, three chiral binaphthyl-based triphenylethylene (HTPE) derivatives were prepared through condensation reactions. Despite their similar structures, these compounds exhibited distinct luminescent properties. Diphenylmethane-derived HTPE displayed dual-state emissions, characterized by dual-wavelength emissions which were insensitive to the polarity of solvents. The dual emissions in solution state could be attributed to the different locally excited (LE) excitons. However, upon aggregation, two stable conformers were generated, probably leading to different emission peaks. In contrast, dibenzocycloheptadiene-derived HTPE aggregates showed only a single emission peak. Surprisingly, fluorene-derived HTPE exhibited obvious luminescence in neither solution nor aggregate states due to inherent π-π interactions. These conclusions were substantiated by X-ray analysis, spectroscopic analysis, and theory calculations. Application studies demonstrated that fluorescence on/off switches could be achieved through exposure to acetone. More importantly, trace amounts of acetone could be detected using luminescent materials in both organic and aqueous phases with a detection limit of 0.08 %. Thus, this work not only presents a strategy for designing chiral triphenylethylene fluorophores but also provides valuable information for dual wavelength emissions resulting from two stable conformations.

Exploring the conformational dynamics and thermodynamics of EGFR S768I and G719X + S768I mutations in non-small cell lung cancer: An in silico approaches

Non-small cell lung cancer (NSCLC) is often driven by mutations in the epidermal growth factor receptor (EGFR) gene. However, rare mutations such as G719X and S768I lack standard anti-EGFR targeted therapies. Understanding the structural differences between wild-type EGFR and these rare mutants is crucial for developing EGFR-targeted drugs. We performed a systematic analysis using molecular dynamics simulations, essential dynamics (ED), molecular mechanics Poisson-Boltzmann surface area, and free energy calculation methods to compare the kinetic properties, molecular motion, and free energy distribution between wild-type EGFR and the rare mutants' structures G719X-EGFR, S768I-EGFR, and G719X + S768I-EGFR. Our results showed that S768I-EGFR and G719X + S768I-EGFR have higher global and local conformational flexibility and lower thermal and global structural stability than WT-EGFR. ED analysis revealed different molecular motion patterns between S768I-EGFR, G719X + S768I-EGFR, and WT-EGFR. The A-loop and αC-helix, crucial structural elements related to the active state, showed a tendency toward active state development, providing a molecular mechanism explanation for NSCLC caused by EGFR S768I and EGFR G719C + S768I mutations. The present study may be helpful in the development of new EGFR-targeted drugs based on the structure of rare mutations. Our findings may aid in developing new targeted treatments for patients with EGFR S768I and EGFR G719X + S768I mutations.

Conformational Analysis of 1,5-Diaryl-3-Oxo-1,4-Pentadiene Derivatives: A Nuclear Overhauser Effect Spectroscopy Investigation

1,5-Diaryl-3-Oxo-1,4-Pentadiene derivatives are intriguing organic compounds with a unique structure featuring a pentadiene core, aryl groups, and a ketone group. This study investigates the influence of fluorine atoms on the conformational features of these derivatives in deuterated chloroform (CDCl3) solution. Through nuclear magnetic resonance (NMR) spectroscopy and quantum chemical calculations, we discerned variations in interatomic distances and established predominant conformer proportions. The findings suggest that the non-fluorinated entity exhibits a uniform distribution across various conformer groups. The introduction of a fluorine atom induces substantial alterations, resulting in the predominance of a specific conformer group. This structural insight may hold the key to their diverse anticancer activities, previously reported in the literature.

