Superposition Of Structures Research Articles

Biochemical properties and crystal structure of formate-tetrahydrofolate ligase from Methylobacterium extorquens CM4

Methylobacterium extorquens is a methylotroph model organism that has the ability to assimilate formate using the tetrahydrofolate (THF) pathway. The formate-tetrahydrofolate ligase from M. extorquens (MeFtfL) is an enzyme involved in the THF pathway that catalyzes the conversion of formate, THF, and ATP into formyltetrahydrofolate and ADP. To investigate the biochemical properties of MeFtfL, we evaluated the metal usage and enzyme kinetics of the enzyme. MeFtfL uses the Mg ion for catalytic activity, but also has activity for Mn and Ca ions. The enzyme kinetics analysis revealed that Km value of farmate was much higher than THF and ATP, which shows that the ligation activity of MeFtfL is highly dependent on formation concentration. We also determined the crystal structure of MeFtfL at 2.8 Å resolution. MeFtfL functions as a tetramer, and each monomer consists of three domains. The structural superposition of MeFtfL with FtfL from Moorella thermoacetica allowed us to predict the substrate binding site of the enzyme.

Global Cities as the Hubs of New Transnational Actors

In the context of the world development paradigm shift and the transition to a network structure, so-called new transnational actors are beginning to play an increasing role in global governance processes, their activity is constantly growing and their composition is expanding. In the economic sphere their core is made up of transnational corporations (TNC), in the political sphere – of international organizations of different profiles and status. Placing their headquarters in cities, such structures, together with the institutions of traditional subjects of international relations, largely determine both the set of command and control functions over urban agglomerations, their competitiveness, sustainability of development and the variability of the configuration of the General framework of “centers of power” operating on the world stage. Their influence growth in the context of desovereignization process development means the approximation of the historical transition in the spatial organization of the international community from its traditional “countries-nations” model to the “archipelago of cities”, which is a set of centers of different rank and functional profile, closely interacting on a global scale.The global cities concept, which emerged in the 1990s, is aimed at revealing this phenomenon. The explanatory part of this concept is based on the superposition of network structures of global firms highly specialized business services in global cities. The article discusses the main directions in modern research of global cities, argues for the need for a qualitative update of existing approaches, and the importance of new transnational actors in their formation. An assessment of the dynamics and localization of the headquarters of the world’s leading TNCs and international organizations is given. The revealed asymmetry in their placement refutes the hypothesis that global cities are equally attractive. Based on the rating and grouping of centers, several types of hubs of new transnational actors were identified, including complex ones headed by “hegemonic cities” (New York, London, Paris), and specialized ones of various ranks – geoeconomic and geopolitical. Given the relevance and significance of the phenomenon of new transnational actors based in urban agglomerations, it is assumed that a productive study of the features of their formation, composition, specialization, placement and interaction mechanisms can become the subject field of a new scientific problem area at the intersection of a number of disciplines – geopolitical urbanism, which can make a significant contribution to the study of the contours of future global transformations.

Characterization of cold-tolerant trehalose-6-phosphate synthase from the deep-sea bacterium Microbacterium sediminis YLB-01.

A gene encoding the enzyme trehalose-6-phosphate synthase (TPS), which is part of the TPS trehalose synthesis pathway, was cloned from the deep-sea psychrotolerant bacterium Microbacterium sediminis YLB-01 and expressed in Escherichia coli BL21. The exogenously expressed TPS exhibited highest similarity (80.93% identity) to Microbacterium sp. TPS. The purified recombinant TPS was cold-tolerant, with low thermostability. The optimum temperature for TPS activity was 40°C, and the enzyme retained 72.6% of its maximal activity at 4°C. The optimum pH was 7.5. TPS activity was cation-dependent, with Mg2+, Co2+, or Ba2+ being essential for maximum activity. The kinetic constants of the recombinant TPS reaction rates confirmed that it was cold-tolerant. Molecular dynamics analysis showed that TPS was more flexible (0.8741Å) at 4°C than 1GZ5, its homolog in the mesophilic bacterium E. coli, and superposition of the 3D enzyme structures supported this.

