Conformational Structure Research Articles

Giant pandas in captivity undergo short-term adaptation in nerve-related pathways.

Behaviors in captive animals, including changes in appetite, activity level, and social interaction, are often seen as adaptive responses. However, these behaviors may become progressively maladaptive, leading to stress, anxiety, depression, and other negative reactions in animals. In this study, we investigated the whole-genome sequencing data of 39 giant panda individuals, including 11 in captivity and 28 in the wild. To eliminate the mountain range effect and focus on the factor of captivity only, we first performed a principal component analysis. We then enumerated the 21,474,180 combinations of wild giant pandas (11 chosen from 28) and calculated their distances from the 11 captive individuals. The 11 wild individuals with the closest distances were used for the subsequent analysis. The linkage disequilibrium (LD) patterns demonstrated that the population was almost eliminated. We identified 505 robust selected genomic regions harboring at least one SNP, and the absolute frequency difference was greater than 0.6 between the two populations. GO analysis revealed that genes in these regions were mainly involved in nerve-related pathways. Furthermore, we identified 22 GO terms for which the selection strength significantly differed between the two populations, and there were 10 nerve-related pathways among them. Genes in the differentially abundant regions were involved in nerve-related pathways, indicating that giant pandas in captivity underwent minor genomic selection. Additionally, we investigated the relationship between genetic variation and chromatin conformation structures. We found that nucleotide diversity (θπ) in the captive population was correlated with chromatin conformation structures, which included A/B compartments, topologically associated domains (TADs) and TAD-cliques. For each GO term, we then compared the expression level of genes regulated by the above four factors (AB index, TAD intactness, TAD clique and PEI) with the corresponding genomic background. The retained 10 GO terms were all coordinately regulated by the four factors, and three of them were associated with nerve-related pathways. This study revealed that giant pandas in captivity undergo short-term adaptation in nerve-related pathways. Furthermore, it provides new insights into the molecular mechanism of gene expression regulation under short-term adaptation to environmental change.

Influence of different pH milieu on the structure and function of human Aurora kinase B protein (AURK-B): Amalgamation of both spectroscopic and computational approach

Aurora kinase B (AURK-B) is a serine/threonine kinase protein that plays an essential role in chromosomal separation during the cell cycle event. AURK-B is highly expressed in various types of cancer such as human seminoma, thyroid carcinoma, non-small cell lung carcinoma (NSCLC), oral carcinoma, and gastric cancer. Hence, it is a potential therapeutic target in the treatment of various cancers. The structure of AURK-B in complex with one of its substrate inner centromeric protein (INCENP) is present, but the structural and functional characterization of native AURK-B at different pH environment is still unexplored.This study determines the effect of different pH milieu on the structure and function of AURK-B protein wherein the influence of pH on the protein conformation was probed using Circular dichroism (CD) and fluorescence spectroscopy. The structural studies were further combined with functional activity assay to observe the change in kinase activity at various pH milieu (2.0–11.0). CD and fluorescence spectroscopy experiments dictate that at high acidic conditions (pH 2.0 – 5.0), the secondary and tertiary structures of AURK-B become distorted, leading to diminished activity. The protein, however, was observed to stabilize towards pH 7.0 – 8.0 with minimal structure alteration over the basic pH range (pH 9.0 –11.0). The measured spectroscopic structural features were found to be in-line with obtained experimental kinase activity assays.Further, in-vitro experiments indicate that the enzyme is maximally active at pH 8.0. More ordered conformation and compact structure was observed at this pH (pH 8.0) as compared to other pH values through molecular dynamics simulation studies (MDS). As AURK-B localizes itself in the intracellular compartment, this study may provide a clue about the role of different pH environments in enhancing cancer growth, proliferation, and invasion.

Predicted deleterious variants in ABCA1, LPL, LPA and KIF6 are associated with statin response and adverse events in patients with familial hypercholesterolemia and disturb protein structure and stability.

