Complete Structural Model Research Articles

Molecular basis of global promoter sensing and nucleosome capture by the SWR1 chromatin remodeler.

The SWR1 chromatin remodeling complex is recruited to+1 nucleosomes downstream of transcription start sites of eukaryotic promoters, where it exchanges histone H2A for the specialized variant H2A.Z. Here, we use cryoelectron microscopy (cryo-EM) to resolve the structural basis of the SWR1 interaction with free DNA, revealing a distinct open conformation of the Swr1 ATPase that enables sliding from accessible DNA to nucleosomes. A complete structural model of the SWR1-nucleosome complex illustrates critical roles for Swc2 and Swc3 subunits in oriented nucleosome engagement by SWR1. Moreover, an extended DNA-binding α helix within the Swc3 subunit enables sensing of nucleosome linker length and is essential for SWR1-promoter-specific recruitment and activity. The previously unresolved N-SWR1 subcomplex forms a flexible extended structure, enabling multivalent recognition of acetylated histone tails by reader domains to further direct SWR1 toward the+1 nucleosome. Altogether, our findings provide a generalizable mechanism for promoter-specific targeting of chromatin and transcription complexes.

De novo atomic protein structure modeling for cryoEM density maps using 3D transformer and HMM

Accurately building 3D atomic structures from cryo-EM density maps is a crucial step in cryo-EM-based protein structure determination. Converting density maps into 3D atomic structures for proteins lacking accurate homologous or predicted structures as templates remains a significant challenge. Here, we introduce Cryo2Struct, a fully automated de novo cryo-EM structure modeling method. Cryo2Struct utilizes a 3D transformer to identify atoms and amino acid types in cryo-EM density maps, followed by an innovative Hidden Markov Model (HMM) to connect predicted atoms and build protein backbone structures. Cryo2Struct produces substantially more accurate and complete protein structural models than the widely used ab initio method Phenix. Additionally, its performance in building atomic structural models is robust against changes in the resolution of density maps and the size of protein structures.

МОДЕЛЮВАННЯ ХАРАКТЕРИСТИК ГІДРАВЛІЧНИХ ПРИСТРОЇВ АВТОМАТИКИ

The paper presents the results of calculations of the regression model of hydraulic losses of technological equipment, in particular, the gate pump SV1-25, which is used in the practice of laboratory research of hydraulic equipment (GЕ) as part of the educational process at the Department of Theoretical Mechanics, Mechanical Science and Robotic Systems of NAU "KHAI". The task of the work was to establish the nature and actual hydraulic losses depending on the hydraulic load. According to the obtained data, in turn, the goal was to establish a mathematical model of the dependence of losses on the load of the public utility. In the course of conducting a number of experiments with a successive increase in the hydraulic load, the flow rate of the working fluid and the hydraulic power of the system were recorded; power losses and hydraulic efficiency of the system were calculated. As a result of the experiment, the nonlinear theoretical, namely, the parabolic dependence of the losses on the load, which is described by parabolic regression with a looseness of the model that does not exceed 4%, was confirmed. The obtained mathematical model of losses can be used in the future to build a complete structural model of the GЕ and a detailed analysis of the factors that determine the occurrence of its power losses. The mathematical model of losses of real equipment obtained in the course of experimental research can be added to the already existing model of the GЕ for the purpose of non-linear correction of its efficiency under variable hydraulic load in real conditions of use. During the calculation of the mathematical model, some stages of mathematical modeling were simplified, namely: models with a higher degree of polynomial were not considered (that is, the type of regressive dependence was not changed), the significance of the obtained coefficients was not characterized by their dispersion when the external conditions of the application of the GЕ were changed. The use of the powerful mathematical CAD Sim Hidraulics (MATLAB) provides an opportunity to simplify the process of designing the latest hydraulic automation systems, taking into account the studied dependencies.

Parallel β-Sheet Structure and Structural Heterogeneity Detected within Q11 Self-Assembling Peptide Nanofibers.

