Solution Structure Research Articles

Ligand-induced CaMKIIα hub Trp403 flip, hub domain stacking, and modulation of kinase activity.

γ-Hydroxybutyric acid (GHB) analogs are small molecules that bind competitively to a specific cavity in the oligomeric CaMKIIα hub domain. Binding affects conformation and stability of the hub domain, which may explain the neuroprotective action of some of these compounds. Here, we describe molecular details of interaction of the larger-type GHB analog 2-(6-(4-chlorophenyl)imidazo[1,2-b]pyridazine-2-yl)acetic acid (PIPA). Like smaller-type analogs, PIPA binding to the CaMKIIα hub domain promoted thermal stability. PIPA additionally modulated CaMKIIα activity under sub-maximal CaM concentrations and ultimately led to reduced substrate phosphorylation. A high-resolution X-ray crystal structure of a stabilized CaMKIIα (6x mutant) hub construct revealed details of the binding mode of PIPA, which involved outward placement of tryptophan 403 (Trp403), a central residue in a flexible loop close to the upper hub cavity. Small-angle X-ray scattering (SAXS) solution structures and mass photometry of the CaMKIIα wild-type hub domain in the presence of PIPA revealed a high degree of ordered self-association (stacks of CaMKIIα hub domains). This stacking neither occurred with the smaller compound 3-hydroxycyclopent-1-enecarboxylic acid (HOCPCA), nor when Trp403 was replaced with leucine (W403L). Additionally, CaMKIIα W403L hub was stabilized to a larger extent by PIPA compared to CaMKIIα hub wild type, indicating that loop flexibility is important for holoenzyme stability. Thus, we propose that ligand-induced outward placement of Trp403 by PIPA, which promotes an unforeseen mechanism of hub domain stacking, may be involved in the observed reduction in CaMKIIα kinase activity. Altogether, this sheds new light on allosteric regulation of CaMKIIα activity via the hub domain.

A Data-Driven Image-Based Visual Servoing Scheme for Redundant Manipulators With Unknown Structure and Singularity Solution

A Data-Driven Image-Based Visual Servoing Scheme for Redundant Manipulators With Unknown Structure and Singularity Solution

Surface Plasmon Resonance Allows to Correlate Molecular Properties with Diffusion Coefficients of Linear Chain Alcohols.

Every biological and physicochemical process occurring in a fluid phase depends on the diffusion coefficient (D) of the species in solution. In the present work, a model to describe and fit the behaviour of D as a function of structure and extensive thermodynamics parameters in binary solutions of linear chain organic molecules is developed. Supporting experimental and computational evidences for this model are obtained by measuring D for a series of n-alcohols through a novel surface plasmon resonance method and molecular dynamics simulations. This allows to propose a kind of combined analysis to explain the dependence of D on various thermodynamic and structural parameters. The results suggest that for small linear systems in the range from 0 to 200 g mol-1 and under the assumption that the diffusive activation energy is a linear function of mass, D is strictly dependent on the molecular shape and on the relative strength of the solute-solvent intermolecular forces represented by a parameter named R. The newly proposed approach can be utilized to characterize and monitor progressive changes in physicochemical properties for any investigated species upon increasing the dimension of the aggregate/molecule along a certain direction.

Ship Hull Hybrid Structural Design Accounting for Reliability

The optimum ship hull design solution has always been a concern, and in recent years, genetic algorithms to optimise the ship hull structure have been developed. The genetic algorithm’s fundaments generate alternative solutions and compare them with pre-defined constants and objectives. The development of design solutions evolves through competition and controlled variations. Minimising the ship hull structure weight is essential in reducing the ship’s capital (construction) expenditure and increasing the cargo capacity. The risk of the ship is associated with the loss of the ship, cargo, human life, environmental pollution, etc. It is a governing factor impacted by the chosen structural design solution and the measures taken to reduce the structural weight. A genetic algorithm will be employed to study the weight minimisation of a multi-purpose ship hull structure, controlling the associated risk by accounting for several structural design variables. The risk and best design solution are defined by the probability of compressive collapse of the stiffened plates, integral ship hull structure, and the associated cost due to failure. The Pareto frontier solutions, calculated by the non-dominated sorting genetic algorithm, NSGA-II, will be employed to determine feasible solutions for the design variables. The first-order reliability method will estimate the Beta reliability index based on the topology of the stiffened plates and ship hull structure as a part of the Pareto frontier solutions. The algorithm employed will not account for any manufacturing constraints and consequences due to the encountered optimal design solution.

