Methods for Genome-Wide Chromatin Interaction Analysis.

Recent analyses revealed the essential function of chromatin structure in maintaining and regulating genomic information. Advancements in microscopy, nuclear structure observation techniques, and the development of methods utilizing next-generation sequencers (NGSs) have significantly progressed these discoveries. Methods utilizing NGS enable genome-wide analysis, which is challenging with microscopy, and have elucidated concepts of important chromatin structures such as a loop structure, a domain structure called topologically associating domains (TADs), and compartments. In this chapter, I introduce chromatin interaction techniques using NGS and outline the principles and features of each method.

HOMER for Analysis of Hi-C Data and Assessment of Composite Structure of the X Chromosome.

Hi-C reads, which represent ligation events between different regions of the genome, must be processed into matrices of interaction frequencies for downstream analysis. Here, I describe a procedure for mapping Hi-C reads to the genome and conversion of mapped reads into the HOMER tag directory format and interaction matrix format for visualization with Juicebox. The method is demonstrated for the mouse composite X chromosome in which reads from the active and inactive X chromosomes are combined after mock DMSO treatment or targeted degradation of cohesin.

Single-Cell Hi-C Analysis Workflow with Pairtools.

Single-cell Hi-C (scHi-C) is a collection of protocols for studying genomic interactions within individual cells. Although data analysis for scHi-C resembles data analysis for bulk Hi-C, the unique challenges of scHi-C, such as high noise and protocol-specific biases, require specialized data processing strategies. In this tutorial chapter, we focus on using pairtools, a suite of tools optimized for scHi-C data, demonstrating its application on a Drosophila snHi-C dataset. While centered on pairtools for snHi-C data, the principles outlined are applicable across scHi-C variants with minor adjustments. This educational chapter aims to guide researchers in using open-source tools for scHi-C analysis, emphasizing critical steps of contact pair extraction, detection of ligation junctions, filtration, and deduplication.

Synthesis and conformational analysis of pyran inter-halide analogues of á´ -talose.

In this work, we describe the synthesis of halogenated pyran analogues of ᴅ-talose using a halo-divergent strategy from known 1,6-anhydro-2,3-dideoxy-2,3-difluoro-ß-ᴅ-mannopyranose. In solution and in the solid-state, all analogues adopt standard 4 C 1-like conformations despite 1,3-diaxial repulsion between the F2 and the C4 halogen. Moreover, the solid-state conformational analysis of halogenated pyrans reveals deviation in the intra-annular torsion angles arising from repulsion between the axial fluorine at C2 and the axial halogen at C4, which increases with the size of the halogen at C4 (F < Cl < Br < I). Crystal packing arrangements of pyran inter-halides show hydrogen bond acceptor and nonbonding interactions for the halogen at C4. Finally, density functional theory (DFT) calculations corroborate the preference of talose analogues to adopt a 4 C 1-like conformation and a natural bonding orbital (NBO) analysis demonstrates the effects of hyperconjugation from C-F antibonding orbitals.

Shape and joint angle data for seven European horse breeds and their repeatability.

Conformation traits are important in the selection and distinction between horse breeds, but tend to be evaluated subjectively within a breed and cannot be compared between them. The horse shape space model, using a combination of 253 landmarks and semi-landmarks, provides objective information on the shape of a horse photographed from the side that can be compared between breeds. In this dataset, we are providing the full set of 253 landmarks for 1241 horses from seven breeds, including an R code file to extract joint angle information and transform the raw data into csv files for further analysis, such as breed comparisons, heritability or genome-wide association studies (single- or multibreed). The repeatability of the joint angles are also reported.

The Effect of Hyperconjugation and Hydrogen Bonding on the Conformers of Methylated Monosaccharides.