Q11 peptide nanofibers are used as a biomaterial for applications such as antigen presentation and tissue engineering, yet detailed knowledge of molecular-level structure has not been reported. The Q11 peptide sequence was designed using heuristics-based patterning of hydrophobic and polar amino acids with oppositely charged amino acids placed at opposite ends of the sequence to promote antiparallel β-sheet formation. In this work, we employed solid-state nuclear magnetic resonance spectroscopy (NMR) to evaluate whether the molecular organization within Q11 self-assembled peptide nanofibers is consistent with the expectations of the peptide designers. We discovered that Q11 forms a distribution of molecular structures. NMR data from two-dimensional (2D) 13C-13C dipolar-assisted rotational resonance indicate that the K3 and E9 residues between Q11 β-strands are spatially proximate (within ∼0.6 nm). Frequency-selective rotational echo double resonance (fsREDOR) on K3 Nζ and E9 Cδ-labeled sites showed that approximately 9% of the sites are close enough for salt bridge formation to occur. Surprisingly, dipolar recoupling measurements revealed that Q11 peptides do not assemble into antiparallel β-sheets as expected, and structural analysis using Fourier-transform infrared spectroscopy and 2D NMR alone can be misleading. 13C PITHIRDS-CT dipolar recoupling measurements showed that the most abundant structure consists of parallel β-sheets, in contrast to the expected antiparallel β-sheet structure. Structural heterogeneity was detected from 15N{13C} REDOR measurements, with approximately 22% of β-strands having antiparallel nearest neighbors. We cannot propose a complete structural model of Q11 nanofibers because of the complexity involved when examining structurally heterogeneous samples using NMR. Altogether, our results show that while heuristics-based patterning is effective in promoting β-sheet formation, designing a peptide sequence to form a targeted β-strand arrangement remains challenging.

The structure and physical properties of a packaged bacteriophage particle.

A string of nucleotides confined within a protein capsid contains all the instructions necessary to make a functional virus particle, a virion. Although the structure of the protein capsid is known for many virus species1,2, the three-dimensional organization of viral genomes has mostly eluded experimental probes3,4. Here we report all-atom structural models of an HK97 virion5, including its entire 39,732 base pair genome, obtained through multiresolution simulations. Mimicking the action of a packaging motor6, the genome was gradually loaded into the capsid. The structure of the packaged capsid was then refined through simulations of increasing resolution, which produced a 26 million atom model of the complete virion, including water and ions confined within the capsid. DNA packaging occurs through a loop extrusion mechanism7 that produces globally different configurations of the packaged genome and gives each viral particle individual traits. Multiple microsecond-long all-atom simulations characterized the effect of the packaged genome on capsid structure, internal pressure, electrostatics and diffusion of water, ions and DNA, and revealed the structural imprints of the capsid onto the genome. Our approach can be generalized to obtain complete all-atom structural models of other virus species, thereby potentially revealing new drug targets at the genome-capsid interface.

Mathematics study habits through an ethnomathematics approach and entrepreneurial behavior of mathematics education students

This research aims to determine whether there is a positive correlation between mathematics learning habits through an ethnomathematics approach and entrepreneurial behavior. This research is survey research conducted by mathematics education students in Bengkulu and Lubuklinggau. The sample for this research consisted of 70 students. There are two questionnaires as research instruments. Both are a questionnaire on mathematics learning habits using an ethnomathematics approach, and an entrepreneurial behavior questionnaire. The result of this research is that the complete structural equation model fit test is a good fit, which means that the empirical structural equation model is suitable with the theoretical (conceptual) structural equation model. The results of the hypothesis test show that the calculated t value is 11.364 > 1.96, which means Ho is rejected, meaning that this research hypothesis is accepted. The conclusion is that there is a positive correlation between mathematics learning habits through an ethnomathematics approach and entrepreneurial behavior.

Structure and evolution of disordered deep-charge phases in NaxCrO2 Na-ion battery electrodes

Layered sodium chromium oxide, O3–NaCrO2, is a promising electrode material for Na-ion batteries due to the high thermal stability, high rate-capability, and good coulombic efficiency of the material. However, it is well-known that the material loses crystallinity and the ability to store Na-ions reversibly when taken to high states of charge. While the structural identity of the disordered state has been investigated, a bulk structural model has so far been lacking, as has the mechanism for the order-disorder transition from the P′3-NaxCrO2 (the last crystalline phase observed during charge) to the disordered state. In this work, we combine pair distribution function analysis from total X-ray scattering and powder X-ray diffraction to obtain a complete structural model for the disordered O3-like NaxCrO2 forming at high states-of-charge, and from operando pair distribution function analysis and X-ray absorption spectroscopy, we elucidate the structural evolution of the order-disorder transition and shed new light on the Cr-migration in the disordered state, which is the cause of the irreversibility of the Na-ion storage.

