Bond Pattern Research Articles

Assignment of Disulfide Bonds in HNTX-XXI by Double-Enzymatic Digestion and Edman Degradation.

HNTX-XXI, a peptide toxin derived from the venom of the spider Ornithoctonus hainana, comprises a 64-amino-acid protein architecture that notably incorporates eight cysteine residues positioned at positions 2, 10, 14, 16, 17, 23, 36, and 63. The close spatial proximity of Cys16 and Cys17 poses a challenge in resolving their disulfide bridge configurations using standard methodologies. In this study, we introduce an innovative and highly efficient approach for delineating disulfide pairings in peptides containing adjacent cysteines. Our methodology integrates a two-step proteolytic digestion strategy utilizing trypsin and Glu-specific staphylococcal V8 protease coupled with a subsequent round of Edman degradation. This multifaceted approach enables the precise characterization of the disulfide bonds within the peptide. Specifically, targeted proteolysis by trypsin and V8, followed by reversed-phase HPLC separation of the resulting peptides, facilitated the unambiguous identification of disulfide linkages between Cys10-Cys23 and Cys14-Cys63. For the fragment containing the four remaining cysteines, a single cycle of Edman degradation was employed, strategically breaking the peptide bond between the adjacent cysteines. This pivotal step enabled the isolation and analysis of the resulting fragments. Subsequently, matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) was utilized, revealing the presence of two additional disulfide bonds: Cys2-Cys17 and Cys16-Cys36. Collectively, these findings allow for the definitive assignment of the four disulfide linkages in HNTX-XXI as Cys2-Cys17, Cys10-Cys23, Cys14-Cys63, and Cys16-Cys36. This rapid and sensitive methodology represents a significant advancement in the structural characterization of peptide toxins with complex disulfide bond patterns, underscoring its potential for broad application in the field of venom peptide research.

Dynamic interactions of negatively charged gold nanoparticles (AuNPs) in aqueous environments with different ionic compositions

This study provides a comprehensive analysis of the interactions between negatively charged gold nanoparticles (Au)144(SRCOO1−)60 and both divalent (Mg2+, Ca2+) and monovalent (Na+, K+) ions in aqueous solution, employing molecular dynamics simulations. The investigation focuses on elucidating the energetics, hydrogen bond patterns and radial distribution of ions surrounding gold nanoparticles. Our results reveal distinct differences in the Coulombic and van der Waals energies between gold nanoparticles and ions, as well as between gold nanoparticles and water, which exert influence on hydrogen bond patterns and lifetimes, as even as ion and water mobility. These findings have important implications for potential applications in nanotechnology and materials science. This research contributes to a deeper understanding of ion-nanoparticle interactions and provides valuable insights for the design and development of new nanomaterials with properties and functionalities.

Bridging the Gap between Sequence and Structure Classifications of Proteins with AlphaFold Models

Classification of protein domains based on homology and structural similarity serves as a fundamental tool to gain biological insights into protein function. Recent advancements in protein structure prediction, exemplified by AlphaFold, have revolutionized the availability of protein structural data. We focus on classifying about 9000 Pfam families into ECOD (Evolutionary Classification of Domains) by using predicted AlphaFold models and the DPAM (Domain Parser for AlphaFold Models) tool. Our results offer insights into their homologous relationships and domain boundaries. More than half of these Pfam families contain DPAM domains that can be confidently assigned to the ECOD hierarchy. Most assigned domains belong to highly populated folds such as Immunoglobulin-like (IgL), Armadillo (ARM), helix-turn-helix (HTH), and Src homology 3 (SH3). A large fraction of DPAM domains, however, cannot be confidently assigned to ECOD homologous groups. These unassigned domains exhibit statistically different characteristics, including shorter average length, fewer secondary structure elements, and more abundant transmembrane segments. They could potentially define novel families remotely related to domains with known structures or novel superfamilies and folds. Manual scrutiny of a subset of these domains revealed an abundance of internal duplications and recurring structural motifs. Exploring sequence and structural features such as disulfide bond patterns, metal-binding sites, and enzyme active sites helped uncover novel structural folds as well as remote evolutionary relationships. By bridging the gap between sequence-based Pfam and structure-based ECOD domain classifications, our study contributes to a more comprehensive understanding of the protein universe by providing structural and functional insights into previously uncharacterized proteins.