The conformational landscapes of four 1-O-methylated monosaccharides-methyl a-glucose, methyl b-glucose, methyl a-galactose, and methyl b-galactose-were characterized using jet-cooled broadband rotational spectroscopy, supported by density functional theory calculations. A newly designed, simple pulsed nozzle assembly was used to introduced the sugar samples into a jet expansion without thermal degradation, eliminating the need for a complex and expensive laser ablation system. Ten conformers were experimentally identified by assigning their rotational spectra, and the intricate methyl internal rotation splittings were analysed. Notably, methylation alters the directionality of intramolecular hydrogen bonding of a-galactose highlighting its impact on structural preference. Natural bond orbital, intrinsic bond strength, and non-covalent interaction analyses were conducted to explore the interplay between hydrogen bonding and hyperconjugation. A set of σ to σ* neutral hyperconjugative interactions were found to override a strong hydrogen bond, driving a preference for the gauche conformers.

End-To-End FRET Enabling Direct Measurement of Oligomer Chain Conformations and Molecular Weight in Reaction Solutions.

Förster resonance energy transfer (FRET) is an established tool for measuring distances between two molecules (donor and acceptor) on the nanometer scale. In the field of polymer science, the use of FRET to measure polymer end-to-end distances (Ree) often requires complex synthetic steps to label the chain ends with the FRET pair. This work reports an anthracene-functionalized chain-transfer agent for reversible addition-fragmentation chain-transfer (RAFT) polymerization, enabling the synthesized chains to be directly end-labeled with a donor and acceptor without the need for any post-polymerization functionalization. Noteworthily, this FRET method allows for chain conformation measurements of low molecular weight oligomers in situ, without any work-up steps. Using FRET to directly measure the average Ree of the oligomer chains during polymerization, the chain growth of methyl methacrylate, styrene, and methyl acrylate is investigated as a function of reaction time, including determining their degree of polymerization (DP). It is found that DP results from FRET are consistent with other established measurement methods, such as nuclear magnetic resonance (NMR) spectroscopy. Altogether, this work presents a broadly applicable and straightforward method to in situ characterize Ree of low molecular weight oligomers and their DP during reaction.

Conformation-Confined Organic Butterfly-Molecule with High Photoluminescence Efficiency, Deep-Blue Amplified Spontaneous Emission, and Unique Piezochromic Luminescence.

Organic fluorophores with tunable π-conjugated paths have attracted considerable attention owing to their diverse properties and promising applications. Herein, we present a tailored butterfly like molecule, 2,2'-(2,5-bis (2,2-diphenylvinyl)-1,4-phenylene)dinaphtha-lene (BDVPN), which exhibits diverse photophysical features in its two polymorphs. The BP phase crystal, with its "aligned wings" conformation, possesses emissive characteristics that are nearly identical to those in dilute solutions. In contrast, the BN phase crystal, which adopts an "orthogonal wings" conformation, exhibits an unusual hypsochromic-shifted emission compared to its dilute solution counterparts. This intriguing hypsochromic-shifted emission originates from the reduction in the effective conjugated length of the molecular skeleton. Notably, BN phase crystals also exhibit exceptional optical performance, featuring high-efficiency emission (76.6%), low-loss optical waveguides (0.571 dB mm-1), deep-blue amplified spontaneous emission (ASE) with a narrow full width at half maximum (FWHM: 6.4 nm), and a unique 200 nm bathochromic shift of piezochromic luminescence.

High Yield of L-Sorbose via D-Glucose Isomerization in Ethanol over a Bifunctional Titanium-Boron-Beta Zeolite.

D-Glucose-to-L-sorbose isomerization on Lewis acidic zeolite is a highly attractive avenue for sorbose production. But the L-sorbose yield is limited by the competing D-glucose-to-D-fructose isomerization and reaction equilibrium. In this work, it is suggested that ethanol directs the glucose conformation for selective D-glucose-to-L-sorbose isomerization. It also reacts with the produced L-sorbose to form ethyl-sorboside, which allows the D-glucose-to-L-sorbose isomerization to proceed beyond the thermodynamic equilibrium limit.  It is shown that a bifunctional zeolite Beta containing framework titanium (Ti) and boron (B) is a selective catalyst for this tandem reaction: Lewis acidic framework Ti catalyzes the D-glucose-to-L-sorbose isomerization via an intramolecular 5,1-hydride shift process as confirmed by isotopic tracing experiments followed by 13C-NMR, while weak Brønsted acid framework B selectively promotes the sorbose ketalization with ethanol. A remarkably high yield of L-sorbose with a high fraction of sugar (>95%: 27% unreacted glucose, 11.4% fructose, 57% sorbose) was obtained after the mixture produced in ethanol was hydrolyzed.

