Multiple Complex Structures Research Articles

Tracing the substrate translocation mechanism in P-glycoprotein.

P-glycoprotein (Pgp) is a prototypical ATP-binding cassette (ABC) transporter of great biological and clinical significance.Pgp confers cancer multidrug resistance and mediates the bioavailability and pharmacokinetics of many drugs (Juliano and Ling, 1976; Ueda et al., 1986; Sharom, 2011). Decades of structural and biochemical studies have provided insights into how Pgp binds diverse compounds (Loo and Clarke, 2000; Loo et al., 2009; Aller et al., 2009; Alam et al., 2019; Nosol et al., 2020; Chufan et al., 2015), but how they are translocated through the membrane has remained elusive. Here, we covalently attached a cyclic substrate to discrete sites of Pgp and determined multiple complex structures in inward- and outward-facing states by cryoEM. In conjunction with molecular dynamics simulations, our structures trace the substrate passage across the membrane and identify conformational changes in transmembrane helix 1 (TM1) as regulators of substrate transport. In mid-transport conformations, TM1 breaks at glycine 72. Mutation of this residue significantly impairs drug transport of Pgp in vivo, corroborating the importance of its regulatory role. Importantly, our data suggest that the cyclic substrate can exit Pgp without the requirement of a wide-open outward-facing conformation, diverting from the common efflux model for Pgp and other ABC exporters. The substrate transport mechanism of Pgp revealed here pinpoints critical targets for future drug discovery studies of this medically relevant system.

Tracing the substrate translocation mechanism in P-glycoprotein

P-glycoprotein (Pgp) is a prototypical ATP-binding cassette (ABC) transporter of great biological and clinical significance.Pgp confers cancer multidrug resistance and mediates the bioavailability and pharmacokinetics of many drugs (Juliano and Ling, 1976; Ueda et al., 1986; Sharom, 2011). Decades of structural and biochemical studies have provided insights into how Pgp binds diverse compounds (Loo and Clarke, 2000; Loo et al., 2009; Aller et al., 2009; Alam et al., 2019; Nosol et al., 2020; Chufan et al., 2015), but how they are translocated through the membrane has remained elusive. Here, we covalently attached a cyclic substrate to discrete sites of Pgp and determined multiple complex structures in inward- and outward-facing states by cryoEM. In conjunction with molecular dynamics simulations, our structures trace the substrate passage across the membrane and identify conformational changes in transmembrane helix 1 (TM1) as regulators of substrate transport. In mid-transport conformations, TM1 breaks at glycine 72. Mutation of this residue significantly impairs drug transport of Pgp in vivo, corroborating the importance of its regulatory role. Importantly, our data suggest that the cyclic substrate can exit Pgp without the requirement of a wide-open outward-facing conformation, diverting from the common efflux model for Pgp and other ABC exporters. The substrate transport mechanism of Pgp revealed here pinpoints critical targets for future drug discovery studies of this medically relevant system.

Inhibitory effect of truncated isoforms on GPCR dimerization predicted by combinatorial computational strategy

G protein-coupled receptors (GPCRs) play a pivotal role in fundamental biological processes and disease development. GPCR isoforms, derived from alternative splicing, can exhibit distinct signaling patterns. Some highly-truncated isoforms can impact functional performance of full-length receptors, suggesting their intriguing regulatory roles. However, how these truncated isoforms interact with full-length counterparts remains largely unexplored. Here, we computationally investigated the interaction patterns of three human GPCRs from three different classes, ADORA1 (Class A), mGlu2 (Class C) and SMO (Class F) with their respective truncated isoforms because their homodimer structures have been experimentally determined, and they have truncated isoforms deposited and identified at protein level in Uniprot database. Combining the neural network-based AlphaFold2 and two physics-based protein-protein docking tools, we generated multiple complex structures and assessed the binding affinity in the context of atomistic molecular dynamics simulations. Our computational results suggested all the four studied truncated isoforms showed potent binding to their counterparts and overlapping interfaces with homodimers, indicating their strong potential to block homodimerization of their counterparts. Our study offers insights into functional significance of GPCR truncated isoforms and supports the ubiquity of their regulatory roles.