Strong Triel Bonds with Be as Electron Donor.

A systematic theoretical study was conducted on the triel bonds (TrBs) within the TrX3···Be(CO)3 complexes (Tr = B, Al, Ga, In, Tl; X = H, F, Cl, Br, I). The interaction energies of these systems range between 4 and 38 kcal/mol. The TrB weakens as X becomes more electronegative in the B and Al systems, while the opposite pattern of stronger bonds is observed in the In and Tl analogues. The dominant component of the TrB is polarization energy, which arises from charge transfer from Be(CO)3 to TrX3. The source of the density is a confluence of CO π-bonding orbitals at the Be center that resembles a Be lone pair, and which makes the molecular electrostatic potential above the Be somewhat negative. This π-lump is paired with the highly positive π-hole above the Tr, and a large amount of charge is transferred to the empty pz orbital of Tr. These factors, when considered in conjunction with large AIM measures, confer on this TrB a certain degree of covalency.

Streamlining the Analysis of Proteins from Snake Venom.

Investigating snake venom is necessary for developing new treatments for envenoming and harnessing the therapeutic potential that lies within venom toxins. Despite considerable efforts in previous research, several technical challenges remain for characterizing the individual components within such complex mixtures. Here, we present native and top-down mass spectrometry (MS) workflows that enable the analysis of individual venom proteins within complex mixtures and showcase the utility of these methodologies on King cobra (Ophiophagus hannah) venom. First, we coupled ion mobility spectrometry for separation and electron capture dissociation for charge reduction to resolve highly convoluted mass spectra containing multiple proteins with masses ranging from 55 to 127 kDa. Next, we performed a top-down glycomic analysis of a 25.5 kDa toxin, showing that this protein contains a fucosylated complex glycan. Finally, temperature-controlled nanoelectrospray mass spectrometry facilitated the top-down sequence analysis of a β-cardiotoxin, which cannot be fragmented by collisional energy due to its disulfide bond pattern. The work presented here demonstrates the applicability of new and promising MS methods for snake venom analysis.

In-plane seismic performance of historical masonry walls with various brick bond patterns using micro-modeling approach

In-plane seismic performance of historical masonry walls with various brick bond patterns using micro-modeling approach

Kinematic analysis of kinases and their oncogenic mutations - Kinases and their mutation kinematic analysis.

Protein kinases are crucial cellular enzymes that facilitate the transfer of phosphates from adenosine triphosphate (ATP) to their substrates, thereby regulating numerous cellular activities. Dysfunctional kinase activity often leads to oncogenic conditions. Chosen by using structural similarity to 5UG9, we selected 79 crystal structures from the PDB and based on the position of the phenylalanine side chain in the DFG motif, we classified these 79 crystal structures into 5 group clusters. Our approach applies our kinematic flexibility analysis (KFA) to explore the flexibility of kinases in various activity states and examine the impact of the activation loop on kinase structure. KFA enables the rapid decomposition of macromolecules into different flexibility regions, allowing comprehensive analysis of conformational structures. The results reveal that the activation loop of kinases acts as a "lock" that stabilizes the active conformation of kinases by rigidifying the adjacent α-helices. Furthermore, we investigate specific kinase mutations, such as the L858R mutation commonly associated with non-small cell lung cancer, which induces increased flexibility in active-state kinases. In addition, through analyzing the hydrogen bond pattern, we examine the substructure of kinases in different states. Notably, active-state kinases exhibit a higher occurrence of α-helices compared to inactive-state kinases. This study contributes to the understanding of biomolecular conformation at a level relevant to drug development.

The structural landscape and diversity of Pyricularia oryzae MAX effectors revisited.