Finite Element Modeling and Analysis of RC Shear Walls with Cutting-Out Openings

In recent decades, reinforced concrete (RC) shear walls have been one of the best structural solutions to resist lateral load in high-rise buildings. Shear wall openings are essential for preparations and architectural requirements, which weaken the wall, reducing bearing capacity, energy absorption, and stiffness while also causing stress concentrations. This paper presents a comprehensive finite element (FE) investigation of the behavior and performance of RC shear walls with openings and subjected to lateral loads. The study aims to evaluate the influence of various parameters, such as opening location, size, wall aspect ratio, axial load, and concrete strength, which affect the performance of shear walls. FE models were developed to simulate the seismic response of RC shear walls under the combined effect of constant axial and lateral loads. The obtained results from the FE model showed a successful validation using the experimental data available in the literature. The FE analysis results demonstrate that the inclusion of lower openings leads to a 25% decrease in the bearing capacity of the wall when compared to the upper openings. Moreover, it was observed that augmenting the sizes of the openings and the aspect ratios of the wall resulted in declines in the strength, stiffness, and energy absorption capacity of the wall while simultaneously enhancing the ductility and displacement of the RC shear walls.

DESIGN TASK IN THE MODERN CONDITIONS OF INVESTMENT AND CONSTRUCTION PROJECTS

The article is devoted to the organizational aspect of solving the urgent problem of shortening the terms of implementation of investment and construction projects in modern conditions at the stage design The article examines the procedure for drawing up a design task by the customer at the stage of preparing tender documentation for construction objects in Ukraine, the financing of which is carried out with the involvement of budget funds, funds of state and communal enterprises, institutions and organizations, loans provided under state guarantees and defined and disadvantages The provisions of regulatory and technical documents regulating the procedure for drawing up a design assignment and its content have been reviewed. The list of problems that arise at the design and construction stage during the implementation of investment and construction projects due to the uncertainty and variability of data for project development, provided by the customer in the design task, is defined. The analysis of open sources of information regarding the procurement of design works showed that customers fill out the design task form, defined by the regulatory framework, on a formal basis, without actually expressing their real requirements for the future construction inspection. In "design and build" projects, the design task occupies a special place, since the contractor, on the basis of the customer's technical task, can determine not only the cost of the design work, but also the price of the construction work for which he is willing to perform it, while this price depends on technical and economic parameters of the building, which has not yet been designed, from the applied finishing materials, engineering systems, structural solutions, etc. An analysis of completed contracts for the purchase of construction works on "design and build" schemes was carried out, and they were divided into groups depending on the sufficiency of information in the design task. The foreign experience of organizing design works was analyzed, in particular, when implementing the "design and build" approach. It is proposed to improve the organization of the design process by separating the process of drawing up the design task into a separate procedure with a toolkit based on digital technologies, formulating the customer's requirements for design solutions and checking the validity of the customer's requirements. The feasibility of developing a toolkit based on digital technologies, which can be applied by the customer for drawing up a design task in investment and construction projects.

Semi-analytical layerwise solutions for FG MEE complex shell structures

This paper presents a unique analytical layerwise solution for functionally graded magneto-electric-elastic shell with complex geometry. The middle surface of the shell is modeled by a parametric equation and the Lamé parameter and radii of curvature is modeled by Differential Geometry. The mechanical displacements, electrical and magnetic potentials are written in term of a simple cosine layerwise based on a unified formulation. The highly coupled differential equations are discretized by the Chebyshev-Gauss-Lobatto grid points and solved numerically via the Differential Quadrature Method (DQM). Lagrange interpolation polynomials are employed as the basis functions. The highly coupled differential equations are solved for shells subjected to different loads and boundary conditions. Since extremely few results on this topic is available in the literature, benchmarks complex shell problems and their solutions are introduced in this paper for the very first time.