This study explored the association of deleterious variants in pharmacodynamics (PD) genes with statin response and adverse effects in patients with familial hypercholesterolemia (FH) and analyzed their potential effects on protein structure and stability. Clinical and laboratory data were obtained from 144 adult FH patients treated with statins. A panel of 32 PD genes was analyzed by exon-targeted gene sequencing. Deleterious variants were identified using prediction algorithms and their structural effects were analyzed by molecular modeling studies. A total of 102 variants were predicted as deleterious (83 missense, 8 stop-gain, 4 frameshift, 1 indel, 6 splicing). The variants ABCA1 rs769705621 (indel), LPA rs41267807 (p.Tyr2023Cys) and KIF6 rs20455 (p.Trp719Arg) were associated with reduced low-density lipoprotein cholesterol (LDLc) response to statins, and the LPL rs1801177 (p.Asp36Asn) with increased LDLc response (P < 0.05). LPA rs3124784 (p.Arg2016Cys) was predicted to increase statin response (P = 0.022), and ABCA1 rs769705621 to increase the risk of statin-related adverse events (SRAE) (P = 0.027). LPA p.Arg2016Cys and LPL p.Asn36Asp maintained interactions with solvent, LPA p.Tyr2023Cys reduced intramolecular interaction with Gln1987, and KIF6 p.Trp719Arg did not affect intramolecular interactions. DDMut analysis showed that LPA p.Arg2016Cys and p.Tyr2023Cys and LPL p.Asp36Asn caused energetically favorable changes, and KIF6 p.Trp719Arg resulted in unfavorable energetic changes, affecting protein stability. Deleterious variants in ABCA1, LPA, LPL and KIF6 are associated with variability in LDLc response to statins, and ABCA1 rs769705621 is associated with SRAE risk in FH patients. Molecular modeling studies suggest that LPA p.Tyr2023Cys and KIF6 p.Trp719Arg disturb protein conformational structure and stability.

ASPSCR1-TFE3 reprograms transcription by organizing enhancer loops around hexameric VCP/p97

The t(X,17) chromosomal translocation, generating the ASPSCR1::TFE3 fusion oncoprotein, is the singular genetic driver of alveolar soft part sarcoma (ASPS) and some Xp11-rearranged renal cell carcinomas (RCCs), frustrating efforts to identify therapeutic targets for these rare cancers. Here, proteomic analysis identifies VCP/p97, an AAA+ ATPase with known segregase function, as strongly enriched in co-immunoprecipitated nuclear complexes with ASPSCR1::TFE3. We demonstrate that VCP is a likely obligate co-factor of ASPSCR1::TFE3, one of the only such fusion oncoprotein co-factors identified in cancer biology. Specifically, VCP co-distributes with ASPSCR1::TFE3 across chromatin in association with enhancers genome-wide. VCP presence, its hexameric assembly, and its enzymatic function orchestrate the oncogenic transcriptional signature of ASPSCR1::TFE3, by facilitating assembly of higher-order chromatin conformation structures demonstrated by HiChIP. Finally, ASPSCR1::TFE3 and VCP demonstrate co-dependence for cancer cell proliferation and tumorigenesis in vitro and in ASPS and RCC mouse models, underscoring VCP’s potential as a novel therapeutic target.

Microsecond dynamics control the HIV-1 Envelope conformation.

The HIV-1 Envelope (Env) glycoprotein facilitates host cell fusion through a complex series of receptor-induced structural changes. Although remarkable progress has been made in understanding the structures of various Env conformations, microsecond timescale dynamics have not been studied experimentally. Here, we used time-resolved, temperature-jump small-angle x-ray scattering to monitor structural rearrangements in an HIV-1 Env SOSIP ectodomain construct with microsecond precision. In two distinct Env variants, we detected a transition that correlated with known Env structure rearrangements with a time constant in the hundreds of microseconds range. A previously unknown structural transition was also observed, which occurred with a time constant below 10 μs, and involved an order-to-disorder transition in the trimer apex. Using this information, we engineered an Env SOSIP construct that locks the trimer in the prefusion closed state by connecting adjacent protomers via disulfides. Our findings show that the microsecond timescale structural dynamics play an essential role in controlling the Env conformation with impacts on vaccine design.