Magnaporthe AVRs and ToxB-like (MAX) effectors constitute a family of secreted virulence proteins in the fungus Pyricularia oryzae (syn. Magnaporthe oryzae), which causes blast disease on numerous cereals and grasses. In spite of high sequence divergence, MAX effectors share a common fold characterized by a ß-sandwich core stabilized by a conserved disulfide bond. In this study, we investigated the structural landscape and diversity within the MAX effector repertoire of P. oryzae. Combining experimental protein structure determination and in silico structure modeling we validated the presence of the conserved MAX effector core domain in 77 out of 94 groups of orthologs (OG) identified in a previous population genomic study. Four novel MAX effector structures determined by NMR were in remarkably good agreement with AlphaFold2 (AF2) predictions. Based on the comparison of the AF2-generated 3D models we propose a classification of the MAX effectors superfamily in 20 structural groups that vary in the canonical MAX fold, disulfide bond patterns, and additional secondary structures in N- and C-terminal extensions. About one-third of the MAX family members remain singletons, without strong structural relationship to other MAX effectors. Analysis of the surface properties of the AF2 MAX models also highlights the high variability within the MAX family at the structural level, potentially reflecting the wide diversity of their virulence functions and host targets.

Convergence behavior of sovereign bond yields in the EU and COVID-19 government responses

This paper aims to investigate the convergence pattern of sovereign bond yields in European Union (EU) countries during the Covid-19 pandemic. To this purpose we employ the Phillips and Sul convergence methodology. We further test whether the above pattern was affected by the intensity of government responses against the Covid-19 dispersion. Our findings indicate the existence of two convergence clubs. Both clubs are composed of countries that have previously been classified as either ‘core’ or ‘periphery’ countries, indicating that in this particular health crisis, this classification is too simplistic. Moreover, our results suggest that the intensity of Covid-19 containment policies had little to no effect in shaping the convergence pattern of sovereign bond yields in the EU. These conclusions are robust even after accounting for the size of the fiscal sector of each country.

Characterisation of bond between cement paste and steel fibres with different surface roughness using SEM.

The performance of cementitious composites reinforced with fibres or/and bars depends on the bond strength between inclusion and cementitious matrix. The nature of formation of fibre-matrix bond is crucial for enhancing the reliability and utilisation of reinforced composites. The research provides a review on the recently published result about the changes in the microstructure of cement matrix surrounding steel fibres with different surface roughness, using a scanning electron microscope (SEM) coupled with k-means clustering algorithm for image segmentation. The debonding pattern of the fibre-matrix bond after the tensile loading cycles was discussed by observing the amount of adhered cement paste to the pulled out fibre surface with SEM. Therefore, analysis of SEM images enabled to explain the connection between the micro-scale properties of cement paste and fibre after application of cyclic loading.

Identification of TBK1 inhibitors against breast cancer using a computational approach supported by machine learning.

Introduction: The cytosolic Ser/Thr kinase TBK1 is of utmost importance in facilitating signals that facilitate tumor migration and growth. TBK1-related signaling plays important role in tumor progression, and there is need to work on new methods and workflows to identify new molecules for potential treatments for TBK1-affecting oncologies such as breast cancer. Methods: Here, we propose the machine learning assisted computational drug discovery approach to identify TBK1 inhibitors. Through our computational ML-integrated approach, we identified four novel inhibitors that could be used as new hit molecules for TBK1 inhibition. Results and Discussion: All these four molecules displayed solvent based free energy values of -48.78, -47.56, -46.78 and -45.47Kcal/mol and glide docking score of -10.4, -9.84, -10.03, -10.06Kcal/mol respectively. The molecules displayed highly stable RMSD plots, hydrogen bond patterns and MMPBSA score close to or higher than BX795 molecule. In future, all these compounds can be further refined or validated by in vitro as well as in vivo activity. Also, we have found two novel groups that have the potential to be utilized in a fragment-based design strategy for the discovery and development of novel inhibitors targeting TBK1. Our method for identifying small molecule inhibitors can be used to make fundamental advances in drug design methods for the TBK1 protein which will further help to reduce breast cancer incidence.

β-sheets mediate the conformational change and allosteric signal transmission between the AsLOV2 termini.