Magnetically-assisted digital light processing 4D printing of flexible anisotropic soft-Magnetic composites

ABSTRACT Flexible anisotropic soft-magnetic composite (FASMC) presents superior magnetic properties in one or more specified directions, showing great potential in the application of microwave absorption, soft robots, and other smart sensors/actuators. However, the fabrication of FASMC using additive manufacturing is challenging due to a trade-off between magnetic properties of the composites enhanced by iron particles and printability during printing. Here, we developed a 4D printing scheme using flexible soft-magnetic photosensitive resin consisting of flexible long-chin acrylic resin monomer and soft magnetic iron particles. Multiple complex structures with good spatial resolution of ∼170 μm were fabricated using magnetic field-assisted digital light processing (MF-DLP). Directional magnetic field was applied during printing, enabling the fabrication of FASMC with strong anisotropic magnetic properties. FASMC with high CIP (carbonyl iron powder, CIP) concentration of up to 45 wt.% was fabricated with excellent tensile strength and elongation up to 460%. Strong anisotropic magnetic properties were demonstrated through a series of stimuli-response testing such as large deformation, anti-deflection, controlled motion, variable stiffness metamaterial, and array assembly, under external magnetic field. This study demonstrates the feasibility and potential of MF-DLP technique for fabrication of FASMC, shedding light on the design and fabrication of next-generation sensors and actuators.

OLFF-Net: Robust Registration of 3D Point Cloud based on Overlapped Local Feature Fusion

Recent advance in high-accuracy sensors has made point cloud become the main data format to characterize the three-dimensional world. Since the sensor can only scan and capture the 3D data within a limited field of view, an alignment algorithm is needed to generate the complete 3D scene. Point cloud registration is the solution for alignment problem that aims to estimate the transformation matrix between two frames of different point cloud sets. In this paper, we propose a neural network called OLFF-Net to achieve robust registration of 3D point clouds based on overlapped local feature fusion, which focuses on extracting rotational-invariant local features while providing enough information to achieve accurate alignment. Extensive experiments on representative datasets indicate that the framework can largely outperform competing methods with an average improvement of 16.82% in the metrics over the compared methods. More importantly, it shows significant generalization capability and can be widely applied to point cloud data with multiple complex structures.

On multiple complex structure formations in expanding hollow cathode discharge

On multiple complex structure formations in expanding hollow cathode discharge

Probabilistic analyses of structural dynamic response with modified Kriging-based moving extremum framework

Mechanical system is usually composed of multiple complex structures, which endure the combine action of multi-physical fields (e.g., flow field, thermal field, structural field, and so forth) during operation. Structural response, for instance, deformation, stress, strain, fatigue life, etc., have dynamic and time-varying attributes, their values play an important role in safeguarding function properly, and affects the safety of entire system. Probabilistic analyses (including reliability evaluation and sensitivity analysis) can effectively identify potential risk and improve the reliability level. The traditional way is to use Monte Carlo (MC) simulation to achieve probabilistic analyses of complex structures. However, the MC simulation needs to perform a large amount of calculations to complete the specified task analysis, the computational burden is too heavy for the reliability evaluation and sensitivity analysis of structural dynamic response. To efficiently perform probabilistic analyses of structural dynamic response, we therefore developed a surrogate model method, namely modified Kriging-based moving extremum framework (MKMEF, short for), absorbing extremum thought, moving least squares (MLS) technique, Kriging model and collaborative evolution genetic algorithm (CEGA). For this proposed MKMEF, the extremum thought is used to transform dynamic output response into extremum values within a time domain, and the MLS method is applied to obtain efficient samples to derive Kriging model. Besides, the CEGA is employed to replace gradient descent method to resolve maximum likelihood equation (MLE) and find the optimal hyperparameters of Kriging model. Furthermore, an aeroengine high-pressure turbine blisk is treated as a case study, the probabilistic analyses of radial running deformation is executed to validate the effectiveness of the proposed method by considering the fluid-thermal-solid interaction. The analytical results show that the reliability degree of turbine blisk is 99.78%, when the allowable value of radial running deformation is 2.5071 × 10−3 m (determined by 3 sigma levels), and the highest impact on the turbine blisk radial running deformation is gas temperature, followed by inlet velocity, rational speed, material density and outlet pressure. The comparison of methods including direct simulation, response surface method-based extremum thought (ERSM) and traditional Kriging model, shows that the developed MKMEF holds high-efficiency and high-accuracy for the probabilistic analyses of turbine blisk radial running deformation. The presented efforts provide a useful insight for assessing probabilistic analyses of structural dynamic response and enrich mechanical reliability theory.