Mass Spectrometry Analysis on the Breakage of Allergens in High-Molecular-Mass Polymer of Roasted Peanuts.

Peanut allergy is a prevalent and concerning food allergy. Roasting can introduce structural changes to peanut allergens, affecting their allergenicity, but the structure on the primary structure is unclear. Here, the breakage sites were identified by mass spectrometry and software tools, and structural changes were simulated by molecular dynamics and displayed by PyMOL software. Results revealed that the appearance frequencies of L, Q, F, and E were high at the N-terminal of the breakage site, while S and E were dominant at the C-terminal. In the conformational structure, breakage sites were found close to disulfide bonds and the Cupin domains of Ara h 1 and Ara h 3. The breakage of allergens destroyed linear epitopes and might change the conformation of epitopes, which could influence peanuts' potential allergenicity.

Structure and molecular interactions in 1‑ethyl-3-methylimidazolium bis(trifluoromethylsulfonyl)imide ion pair conformers: abinitio DFT based study

Density functional theory (DFT) calculations with Grimme’s B97D functional including dispersion are employed to provide both structural and electronic insight into the multifold interactions occurring in 1-ethyl-3-methylimidazolium bis(trifluoromethylsulfonyl)imide ionic liquid [EMI][TFSI], which is currently being targeted for applications in next-generation Li-ion battery electrolytes. The geometric structure, interaction energy and natural bond orbital analysis of the ion-pair conformers of [EMI][TFSI] show differences from the conventional H-bonds. A total of six stable [EMI][TFSI] ion pair conformers were observed. Our results show that a doubly ionic H-bond exists between [EMI]+ and [TFSI]− ion pair conformers. The greater the number of multiple H-bond type interactions, the greater the absolute value of the interaction energy. Moreover, results from the NBO analysis show that, for [EMI][TFSI] ion pair conformers, charge transfer occurs mainly from the lone pairs of oxygen and nitrogen atom to the σ-type anti-bonding orbital of the C–H and π-type anti-bonding orbitals of N–C bonds. This was evident from the values of the stabilization energy E(2) associated with each electron delocalization from the donor to acceptor orbitals. There exist large numbers of multiple concomitant hydrogen bonds, but the values of the stabilization energy E(2) are generally small (E(2)n→\\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document}$$\ o$$\\end{document}σ* < 3 kcal/mol) for the individual H-bond interactions. The shorter the C–H···O and/or C–H···N bond is, the larger charge transfer, and the larger the stabilization energy E(2) associated with electron delocalization from donor to acceptor. Generally, the [EMI][TFSI] ion pair conformers tend to form multiple but bent H bonds, reducing the strength of the individual H bonds from a potential (linear) maximum.

CaO:Tb&lt;sup&gt;3+ &lt;/sup&gt; green-emitting phosphor for white light-emitted diode-phosphor applications: the improvement of light output intensity

The use of CaO:Tb3+ with light green emission on for improvement of both luminescent output and chromatic fidelity of the white light emitted from a light-emitting diode (LED). The CaO:Tb3+ is combined with the yellow-emitting phosphor of YAG:Ce3+ to provide sufficient colored spectral proportion for the white light generation, enhancing the color performance. The phosphor combination is utilized for the three most applied LED structures: conformal, in-cup, and remote phosphor structures. The changes in optical properties of these three LEDs are monitored with adjustments in the proportion of CaO:Tb3+. The higher proportion of the green phosphor results in higher scattering efficiency in all structures, offering better color coordination and stronger luminous flux. The color quality scale is somehow reduced when CaO:Tb3+ concentration is more than a certain level. Therefore, depending on the phosphor configuration of the white light-emitting diode (WLED), the concentration of CaO:Tb3+ should be modified to achieve a good color rendition with improved color consistency and luminous properties.