Dose and spatial resolution analysis of grating-based phase-contrast mammography using an inverse Compton x-ray source.

Purpose: Although the mortality rate of breast cancer was reduced with the introduction of screening mammography, many women undergo unnecessary subsequent examinations due to inconclusive diagnoses. Superposition of anatomical structures especially within dense breasts in conjunction with the inherently low soft tissue contrast of absorption images compromises image quality. This can be overcome by phase-contrast imaging.Approach: We analyze the spatial resolution of grating-based multimodal mammography using a mammographic phantom and one freshly dissected mastectomy specimen at an inverse Compton x-ray source. Here, the focus was on estimating the spatial resolution with the sample in the beam path and discussing benefits and drawbacks of the method used and the estimation of the mean glandular dose. Finally, the possibility of improving the spatial resolution is investigated by comparing monochromatic grating-based mammography with the standard one.Results: The spatial resolution is constant or also higher for the image acquired with monochromatic radiation and the contrast-to-noise ratio (CNR) is higher in our approach while the dose can be reduced by up to 20%.Conclusions: In summary, phase-contrast imaging helps to improve tumor detection by advanced diagnostic image quality. We demonstrate a higher spatial resolution for one mastectomy specimen and increased CNR at an equal or lower dose for the monochromatic measurements.

Basement-cover interaction in the mountain front of the Northern Neuquén fold and thrust belt (37°10’ – 37°40’ S), Argentina

The deformation front of the Neuquén fold and thrust belt (~37°30′S) comprises kilometer-scale basement-involved anticlines, related to development of the Las Yeseras and Pampa Tril thrust systems, connected with a wide frontal syncline. The interpretation of more than 70 seismic lines led to the construction of a time-structure map at top of the Cuyo Group (Middle Jurassic), which shows a structural high east of the Tromen volcano produced by the superposition of thick-skinned structures. Moreover, data from 35 oil wells constrain the along-strike variations in structural reliefs. The structural relief of the Las Yeseras anticline increase from north to south, between ~1000 m and 2000 m, while the structural relief of the Pampa Tril anticline reaches its maximum height of 3700 m in the north and decreases southwards to only 1600 m height and then disappears. Three structural cross-sections based on surface and subsurface information show the overall structural style dominated by north-trending basement-involved anticlines, with subhorizontal backlimbs and maximum structural reliefs around 3–4 km, associated with thick-skinned thrust systems and without significant participation of inverted normal faults. Calculated thick-skinned shortenings are ~8.3 km (14.8%) in the north and ~4 km (7.8%) in the south, which principally reflects the decreasing displacement of the Pampa Tril thrust system. Along-strike structural changes were locally controlled by WNW transfer zones that can be interpreted as SSW-dipping preexisting normal faults with minor positive inversion. Thin-skinned structures that form oil fields at depth are genetically associated with the thick-skinned thrust systems, thus the understanding of basement-cover interaction in the mountain fronts will aid to future hydrocarbon explorations and to comprehend the mechanisms of Andean mountain building.

Accretionary processes and metallogenesis of the Central Asian Orogenic Belt: Advances and perspectives