Conformation-selective rather than avidity-based binding to tumor associated antigen derived peptide-MHC enables targeting of WT1-pMHC low expressing cancer cells by anti-WT1-pMHC/CD3 T cell engagers

T cell engagers, a category of T cell-retargeting immunotherapy, are rapidly transforming clinical cancer care. However, the lack of tumor-specific targets poses a significant roadblock for broad adaptation of this therapeutic modality in many indications, often resulting in systemic on-target off-tumor toxicity. Though various tumor-derived intracellular mutations provide a massive pool of potential tumor-specific antigens, targeting them is extremely challenging, partly due to the low copy number of tumor associated antigen (TAA)-derived pMHC on tumor cell surface. Further, the interplay of binding geometry and format valency in relation to the capacity of a T cell engager to efficiently target low density cell-surface pMHC is not well understood. Using the Wilms' tumor 1 (WT1) oncoprotein as a proof-of-principle TAA, combined with an array of IgG-like T cell engager modalities that differ in their anti-TAA valency and binding geometry, we show that the ability to induce an immunological synapse formation, resulting in potent killing of WT1 positive cancer cell lines is primarily dependent on the distinct geometrical conformations between the Fab arms of anti-WT1-HLA-A*02:01 and anti-CD3. The augmented avidity conferred by the binding of two anti-WT1-HLA-A*02:01 Fab arms has only minimal influence on cell killing potency. These findings demonstrate the need for careful examination of key design parameters for the development of next-generation T cell engagers targeting low density TAA-pMHCs on tumor cells.

Anion-Dependent Hydrogen-Bond Polarity Switching in Ethylene-bridged Urea Oligomers

The reversible coordination of anions to an N,N'-disubstituted 3,5-bis(trifluoromethyl)phenylurea located at a terminus of a linear chain of ethylene-bridged hydrogen-bonded ureas triggers a cascade of conformational changes. A series of hydrogen-bond polarity reversals propagates along the oligomer, leading to a global switch of its hydrogen-bond directionality. The induced polarity switch, transmitted through four reversible urea groups, results in a change in emission and excitation wavelengths of a fluorophore located at the opposite terminus of the oligomer. The molecule thus behaves as a chemical sensor with a relayed remote spectroscopic response to variations in anion concentration. The polarity switch induced by anion concentration constitutes an artificial communication mechanism for conveying information through oligomeric structures.

Conformation Dependent Architectures of Assembled Antimicrobial Peptides with Enhanced Antimicrobial Ability

Antimicrobial peptides (AMPs) are a developing class of natural and synthetic oligopeptides with host defense mechanisms against a broad spectrum of microorganisms. With in-depth research on the structural conformations of AMPs, synthesis or modification of peptides has shown great potential in effectively obtaining new therapeutic agents with improved physicochemical and biological properties. Notably, AMPs with self-assembled properties have gradually become a hot research topic for various biomedical applications. Compared to monomeric peptides, these peptides can exist in diverse forms (e.g., nanoparticles, nanorods, and nanofibers) and possess several advantages, such as high stability, good biocompatibility, and potent biological functions, after forming aggregates under specific conditions. In particular, the stability and antibacterial property of these AMPs can be modulated by rationally regulating the peptide sequences to promote self-assembly, leading to the reconstruction of molecular structure and spatial orientation while introducing some peptide fragments into the scaffolds. In this work, four self-assembled AMPs are developed, and the relationship between their chemical structures and antibacterial activity is explored extensively through different experiments. Importantly, the evaluation of antibacterial performance in both in vitro and in vivo studies has provided a general guide for using self-assembled AMPs in subsequent treatments for combating bacterial infections.

Anti-tau antibodies targeting a conformation-dependent epitope selectively bind seeds