Codimension two spacelike submanifolds in Lorentzian manifolds and conformal structures

Starting from a Riemannian conformal structure on a manifold M, we provide a method to construct a family of Lorentzian manifolds. The construction relies on the choice of a metric in the conformal class and a smooth 1-parameter family of self-adjoint tensor fields. Then, every metric in the conformal class corresponds to the induced metric on M seen as a codimension two spacelike submanifold into these Lorentzian manifolds. Under suitable choices of the 1-parameter family of tensor fields, there exists a lightlike normal vector field along such spacelike submanifolds whose Weingarten endomorphism provide a Möbius structure on the Riemannian conformal structure. Conversely, every Möbius structure on a Riemannian conformal structure arises in this way. Flat Möbius structures are characterized in terms of the extrinsic geometry of the corresponding spacelike surfaces.

Deformation of discrete conformal structures on surfaces

Deformation of discrete conformal structures on surfaces

Acetal Substitution Reactions: Stereoelectronic Effects, Conformational Analysis, Reactivity vs. Selectivity, and Neighboring-Group Participation.

Acetal substitution reactions can proceed by a number of mechanisms, but oxocarbenium ion intermediates are involved in many of these reactions. Our research has focused on understanding the conformational preferences, structures, and reactions of these intermediates. This Account summarizes our observations that electrostatic effects play a significant role in defining the preferred conformations, and that torsional effects determine how those intermediates react. Neighboring-group effects are not as straightforward as they might seem, considering that oxocarbenium ion intermediates are in equilibrium with structures that involve stabilization by a nearby substituent.

Determining Structural Changes for Ligand Recognition between Human and Rat Phosphorylated BACE1 in Silico and Its Phosphorylation by GSK3β at Thr252 by in Vitro Studies.

Alzheimer's disease (AD) is a neurodegenerative disease affecting older adults. AD pathogenesis involves the production of the highly neurotoxic amyloid-β peptide 1-42 (Aβ1-42) from β-site amyloid precursor protein cleaving enzyme 1 (BACE1). The phosphorylation of BACE1 at Thr252 increases its enzymatic activity. This study examined the phosphorylation of BACE1 from human and rat BACE1 in silico through phosphorylation predictors. Besides, we explored how phosphorylation at various sites affected the BACE1 structure and its affinity with amyloid precursor protein (APP) and six BACE1 inhibitors. Additionally, we evaluated the phosphorylation of Thr252-BACE1 by glycogen synthase kinase 3 β (GSK3β) in vitro. The phosphorylation predictors showed that Thr252, Ser59, Tyr76, Ser71, and Ser83 could be phosphorylated. Also, Ser127 in rat BACE1 can be phosphorylated, but human BACE1 has a Gly at this position. Molecular dynamics simulations showed that Ser127 plays an important role in the open and closed BACE1 conformational structures. Docking studies and the molecular mechanics generalized Born surface area (MMGBSA) approach showed that human BACE1 phosphorylated at Thr252 and rat BACE1 phosphorylated at Ser71 have the best binding and free energy with APP, forming hydrogen bonds with Asp672. Importantly, inhibitors have a higher affinity for the phosphorylated rat BACE1 than for its human counterpart, which could explain their failure during clinical trials. Finally, in vitro experiments showed that GSK3β could phosphorylate BACE1. In conclusion, BACE1 phosphorylation influences the BACE1 conformation and its recognition of ligands and substrates. Thus, these features should be carefully considered in the design of BACE1 inhibitors.