As one of the largest Phanerozoic orogens in the world, the Central Asian Orogenic Belt (CAOB) is a natural laboratory for studies of continental dynamics and metallogenesis. This paper summarizes the research progresses of the accretionary processes and metallogenesis of the CAOB since the People’s Republic of China was founded, and puts forward the prospect for future research. During the early period (1950s–1970s), several geological theories were applied to explain the geological evolution of Central Asia. In the early period of China’s reform and opening-up, the plate tectonics theory was applied to explain the evolution of the northern Xinjiang and Xingmeng regions, and the opinion of subduction-collision between Siberian, Kazakhstan, and China-North Korea-Tarim plates was proposed. The idea of the Solonker-Yanbian suture zone was established. In the 1990s, the study of the CAOB entered a period of rapid development. One school of scholars including geologists from the former Soviet Union proposed a multi-block collision model for the assemblage of the CAOB. In contrast, another school of scholars, led by a Turkish geologist, Celal Şengor, proposed that the Altaids was formed through the growth and strike-slip duplicates of a single island arc, and pointed out that the Altaids is a special type of collisional orogen. During this period, Chinese geologists carried out a lot of pioneering researches on ophiolites and high-pressure metamorphic rocks in northern China, and confirmed the main suture zones accordingly. In 1999, the concept of “Central Asian metallogenic domain” was proposed, and it became one of the three major metallogenic domains in the world. Since the 21st century, given the importance for understanding continental accretion and metallogenic mechanism, the CAOB has become the international academic forefront. China has laid out a series of scientific research projects in Central Asia. A large number of important scientific research achievements have been spawned, including the tectonic attribution of micro-continents, timing and tectonic settings of ophiolites, magmatic arcs, identification and anatomy of accretionary wedges, regional metamorphism-deformation, (ultra)high-pressure metamorphism, ridge subduction, plume-plate interaction, archipelagic paleogeography and spatio-temporal framework of multiple accretionary orogeny, continental growth, accretionary metallogenesis, structural superposition and transformation, etc. These achievements have made important international influences. There still exist the following aspects that need further study: (1) Early evolution history and subduction initiation of the Paleo-Asian Ocean; (2) The accretionary mechanism of the extroversion Paleo-Asian Ocean; (3) The properties of the mantle of the Paleo-Asian Ocean and their spatio-temporal distribution; (4) The interaction between the Paleo-Asian Ocean and the Tethys Ocean; (5) Phanerozoic continental growth mechanism and its global comparison; (6) Accretionary metallogenic mechanism of the Central Asian metallogenic domain; and (7) Continental transformation mechanism.

Latest fold and thrust tectonics conceals extensional structures inherited from Cretaceous syn-sedimentary deformation: insights for exploration in fold-and-thrust belts from the Maiella Mountain

Abstract The superposition of structures produced by different tectonic phases is common in sedimentary basins. Yet the earlier structures often remain overlooked with potentially negative exploration consequences. In the Maiella anticline, Pliocene compression has folded carbonate sequences containing Cretaceous extensional structures. The geometry and evolution of the Apulian carbonate platform margin outcropping on the Maiella Mountain are described by two opposing groups of models. One proposes a structurally controlled platform margins cut by syn-sedimentary Cretaceous faults; the other assumes a passive Cretaceous palaeo-escarpments progressively filled by Cretaceous to Tertiary sediments later deformed by the Pliocene compression. Assuming models in line with either one of these two groups has significant implications for exploration plays on both platforms and adjacent basins of analogous subsurface systems. These include: hypothesized margin geometries; sediment transport mechanisms (directions and distribution); size of sequences; type and size of traps and associated exploration targets, risks and uncertainties. We demonstrate that during the Late Cretaceous the platform margin was cut by normal faults which controlled the palaeogeography of the platform and the sediment input into the adjacent basin in which thick, resedimented, carbonate megabreccia and turbidites were deposited. These carbonates represent exploration targets in similar settings worldwide.

Analytical Solution of Heat Conduction in a Symmetrical Cylinder Using the Solution Structure Theorem and Superposition Technique

In this paper, non-Fourier heat conduction in a cylinder with non-homogeneous boundary conditions is analytically studied. A superposition approach combining with the solution structure theorems is used to get a solution for equation of hyperbolic heat conduction. In this solution, a complex origin problem is divided into, different, easier subproblems which can actually be integrated to take the solution of the first problem. The first problem is split into three sub-problems by setting the term of heat generation, the initial conditions, and the boundary condition with specified value in each sub-problem. This method provides a precise and convenient solution to the equation of non-Fourier heat conduction. The results show that at low times (t = 0.1) up to about r = 0.4, the contribution of T1 and T3 dominate compared to T2 contributing little to the overall temperature. But at r > 0.4, all three temperature components will have the same role and less impact on the overall temperature (T).

The structure of the Thermococcus gammatolerans McrB N-terminal domain reveals a new mode of substrate recognition and specificity among McrB homologs.