All-Atom Protein Sequence Design Based on Geometric Deep Learning.

Designing sequences for specific protein backbones is a key step in creating new functional proteins. Here, we introduce GeoSeqBuilder, a deep learning framework that integrates protein sequence generation with side chain conformation prediction to produce the complete all-atom structures for designed sequences. GeoSeqBuilder uses spatial geometric features from protein backbones and explicitly includes three-body interactions of neighboring residues. GeoSeqBuilder achieves native residue type recovery rate of 51.6%, comparable to ProteinMPNN and  other leading methods, while accurately predicting side chain conformations. We first used GeoSeqBuilder to design sequences for thioredoxin and a hallucinated three-helical bundle protein. All the 15 tested sequences expressed as soluble monomeric proteins with high thermal stability, and the 2 high-resolution crystal structures solved closely match the designed models. The generated protein sequences exhibit low similarity (minimum 23%) to the original sequences, with significantly altered hydrophobic cores. We further redesigned the hydrophobic core of glutathione peroxidase 4, and 3 of the 5 designs showed improved enzyme activity. Although further testing is needed, the high experimental success rate in our testing demonstrates that GeoSeqBuilder is a powerful tool for designing novel sequences for predefined protein structures with atomic details. GeoSeqBuilder is available at https://github.com/PKUliujl/GeoSeqBuilder.

Conformational Tuning of Magnetic Interactions in Coupled Nanographenes.

Phenalenyl (C13H9) is an open-shell spin-1/2 nanographene. Using scanning tunneling microscopy (STM) inelastic electron tunneling spectroscopy (IETS), covalently bonded phenalenyl dimers have been shown to feature conductance steps associated with singlet-triplet excitations of a spin-1/2 dimer with antiferromagnetic exchange. Here, we address the possibility of tuning the magnitude of the exchange interactions by varying the dihedral angle between the two molecules within a dimer. Theoretical methods ranging from density functional theory calculations to many-body model Hamiltonians solved within different levels of approximation are used to explain STM-IETS measurements of phenalenyl dimers on a hexagonal boron nitride (h-BN)/Rh(111) surface, which exhibit signatures of twisting. By means of first-principles calculations, we also propose strategies to induce sizable twist angles in surface-adsorbed phenalenyl dimers via functional groups, including a photoswitchable scheme. This work paves the way toward tuning magnetic couplings in carbon-based spin chains and two-dimensional lattices.

Conformational variability in the D2 loop of Plasmodium Apical Membrane antigen 1.

Apical Membrane Antigen 1 (AMA1) plays a vital role in the invasion of the host erythrocyte by the malaria parasite, Plasmodium. It is thus an important target for vaccine and anti-malaria therapeutic strategies that block the invasion process. AMA1, present on the surface of the parasite, interacts with RON2, a component of the parasite's rhoptry neck (RON) protein complex, which is transferred to the erythrocyte membrane during invasion. The D2 loop of AMA1 plays an essential role in invasion as it partially covers the RON2-binding site and must therefore be displaced for invasion to proceed. Several structural studies have shown that the D2 loop is very mobile, a property that is probably important for the function of AMA1. Here we present three crystal structures of AMA1 from P. falciparum (strains 3D7 and FVO) and P. vivax (strain Sal1), in which the D2 loop could be largely traced in the electron density maps. The D2 loop of PfAMA1-FVO and PvAMA1 (as a complex with a monoclonal antibody Fab) has a conformation previously noted in the P. knowlesi AMA1 structure. The D2 loop of PfAMA1-3D7, however, reveals a novel conformation. We analyse the conformational variability of the D2 loop in these structures, together with those previously reported. Three different conformations can be distinguished, all of which are highly helical and show some similarity in their secondary structure organisation. We discuss the significance of these observations in the light of the flexible nature of the D2 loop and its role in AMA1 function.