Changes in molecular conformation and electronic structure of DNA under 12C ions based on first-principles calculations

Fundamental studies on the interaction between ionizing radiation and deoxyribonucleic acid (DNA) can contribute to understanding the biological effects of radiation protection and radiotherapy. The transitional process from ionized and excited DNA to DNA lesions, such as strand breaks and base lesions, remains uncertain. In this study, we focused in particular on the direct effects of radiation on DNA and calculated the number of ionizations induced within 10 base pairs of DNA using the Particle and Heavy Ion Transport code System, a general-purpose Monte Carlo code for radiation transport. The electronic structure of the ionized DNA is subsequently calculated using the first-principles calculation software OpenMX. Through these calculations, we successfully identified the redox site of DNA and quantitatively evaluated the amount of molecular bond cleavage. The scientific findings of this study will elucidate the cleavage mechanism of DNA in the high-density radiation field realized by ion beam irradiation by determining the redox sites.

Synthesis and physical properties of new 1,6-diazabicyclo[4.1.0]heptanes: Quantum-chemistry calculations and crystal structures simulations

Nine new 1,6-diazabicyclo[4.1.0]heptanes with alkyl substituents in position 7 were synthesized for the first time. The compounds were characterized by NMR and mass spectrometry, their densities were measured, and X-ray diffraction data were obtained for compounds 8, 12 and 13. The structure of conformers for 1,6-diazabicyclo[4.1.0]heptanes was studied using quantum chemistry methods. Crystal packings for 25 different compounds of the class 1,6-diazabicyclo[4.1.0]heptanes and 1,5-diazabicyclo[3.1.0]hexanes were modeled based on the Atom-Atom potential method. The enthalpies of formation and combustion of 1,6-diazabicyclo[4.1.0]heptanes and 1,5-diazabicyclo[3.1.0]hexanes are estimated and compared with their naphthenic analogs.

Developing of SARS-CoV-2 fusion protein expressed in E. coli Shuffle T7 for enhanced ELISA detection sensitivity – an integrated experimental and bioinformatic approach

In the recent COVID-19 pandemic, developing effective diagnostic assays is crucial for controlling the spread of the SARS-CoV-2 virus. Multi-domain fusion proteins are a promising approach to detecting SARS-CoV-2 antibodies. In this study, we designed an antigen named CoV2-Pro, containing two RBD domains from SARS-CoV-2 Omicron and Delta variants and one CTD domain of the nucleoprotein in the order of RBD-RBD-N, linked by a super flexible glycine linker. We evaluated the suitability of E. coli Shuffle T7 and BL21 (DE3) strain for expressing CoV2-Pro. Moreover, Bioinformatic studies were conducted first to analyze the tertiary structure of CoV2-Pro. The CoV2-Pro sequences were cloned into a pET-32b (+) vector for expression in E. coli Shuffle T7 and BL21 (DE3). SDS-PAGE and western blot confirmed the protein expression and folding structure. The CoV2-Pro-TRX was purified by Ni-NTA affinity chromatography. Dot blot analysis was performed to evaluate the antigenic characterization of the CoV2-Pro. A molecular docking simulation was conducted to assess the binding affinity of CoV2-Pro with LY-COV555 (Bamlanivimab) monoclonal antibody. A molecular dynamic was performed to analyze the stability of the structure. Bioinformatic and experimental studies revealed a stable conformational 3D structure of the CoV2-Pro. The CoV2-Pro interacted with SARS-CoV-2 antibodies, confirming the correct antigenic structure. We assert with confidence that CoV2-Pro is ideal for developing an ELISA assay for precise diagnosis and rigorous vaccine evaluation during the COVID-19 prevalence. Communicated by Ramaswamy H. Sarma

Morphological Characterization of Self-Amplifying mRNA Lipid Nanoparticles.

