Search Results (17)

The accurate prediction of secondary structures of proteins (SSPs) is a critical challenge in molecular biology and structural bioinformatics. Despite recent advancements, this task remains complex and demands further exploration. This study presents a novel approach to SSP prediction using atom-centric substructural multilevel neighborhoods of atoms (MNA) descriptors for protein molecular fragments. A dataset comprising over 335,000 SSPs, annotated by the Dictionary of Secondary Structure in Proteins (DSSP) software from 37,000 proteins, was constructed from Protein Data Bank (PDB) records with a resolution of 2 Å or better. Protein fragments were converted into structural formulae using the RDKit Python package and stored in SD files using the MOL V3000 format. Classification sequence–structure–property relationships (SSPR) models were developed with varying levels of MNA descriptors and a Bayesian algorithm implemented in MultiPASS software. The average prediction accuracy (AUC) for eight SSP types, calculated via leave-one-out cross-validation, was 0.902. For independent test sets (ASTRAL and CB513 datasets), the best SSPR models achieved AUC, Q3, and Q8 values of 0.860, 77.32%, 70.92% and 0.889, 78.78%, 74.74%, respectively. Based on the created models, a freely available web application MNA-PSS-Pred was developed. Full article

Polyamides’ properties are greatly influenced by the polymerization process and the type of feedstock used. The solid forms of nylon salts play a significant role in determining the final characteristics of the material. This study focuses on the long-chain bio-nylon 512. Firstly, we systematically investigated the possible solid forms of the nylon 512 salt, including crystal forms and morphologies, by massive experimental screening, single-crystal X-ray diffraction, Hirshfeld surface analysis, and TG-DSC measurements. The regulation and control of the various solid forms were achieved through solid-state transformations (SSTs) and solution-mediated phase transformations (SMPTs). Our findings shows that the nylon 512 salt exists in two crystal forms (anhydrate and dihydrate) and four morphologies (needle-like, plate-like, rod-like, and massive block crystal). Many factors will influence the formation of these solid forms, such as water activity, temperature, solvent, and ultrasonic physical fields. We can choose the right factors to regulate this as needed. On this basis, we studied the effects of different solid forms (crystal forms and morphologies) on the properties of the resulting polyamides prepared using direct solid-state polymerization (DSSP). The solid form of the salt had many effects on the polymer, including its structure, melting point, and mechanical properties. The polyamide obtained through DSSP of the anhydrate salt exhibited a higher melting point (204.22 °C) and greater elastic modulus (3.366 GPa) compared to that of the dihydrate salt, especially for the anhydrate salt of plate-like crystals. Full article

Double-wall steel sheet piles (DSSPs) are widely used in large-span cofferdams for docks due to their good performance against wave action during storm surges. This paper describes a study of the dynamic behavior of a DSSP cofferdam under wave action through flume tests and a numerical simulation that combined computational fluid dynamics (CFD) and the finite element method. The influences of the water level and wave height on the DSSP cofferdam were investigated experimentally and numerically. Tall waves in shallow water broke upon and impacted the seaside pile with large dynamic wave pressure, dramatically increasing the stress and displacement of the seaside pile. The overlap of the traveling and reflected waves increased the excess pore water pressure near the seaside pile due to taller overlapped waves and higher wave frequency. The DSSP cofferdam failed under the combined actions of the dynamic wave pressure and erosion of the landside seabed. The leakage and overflow of the breaking waves resulted in significant erosion of the landside seabed and greatly weakened the support of the seabed. The dynamic wave pressure then pushed the DSSP cofferdam until it failed. The simulation with the combined methods of CFD and FEM resulted in trends that were similar to those of the test measurements. Compared to the quasi-static method and pseudo-dynamic method, the results of the simulation via the present method were much closer to the test results because the simulation included the effects of breaking waves. The reinforced measure worked well to prevent the DSSP cofferdam in a sandy seabed foundation from continuous failures of deformation–leakage–erosion–tilting. However, it failed in a clay interlayer seabed foundation due to the large settlement. Full article