Cellulose Fiber with Enhanced Mechanical Properties: The Role of Co-Solvents in Gel-like NMMO System.

Cellulose has garnered attention in the textile industry, but it exhibits limitations in applications that require high strength and modulus. In this study, regenerated cellulose fiber with enhanced mechanical properties was fabricated from a gel-like N-methylmorpholine N-oxide (NMMO)-cellulose solution by modulating the intermolecular interaction and conformation of the cellulose chains. To control the interaction, two types of co-solvents (dimethyl acetamide (DMAc) and dimethyl formamide (DMF)) were added to the cellulose solutions at varying concentrations (10, 20, and 30 wt%). Rheological analysis showed that the co-solvents reduced the solution viscosity by weakening intermolecular interactions. The calculated distance parameter (Ra) in Hansen space confirmed that the co-solvent disrupted intermolecular hydrogen bonding within cellulose chains. The solutions were spun into fiber via a simple wet spinning process and were characterized by X-ray diffraction (XRD) and universal testing machine (UTM). The addition of co-solvent led to an increased crystallinity index (C.I.) owing to the extended cellulose chains. The modulus of the resulting fiber was increased when the co-solvent concentration was 10 wt%, regardless of the co-solvent type. This study demonstrates the potential for enhancing the mechanical properties of cellulose-based products by modulating the conformation and interaction of cellulose chains through the addition of co-solvent.

Potential Bioactivities, Chemical Composition, and Conformation Studies of Exopolysaccharide-Derived Aspergillus sp. Strain GAD7.

This research identified a marine fungal isolate, Aspergillus sp. strain GAD7, which produces an acidic and sulfated extracellular polysaccharide (EPS) with notable anticoagulant and antioxidant properties. Six fungal strains from the Egyptian Mediterranean Sea were screened for EPS production, with Aspergillus sp. strain GAD7 (EPS-AG7) being the most potent, yielding ~5.19 ± 0.017 g/L. EPS-AG7 was characterized using UV-Vis and FTIR analyses, revealing high carbohydrate (87.5%) and sulfate (24%) contents. HPLC and GC-MS analyses determined that EPS-AG7 is a heterogeneous acidic polysaccharide with an average molecular weight (Mw¯) of ~7.34 × 103 Da, composed of mannose, glucose, arabinose, galacturonic acid, galactose, and lyxose in a molar ratio of 6.6:3.9:1.8:1.3:1.1:1.0, linked through α- and ß-glycosidic linkages as confirmed by NMR analysis. EPS-AG7 adopted a triple helix-like conformation, as evidenced by UV-Vis (Congo Red experiment) and circular dichroism (CD) studies. This helical arrangement demonstrated stability under various experimental conditions, including concentration, ionic strength, temperature, and lipid interactions. EPS-AG7 exhibited significant anticoagulant activity, doubling blood coagulation time at a concentration of 3.0 mg/mL, and showed significant antioxidant activity, with scavenging activities reaching up to 85.90% and 58.64% in DPPH and ABTS+ assays at 5.0 mg/mL, and EC50 values of 1.40 mg/mL and 3.80 mg/mL, respectively. These findings highlight the potential of EPS-AG7 for therapeutic applications due to its potent biological activities.

Peptides Evaluated In Silico, In Vitro, and In Vivo as Therapeutic Tools for Obesity: A Systematic Review.