Predicting the Crystal Structure of Beryl from the Chemical Composition

Abstract Crystal-structure prediction is a challenging topic. Few models have been developed that use the chemical composition of a known compound to determine a complete crystal structure. A complete structural model should include all major bond lengths and angles, atomic coordinates, polyhedral volumes and distortions, and unit-cell parameters. The mineral beryl is used here to develop such a model. Beryl (Be3Al2Si6O18) is an ideal mineral to show that predicting the crystal structure using chemistry is possible: the framework structure is known, this structure has only two cation sites that experience substitutions, and these substitutions only minimally occur simultaneously. Vacant channel sites are involved in coupled substitutions, allowing alkali cations (typically Na+) to enter the structure, and the channel regularly contains molecular H2O correlated to Na content (Henry et al. 2022). The research employed single-crystal X-ray diffraction and electron probe microanalyses of 80 samples to create a model which was subsequently tested using 33 samples. Results show that the complete crystal structure of beryl can be accurately calculated using the Al-site average ionic radius (Al-SAIR) for octahedrally trending beryl, or the Be-site average ionic radius (Be-SAIR) for tetrahedrally trending beryl. Beryl for which Al-SAIR > (0.45 × Be-SAIR) + 0.414 is considered octahedrally trending and that for which Al-SAIR ≤ (0.45 × Be-SAIR) + 0.414 is considered tetrahedrally trending. Red beryl (differentiated by high Fe and Mn) exhibits a different trend, forming a subset of the octahedrally trending beryl. There is an upper limit to the predictable range of beryl structures of 0.604 Å Al-SAIR or 0.326 Å Be-SAIR. This model makes it possible to explore limitations on the crystal structure of beryl and the potential for unusual cation substitutions, or conversely, to compute the structure of a hypothetical pure endmember beryl. It is robust for true beryl (beryl for which Be and Al are the dominant non-Si cations) up to a high limit of cation substitutions, but not for other beryl-group minerals, including stoppaniite, bazzite, avdeevite, and johnkoivulaite. Future studies on beryl will be able to estimate basic crystal-structure features arising from standard chemical analyses as used in this research. It enables the creation of an extensive beryl database, aids comparisons of natural beryl to synthetics, and helps provide further guidance on provenance studies. It also invites future crystal-structure prediction research. This approach is applicable to broader fields, as crystal structures are linked to the physical characteristics of minerals and rocks in which they form.

Structure of the endosomal Commander complex linked to Ritscher-Schinzel syndrome

The Commander complex is required for endosomal recycling of diverse transmembrane cargos and is mutated in Ritscher-Schinzel syndrome. It comprises two sub-assemblies: Retriever composed of VPS35L, VPS26C, and VPS29; and the CCC complex which contains twelve subunits: COMMD1-COMMD10 and the coiled-coil domain-containing (CCDC) proteins CCDC22 and CCDC93. Combining X-ray crystallography, electron cryomicroscopy, and in silico predictions, we have assembled a complete structural model of Commander. Retriever is distantly related to the endosomal Retromer complex but has unique features preventing the shared VPS29 subunit from interacting with Retromer-associated factors. The COMMD proteins form a distinctive hetero-decameric ring stabilized by extensive interactions with CCDC22 and CCDC93. These adopt a coiled-coil structure that connects the CCC and Retriever assemblies and recruits a 16th subunit, DENND10, to form the complete Commander complex. The structure allows mapping of disease-causing mutations and reveals the molecular features required for the function of this evolutionarily conserved trafficking machinery.