Backbone assignment of CcdB_G100T toxin from E.coli in complex with the toxin binding C-terminal domain of its cognate antitoxin CcdA.

The CcdAB system expressed in the E.coli cells is a prototypical example of the bacterial toxin-antitoxin (TA) systems that ensure the survival of the bacterial population under adverse environmental conditions. The solution and crystal structures of CcdA, CcdB and of CcdB in complex with the toxin-binding C-terminal domain of CcdA have been reported. Our interest lies in the dynamics of CcdB-CcdA complex formation. Solution NMR studies have shown that CcdB_G100T, in presence of saturating concentrations of CcdA-c, a truncated C-terminal fragment of CcdA exists in equilibrium between two major populations. Sequence specific backbone resonance assignments of both equilibrium forms of the ~ 27kDa complex, have been obtained from a suite of triple resonance NMR experiments acquired on 2H, 13C, 15N enriched samples of CcdB_G100T. Analysis of 1H, 13Cα, 13Cβ secondary chemical shifts, shows that both equilibrium forms of CcdB_G100T have five beta-strands and one alpha-helix as the major secondary structural elements in the tertiary structure. The results of these studies are presented below.

Structural Study of Aqueous Electrolyte Solution by MeV Liquid Electron Scattering.

The impact of ions on water has long been a subject of great interest, as it is closely tied to the hydration structure, dynamics, and properties of electrolyte solutions. Over centuries of investigation, the influence of ions on water's structure remains highly debated. Prevailing techniques, such as neutron and X-ray scattering, primarily focus on the microscopic structure of salt solutions at very high concentrations, mostly above 1 mol/L. In this study, we measured the structure of aqueous potassium iodide (KI) and potassium chloride (KCl) solutions using MeV liquid electron scattering (MeV-LES) across a concentration range of 0.10 to 0.75 mol/L. The obtained results provide detailed insights into the variations in ion-oxygen and oxygen-oxygen correlations as a function of concentration. The observed structural differences between KI and KCl solutions are in line with the structure maker/breaker theory, which suggests that iodide ions exert a more pronounced effect than chloride ions on disrupting the water shell. This work demonstrates the potency of MeV-LES for investigating the atomic structure in liquids, augmenting the modern analytical toolbox.

Why is Dimeric 3D Domain Swapping in Antibody Light Chains Missing from the Solution? Atomistic Insights Mechanisms.

Misfolding of antibody light chains can lead to systemic light chain amyloidosis, which is associated with misfolding and aggregation. The antibody light chain may engage in 3D domain swapping within the variable region (#4VL) through hydrogen bonding (HB) interactions, potentially forming the tetramer, as revealed in solution and crystal structures. However, the 3D-domain swapping (3D-DS) dimers could not be detected experimentally. This study investigates the absence of 3D-DS using computational approaches, focusing on structural dynamics, solvation effects, and stability relevant to the loss of 3D-DS. Microscale molecular dynamics simulations of #4VL and 3D-DS confirm that native HB interactions are essential to maintain β-sheet structures in both #4VL and 3D-DS. A flickering native HB interaction in the 3D-DS system, caused by repulsive interaction with water molecules in the hydrophobic region, leads to intramolecular breathing motions and oligomerization in another 3D-DS. Structural dynamics of the 3D-DS dimer in long-run simulations were analyzed using the newly developed integrated solvation-based principal component analysis (3D-RISM/PCA) and density-based spatial clustering of applications with noise, confirm that if the 3D-DS cannot form the tetramer within the breathing motion process, the 3D-DS will collapse. This finding provides insights into why the 3D-DS dimer is missing from the solution and can be used to design and develop 3D-DS in other antibodies.

Molecular Mechanism of pH-Induced Protrusion Configuration Switching in Piscine Betanodavirus Implies a Novel Antiviral Strategy.