Neurodegenerative tauopathies are caused by the transition of tau protein from a monomer to a toxic aggregate. They include Alzheimer disease (AD), progressive supranuclear palsy (PSP), corticobasal degeneration (CBD), and Pick disease (PiD). We have previously proposed that tau monomer exists in two conformational ensembles: an inert form (Mi), which does not self-assemble, and seed-competent form (Ms), which self-assembles and templates ordered assembly growth. We proposed that cis/trans isomerization of tau at P301, the site of dominant disease-associated S/L missense mutations, might underlie the transition of wild-type tau to a seed-competent state. Consequently, we created monoclonal antibodies using non-natural antigens consisting of fluorinated proline (P∗) at the analogous P270 in repeat 1 (R1), biased toward the trans-configuration at either the R1/R2 (TENLKHQP∗GGGKVQIINKK) or the R1/R3 (TENLKHQP∗GGGKVQIVYK) interfaces. Two antibodies, MD2.2 and MD3.1, efficiently immunoprecipitated soluble seeds from AD and PSP but not CBD or PiD brain samples. The antibodies efficiently stained brain samples of AD, PSP, and PiD, but not CBD. They did not immunoprecipitate or immunostain tau from the control brain. Creation of potent anti-seed antibodies based on the trans-proline epitope implicates local unfolding around P301 in pathogenesis. MD2.2 and MD3.1 may also be useful for therapy and diagnosis.

Preferential Regulation of Γ-Secretase-Mediated Cleavage of APP by Ganglioside GM1 Reveals a Potential Therapeutic Target for Alzheimer's Disease

A hallmark of Alzheimer's disease (AD) is the senile plaque, which contains β-amyloid peptides (Aβ). Ganglioside GM1 is the most common brain ganglioside. However, the mechanism of GM1 in modulating Aβ processing is rarely known. Aβ levels are detected by using Immunohistochemistry (IHC) and enzyme-linked immune-sorbent assay (ELISA). Cryo-electron microscopy (Cryo-EM) is used to determine the structure of γ-secretase supplemented with GM1. The levels of the cleavage of amyloid precursor protein (APP)/Cadherin/Notch1 are detected using Western blot analysis. Y maze, object translocation, and Barnes maze are performed to evaluate cognitive functions. GM1 leads to conformational change of γ-secretase structure and specifically accelerates γ-secretase cleavage of APP without affecting other substrates including Notch1, potentially through its interaction with the N-terminal fragment of presenilin 1 (PS1). Reduction of GM1 levels decreases amyloid plaque deposition and improves cognitive dysfunction. This study reveals the mechanism of GM1 in Aβ generation and provides the evidence that decreasing GM1 levels represents a potential strategy in AD treatment. These results provide insights into the detailed mechanism of the effect of GM1 on PS1, representing a step toward the characterization of its novel role in the modulation of γ-secretase activity and the pathogenesis of AD.

Chain-Kinked Design: Improving Stretchability of Polymer Semiconductors through Nonlinear Conjugated Linkers

The manipulation of the polymer backbone structure has a profound influence on the crystalline behavior and charge transport characteristics of polymers. These strategies are commonly employed to optimize the performance of stretchable polymer semiconductors. However, a universal method that can be applied to conjugated polymers with different donor-acceptor combinations is still lacking. In this study, we propose a universal strategy to boost the stretchability of polymers by incorporating the nonlinear conjugated linker (NCL) into the main chain. Specifically, we incorporate meta-dibromobenzene (MB), characterized by its asymmetric linkage sites, as the NCL into the backbone of diketopyrrolopyrrole-thiophene-based (DPP-based) polymers. Our research demonstrates that the introduction of MB prompts chain-kinking, thereby disrupting the linearity and central symmetry of the DPP conjugated backbone. This modification reshapes the polymer conformation, decreasing the radius of gyration and broadening the free volume, which consequently adjusts the level of crystallinity, leading to a considerable increase in the stretchability of the polymer. Importantly, this method increases stretchability without compromising mobility and exhibits broad applicability across a wide range of donor-acceptor pair polymers. Leveraging this strategy, fully stretchable transistors were fabricated using a DPP polymer that incorporates 10 mol % of MB. These transistors display a mobility of approximately 0.5 cm2 V-1 s-1 and prove remarkably durable, maintaining 90% of this mobility even after enduring 1000 cycles at 25% strain. Overall, we propose a method to systematically control the main-chain conformation, thereby enhancing the stretchability of conjugated polymers in a widely applicable manner.