Avena sativa phototropin 1 light-oxygen-voltage 2 domain (AsLOV2) is a model protein of Per-Arnt-Sim (PAS) superfamily, characterized by conformational changes in response to external environmental stimuli. This conformational change begins with the unfolding of the N-terminal A'α helix in the dark state followed by the unfolding of the C-terminal Jα helix. The light state is characterized by the unfolded termini and the subsequent modifications in hydrogen bond patterns. In this photoreceptor, β-sheets are identified as crucial components for mediating allosteric signal transmission between the two termini. Through combined experimental and computational investigations, the Hβ and Iβ strands are recognized as the most critical and influential β-sheets in AsLOV2's allosteric mechanism. To elucidate the role of these β-sheets, we introduced 13 distinct mutations (F490L, N492A, L493A, F494L, H495L, L496F, Q497A, R500A, F509L, Q513A, L514A, D515V, and T517V) and conducted comprehensive molecular dynamics simulations. In-depth hydrogen bond analyses emphasized the role of two hydrogen bonds, Asn482-Leu453 and Gln479-Val520, in the observed distinct behaviors of L493A, L496F, Q497A, and D515V mutants. This illustrates the role of β-sheets in the transmission of the allosteric signal upon the photoactivation of the light state.

EXPERIMENTAL STUDY ON THE STRUCTURAL BEHAVIOUR OF RECYCLED PLASTIC ONE STORY HOUSES

Recycling plastic materials may constitute a relief measure to the global plastic problem. Several companies are now producing recycled plastic for use as construction material in single-story houses. One commercially available layout involves assembling Recycled Plastic Lumber units in a running bond pattern, forming panels confined by horizontal and vertical tie elements joined through bolted steel plate connections. As production of houses is industrialized, the architectural layouts are standardized according to specific distribution and dimensions. This paper presents the findings of an experimental program aimed to characterize the seismic behavior and properties of a one-story house model. To facilitate practical application, the model is referred here as Architectural Standard Model (ASM). The objectives of the test campaign were to investigate the structural behavior of the constituting members and assemblies, and the response of structural walls to cyclic static lateral loads. Three natural scale wall specimens were tested in-plane and two out of plane. Results of natural scale cyclic loading tests demonstrated that structural system of the ASM can perform acceptably safely under high seismic loads if it is adequately fixed to the foundation. The results showed that out of plane loading was the critical pattern and behaved like a unidirectional plate that transmitted load to the columns. In plane observed behavior exhibited predominating rocking component, which suggests considering an evaluation of the system's response using dynamic methods.

Oligo-Condensation Reactions of Silanediols with Conservation of Solid-State-Structural Features.

Oligo- and polysiloxanes are usually prepared by condensation reactions in solvents without control of stereochemistry. Here we present a solventless thermal condensation of stable organosilanols. We investigated the condensation reactions of organosilanediols with different organic substituents, having in common at least one aromatic group. The condensation kinetics of the precursors observed by NMR spectroscopy revealed a strong dependence on temperature, time, and substitution pattern at the silicon atom. SEC measurements showed that chain length increases with increasing condensation temperature and time and lower steric demand of the substituents, which also influences the glass transition temperatures (Tg) of the resulting oligo- or polymers. X-ray diffraction studies of the crystalline silanediols and their condensation products revealed a structural correlation between the substituent location in the crystalline precursors and the formed macromolecules induced by the hydrogen bonding pattern. In certain cases, it is possible to carry out topotactic polymerization in the solid-state, which has its origin in the crystal structure.

Tuning the dimensionality of H bonded networks using different chalcogen atoms in [Re6Q8(CN)6]4– (Q = S, Se) clusters

Two novel compounds based on [Re6Q8(CN)6]4– (Q = S, Se) and small H bond donor bis-amidinium dication of 2,2’-methylenediimidazolium (Cat) (Cat)2[Re6S8(CN)6]∙2H2O (1) and (Cat)2[Re6Se8(CN)6]∙2H2O (2) were synthesized and structurally characterized. Depending of the chalcogen atom (S or Se) in the cluster anion, the dimensionality of the obtained (2D and 3D) network and the nature of the H bond pattern change.

Physicochemical differences between camelid single-domain antibodies and mammalian antibodies.