The application of structural equation model in psychological research

The application of structural equation model in psychological research

Complete Models of p53 Better Inform the Impact of Hotspot Mutations

Mutations in tumor suppressor genes often lead to cancerous phenotypes. Current treatments leverage signaling pathways that are often compromised by disease-derived deficiencies in tumor suppressors. P53 falls into this category as genetic mutations lead to physical changes in the protein that impact multiple cellular pathways. Here, we show the first complete structural models of mutated p53 to reveal how hotspot mutations physically deviate from the wild-type protein. We employed a recently determined structure for the p53 monomer to map seven frequent clinical mutations using computational modeling approaches. Results showed that missense mutations often changed the conformational structure of p53 in the DNA-binding site along with its electrostatic surface charges. We posit these changes may amplify the toxic effects of these hotspot mutations by destabilizing an important zinc ion coordination region in p53 to impede proper DNA interactions. These results highlight the imperative need for new studies on patient-derived proteins that may assist in redesigning structure-informed targeted therapies.

Prediction of spectral radiative property based on the microscopic ligament morphology and pore-level structure of open-cell alumina foam

In this work, based on the complete structure model consisting of microscopic ligament morphology and pore-level structure, a trans-scale analysis method is presented for accurately predicting the spectral radiative properties of open-cell ceramic foams. The characteristic models of microscopic ligament morphologies are obtained by the SEM technique, while the network structure of ligaments is reconstructed by the μ-CT technique. According to the SEM data, the microscopic statistical models are developed for the rough surfaces and the internal porous media of ligaments. Additionally, based on the statistical models, the FDTD method is employed to analyze the spectral radiative transfer behaviors on the surfaces and inside the ligament media. The spectral directional-hemispherical reflectivity and specularity parameter for the ligament surface, as well as the extinction coefficient, the scattering albedo and the scattering phase function for the ligament medium are extracted from the FDTD simulations. The above parameters are used as the input data for the pore-level simulations of spectral radiative transfer inside the ligament network, where the Monte Carlo method is conducted. The apparent spectral absorptivity and reflectivity, as well as the equivalent volumetric spectral radiative properties of alumina foam sheets are predicted by the presented trans-scale analysis method. The trans-scale predicting method is verified and compared with the single pore-level simulations of radiative transfer inside alumina foams. The spectral radiative characteristics of alumina foams are analyzed for various wavelengths and incident angles. From the analysis, only when the specularity parameter is properly chosen, the pore-level simulation is also reliable for predicting the spectral radiative properties of ceramic foams.

Multigroup Analysis in Information Systems Research using PLS-PM

Heterogeneity is a pertinent issue in Information Systems (IS) research because human behavior often differs across groups. In the partial least squares path modeling (PLS-PM) context, several approaches have been proposed to investigate potential group differences. Despite the availability of numerous approaches, literature that compares their efficacy is sparse. Consequently, IS researchers lack guidance on which approach is best suited to detect group differences. We address this issue by presenting the results of an extensive Monte Carlo simulation study that juxtaposes the various approaches' behavior under numerous conditions. In doing so, we first provide an overview on existing approaches proposed for multigroup analysis (MGA) in the PLS-PM context. Moreover, we derive important implications for applied research: Firstly, we show that the omnibus test of group differences (OTG) and approaches based on the comparison of confidence intervals are not recommendable for MGA. Secondly, we provide detailed information as to which approaches are suitable for comparing one specific path coefficient and which are recommended if the complete structural model is compared across groups. Finally, we show that approaches which are designed to compare a single parameter require an adjustment for multiple comparisons when used to compare more than two groups.

Does Trust Mediate in Corporate Social Responsibility (CSR) and Brand Equity Nexus? Empirical Evidence from the Banking Sector

The purpose of this study is to examine the role of trust on the CSR and brand-equity nexus in the banking sector of Bangladesh. Using the convenient sampling method and structured questionnaire, the study conducted an online survey of 275 customers of private commercial banks from Bangladesh. This study applied structural equation modelling (SEM) to define the complete structural model to analyse the direct and indirect relationships between study constructs. The results reveal a positive and significant impact of CSR on brand equity. Regarding the mediating effect of trust, the study found a significant impact of trust on the CSR components and the brand-equity nexus. The study’s outcomes enrich the existing literature as a dimension of trust is added as mediating effect on the CSR and brand equity relationship in Bangladesh.