The mRNA technology has emerged as a rapid modality to develop vaccines during pandemic situations with the potential to protect against endemic diseases. The success of mRNA in producing an antigen is dependent on the ability to deliver mRNA to the cells using a vehicle, which typically consists of a lipid nanoparticle (LNP). Self-amplifying mRNA (SAM) is a synthetic mRNA platform that, besides encoding for the antigen of interest, includes the replication machinery for mRNA amplification in the cells. Thus, SAM can generate many antigen encoding mRNA copies and prolong expression of the antigen with lower doses than those required for conventional mRNA. This work describes the morphology of LNPs containing encapsulated SAM (SAM LNPs), with SAM being three to four times larger than conventional mRNA. We show evidence that SAM changes its conformational structure when encapsulated in LNPs, becoming more compact than the free SAM form. A characteristic "bleb" structure is observed in SAM LNPs, which consists of a lipid-rich core and an aqueous RNA-rich core, both surrounded by a DSPC-rich lipid shell. We used SANS and SAXS data to confirm that the prevalent morphology of the LNP consists of two-core compartments where components are heterogeneously distributed between the two cores and the shell. A capped cylinder core-shell model with two interior compartments was built to capture the overall morphology of the LNP. These findings provide evidence that bleb two-compartment structures can be a representative morphology in SAM LNPs and highlight the need for additional studies that elucidate the role of spherical and bleb morphologies, their mechanisms of formation, and the parameters that lead to a particular morphology for a rational design of LNPs for mRNA delivery.

Direct Ink writing of high conductive PEDOT:PSS dispersion with an engineered conformation and electronic structure for printed electronic circuits

PEDOT:PSS dispersions with engineered conformation and electronic structure are obtained by controlling polymerization parameters. Outstanding electrical conductivity makes them promising candidates for conductive inks in printed electronic circuits.

Porphyrin(2.1.2.1) organopalladium complexes as efficient singlet oxygen sensitizers.

Four new non-planar and non-aromatic porphyrin organopalladium complexes were synthesized. Conformational structures and optical and electronic properties of the obtained organopalladium complexes containing meso-substituted phenyl, p-tert-butylphenyl, or pentafluorophenyl groups were fully investigated. These complexes showed potent capacity for singlet oxygen (1O2) generation under blue-light irradiation, and the 1O2 quantum yields were in the range of 41%-56%, which were comparable to that of Ru(bpy)3Cl2 (57%), and such potency made these organopalladium complexes potential 1O2 photo sensitizers for photodynamic therapy.

Conformal symplectic, foliated and contact structures

Conformal symplectic, foliated and contact structures

ЛИНЕЙНАЯ ОЦЕНКА БЫКОВ ГОЛШТИНСКОЙ ПОРОДЫ ПО ЭКСТЕРЬЕРНОМУ ТИПУ ИХ ДОЧЕРЕЙ В ТОО «БЕК+»

The article presents the characteristics of linear evaluation of exterior of the first calving heifers of different lineage in the conditions of dairy complex of Beck+ LLP located in the Fyodorov district of the Kostanay region. Three experimental groups of cows were formed based on the different lineage of their first calving: Vis Back Ideal, Reflection Sovereign, and Osborndale Ivanhoe. The assessment of first-calving cows' exterior traits was conducted using 24 indicators and 9-point scale from day 30 to day 150 of lactation. Throughout the study, cows from the Vis Back Ideal and Reflection Sovereign lines demonstrated their superiority in overall body conformation, dairy type, and limb structure compared to their herd mates from the Osborndale Ivanhoe line. Across most of the evaluated traits such as hip height, rear width, udder depth, udder attachment, and hind leg posture, first-calving cows from the Vis Back Ideal line exhibited an advantage over those from the Reflection Sovereign and Osborndale Ivanhoe lines. A comprehensive evaluation of exterior traits was conducted, revealing that first-calving cows from the Vis Back Ideal and Reflection Sovereign lines are classified as "good," while their herd mates from the Osborndale Ivanhoe line are classified as "satisfactory." These finding confirm that servicing bulls significantly influence the expression of linear exterior traits in offspring.