Hydrophobic recognition allows the glycosyltransferase UGT76G1 to catalyze its substrate in two orientations

Diets high in sugar are recognized as a serious health problem, and there is a drive to reduce their consumption. Steviol glycosides are natural zero-calorie sweeteners, but the most desirable ones are biosynthesized with low yields. UGT76G1 catalyzes the β (1–3) addition of glucose to steviol glycosides, which gives them the preferred taste. UGT76G1 is able to transfer glucose to multiple steviol substrates yet remains highly specific in the glycosidic linkage it creates. Here, we report multiple complex structures of the enzyme combined with biochemical data, which reveal that the enzyme utilizes hydrophobic interactions for substrate recognition. The lack of a strict three-dimensional recognition arrangement, typical of hydrogen bonds, permits two different orientations for β (1–3) sugar addition. The use of hydrophobic recognition is unusual in a regio- and stereo-specific catalysis. Harnessing such non-specific hydrophobic interactions could have wide applications in the synthesis of complex glycoconjugates.

Photonic bandgap properties of two dimensional photonic quasicrystals with multiple complex structures

Abstract Two dimensional photonic quasicrystals (PQCs) with different rotational symmetries are constructed based on holographic interference patterns. Their photonic bandgap (PBG) properties are obtained by using finite element method (FEM) to calculate the transmission and reflection spectra with different directions. The maximum gap-midgap ratio among different dielectric constant contrast and fill factor is given for all the PQCs to compare their abilities to produce bandgaps. The results show that 10-fold (five beams interference) and 12-fold quasicrystals are easier to form bandgaps than others. This may provide a reference to select appropriate quasicrystal structures for photonic devices and optimize device performance.

Fold 2D Woven DNA Origami to Origami+ Structures

AbstractDNA origami strategy has greatly promoted the development of DNA nanotechnology as it can construct delicate 2D/3D nanostructures. The current method to prepare DNA origami is through a woven approach to fix a long strand of DNA into certain shapes. This article describes a novel strategy to fold the same 2D DNA sheet into multiple complex structures driven by introducing hydrophobic interaction. The pathway of the folding process can be adjusted by tuning the distribution and chronic order of cholesterol, resulting in different complicated structures. This method is proven efficient for constructing variable nanostructures based on the same DNA origami sheet, and termed as origami+. This work represents a new strategy in DNA nanotechnology and will improve the ability to manipulate objects at nanoscale.

Threshold response to stochasticity in morphogenesis.

During development of biological organisms, multiple complex structures are formed. In many instances, these structures need to exhibit a high degree of order to be functional, although many of their constituents are intrinsically stochastic. Hence, it has been suggested that biological robustness ultimately must rely on complex gene regulatory networks and clean-up mechanisms. Here we explore developmental processes that have evolved inherent robustness against stochasticity. In the context of the Drosophila eye disc, multiple optical units, ommatidia, develop into crystal-like patterns. During the larva-to-pupa stage of metamorphosis, the centers of the ommatidia are specified initially through the diffusion of morphogens, followed by the specification of R8 cells. Establishing the R8 cell is crucial in setting up the geometric, and functional, relationships of cells within an ommatidium and among neighboring ommatidia. Here we study an PDE mathematical model of these spatio-temporal processes in the presence of parametric stochasticity, defining and applying measures that quantify order within the resulting spatial patterns. We observe a universal sigmoidal response to increasing transcriptional noise. Ordered patterns persist up to a threshold noise level in the model parameters. In accordance with prior qualitative observations, as the noise is further increased past a threshold point of no return, these ordered patterns rapidly become disordered. Such robustness in development allows for the accumulation of genetic variation without any observable changes in phenotype. We argue that the observed sigmoidal dependence introduces robustness allowing for sizable amounts of genetic variation and transcriptional noise to be tolerated in natural populations without resulting in phenotype variation.

An uracil-linked hydroxyflavone probe for the recognition of ATP.

Background: Nucleotides are essential molecules in living systems due to their paramount importance in various physiological processes. In the past years, numerous attempts were made to selectively recognize and detect these analytes, especially ATP using small-molecule fluorescent chemosensors. Despite the various solutions, the selective detection of ATP is still challenging due to the structural similarity of various nucleotides. In this paper, we report the conjugation of a uracil nucleobase to the known 4’-dimethylamino-hydroxyflavone fluorophore.Results: The complexation of this scaffold with ATP is already known. The complex is held together by stacking and electrostatic interactions. To achieve multi-point recognition, we designed the uracil-appended version of this probe to include complementary base-pairing interactions. The theoretical calculations revealed the availability of multiple complex structures. The synthesis was performed using click chemistry and the nucleotide recognition properties of the probe were evaluated using fluorescence spectroscopy.Conclusions: The first, uracil-containing fluorescent ATP probe based on a hydroxyflavone fluorophore was synthesized and evaluated. A selective complexation with ATP was observed and a ratiometric response in the excitation spectrum.