Modeling self-identification, memorable tourism experience, overall satisfaction and destination loyalty: empirical evidence from small island destinations

PurposeAlthough many studies addressed destination marketing concepts, the relationship between self-identification, memorable tourism experiences, overall satisfaction, and destination loyalty in small island destinations remains unknown. To address this issue, the authors established a model based on social identity theory to investigate the effects of self-identification on overall satisfaction and loyalty, taking into account the mediating role of memorable tourism experiences.Design/methodology/approachDrawing on 335 useable questionnaires from the visitors of Princes' Islands in Turkey, a quantitative study approach was administrated to empirically analyze a partial least squares path model in PLS-SEM.FindingsThe findings revealed that self-identification positively affects memorable tourism experiences, overall satisfaction, and destination loyalty. The findings also confirm the indirect effects of self-identification on overall satisfaction and destination loyalty through mediating the role of memorable tourism experiences.Research limitations/implicationsThe findings of the study will be useful both theoretically and practically. Theoretically, this research will be important to determine tourist behavior through the viewpoint of self-identification in the context of a small island destination. Practically, the findings of this study will assist small island destinations' policymakers and practitioners to develop strategies and make effective future actions.Originality/valueThis is the first study that uses a complete structural model linking self-identification, memorable tourism experiences, overall satisfaction, and destination loyalty.

Structural model of tissue factor (TF) and TF-factor VIIa complex in a lipid membrane: A combined experimental and computational study

Tissue factor (TF) is a membrane protein involved in blood coagulation. TF initiates a cascade of proteolytic reactions, ultimately leading to the formation of a blood clot. The first reaction consists of the binding of the coagulation factor VII and its conversion to the activated form, FVIIa. Here, we combined experimental, i.e. quartz crystal microbalance with dissipation monitoring and neutron reflectometry, and computational, i.e. molecular dynamics (MD) simulation, methods to derive a complete structural model of TF and TF/FVIIa complex in a lipid bilayer. This model shows that the TF transmembrane domain (TMD), and the flexible linker connecting the TMD to the extracellular domain (ECD), define the location of the ECD on the membrane surface. The average orientation of the ECD relative to the bilayer surface is slightly tilted towards the lipid headgroups, a conformation that we suggest is promoted by phosphatidylserine lipids, and favours the binding of FVIIa. On the other hand, the formation of the TF/FVIIa complex induces minor changes in the TF structure, and reduces the conformational freedom of both TF and FVIIA. Altogether we describe the protein-protein and protein-lipid interactions favouring blood coagulation, but also instrumental to the development of new drugs.

Structural equation fit test of mathematical connection ability, mathematical reasoning, and mathematics problem-solving ability of junior high school students

The purpose of this study was to test the compatibility of theoretical and empirical structural equations on the relationship between mathematical connection skills, mathematical reasoning, and mathematical problem-solving abilities of junior high school students. This is an ex-post facto research at SMP N 1 Bengkulu City. The population of this study was 296 people, and the sample was selected through a simple random technique of 100 people. Data collection techniques through tests with three research instruments. The three instruments are a mathematical problem-solving ability test, a mathematical reasoning ability test, and a mathematical connection ability test that have been valid and reliable based on expert tests and field tests. The data was tested using the Lisrel 8.8 application program. The results of the study are the P-valued of 0.05, RMSEA ≤ 0.08; NFI ≥ 0.90, NNFI ≥ 0.90; CFI ≥ 0.90; IFI ≥ 0.90; RFI ≥ 0.90; RMR ≤ 0.05; SRMR ≤ 0.05; GFI ≥ 0.90; and 0.8≤AGFI≤0.9; then the fit test for the complete structural equation model is good fit. It means that the theoretical structural equation model is compatible with the empirical structural equation model. Thus, the overall fit test of the model shows a fit model, and it can be concluded that the empirical structural equation model is compatible with the theoretical model.