Shoshonitic rocks are widely distributed in post-collisional settings and provide key information on deep geodynamic mechanisms and magmatic evolution. In this paper, we present petrographic, zircon U-Pb age-related, trace elemental, Hf isotopic, bulk-rock elemental, and Sr-Nd isotopic data of the Dalongtan shoshonitic syenite porphyries (DSSPs) in central Yunnan, southeastern Tibet. The DSSPs formed at 33.2 ± 0.3 Ma in a post-collisional setting. They define linear trends on Harker diagrams, and they display similar trace element patterns and enriched bulk-rock Sr-Nd isotopes [(⁸⁷Sr/⁸⁶Sr)_i = 0.70964–0.70968, ε_Nd(t) = −12.9 to −12.7] and zircon Hf isotopes (ε_Hf(t) = −15.7 to −13.1) to the coeval mantle-derived potassic mafic rocks. This suggests that the DSSPs were fractionated from the lithospheric mantle-derived mafic magmas. The DSSPs, along with the coeval felsic and mafic magmatic rocks (37.2–32.3 Ma), exhibit a planar distribution on the SE Tibet and predate the left-lateral shearing of the Ailaoshan–Red River shear zone (ARSZ) (32–22 Ma), suggesting that there are no genetic relationships between them. The DSSPs have geochemical characteristics similar to those of A-type granites, with high total alkalinity (10.39–11.17 wt.%), HFSE concentrations (Zr + Nb + Ce + Y = 890.2–1054.3 ppm), Ga/Al ratios (10,000 × Ga/Al = 2.95–3.46), whole-rock zircon saturation temperatures (906–947 °C), and oxygen fugacity (ΔFMQ = +3.30–+4.65), indicating that they are products of the high-temperature melting of the lithosphere as a result of asthenosphere upwelling in extensional settings. Based on our data and regional observations, it is proposed that the generation of the DSSPs may be linked to the convective thinning of the thickened lithospheric mantle following the India–Asia collision. Full article

Protein structure prediction continues to pose multiple challenges despite outstanding progress that is largely attributable to the use of novel machine learning techniques. One of the widely used representations of local 3D structure—protein blocks (PBs)—can be treated in a similar way to secondary structure classes. Here, we present a new approach for predicting local conformation in terms of PB classes solely from amino acid sequences. We apply the RMSD metric to ensure unambiguous future 3D protein structure recovery. The selection of statistically assessed features is a key component of the proposed method. We suggest that ML input features should be created from the statistically significant predictors that are derived from the amino acids’ physicochemical properties and the resolved structures’ statistics. The statistical significance of the suggested features was assessed using a stepwise regression analysis that permitted the evaluation of the contribution and statistical significance of each predictor. We used the set of 380 statistically significant predictors as a learning model for the regression neural network that was trained using the PISCES30 dataset. When using the same dataset and metrics for benchmarking, our method outperformed all other methods reported in the literature for the CB513 nonredundant dataset (for the PBs, Q16 = 81.01%, and for the DSSP, Q3 = 85.99% and Q8 = 79.35%). Full article

The use of pre-alloyed powders as high-entropy alloy (HEA) coating precursors ensures a predetermined (unaltered) elemental composition of the coating with regard to the feedstock powder. At the same time, it is interesting to tackle a more challenging task: to form alloy coatings from powder blends (not previously alloyed). The powder-blend-based route of coating formation eliminates the need to use atomization or ball milling equipment for powder preparation and allows for the introduction of additives into the material in a flexible manner. In this work, for the first time, a HEA was obtained using detonation spraying (DS) followed by spark plasma sintering (SPS). A powder mixture with a nominal composition of 10Al-22.5Fe-22.5Co-22.5Ni-22.5Cu (at.%) was detonation-sprayed to form a multicomponent metallic coating on a steel substrate. The elemental composition of the deposited layer was (9 ± 1)Al-(10 ± 1)Fe-(20 ± 1)Co-(34 ± 1)Ni-(27 ± 1)Cu (at.%), which is different from that of the feedstock powder because of the differences in the deposition efficiencies of the metals during DS. Despite the compositional deviations, the deposited layer was still suitable as a precursor for a HEA with a configurational entropy of ~1.5R, where R is the universal gas constant. The subsequent SPS treatment of the substrate/coating assembly was carried out at 800–1000 °C at a uniaxial pressure of 40 MPa. The SPS treatment of the deposited layer at 1000 °C for 20 min was sufficient to produce an alloy with a single-phase face-centered cubic structure and a porosity of <1%. Interestingly, the hardness values of the as-sprayed and SPS-treated coatings were close to each other (~320 HV_0.3). The hardness of the coatings measured in two perpendicular directions did not differ significantly. The features of the DS–SPS route of the formation of HEA coatings and its potential applications are discussed. Full article