In recent years, single-domain antibodies, also known as nanobodies, have emerged as an alternative to full immunoglobulin Gs (IgGs), due to their various advantages, including increased solubility, faster clearance, and cheaper production. Nanobodies are generally derived from the variable domain of the camelid heavy-chain-only immunoglobulin Gs (hcIgGs). Due to the high sequence homology between variable heavy chains of camelids (VHHs) and humans (VHs), hcIgGs are ideal candidates for nanobody development. However, further examination is needed to understand the structural differences between VHs and VHHs. This analysis is essential for nanobody engineering to mitigate potential immunogenicity, while preserving stability, functionality, and antigen specificity. We obtained the VH and VHH sequences of various camelid and non-camelid mammalian antibodies from public databases and used multiple sequence alignment based on the Chothia numbering scheme. Aligned sequences were subjected to diverse analyses encompassing paratope length, binding prediction, motif, disulfide bridge, salt bridge profiling, and physicochemical characteristic distribution. Logistic Regression coupled with the Boruta - Random Forest algorithm facilitated the comprehensive examination of physicochemical properties. Our findings revealed longer, less variable paratope sequences in VHHs, along with specific antigen binding residues with increased binding potential compared to VHs. Although the VHs showed more heterogeneous noncanonical disulfide bond patterns, the VHHs had a higher number of noncanonical disulfide bridges. Intriguingly, a typical salt bridge between the 94th and 101st positions in the VHs had a very low encounter rate in the VHHs. Surprisingly, we also identified notable differences in the physicochemical patterns of mostly conserved frameworks (FWs), especially the FW2 and FW3 regions, between VHs and VHHs. Our findings point to possible key sites in VHHs as candidate residues for nanobody engineering efforts.

Higher-Order Topological Peierls Insulator in a Two-Dimensional Atom-Cavity System.

In this work, we investigate a two-dimensional system of ultracold bosonic atoms inside an optical cavity, and show how photon-mediated interactions give rise to a plaquette-ordered bond pattern in the atomic ground state. The latter corresponds to a 2D Peierls transition, generalizing the spontaneous bond dimerization driven by phonon-electron interactions in the 1D Su-Schrieffer-Heeger (SSH) model. Here the bosonic nature of the atoms plays a crucial role to generate the phase, as similar generalizations with fermionic matter do not lead to a plaquette structure. Similar to the SSH model, we show how this pattern opens a nontrivial topological gap in 2D, resulting in a higher-order topological phase hosting corner states, that we characterize by means of a many-body topological invariant and through its entanglement structure. Finally, we demonstrate how this higher-order topological Peierls insulator can be readily prepared in atomic experiments through adiabatic protocols. Our work thus shows how atomic quantum simulators can be harnessed to investigate novel strongly correlated topological phenomena beyond those observed in natural materials.

Crystal structure, hydrogen bond patterns, Hirshfeld surface analysis, and topological studies (NCI) of 1,5,5-trimethyl-imidazolidine-2,4-dione; an organic compound with high symmetry crystallizing in the tetragonal space group I4/m

The title compound, 1,5,5-trimethyl-imidazolidine-2,4‑dione was characterized by FT-IR, 1H NMR, and 13C NMR spectroscopy techniques. The crystal structure was established by single-crystal X-ray diffraction. The powder X-ray powder diffraction analysis confirms the phase purity of the crystalline sample. The hydantoin with formula C6H10N2O2 crystallizes in the tetragonal space group I4/m (N°87), Z=8, and unit cell parameters a=15.554(2) Å, c=6.623(6) Å. This space group is very infrequent to find in purely organic molecules and is since, in the asymmetric unit, the hydantoin ring lies on a mirror plane m. The crystalline packing is stabilized by the formation of intermolecular interactions of the strong hydrogen bond type of the N–H···O between the neighboring hydantoin rings. In addition, the crystalline structure presents the formation of weaker unconventional hydrogen bonds of the C–H···O type. These hydrogen bonds give rise to the formation of 8, 24, and 36-membered ring-type supramolecular structures described by the graphs R22(8), R44(24), and R88(36), respectively, which govern the packing of the supramolecular structure of 1,5,5-trimethyl-imidazolidine-2,4‑dione.Hirshfeld surface analysis of the crystal structure shows that the most important contributions for the crystal packing are from H···H (58.3%) and H··O/O··H (34.0%) interactions, which indicate that van der Waals interactions are the dominant forces in the crystal packing. Energy framework calculations suggest that the contacts formed between molecules are slightly electrostatic.These intermolecular interactions were also investigated through topological analysis of the electron density (ρ) employing the NCI method. Experimental and theoretical results obtained for this new hydantoin compound suggest that N–H···O and C–H···O interactions play an important role in the stabilization of its supramolecular structure.