Antifouling Surfaces Based on Polyzwitterion Loop Brushes

Antifouling surfaces have attracted increasing interest in recent years due to their potential application in various fields. In this work, we report a loop polyzwitterionic coating that exhibits excellent resistance to protein adsorption. Triblock and diblock copolymers of 2-[(2-hydroxyethyl)disulfanyl]ethyl methacrylate) (HSEMA) and 2-(dimethylamino)ethyl methacrylate) (DMAEMA) were synthesized by atom-transferred radical polymerization, followed by betainization of the DMAEMA block with 1,3-propane sultone and reduction of the disulfide bond in HSEMA to yield a triblock copolymer comprising a zwitterionic poly(sulfobetaine methacrylate) (PSBMA) midblock and poly(2-sulfanylethyl methacrylate) (PSEMA) terminal blocks as well as its diblock analogue that was of the same composition as the former and half the chain length. Both copolymers adsorbed to the gold substrate via the thiol groups in the terminal PSEMA block(s), creating loop and linear PSBMA brush coatings of comparable thickness, as revealed by X-ray photoelectron spectroscopy and ellipsometry. Adsorption of bovine serum albumin and fibrinogen as model proteins from solution to these surfaces was investigated by a quartz crystal microbalance with dissipation and confocal laser scanning microscopy (CLSM), and platelet and bacterial adhesions were assessed by scanning electron microscopy and CLSM. The results demonstrate that both linear and loop polyzwitterion brushes are excellent in resisting the adsorption of the foulants, and the loop brushes are superior to the linear analogues.

Linear (-)-Zampanolide: Flexibility in Conformation-Activity Relationships

Through an understanding of the conformational preferences of the polyketide natural product (-)-zampanolide, and the structural motifs that control these preferences, we developed a linear zampanolide analogue that exhibits potent cytotoxicity against cancer cell lines. This discovery provides a set of three structural handles for further structure-activity relationship (SAR) studies of this potent microtubule-stabilizing agent. Moreover, it provides additional evidence of the complex relationship between ligand preorganization, conformational flexibility, and biological potency. In contrast to medicinal chemistry dogma, these results demonstrate that increased overall conformational flexibility is not necessarily detrimental to protein binding affinity and biological activity.

Comparison of Conformation and Movement Characteristics in Dressage and Jumping Sport Warmblood Mares Based on Point Evaluation and Linear Scoring System

The aim of this study was to analyze the influence of factors on the results of 100-point judging systems, linear scoring and basic measurements, as well as differences between systems for dressage and jumping warmblood mares. The research covered official data on 1547 warmblood mares. Analysis of variance and phenotypic correlations (Pearson and partial) were used. The analysis showed that sport type significantly influenced 1/3 of biometric measurements, 2/9 traits on the 100-point system and 7/37 of linear scored traits. The influence of horse type evaluation is more significant in linear scoring than in the 100-point evaluation, which provides an argument for using the first system in breeding. In the linear evaluation for warmblood mares grouped as jumping or dressage, the most significant differences (p < 0.001) were noted between the traits of shoulder position, line of the loins and shape of the croup. In the point-based evaluation, differences (p < 0.05) were found in forelimbs and walking, as well as chest circumference in basic measurements. None of the traits in the two evaluation systems is identical to any other (r > 0.8). The comparison of systems showed meaningful correlations only between general traits. The differences between sport types of warmblood mares were smaller than expected. More objective traits should be discovered to increase accuracy in discriminating between horse types.