Catastrophic Emulsion Inversion Process of Highly Viscous Isosorbide Biobased Polyester Monitoredin situ by Torque and Light Backscattering.

Highly viscous hydrophobic isosorbide biobased polyester O/W emulsions are prepared through catastrophic phase inversion. The process is followed in situ with two different methods: torque and light backscattering (LBS). Considering high viscosity of the system, only discontinuous conductivity monitoring is performed for comparison. Torque and LBS allow to highlight the emulsion inversion point (EIP) with relatively close water weight fraction values (fw≈0.20). The torque and LBS signals are rather noisy before inversion (evolution of different structures) and more smooth after phase inversion (continuous aqueous phase). Torque gives a more macroscopic information, representative of the global state of the dispersion. Consistent conductivity and torque measurements suggest indeed an inversion pathway through multiple o/W/O emulsions leading to multiple complex structures before getting continuous aqueous final emulsion. This hypothesis is confirmed with continuous LBS monitoring and microscopic observations. LBS signal seems more complete because it combines the information of conductivity and torque and allows to clearly follow in situ the inversion from the beginning to the end of the process.

Vulnerability of international freight flows to shipping network disruptions: A multiplex network perspective

As freight flows through global supply chains intensify, dependence upon maritime transportation increases. This paper explores the risks that international freight flows are exposed to as a function of the multiple complex structure of liner shipping networks. Based on network modelling of over 80 networks and simulation of attacks to seven strategic nodes in the Americas, the paper shows that the vulnerability of international freight flows to disruptions in maritime transportation services varies according to the country of origin of such flows and the role that the country plays in the multi-layered maritime transportation network.

Robust Locally Weighted Regression For Ground Surface Extraction In Mobile Laser Scanning 3D Data

Abstract. A new robust way for ground surface extraction from mobile laser scanning 3D point cloud data is proposed in this paper. Fitting polynomials along 2D/3D points is one of the well-known methods for filtering ground points, but it is evident that unorganized point clouds consist of multiple complex structures by nature so it is not suitable for fitting a parametric global model. The aim of this research is to develop and implement an algorithm to classify ground and non-ground points based on statistically robust locally weighted regression which fits a regression surface (line in 2D) by fitting without any predefined global functional relation among the variables of interest. Afterwards, the z (elevation)-values are robustly down weighted based on the residuals for the fitted points. The new set of down weighted z-values along with x (or y) values are used to get a new fit of the (lower) surface (line). The process of fitting and down-weighting continues until the difference between two consecutive fits is insignificant. Then the final fit represents the ground level of the given point cloud and the ground surface points can be extracted. The performance of the new method has been demonstrated through vehicle based mobile laser scanning 3D point cloud data from urban areas which include different problematic objects such as short walls, large buildings, electric poles, sign posts and cars. The method has potential in areas like building/construction footprint determination, 3D city modelling, corridor mapping and asset management.

Sparse-plus-dense-RANSAC for estimation of multiple complex curvilinear models in 2D and 3D

The detection of multiple complex structures in noisy, outlier-rich two- and three-dimensional data is a challenging model estimation problem. In this paper, we build on the RANSAC method to select multiple model instances, focusing especially on curve estimation. Estimation of complex curves such as splines has so far received little attention in the context of model estimation, but has primarily been considered as a segmentation problem. Our proposed curve estimation is based on Sparse-Plus-Dense RANSAC, a framework in which estimation is performed on sparse points, guided by dense image data. This approach is extended to complex curvilinear models, in two- and three-dimensional data. The estimation is hierarchical, based on a merging step that uses an intuitive cost function. Results are presented on synthetic and real X-ray data, showing that the proposed approach performs comparably to state-of-the-art multiple model estimation in the synthetic data, while it significantly outperforms state-of-the-art in the real X-ray sequences. It also achieves correct localization of the model endpoints, which is a crucial aspect in the context of the clinical application.

CRIB

Conventional high-performance processors utilize register renaming and complex broadcast-based scheduling logic to steer instructions into a small number of heavily-pipelined execution lanes. This requires multiple complex structures and repeated dependency resolution, imposing a significant dynamic power overhead. This paper advocates in-place execution of instructions, a power-saving, pipeline-free approach that consolidates rename, issue, and bypass logic into one structure---the CRIB---while simultaneously eliminating the need for a multiported register file, instead storing architected state in a simple rank of latches. CRIB achieves the high IPC of an out-of-order machine while keeping the execution core clean, simple, and low power. The datapath within a CRIB structure is purely combinational, eliminating most of the clocked elements in the core while keeping a fully synchronous yet high-frequency design. Experimental results match the IPC and cycle time of a baseline out-of-order design while reducing dynamic energy consumption by more than 60% in affected structures.