Ladder-like Organostannoxane: Synthesis and Crystal Structure of the Second Polymorph {[(C6H5)2Sn]2[(C6H5)2ClSn]2(μ3-O)2(μ2-OH)2}∙[DMF

A ladder-like organostannoxane identified as a polymorph of bis-[chloro-(m2-hydroxo)-(m3-oxo)-tetraphenyl-di-tin] dimethylformamide solvate, {[(C6H5)2Sn]2[(C6H5)2ClSn]2(μ3-O)2(μ2-OH)2}[DMF]2 (1), has been synthesized and structurally characterized by means of single-crystal X-ray diffraction analysis. Compound 1 crystallizes in the monoclinic space group P21/c with a = 23.4137(12) Å, b = 11.2525(6) Å, c = 20.2719(11) Å, β = 100.461(2)°, V = 5252.1(5) Å3, Z = 4 and Z’ = 1. The XRD discloses that the polymorph reported in this work is the full molecule which does not crystallize about any inversion center. Complex 1 exhibits a tetranuclear organotin(IV) ladder-like structure containing two external chlorides. The tetranuclear structure is comprised of a three-rung-staircase Sn4O4 cluster which consists of a ladder of four Sn2O2 units. The central Sn2O2 core forms dihedral angles of 4.00(7)° and 1.62(8)° with its two fused four-membered rings, describing a slightly bent ladder. This folding is further noticed with the dihedral angle between the two external Sn2O2 cores of 4.65(8)°. In the structure, two types of distorted trigonal bipyramid geometry at tin centers like-arrangement are disclosed. The most Sn–O bridges bond lengths describe a static trans effect affording dissymmetrical bonds. The dimethylformamide solvate molecules form a dihedral angle of 74.5(2)° and are interlinked to the tetranuclear organotin(IV) ladder via O–H···O hydrogen bond patterns. Additional inner C–H···Cl and C–H···O hydrogen bonds as well the C–H···O interactions are present. Moreover, the intermolecular C–H···O hydrogen bonds do not contribute to direct the crystal structure framework; they do not play an important function in forming a supramolecular architecture.

A Comparative Analysis of the Physico-Chemical Properties of Pectin Isolated from the Peels of Seven Different Citrus Fruits.

In the present research work, pectin was isolated from the peels of seven citrus fruits (Citrus limon, Citrus limetta, Citrus sinensis, Citrus maxima, Citrus jambhiri, Citrus sudachi, and Citrus hystrix) for a comparison of its physicochemical parameters and its potential use as a thickening agent, gelling agent, and food ingredient in food industries. Among the seven citrus fruits, the maximum yield of pectin was observed from Citrus sudachi, and the minimum yield of pectin was observed from Citrus maxima. The quality of each pectin sample was compared by using parameters such as equivalent weight, anhydrouronic acid (AUA) content, methoxy content, and degree of esterification. It was observed that all seven pectin samples had a high value of equivalent weight (more than 1000), suggesting that all the pectin samples had a high content of non-esterified galacturonic acid in the molecular chains, which provides viscosity and water binding properties. The methoxy content and degree of esterification of all the pectins was lower than 50%, which suggests that it cannot easily disperse in water and can form gel only in presence of divalent cations. The AUA content of all isolated pectins samples was above 65%, which suggests that the pectin was pure and can be utilized as a food ingredient in domestic foods and food industries. From the FTIR analysis of pectin, it was observed that the bond pattern of Citrus maxima, Citrus jambhiri, and Citrus hystrix was similar. The bond pattern of Citrus limon, Citrus limetta, and Citrus sinensis was similar. However, the bond pattern of Citrus sudachi was different from that of all other citrus fruits. The difference in the bond pattern was due to the hydrophobic nature of pectin purified from Citrus limon, Citrus limetta, Citrus sudachi, and Citrus sinensis and the hydrophilic nature of pectin purified from Citrus maxima, Citrus jambhiri, and Citrus hystrix. Hence, hydrophobic pectin can be utilized in the preparation of hydrogels, nanofibers, food packaging material, polysoaps, drug delivery agents, and microparticulate materials, whereas hydrophilic pectin can be utilized for the preparation of gelling and thickening agents.