Analytical Ultracentrifugation Detects Quaternary Rearrangements and Antibody-Induced Conformational Selection of the SARS-CoV-2 Spike Trimer

Analytical ultracentrifugation (AUC) analysis shows that the SARS-CoV-2 trimeric Spike (S) protein adopts different quaternary conformations in solution. The relative abundance of the "open" and "close" conformations is temperature-dependent, and samples with different storage temperature history have different open/close distributions. Neutralizing antibodies (NAbs) targeting the S receptor binding domain (RBD) do not alter the conformer populations; by contrast, a NAb targeting a cryptic conformational epitope skews the Spike trimer toward an open conformation. The results highlight AUC, which is typically applied for molecular mass determination of biomolecules as a powerful tool for detecting functionally relevant quaternary protein conformations.

Quantum chemical investigation of predominant conformation of the antibiotic azithromycin in water and DMSO solutions: thermodynamic and NMR analysis

Azithromycin (AZM) is a macrolide-type antibiotic used to prevent and treat serious infections (mycobacteria or MAC) that significantly inhibit bacterial growth. Knowledge of the predominant conformation in solution is of fundamental importance for advancing our understanding of the intermolecular interactions of AZM with biological targets. We report an extensive density functional theory (DFT) study of plausible AZM structures in solution considering implicit and explicit solvent effects. The best match between the experimental and theoretical nuclear magnetic resonance (NMR) profiles was used to assign the preferred conformer in solution, which was supported by the thermodynamic analysis. Among the 15 distinct AZM structures, conformer M14, having a short intramolecular C6-OH … N H-bond, is predicted to be dominant in water and dimethyl sulfoxide (DMSO) solutions. The results indicated that the X-ray structure backbone is mostly conserved in solution, showing that large flexible molecules with several possible conformations may assume a preferential spatial orientation in solution, which is the molecular structure that ultimately interacts with biological targets.

Effect of Soft Preheating of Bovine Serum Albumin on the Complexation with Oligochitosan: Structure and Conformation of BSA in the Complex

Phase analysis, spectroscopic, and light scattering methods are applied to investigate the peculiarities of the interaction of oligochitosan (OCHI) with native and preheated bovine serum albumin (BSA) as well as the conformational and structural changes of BSA in BSA/OCHI complex. As shown, untreated BSA binds with OCHI mainly forming soluble electrostatic nanocomplexes, with the binding causing an increase in BSA helicity without a change in the local tertiary structure and thermal stability of BSA. In contrast, soft preheating at 56 °C enhances the complexation of BSA with OCHI and slightly destabilizes the secondary and local tertiary structures of BSA within the complex particles. Preheating at 64 °C (below the irreversible stage of BSA thermodenaturation) leads to further enhancement in the complexation and formation of insoluble complexes stabilized by both Coulomb forces and hydrophobic interactions. The finding can be promising for the preparation of biodegradable BSA/chitosan-based drug delivery systems.

Genetic selection for reduced health treatment costs in Holstein cows: implications from a long-term study

The objective of this study was to estimate genetic parameters of health treatment cost of Holstein cows from producer-recorded health treatments in 8 herds over an 8-yr period of time. Genetic parameters of health treatment cost were estimated in first (n = 2,214), second (n = 1,487) and third (n = 800) parities of US Holstein cows. The health treatments were uniformly defined and consistently recorded by 8 high-performance dairy herds in Minnesota from 2008 to 2015. A fixed treatment cost was assigned to 14 types of health treatments, and the cost included the mean veterinary expense obtained from the veterinary clinics that serviced the 8 herds, pharmaceuticals, and labor cost. The labor cost was $18/h, and the time incurred for each type of health treatment was determined from interviews with the herd owners. The 14 types of health treatment costs were partitioned into 5 categories: mastitis (including mastitis diagnostic test), reproduction (cystic ovary, retained placenta, and metritis), lameness (hoof treatments), metabolic (milk fever, displaced abomasum, ketosis, and digestive), and miscellaneous (respiratory, injury, and other). Health treatment cost for each cow was summed by category within lactation and also across categories within lactation. The estimates of heritability for health treatment cost were 0.13, 0.04, 0.10, 0.12, and 0.04 for the mastitis, reproduction, lameness, metabolic, and miscellaneous categories, respectively, in first parity. Genetic correlations between categories of health treatment cost in first parity were greatest for mastitis and reproduction (r = 0.85); however, phenotypic correlations between all categories were small (r < 0.16). Total health treatment cost had a large genetic correlation with somatic cell score (0.93) and 305-d milk production (0.44) in first parity; however, the genetic correlation (-0.60) between total health treatment cost and udder depth in first parity indicated a genetic relationship exists between shallow udders and less total health treatment cost. Total health treatment cost across categories had a heritability estimate of 0.25 in first parity, 0.16 in second parity, and 0.17 in third parity. Consequently, genetic selection for reduced health treatment cost should be possible by using producer-recorded health treatment records supplemented with treatment costs.