Many viruses contain surface spikes or protrusions that are essential for virus entry. These surface structures can thereby be targeted by antiviral drugs to treat viral infections. Nervous necrosis virus (NNV), a simple nonenveloped virus in the genus of betanodavirus, infects fish and damages aquaculture worldwide. NNV has 60 conspicuous surface protrusions, each comprising three protrusion domains (P-domain) of its capsid protein. NNV uses protrusions to bind to common receptors of sialic acids on the host cell surface to initiate its entry via the endocytic pathway. However, structural alterations of NNV in response to acidic conditions encountered during this pathway remain unknown, while detailed interactions of protrusions with receptors are unclear. Here, we used cryo-EM to discover that Grouper NNV protrusions undergo low-pH-induced compaction and resting. NMR and molecular dynamics (MD) simulations were employed to probe the atomic details. A solution structure of the P-domain at pH 7.0 revealed a long flexible loop (amino acids 311-330) and a pocket outlined by this loop. Molecular docking analysis showed that the N-terminal moiety of sialic acid inserted into this pocket to interact with conserved residues inside. MD simulations demonstrated that part of this loop converted to a β-strand under acidic conditions, allowing for P-domain trimerization and compaction. Additionally, a low-pH-favored conformation is attained for the linker connecting the P-domain to the NNV shell, conferring resting protrusions. Our findings uncover novel pH-dependent conformational switching mechanisms underlying NNV protrusion dynamics potentially utilized for facilitating NNV entry, providing new structural insights into complex NNV-host interactions with the identification of putative druggable hotspots on the protrusion.

Ion Correlations Decrease Particle Aggregation Rate by Increasing Hydration Forces at Interfaces.

The connection between solution structure, particle forces, and emergent phenomena at solid-liquid interfaces remains ambiguous. In this case study on boehmite aggregation, we established a connection between interfacial solution structure, emerging hydration forces between two approaching particles, and the resulting structure and kinetics of particle aggregation. In contrast to expectations from continuum-based theories, we observed a nonmonotonic dependence of the aggregation rate on the concentration of sodium chloride, nitrate, or nitrite, decreasing by 15-fold in 4 molal compared to 1 molal solutions. These results are accompanied by an increase in repulsive hydration forces and interfacial oscillatory features from 0.27-0.31 nm in 0.01 molal to 0.38-0.52 nm in 2 molal. Moreover, molecular dynamics (MD) simulations indicated that these changes correspond to enhanced ion correlations near the interface and produced loosely bound aggregates that retain electrolyte between the particles. We anticipate that these results will enable the prediction of particle aggregation, attachment, and assembly, with broad relevance to interfacial phenomena.

When can we trust structural models derived from pair distribution function measurements?

The pair distribution function (PDF) is an important metric for characterising structure in complex materials, but it is well known that meaningfully different structural models can sometimes give rise to equivalent PDFs. In this paper, we discuss the use of model likelihoods as a general approach for discriminating between such homometric structure solutions. Drawing on two main case studies-one concerning the structure of a small peptide and the other amorphous calcium carbonate-we show how consideration of model likelihood can help drive robust structure solution, even in cases where the PDF is particularly information-poor. The obvious thread of these individual case studies is the potential role for machine-learning approaches to help guide structure determination from the PDF, and our paper finishes with some forward-looking discussion along these lines.

Ellipsoidal micelle formation of quaternary ammonium salt-based gemini surfactants: structural analysis through small-angle X-ray scattering.

Gemini surfactants exhibit better adsorption and aggregation properties than those of monomeric surfactants. However, to enhance the functional properties of gemini surfactants, the effect of spacer structures on their aggregation behavior must be elucidated. Small-angle X-ray scattering (SAXS) has been performed to study the aggregate structures of monomeric surfactants, but its application has not been expanded to the analysis of gemini surfactants. Therefore, in this study, we performed a structural analysis of aggregates formed by quaternary ammonium salt-based gemini surfactants with different spacer structures in aqueous solutions through viscosity, dynamic light scattering (DLS), and SAXS measurements. We also investigated the effects of the spacer structure and surfactant concentration on the aggregation behavior. The DLS results indicated that gemini surfactants with spacers containing cyclic structures, such as diethylene and triethylene chains, formed small micelles (several nanometers in size) at the limiting concentration for dissolution in water. In contrast, gemini surfactants with nitrogen and oxygen atoms at the center of the spacer formed ellipsoidal micelles at low concentrations, as shown by SAXS results. The core and overall radii of the minor and major axes of the ellipsoidal micelles decreased with increasing surfactant concentration and were larger for spacers with two ethylene chains connected to central nitrogen and oxygen atoms than for spacers with rigid diethylene and ethylene chains connected to a central nitrogen atom.