McrBC is a two-component, modification-dependent restriction system that cleaves foreign DNA-containing methylated cytosines. Previous crystallographic studies have shown that Escherichia coli McrB uses a base-flipping mechanism to recognize these modified substrates with high affinity. The side chains stabilizing both the flipped base and the distorted duplex are poorly conserved among McrB homologs, suggesting that other mechanisms may exist for binding modified DNA. Here we present the structures of the Thermococcus gammatolerans McrB DNA-binding domain (TgΔ185) both alone and in complex with a methylated DNA substrate at 1.68 and 2.27 Å resolution, respectively. The structures reveal that TgΔ185 consists of a YT521-B homology (YTH) domain, which is commonly found in eukaryotic proteins that bind methylated RNA and is structurally unrelated to the E. coli McrB DNA-binding domain. Structural superposition and co-crystallization further show that TgΔ185 shares a conserved aromatic cage with other YTH domains, which forms the binding pocket for a flipped-out base. Mutational analysis of this aromatic cage supports its role in conferring specificity for the methylated adenines, whereas an extended basic surface present in TgΔ185 facilitates its preferential binding to duplex DNA rather than RNA. Together, these findings establish a new binding mode and specificity among McrB homologs and expand the biological roles of YTH domains.

Breakdown of the isochronal structural (α) and secondary (JG β) exact superpositioning in probucol - A low molecular weight pharmaceutical

In this paper, Broadband Dielectric Spectroscopy (BDS) has been applied to study the molecular dynamics of the two active pharmaceutical ingredients (APIs), probucol (PRO) and droperidol (DRO), above and below the glass transition temperature, at varying thermodynamic conditions. We found that the structural (α)-relaxation process in both compounds is sensitive to compression. It was reflected in the high pressure coefficients of the glass transition temperature, dTg/dp = 227 K/GPa and dTg/dp = 427 K/GPa for DRO and PRO, respectively. In this context, it is worthwhile to emphasize that dTg/dp calculated for the latter API is the highest reported to date for the low molecular weight glass formers. Furthermore, the data collected upon squeezing samples revealed that the pressure dependence of the relaxation times of the Johari Goldstein (JG) β-process in PRO is weaker with respect to that of structural relaxation. Thus, a breakdown of exact superposition of both modes has been noted. A slightly different scenario was observed in DRO, where relaxation times of the secondary non-JG γ-process, obtained at different T and p, plotted versus Tg/T, collapsed forming a single curve. A breakdown of exact isochronal superpositioning of α- and JG β-relaxation times at varying thermodynamic conditions in PRO, that is weakly H-bonded low molecular weight glass former, is in accordance with the data reported for the strongly associating compounds (e.g., sorbitol). Moreover, recently a similar scenario has been observed for some polymers, i.e., 1,4-polybutadiene (PBD) (Ransom et al., 2018), poly(methyl methacrylate) (PMMA) (Casalini and Roland, 2013) and polyisoprene (PI) (Kołodziej et al., 2018). This phenomenon, which is consistent with the approximate invariance of the ratio of these two relaxation times to change of thermodynamics conditions (as predicted by the Coupling Model), was assigned to the increasing torsional rigidity of the macromolecule backbone or alternatively to the non-uniform responses to variations of temperature and pressure of the distributed modes composing the JG β-process, resulting in changes of the spectral shape and different fβ(p,T) obtained from the fitting procedure. One can suppose that due to the variation in the population of weak H-bonds at elevated pressure in PRO, the latter effect might be enhanced, contributing to the observed experimental finding. Finally, the data reported herein emphasize the impact of molecular aspects related to specific interactions on the correlation between α- and JG β-relaxation at varying T and p conditions.