Molecular Conformations of Shape Anisometrically Variant Mesogens in Liquid Crystalline Phase Studied by 13 C NMR Spectroscopy

Mesogens that vary in shape anisometry have been investigated by 13 C solid-state NMR in the liquid crystalline phase to inspect the conformations. The molecules examined comprise of (i) rod-like mesogen with three-phenyl ring core and terminal hexyloxy chains, (ii) three-ring core linked to the fourth phenyl ring via a spacer, and (iii) trimesic acid connected to three side arms core units through a spacer. The order parameter (Szz ) values for the phenyl rings of the rod-like mesogen are 0.65-0.68, while the mesogen with a three-ring core linked to a phenyl ring via spacer showed dissimilarity. Consequently, for the core unit phenyl rings, Szz is ~0.70, and the terminal phenyl ring showed a low value of 0.12. For the trimesic acid based mesogen, the Szz value for the side arm phenyl rings is ~0.53, and for the central phenyl ring, a very low value of 0.11 is witnessed. By considering the ordering of the rod-like mesogen as a yardstick and employing the ratios of Szz values of the phenyl rings, the average conformations of other mesogens are arrived. Accordingly, for the trimesic acid based mesogen, a tripod-like conformation instead of λ shape is proposed in the liquid crystalline phase.

Novel Conformation-Dependent Tau Antibodies Are Modulated by Adjacent Phosphorylation Sites

Tau proteins within the adult central nervous system (CNS) are found to be abnormally aggregated into heterogeneous filaments in neurodegenerative diseases, termed tauopathies. These tau inclusions are pathological hallmarks of Alzheimer's disease (AD), Pick's disease (PiD), corticobasal degeneration (CBD), and progressive supranuclear palsy (PSP). The neuropathological hallmarks of these diseases burden several cell types within the CNS, and have also been shown to be abundantly phosphorylated. The mechanism(s) by which tau aggregates in the CNS is not fully known, but it is hypothesized that hyperphosphorylated tau may precede and further promote filament formation, leading to the production of these pathological inclusions. In the studies herein, we generated and thoroughly characterized two novel conformation-dependent tau monoclonal antibodies that bind to residues Pro218-Glu222, but are sensitive to denaturing conditions and highly modulated by adjacent downstream phosphorylation sites. These epitopes are present in the neuropathological hallmarks of several tauopathies, including AD, PiD, CBD, and PSP. These novel antibodies will further enable investigation of tau-dependent pathological inclusion formation and enhance our understanding of the phosphorylation signatures within tauopathies with the possibility of new biomarker developments.

Advances, Applications, and Perspectives in Small-Angle X-ray Scattering of RNA

RNAs exhibit a plethora of functions far beyond transmitting genetic information. Often, RNA functions are entailed in their structure, be it as a regulatory switch, protein binding site, or providing catalytic activity. Structural information is a prerequisite for a full understanding of RNA-regulatory mechanisms. Owing to the inherent dynamics, size, and instability of RNA, its structure determination remains challenging. Methods such as NMR spectroscopy, X-ray crystallography, and cryo-electron microscopy can provide high-resolution structures; however, their limitations make structure determination, even for small RNAs, cumbersome, if at all possible. Although at a low resolution, small-angle X-ray scattering (SAXS) has proven valuable in advancing structure determination of RNAs as a complementary method, which is also applicable to large-sized RNAs. Here, we review the technological and methodological advancements of RNA SAXS. We provide examples of the powerful inclusion of SAXS in structural biology and discuss possible future applications to large RNAs.