Bioinformatics has emerged as a valuable tool for screening drugs and understanding their effects. This systematic review aimed to evaluate whether in silico studies using anti-obesity peptides targeting therapeutic pathways for obesity, when subsequently evaluated in vitro and in vivo, demonstrated effects consistent with those predicted in the computational analysis. The review was framed by the question: "What peptides or proteins have been used to treat obesity in in silico studies?" and structured according to the acronym PECo. The systematic review protocol was developed and registered in PROSPERO (CRD42022355540) in accordance with the PRISMA-P, and all stages of the review adhered to these guidelines. Studies were sourced from the following databases: PubMed, ScienceDirect, Scopus, Web of Science, Virtual Heath Library, and EMBASE. The search strategies resulted in 1015 articles, of which, based on the exclusion and inclusion criteria, 7 were included in this systematic review. The anti-obesity peptides identified originated from various sources including bovine alpha-lactalbumin from cocoa seed (Theobroma cacao L.), chia seed (Salvia hispanica L.), rice bran (Oryza sativa), sesame (Sesamum indicum L.), sea buckthorn seed flour (Hippophae rhamnoides), and adzuki beans (Vigna angularis). All articles underwent in vitro and in vivo reassessment and used molecular docking methodology in their in silico studies. Among the studies included in the review, 46.15% were classified as having an "uncertain risk of bias" in six of the thirteen criteria evaluated. The primary target investigated was pancreatic lipase (n = 5), with all peptides targeting this enzyme demonstrating inhibition, a finding supported both in vitro and in vivo. Additionally, other peptides were identified as PPARγ and PPARα agonists (n = 2). Notably, all peptides exhibited different mechanisms of action in lipid metabolism and adipogenesis. The findings of this systematic review underscore the effectiveness of computational simulation as a screening tool, providing crucial insights and guiding in vitro and in vivo investigations for the discovery of novel anti-obesity peptides.

Controlled ethanol-mediated polyphenol removal from sunflower meal: Impact on physicochemical, structural, flow-behavior, and functional characteristics of isolated proteins.

BACKGROUND: Polyphenols present in sunflower meal act on sunflower proteins by reacting directly with their structures and thus influencing their purity, solubility, crystallinity, and functionality. However, the effect on these properties of varying concentrations of ethanol used in dephenolization has yet to be explored. The present study aimed to explore the impact of dephenolization using varying ethanol concentrations (60%, 70%, 80%, and 90%) on the physicochemical, color, thermal, structural, functional, and flow behavior of protein isolates extracted from sunflower meal. RESULTS: Protein isolates originating from meals that were dephenolized using higher ethanol concentrations exhibited a protein content of 836.10 g kg-1. As the concentration of ethanol increased, a reduction in crystallinity was observed from 24% to 14.15%. Fourier transform infrared (FTIR) spectroscopy revealed marked shifts in major peaks within the 1600 to 1700 cm-1 wavelength range, indicating significant structural and conformational changes. Sodium dodecyl-sulfate polyacrylamide gel electrophoresis (SDS-PAGE) results demonstrated that dephenolization caused decline in molecular weight ranging from 25 kDa to 60 kDa. Dephenolization induced significant changes in surface morphology resulting in more heterogeneous and disordered surfaces as indicated by field emission-scanning electron microscopy (FE-SEM) micrographs. Overall improvement in the functional properties was observed, with an increase in solubility from 15.20% to 22.03%. Improvement in the flow behavior with an increase in porosity from 38% to 60% was also observed, due to dephenolization. CONCLUSION: Dephenolization using 90% ethanol induced structural changes that enhanced physicochemical and functional characteristics of sunflower protein isolates by improving purity and solubility, reducing crystallinity, and increasing flow behavior. © 2024 Society of Chemical Industry.

The quest to map STIM1 activation in granular detail.

The conformational change in STIM1 that communicates sensing of ER calcium-store depletion from the STIM ER-luminal domain to the STIM cytoplasmic region and ultimately to ORAI channels in the plasma membrane is broadly understood. However, the structural basis for the STIM luminal-domain dimerization that drives the conformational change has proven elusive. A recently published study has approached this question via molecular dynamics simulations. The report pinpoints STIM residues that may be part of a luminal-domain dimerization interface, and provides unexpected insight into how torsional movements of the STIM luminal domains might trigger release of the cytoplasmic SOAR/CAD domain from its resting tethers to the STIM CC1 segments.

The spatial separation of basic amino acids is similar in RHAMM and hyaluronan binding peptide P15-1 despite different sequences and conformations.