Preliminary evaluation of stationary inverse-geometry digital tomosynthesis system for diagnostic applications: A simulation study

Conventional X-ray imaging systems for diagnosis have several issues such as high radiation dose, structure superposition, and complicated geometry. These issues can be solved by providing 3D cross-sectional images with limited dose and simplifying system geometries. The purpose of this study is to implement a stationary inverse-geometry digital tomosynthesis (s-IGDT) system through simulation and evaluate the performance of the s-IGDT system for diagnostic applications. We also investigated the digital radiography (DR) and conventional digital tomosynthesis (DT) images for comparison. The simulated s-IGDT system was modeled with a linear X-ray source array contained 75 focal spots and a flat-panel detector. The linear X-ray source array and detector were stationary during image acquisition. In order to reduce truncation artifacts, a raw data correction process was performed. We measured profile, signal difference-to-noise ratio (SDNR), contrast-to-noise ratio (CNR) and root-mean-square error (RMSE) for a comparison of image quality among the s-IGDT, DR and conventional DT. The results showed that the SDNR, CNR and quantitative accuracy of the s-IGDT were higher than those of the DR and similar with those of the conventional DT. Also, the spatial resolution of the s-IGDT evaluated by modulation transfer function (MTF) was comparable with the conventional DT. Therefore, the s-IGDT proposed in this study has a feasibility for diagnostic applications and a potential as an alternative to the conventional X-ray imaging system.

Introducing "best single template" models as reference baseline for the Continuous Automated Model Evaluation (CAMEO).

Critical blind assessment of structure prediction techniques is crucial for the scientific community to establish the state of the art, identify bottlenecks, and guide future developments. In Critical Assessment of Techniques in Structure Prediction (CASP), human experts assess the performance of participating methods in relation to the difficulty of the prediction task in a biennial experiment on approximately 100 targets. Yet, the development of automated computational modeling methods requires more frequent evaluation cycles and larger sets of data. The "Continuous Automated Model EvaluatiOn (CAMEO)" platform complements CASP by conducting fully automated blind prediction evaluations based on the weekly pre-release of sequences of those structures, which are going to be published in the next release of the Protein Data Bank (PDB). Each week, CAMEO publishes benchmarking results for predictions corresponding to a set of about 20 targets collected during a 4-day prediction window. CAMEO benchmarking data are generated consistently for all methods at the same point in time, enabling developers to cross-validate their method's performance, and referring to their results in publications. Many successful participants of CASP have used CAMEO-either by directly benchmarking their methods within the system or by comparing their own performance to CAMEO reference data. CAMEO offers a variety of scores reflecting different aspects of structure modeling, for example, binding site accuracy, homo-oligomer interface quality, or accuracy of local model confidence estimates. By introducing the "bestSingleTemplate" method based on structure superpositions as a reference for the accuracy of 3D modeling predictions, CAMEO facilitates objective comparison of techniques and fosters the development of advanced methods.

Contrast-enhanced spectral mammography with a compact synchrotron source.

For early breast cancer detection, mammography is nowadays the commonly used standard imaging approach, offering a valuable clinical tool for visualization of suspicious findings like microcalcifications and tumors within the breast. However, due to the superposition of anatomical structures, the sensitivity of mammography screening is limited. Within the last couple of years, the implementation of contrast-enhanced spectral mammography (CESM) based on K-edge subtraction (KES) imaging helped to improve the identification and classification of uncertain findings. In this study, we introduce another approach for CESM based on a two-material decomposition, with which we expect fundamental improvements compared to the clinical procedure. We demonstrate the potential of our proposed method using the quasi-monochromatic radiation of a compact synchrotron source—the Munich Compact Light Source (MuCLS)—and a modified mammographic accreditation phantom. For direct comparison with the clinical CESM approach, we also performed a standard dual-energy KES at the MuCLS, which outperformed the clinical CESM images in terms of contrast-to-noise ratio (CNR) and spatial resolution. However, the dual-energy-based two-material decomposition approach achieved even higher CNR values. Our experimental results with quasi-monochromatic radiation show a significant improvement of the image quality at lower mean glandular dose (MGD) than the clinical CESM. At the same time, our study indicates the great potential for the material-decomposition instead of clinically used KES to improve the quantitative outcome of CESM.