Hemoglobin-PEG Interactions Probed by Small-Angle X-ray Scattering: Insights for Crystallization and Diagnostics Applications.

Protein-protein interactions, controlling protein aggregation in the solution phase, are crucial for the formulation of protein therapeutics and the use of proteins in diagnostic applications. Additives in the solution phase are factors that may enhance the protein's conformational stability or induce crystallization. Protein-PEG interactions do not always stabilize the native protein structure. Structural information is needed to validate excipients for protein stabilization in the development of protein therapeutics or use proteins in diagnostic assays. The present study investigates the impact of polyethylene glycol (PEG) molecular weight and concentration on the spatial structure of human hemoglobin (Hb) at neutral pH. Small-angle X-ray scattering (SAXS) in combination with size-exclusion chromatography is employed to characterize the Hb structure in solution without and with the addition of PEG. Our results evidence that human hemoglobin maintains a tetrameric conformation at neutral pH. The dummy atom model, reconstructed from the SAXS data, aligns closely with the known crystallographic structure of methemoglobin (metHb) from the Protein Data Bank. We established that the addition of short-chain PEG600, at concentrations of up to 10% (w/v), acts as a stabilizer for hemoglobin, preserving its spatial structure without significant alterations. By contrast, 5% (w/v) PEG with higher molecular weights of 2000 and 4000 leads to a slight reduction in the maximum particle dimension (Dmax), while the radius of gyration (Rg) remains essentially unchanged. This implies a reduced hydration shell around the protein due to the dehydrating effect of longer PEG chains. At a concentration of 10% (w/v), PEG2000 interacts with Hb to form a complex that does not distort the protein's spatial configuration. The obtained results provide a deeper understanding of PEG's influence on the Hb structure in solution and broader knowledge regarding protein-PEG interactions.

Exploring the Distribution of Low Molecular Weight Compounds in Water-Based Two-Phase Systems with Various Salt Additives

The partition coefficients of seven low molecular weight compounds were tested in different aqueous two-phase systems. The ionic composition of each system included specific salt additives, and it was found that there is a linear relationship between the solute partition coefficients and the presence of different salt additives. The study suggests that the solute structure and the type of ions influence the solute response to the ionic environment. Additionally, it was observed that the solutes’ polar surface area and the solvent-accessible surface area are the essential structural features governing partitioning in aqueous two-phase systems.

The structure of water-ammonia mixtures from classical and abinitio molecular dynamics.

The structure of aqueous ammonia solutions is investigated through classical molecular dynamics (MD) and abinitio molecular dynamics (AIMD) simulations. We have preliminarily compared three well-known classical force fields for liquid water (SPC, SPC/E, and TIP4P) in order to identify the most accurate one in reproducing AIMD results obtained at the Generalized Gradient Approximation (GGA) and meta-GGA levels of theory. Liquid ammonia has been simulated by implementing an optimized force field recently developed by Chettiyankandy et al. [Fluid Phase Equilib. 511, 112507 (2020)]. Analysis of the radial distribution functions for different ammonia concentrations reveals that the three water force fields provide comparable estimates of the mixture structure, with the SPC/E performing slightly better. Although a fairly good agreement between MD and AIMD is observed for conditions close to the equimolarity, at lower ammonia concentrations, important discrepancies arise, with classical force fields underestimating the number and strength of H-bonds between water molecules and between water and ammonia moieties. Here, we prove that these drawbacks are rooted in a poor sampling of the configurational space spanned by the hydrogen atoms lying in the H-bonds of H2O⋯H2O and, more critically, H2O⋯NH3 neighbors due to the lack of polarization and charge transfer terms. This way, non-polarizable classical force fields underestimate the proton affinity of the nitrogen atom of ammonia in aqueous solutions, which plays a key role under realistic dilute ammonia conditions. Our results witness the need for developing more suited polarizable models that are able to take into account these effects properly.