Multi-conformers caused by conformational change of A-ring in the C18- and C19-N-dealkyl diterpenoid alkaloids

This paper describes a rare phenomenon of multi-conformers caused by conformational change of A-ring in the C18- and C19- N-dealkyl diterpenoid alkaloids. The possible reasons for the generation of multiple conformational isomers are complex, which could be affected by the substituents at C-1, C-3, C-13, C-14, and C-15, pH, solvents, the intramolecular hydrogen bond between 1α-OCH3/1α-OH and N-H groups, acid-base treatment, preparation methods, and work-up procedures.

The unusual (syn-/anti-)2 conformation of a di-meth-oxy-pyrimidyl-based tennimide

The tennimide macrocycle, (I) (C52H40N16O16.0.167H2O), was synthesized from 2-amino-4,6-di-meth-oxy-pyrimidine and pyridine-2,6-dicarbonyl dichloride. Compound (I) represents the first tennimide incorporating pyridine rings in the macrocycle scaffold. In the macrocycle ring, the carbonyl groups at each successive dicarbon-yl(pyridine) moiety adopt the (syn/anti)2 conformation. This contrasts with all previously reported tetra-imide macrocycles, which exhibit the (syn)4 conformation. The effect is to close any potential cavity or niche by having two of the central pyridine C5N rings aligned close to each other [with closest pyridine Cg⋯Cg ring centroid separations of 3.5775 (19) Å; closest C⋯C = 3.467 (5) Å]. A partial occupancy water mol-ecule (with s.o.f. = 0.167), resides with its oxygen atom on a twofold axis at hydrogen-bonding distances to the carbonyl O atom, in a mol-ecular niche between two pyridine rings. Macrocyles of (I) have all six C=O groups and all eight meth-oxy O atoms present on the macrocycle surface. However, all twelve N atoms are effectively shielded on steric grounds from any potential inter-molecular inter-actions. The remaining two C=O O atoms inter-act with the partial occupancy water mol-ecule via two O-H⋯O=C hydrogen bonds. Macrocycles of (I) stack as one-dimensional chains along the b-axis direction with primary inter-molecular inter-actions involving weak C-H⋯O=C/OCH3/H2O contacts. Chains inter-lock weakly via meth-oxy-meth-oxy C-H⋯O inter-actions into two-dimensional sheets.

Enantio- and Diastereomerically Pure Titanocenes by Dynamic Conformational Locking

The synthesis of enantiomerically pure titanocenes is limited to cases with enantiomerically pure substituents at the cyclopentadienyl ligands and to ansa-titanocenes. For the latter complexes, the use of achiral ligands requires a resolution of enantiomers and frequently also a separation of the diastereoisomers obtained after metalation. Here, we introduce a new synthetic method that relies on the use of enantiomerically pure camphorsulfonate (CSA) ligands as control elements for the absolute and relative configuration of titanocene complexes. Starting from the conformationally flexible (RC5 H4 )2 TiCl2 , the desired conformationally locked and hence enantio- and diastereomerically pure complexes (RC5 H4 )2 Ti(CSA)2 are obtained in just two steps. According to X-ray crystallography the (RC5 H4 )2 Ti fragment is essentially C2 -symmetric and nuclear magnetic resonance displays overall C2 -symmetry. We applied density functional theory methods to unravel the dynamics of the complexes and the mechanisms and selectivities of their formation.

Effects of quercetin on the gel properties of pork myofibrillar proteins and related changes in protein conformation

BACKGROUND

To study the effects of quercetin on the functionality of myofibrillar proteins (MPs), various levels of quercetin (0, 10, 50, 100 and 200 μmol g^-1 protein) were added to MP solution and the structure and gel properties of MPs were determined.