Sequential analysis of variants and optimal design techniques for human-machine systems

The current paper considers automatic design of functioning processes of human-machine systems. The idea of models, methods and techniques that are discussed in the article is based on functional-structural theory and the generalized structural method, which was suggested by prof. A.I. Gubinsky. The process of functioning is presented as a sequence of simple operations - basic functional units, which can be combined into basic functional structures. Efficiency, quality and reliability of the functioning process are considered as local criteria in optimization problems. Basic design strategies for human-machine systems are given: a down-top, top-down approach and their combination. A definition of a system operation process as a notation based on binary relations between elements included in a functional net is presented. A special algorithm to determine whether a functional net defined as a set of binary relations between net elements can be reduced to a superposition of basic functional structures is stated. All alternative processes of operating of a human-machine system are formed by an alternative graph and its traversal ways. A directional search algorithm is applied to finding the optimal solution. It allows building partial solutions step-by-step. For equal (repeated) segments of a functional net the alternative graph is changed and solutions are produced by the specific optimized technique.

Revealing a Mutant-Induced Receptor Allosteric Mechanism for the Thyroid Hormone Resistance.

SummaryResistance to thyroid hormone (RTH) is a clinical disorder without specific and effective therapeutic strategy, partly due to the lack of structural mechanisms for the defective ligand binding by mutated thyroid hormone receptors (THRs). We herein uncovered the prescription drug roxadustat as a novel THRβ-selective ligand with therapeutic potentials in treating RTH, thereby providing a small molecule tool enabling the first probe into the structural mechanisms of RTH. Despite a wide distribution of the receptor mutation sites, different THRβ mutants induce allosteric conformational modulation on the same His435 residue, which disrupts a critical hydrogen bond required for the binding of thyroid hormones. Interestingly, roxadustat retains hydrophobic interactions with THRβ via its unique phenyl extension, enabling the rescue of the activity of the THRβ mutants. Our study thus reveals a critical receptor allosterism mechanism for RTH by mutant THRβ, providing a new and viable therapeutic strategy for the treatment of RTH.

Asymmetric structure of atomic above-threshold ionization spectrum in two-color elliptically polarized laser fields**Project supported by the National Natural Science Foundation of China (Grant Nos. 11474348, 11674198, 11425414, and 11774411).

According to the frequency-domain theory, we investigate the asymmetric structure of above-threshold ionization (ATI) spectrum of an atom in two-color elliptically polarized (EP) laser fields. When both laser fields are linearly polarized (LP), the spectrum shows that the multi-plateau structure is symmetric about the emitted angle of electron at π/2, while the spectrum becomes asymmetric and shifts rightwards with the increase of the EP degree of the IR laser field. Since the total ATI process is regarded as including direct ATI and the rescattering ATI, we analyze the spectrum structure of direct ATI and rescattering ATI separately. Using the saddle-point approximation, we find that for direct ATI, the fringes on the spectrum are mainly attributed to the fact that the ionization probability becomes very small when the direction of emitted electrons is perpendicular to the direction of the XUV laser polarization; while for the rescattering ATI, the interference fringes on the spectrum mainly come from the superposition of the waist structures on the spectra of all sub-channels.

A Comprehensive Superposition of Viral Polymerase Structures.

Nucleic acid polymerases are essential enzymes that replicate the genomes of both RNA and DNA viruses. These enzymes are generally encoded by viruses themselves so as to provide biochemical functions and control elements that differ from those of the host cell polymerases. The core active site structure used by all replicative polymerases is highly conserved and composed of two key aspartate residues from the conserved motifs A and C, but beyond this there is significant divergence among structures. These differences can make it difficult to select which portions of structures to align for comparisons, yet there are extended structural similarities within different groups of viral polymerases that should clearly be considered to generate optimal alignments. This manuscript describes a comprehensive structure-based superposition of every viral polymerase structure solved thus far based on an alignment-tree approach wherein aligned regions grow in complexity as similarity among polymerases increases. The result is a set of 646 structures that have been aligned into a single common orientation. This provides a convenient resource for directly comparing viral polymerases and illustrating structural conservation among them. It also sets the stage for detailed bioinformatics analysis to further assess common structural features. The full set of protein data bank (PDB) formatted files is publicly available via the Polymerase Structures community page at the Zenodo.org open data repository.