Peptides that increase pro-reparative responses to injury and disease by modulating the functional organization of hyaluronan (HA) with its cell surface binding proteins (e.g., soluble receptor for hyaluronan-mediated motility [RHAMM] and integral membrane CD44) have potential therapeutic value. The binding of RHAMM to HA is an attractive target, since RHAMM is normally absent or expressed at low levels in homeostatic conditions, but its expression is significantly elevated in the extracellular matrix during tissue stress, response-to-injury, and in cancers and inflammation-based diseases. The HA-binding site in RHAMM contains two closely spaced sequences of clustered basic amino acids, in an alpha-helical conformation. In the present communication, we test whether an alpha-helical conformation is required for effective peptide binding to HA, and competitive disruption of HA-RHAMM interaction. The HA-binding RHAMM-competitive peptide P15-1, identified using the unbiased approach of phage display, was examined using circular dichroism spectroscopy and the conformation-predictive AI-based AlphaFold2 algorithm. Unlike the HA-binding site in RHAMM, peptide P15-1 was found to adopt irregular conformations in solution rather than alpha helices. Instead, our structural analysis suggests that the primary determinant of peptide-HA binding is associated with a specific clustering and spacing pattern of basic amino acids, allowing favorable electrostatic interaction with carboxylate groups on HA.

The assembly and comparative analysis of the first complete mitogenome of Lindera aggregata.

Lindera aggregata, a member belongs to the genus Lindera of Lauraceae family. Its roots and leaves have been used as traditional Chinese medicine or functional food for thousands of years. However, its mitochondrial genome has not been explored. Our aim is to sequence and assemble the mitogenome of L. aggregata to elucidate the genetic mechanism and evolutionary pathway. The results had shown that the mitogenome was extremely complex and had a unique multi-branched conformation with total size of 912,473 bp. Comprehensive analysis of protein coding genes of 7 related species showed that there were 40 common genes in their mitogenome. Interestingly, positive selection had become an important factor in the evolution of ccmB, ccmFC, rps10, rps11 and rps7 genes. Furthermore, our data highlighted the repeated trend of homologous fragment migrations between chloroplast and mitochondrial organelles, and 38 homologous fragments were identified. Phylogenetic analysis identified a tree that was basically consistent with the phylogeny of Laurales species described in the APG IV system. To sum up, this study will be helpful to the study of population genetics and evolution of Lindera species.

Genome-Wide Association Study of Conformation Traits in Brazilian Holstein Cattle.

The linear conformation of animals exerts an influence on health, reproduction, production, and welfare, in addition to longevity, which directly affects the profitability of milk-producing farms. The objectives of this study were (1) to perform genome-wide association studies (GWASs) of conformation traits, namely the Rump, Feet and Legs, Mammary System, Dairy Strength, and Final Classification traits, and (2) to identify genes and related pathways involved in physiological processes associated with conformation traits in Brazilian Holstein cattle. Phenotypic and genotypic data from 2339 Holstein animals distributed across the states of Rio Grande do Sul, Paraná, São Paulo, and Minas Gerais were used. The genotypic data were obtained with a 100 K SNP marker panel. The single-step genome-wide association study (ssGWAS) method was employed in the analyses. Genes close to a significant SNP were identified in an interval of 100 kb up- and downstream using the Ensembl database available in the BioMart tool. The DAVID database was used to identify the main metabolic pathways and the STRING program was employed to create the gene regulatory network. In total, 36 significant SNPs were found on 15 chromosomes; 27 of these SNPs were linked to genes that may influence the traits studied. Fourteen genes most closely related to the studied traits were identified, as well as four genes that showed interactions in important metabolic pathways such as myogenesis, adipogenesis, and angiogenesis. Among the total genes, four were associated with myogenesis (TMOD2, TMOD3, CCND2, and CTBP2), three with angiogenesis (FGF23, FGF1, and SCG3), and four with adipogenesis and body size and development (C5H12orf4, CCND2, EMILIN1, and FGF6). These results contribute to a better understanding of the biological mechanisms underlying phenotypic variability in conformation traits in Brazilian Holstein cattle.