RESULTS

Compared with the control MPs not treated with quercetin, adding 10, 50 and 100 μmol g^-1 quercetin caused a significant (P < 0.05) loss of sulfhydryls; 10 and 50 μmol g^-1 quercetin enhanced the surface hydrophobicity significantly (P < 0.05), and 50, 100 and 200 μmol g^-1 quercetin reduced the fluorescence intensity of tryptophan. Additions of 50, 100 and 200 μmol g^-1 quercetin resulted in a significant (P < 0.05) reduction in MP solubility. Adding 10, 50 and 100 μmol g^-1 quercetin did not significantly (P > 0.05) change the gel strength and water-holding ability of MPs than control, but 200 μmol g^-1 quercetin declined the gel properties significantly (P < 0.05). The microstructure and dynamic rheological properties confirmed the results of the gel properties of MPs affected by various levels of quercetin.

CONCLUSION

The results obtained in the present study show that mildly high levels of quercetin can maintain the gel properties of MPs, which may be a result of the moderate MP cross-linkage and aggregation caused by the covalent and non-covalent interactions of MPs. © 2023 Society of Chemical Industry.

Wiggle and Shake: Managing and Exploiting Conformational Dynamics during Proteasome Biogenesis

The 26S proteasome is the largest and most complicated protease known, and changes to proteasome assembly or function contribute to numerous human diseases. Assembly of the 26S proteasome from its ~66 individual polypeptide subunits is a highly orchestrated process requiring the concerted actions of both intrinsic elements of proteasome subunits, as well as assistance by extrinsic, dedicated proteasome assembly chaperones. With the advent of near-atomic resolution cryo-electron microscopy, it has become evident that the proteasome is a highly dynamic machine, undergoing numerous conformational changes in response to ligand binding and during the proteolytic cycle. In contrast, an appreciation of the role of conformational dynamics during the biogenesis of the proteasome has only recently begun to emerge. Herein, we review our current knowledge of proteasome assembly, with a particular focus on how conformational dynamics guide particular proteasome biogenesis events. Furthermore, we highlight key emerging questions in this rapidly expanding area.

Hexahexyloxycalix[6]arene, a Conformationally Adaptive Host for the Complexation of Linear and Branched Alkylammonium Guests

Hexahexyloxycalix[6]arene 2b leads to the endo-cavity complexation of linear and branched alkylammonium guests showing a conformational adaptive behavior in CDCl₃ solution. Linear n-pentylammonium guest 6a⁺ induces the cone conformation of 2b at the expense of the 1,2,3-alternate, which is the most abundant conformer of 2b in the absence of a guest. In a different way, branched alkylammonium guests, such as tert-butylammonium 6b⁺ and isopropylammonium 6c⁺, select the 1,2,3-alternate as the favored 2b conformation (6b⁺/6c⁺&sub;2b^1,2,3-alt), but other complexes in which 2b adopts different conformations, namely, 6b⁺/6c⁺&sub;2b^cone, 6b⁺/6c⁺&sub;2b^paco, and 6b⁺/6c⁺&sub;2b^1,2-alt, have also been revealed. Binding constant values determined via NMR experiments indicated that the 1,2,3-alternate was the best-fitting 2b conformation for the complexation of branched alkylammonium guests, followed by cone > paco > 1,2-alt. Our NCI and NBO calculations suggest that the H-bonding interactions (⁺N-H···O) between the ammonium group of the guest and the oxygen atoms of calixarene 2b are the main determinants of the stability order of the four complexes. These interactions are weakened by increasing the guest steric encumbrance, thus leading to a lower binding affinity. Two stabilizing H-bonds are possible with the 1,2,3-alt- and cone-2b conformations, whereas only one H-bond is possible with the other paco- and 1,2-alt-2b stereoisomers.