Comprehensive investigation of crystallographic, spin-electronic and magnetic structure of [formula omitted]: Unraveling the suppression of configuration entropy in high entropy oxides

High entropy oxides (HEOs) are a rapidly emerging class of functional materials consisting of multiple principal cations. The original paradigm of HEOs assumes cationic occupations with the highest possible configurational entropy allowed by the composition and crystallographic structure. However, the fundamental question remains on the actual degree of configurational disorder in HEOs, especially, in systems with low enthalpy barriers for cation anti-site mixing. Considering the experimental limitations due to the presence of multiple principal cations in HEOs, here we utilize a robust and cross-referenced characterization approach using soft X-ray magnetic circular dichroism, hard X-ray absorption spectroscopy, Mössbauer spectroscopy, neutron powder diffraction and SQUID magnetometry to study the competition between crystal field stabilization energy and configurational entropy governing the cation occupation in a spinel HEO (S-HEO), (Co0.2Cr0.2Fe0.2Mn0.2Ni0.2)3O4. In contrast to the previous studies, the derived complete structural and spin-electronic model, (Co0.6Fe0.4)(Cr0.3Fe0.1Mn0.3Ni0.3)2O4, highlights a significant deviation from the hitherto assumed paradigm of entropy-driven non-preferential distribution of cations in HEOs. An immediate correlation of this result can be drawn with bulk as well as the local element specific magnetic properties, which are intrinsically dictated by cationic occupations in spinels. The real local lattice picture presented here provides an alternate viewpoint on ionic arrangement in HEOs, which is of fundamental interest for predicting and designing their structure-dependent functionalities.

Multiscale investigation of the influence of geometrical imperfections, porosity, and size-dependent features on mechanical behavior of additively manufactured Ti-6Al-4V lattice struts

Various manufacturing defects are known to have significant impact on the mechanical properties of lattice structures. Therefore, defects-embedded FE models are essential for accurate mechanical prediction. However, previous studies often focused on the investigation of complete lattice structure models. As a result, the comprehensive investigation of defects in a single strut remained elusive. The present study investigated five different defects on a single strut, namely undersizing/oversizing, diameter variation, offset of the cross section, internal voids, and local mechanical properties. It was found that the undersizing and oversizing were the primary factor affecting the discrepancy between experiments and numerical predictions for most cases. The diameter variation and offset of the cross section were seen to be dominant for small struts, especially those with 45° build orientation. Furthermore, even though the onset of localization could be observed due to the presence of voids, they had a negligible impact on elastic and initial yielding responses, partly because of their low volume fraction. Besides, the effect from geometrical inaccuracies and varied properties were mostly comparable although that of the former was more dominant in smaller samples. In addition, the sensitivity from the µCT voxel size affected both global behaviors and localization.

Protein Predictive Modeling and Simulation of Mutations of Presenilin-1 Familial Alzheimer's Disease on the Orthosteric Site.

Alzheimer’s disease pathology is characterized by β-amyloid plaques and neurofibrillary tangles. Amyloid precursor protein is processed by β and γ secretase, resulting in the production of β-amyloid peptides with a length ranging from 38 to 43 amino acids. Presenilin 1 (PS1) is the catalytic unit of γ-secretase, and more than 200 PS1 pathogenic mutations have been identified as causative for Alzheimer’s disease. A complete monocrystal structure of PS1 has not been determined so far due to the presence of two flexible domains. We have developed a complete structural model of PS1 using a computational approach with structure prediction software. Missing fragments Met1-Glut72 and Ser290-Glu375 were modeled and validated by their energetic and stereochemical characteristics. Then, with the complete structure of PS1, we defined that these fragments do not have a direct effect in the structure of the pore. Next, we used our hypothetical model for the analysis of the functional effects of PS1 mutations Ala246GLu, Leu248Pro, Leu248Arg, Leu250Val, Tyr256Ser, Ala260Val, and Val261Phe, localized in the catalytic pore. For this, we used a quantum mechanics/molecular mechanics (QM/MM) hybrid method, evaluating modifications in the topology, potential surface density, and electrostatic potential map of mutated PS1 proteins. We found that each mutation exerts changes resulting in structural modifications of the active site and in the shape of the pore. We suggest this as a valid approach for functional studies of PS1 in view of the possible impact in substrate processing and for the design of targeted therapeutic strategies.