Towards end-to-end structure determination from x-ray diffraction data using deep learning

Powder crystallography is the experimental science of determining the structure of molecules provided in crystalline-powder form, by analyzing their x-ray diffraction (XRD) patterns. Since many materials are readily available as crystalline powder, powder crystallography is of growing usefulness to many fields. However, powder crystallography does not have an analytically known solution, and therefore the structural inference typically involves a laborious process of iterative design, structural refinement, and domain knowledge of skilled experts. A key obstacle to fully automating the inference process computationally has been formulating the problem in an end-to-end quantitative form that is suitable for machine learning, while capturing the ambiguities around molecule orientation, symmetries, and reconstruction resolution. Here we present an ML approach for structure determination from powder diffraction data. It works by estimating the electron density in a unit cell using a variational coordinate-based deep neural network. We demonstrate the approach on computed powder x-ray diffraction (PXRD), along with partial chemical composition information, as input. When evaluated on theoretically simulated data for the cubic and trigonal crystal systems, the system achieves up to 93.4% average similarity (as measured by structural similarity index) with the ground truth on unseen materials, both with known and partially-known chemical composition information, showing great promise for successful structure solution even from degraded and incomplete input data. The approach does not presuppose a crystalline structure and the approach are readily extended to other situations such as nanomaterials and textured samples, paving the way to reconstruction of yet unresolved nanostructures.

Influence of wet-dry cycles on the disintegration characteristics of cretaceous siltstone, China

The Cretaceous siltstone, widely distributed in the Yichang region, is a type of soft rock characterized by its low strength and susceptibility to softening and disintegration when exposed to water. To gain a better understanding of the impact of wet-dry cycles on the disintegration characteristics and mechanisms of Cretaceous siltstone, a series of rock disintegration experiments were conducted. These experiments involved microscopic structure analysis and solution ion concentration tests on the specimens. The results of the experiments revealed that with an increase in the number of wet-dry cycles, the Cretaceous siltstone progressively fractured and disintegrated, with larger fragments transitioning into smaller ones. Microscopic structure analysis indicated that continuous wet-dry cycles altered the specimen's microscopic structure, resulting in the formation of new microcracks and pores. The results of solution ion concentration tests showed significant mineral dissolution losses during specimen immersion in the solution. Furthermore, a comparative analysis of various disintegration parameters highlighted that each metric emphasized specific aspects of Cretaceous siltstone disintegration characteristics. Therefore, adopting a multi-metric approach allows for comparison validation and assessment of the disintegration features of Cretaceous siltstone from many aspects. Finally, based on the experimental findings, a concise description and summary of the disintegration mechanisms of Cretaceous siltstone under wet-dry cycle conditions are provided, and then combined with its disintegration mechanism, the engineering prevention and control suggestions for timely drainage and reduction of thermal contact are put forward from the perspectives of waterproof and heat insulation, which can be used for reference.

Unveiling the solution structure of a DNA duplex with continuous silver-modified Watson-Crick base pairs

The challenge of transforming organized DNA structures into their metallized counterparts persists in the scientific field. In this context, utilizing DNA molecules modified with 7-deazapurine, provides a transformative solution. In this study, we present the solution structure of a DNA duplex that can be transformed into its metallized equivalent while retaining the natural base pairing arrangement through the creation of silver-modified Watson-Crick base pairs. Unlike previously documented X-ray structures, our research demonstrates the feasibility of preserving the intrinsic DNA self-assembly while incorporating AgI into the double helix, illustrating that the binding of silver does not disrupt the canonical base-pairing organization. Moreover, in our case, the uninterrupted AgI chain deviates from forming conventional straight linear chains; instead, it adheres to a helical arrangement dictated by the underlying DNA structure. This research challenges conventional assumptions and opens the door to precisely design structures based on the organization of highly stable Ag-DNA assemblies.