Infection of Myxobolus turpisrotundus sp. n. in allogynogenetic gibel carp, Carassius auratus gibelio (Bloch), with revision of Myxobolus rotundus (s. l.) Nemeczek reported from C. auratus auratus (L.)

Infection of a Myxobolus species, previously identified as Myxobolus rotundus, was detected in 182 of 7892 (2.31%) allogynogenetic gibel carp, Carassius auratus gibelio, in a closed pond culture system in China. Morphological and molecular data showed that this myxosporean is a different species from M. rotundus parasitizing Abramis brama in Europe and is thus designated as a new species, Myxobolus turpisrotundus. M. rotundus (s.l.) ex C. auratusauratus is a synonym of M. turpisrotundus. Plasmodia of M. turpisrotundus develop in the subepidermal tissues of the body surface resulting in an unaesthetic appearance and causing severe economic losses. Prevalence of infection with the myxosporean plasmodia varied seasonally, increasing in winter and decreasing in spring. Prevalence was positively correlated to host size, but no host sex-specificity was found. No infection was observed in other fish species (grass carp, bighead carp and yellow catfish) reared in the same pond, suggesting that the parasite has a relatively strict host specificity. Plasmodia grew gradually as the parasite developed, and reached up to a maximum 5.6 mm in diameter. Plasmodia ruptured naturally to release the mature spores and host fish completely recovered with no mortality. Release of spores and regeneration of lesions were not correlated with water temperature. Histology showed that plasmodia developed sub-epidermally, and that the wall of the plasmodia was composed of a multiple complex structure, including layers of fibroblasts, a collagenous membrane, melanophores and a layer of cup-like cells of unknown derivation and function. The cup-like cells are in direct contact with pre-sporogonic stages located in the peripheral parts of the large plasmodia. No severe host inflammatory response was seen.

Novel Method for the Evaluation of 3D Conformation Generators

Conformation generation is a common and key process of computer-aided drug design. The reliability of the docking simulations, pharmacophore development, and 3D-QSAR analyses depends on the accuracy of conformations of small molecules used as input information for each program. Many conformation generators have been developed with the aim of efficiently generating all the putative bound conformations that small molecules adopt when they interact with macromolecules. Conformation generators have been evaluated by whether they can reproduce the experimentally determined bioactive conformations of bound small molecules. These bioactive conformations are usually obtained from publicly available crystal structures of protein-ligand complexes. However, it is difficult to obtain 2 or more than 2 bioactive conformations of one compound because multiple complex structures of a single molecule with various macromolecules are rarely available. Present methods, therefore, simply check whether a set of generated conformations includes the corresponding bioactive conformation. The overall validity of the entire set of generated conformations against bioactive conformation space has never been checked. In this work we developed a novel method for the evaluation of conformation generators, which makes it possible to measure the performance of a conformation generator based on its ability to reproduce the overall bioactive conformation space. We also determined the optimum parameter sets for OMEGA (OpenEye) based on the coverage of bioactive conformation space and computational efficiency. Our evaluation method elucidated that increasing the number of generated conformations is not necessary to obtain better reproducibility of the overall bioactive conformation space. Our method can be applied to the evaluation of the algorithm and/or design of the conformation generator program itself.

Flexible nets: disorder and induced fit in the associations of p53 and 14-3-3 with their partners

BackgroundProteins are involved in many interactions with other proteins leading to networks that regulate and control a wide variety of physiological processes. Some of these proteins, called hub proteins or hubs, bind to many different protein partners. Protein intrinsic disorder, via diversity arising from structural plasticity or flexibility, provide a means for hubs to associate with many partners (Dunker AK, Cortese MS, Romero P, Iakoucheva LM, Uversky VN: Flexible Nets: The roles of intrinsic disorder in protein interaction networks. FEBS J 2005, 272:5129-5148).ResultsHere we present a detailed examination of two divergent examples: 1) p53, which uses different disordered regions to bind to different partners and which also has several individual disordered regions that each bind to multiple partners, and 2) 14-3-3, which is a structured protein that associates with many different intrinsically disordered partners. For both examples, three-dimensional structures of multiple complexes reveal that the flexibility and plasticity of intrinsically disordered protein regions as well as induced-fit changes in the structured regions are both important for binding diversity.ConclusionsThese data support the conjecture that hub proteins often utilize intrinsic disorder to bind to multiple partners and provide detailed information about induced fit in structured regions.