A Probabilistic Programming Approach to Protein Structure Superposition.

Optimal superposition of protein structures or other biological molecules is crucial for understanding their structure, function, dynamics and evolution. Here, we investigate the use of probabilistic programming to superimpose protein structures guided by a Bayesian model. Our model THESEUS-PP is based on the THESEUS model, a probabilistic model of protein superposition based on rotation, translation and perturbation of an underlying, latent mean structure. The model was implemented in the probabilistic programming language Pyro. Unlike conventional methods that minimize the sum of the squared distances, THESEUS takes into account correlated atom positions and heteroscedasticity (ie. atom positions can feature different variances). THESEUS performs maximum likelihood estimation using iterative expectation-maximization. In contrast, THESEUS-PP allows automated maximum a-posteriori (MAP) estimation using suitable priors over rotation, translation, variances and latent mean structure. The results indicate that probabilistic programming is a powerful new paradigm for the formulation of Bayesian probabilistic models concerning biomolecular structure. Specifically, we envision the use of the THESEUS-PP model as a suitable error model or likelihood in Bayesian protein structure prediction using deep probabilistic programming.

Structural Characterization of Arabidopsis thaliana NAP1-Related Protein 2 (AtNRP2) and Comparison with its Homolog AtNRP1.

Nucleosome Assembly Protein (NAP) is a highly conserved family of histone chaperones present in yeast, animals, and plants. Unlike other organisms, plants possess an additional class of proteins in its NAP family, known as the NAP1-related proteins or NRP. Arabidopsis thaliana possesses two NRP isoforms, namely AtNRP1 and AtNRP2, that share 87% sequence identity. Both AtNRP1 and AtNRP2 get expressed in all the plant tissues. Most works in the past, including structural studies, have focused on AtNRP1. We wanted to do a comparative study of the two proteins to find why the plant would have two very similar proteins and whether there is any difference between the two for their structure and function as histone chaperones. Here we report the crystal structure of AtNRP2 and a comparative analysis of its structural architecture with other NAP family proteins. The crystal structure of AtNRP2 shows it to be a homodimer, with its fold similar to that of other structurally characterized NAP family proteins. Although AtNRP1 and AtNRP2 have a similar fold, upon structural superposition, we find an offset in the dimerization helix of the two proteins. We evaluated the stability, oligomerization status, and histone chaperoning properties of the two proteins, for a comparison. The thermal melting experiments suggest that AtNRP2 is more stable than AtNRP1 at higher temperatures. In addition, electrophoretic mobility shift assay and isothermal titration calorimetry experiments suggest histone binding ability of AtNRP2 is higher than that of AtNRP1. Overall, these results provide insights about the specific function and relevance of AtNRP2 in plants through structural and biophysical studies.

Discriminative Dictionary Learning-Based Multiple Component Decomposition for Detail-Preserving Noisy Image Fusion

How to effectively preserve the fine-scale details of the image when noises are suppressed is one of the great challenges faced by scholars in the field of noisy image fusion. The traditional noisy image fusion method tends to smooth the fine-scale structures excessively. To overcome the oversmoothing issue, we develop a novel method that can perform fusion, denoising, and preservation of fine structures simultaneously. In this method, the image is modeled as a superposition of coarse structures and fine details. At the same time, a brand new strategy is developed to decompose the input image into coarse and fine components for the further exploitation of afforded discrimination by learned dictionary. Specifically, to preserve the coarse-scale structures and recover the fine details, a novel discriminative dictionary-learning algorithm is proposed to utilize weighted nuclear norm regularization and sparse constraint to characterize coarse structures and fine components, respectively. For image separation, we present a weighted Schatten sparse nuclear norm regularization and integrate it into the separation model to extract the coarse structures. To estimate the fine components submerged in the noise, we propose to exploit the image’s nonlocal self-similarity and develop gradient-preservation term based on the gradient histogram constraint. Finally, we develop an innovative fusion rule based on the activity level of the recovered patch to construct the fused coding coefficients of different components. Our experiments show that the proposed method has impressive subjective visual quality and objective metric performance.