Determining Secondary Structure Elements (SSEs) for any protein is crucial as an intermediate step for experimental tertiary structure determination. SSEs are identified using popular tools such as DSSP and STRIDE. These tools use atomic information to locate hydrogen bonds to identify SSEs. When some spatial atomic details are missing, locating SSEs becomes a hinder. To address the problem, when some atomic information is missing, three approaches for classifying SSE types using $C\alpha$ atoms in protein chains were developed: (1) a mathematical approach, (2) a deep learning approach, and (3) an ensemble of five machine learning models. The proposed methods were compared against each other and with a state-of-the-art approach, PCASSO. Full article

The β-turn is the third defined secondary structure after the α-helix and the β-sheet. The β-turns were described more than 50 years ago and account for more than 20% of protein residues. Nonetheless, they are often overlooked or even misunderstood. This poor knowledge of these local protein conformations is due to various factors, causes that I discuss here. For example, confusion still exists about the assignment of these local protein structures, their overlaps with other structures, the potential absence of a stabilizing hydrogen bond, the numerous types of β-turns and the software’s difficulty in assigning or visualizing them. I also propose some ideas to potentially/partially remedy this and present why β-turns can still be helpful, even in the AlphaFold 2 era. Full article

In this study, a novel peptide VNAVL was synthesized by removing the C-terminal histidine on the basis of a bioactive peptide VNAVLH obtained from pine nut (Pinus koraiensis Sieb. et Zucc) protein. The effects of removing histidine on antioxidant activity, immunomodulatory activity, and secondary structure of the PEF-treated peptide were discussed. Compared with VNAVLH, VNAVL only exhibited lower antioxidant activity, but no immunomodulatory activity to release TNF-α, IL-6, and NO by activating RAW 264.7 cells. In addition, both antioxidant and immune activities of VNAVLH were significantly more sensitive to treatment with 40 kV/cm than other field intensities, whereas VNAVL was not sensitive to field strength changes. CD spectra and DSSP analysis verified that both peptides consisted of a β structure and random coil, but the ability of VNAVL to transform the random coil via PEF treatment is weaker than that of VNAVLH. Therefore, PEF treatment might expose the key active site located on the C-terminal histidine by altering the secondary structure of the peptide. Full article

The direct solid state polymerization (DSSP) of hexamethylene diammonium dodecanoate (PA 612 salt) was investigated for two different salt grades, fossil-based and bio-based. Aliphatic polyamide salts (such as PA 612 salt) are highly susceptible to solid melt transition (SMT) phenomena, which restrain the industrial application of DSSP. To that end, emphasis was given on reactor design, being the critical parameter influencing byproduct diffusion, amine loss and inherent DSSP kinetics. Experiments took place both at the microscale and the laboratory scale, in which two different reactors were tested in terms of bypassing SMT phenomena. The new reactor designed here proved quite successful in maintaining the solid state during the reaction. Scouting experiments were conducted in order to assess the effect of critical parameters and determine appropriate reaction conditions. Fossil-based PA 612 products proved to have a better end-group imbalance in comparison to bio-based ones, which is critical in terms of achieving high molecular weight. Finally, a real DSSP process was demonstrated, starting from PA 612 salt crystals and ending with PA 612 particles. Full article

This paper deals with a well-known problem of the transient DC-bias current occurring during a phase shift transition in dual active bridge (DAB) DC/DC converters. This phenomenon, if not compensated, can cause damage to the converter or deteriorate its performance. One aim of this paper is to present a solution which allows for the elimination of the undesired transient DC-bias component in current waveforms. This solution is the dual rising edge shift (DRES) compensation algorithm. It provides a very simple implementation and fast settling time within the first half of a switching period. Moreover, the solution is independent on any measurements or system parameter values. It is based on the double-sided single phase shift (DSSPS) modulation, which is described in detail along with a converter model in steady-state. Then, the mechanisms leading to the transient DC-bias are explained, and the compensation algorithm is derived. The performance of the algorithm has been tested using a laboratory prototype. A comprehensive set of tests, involving rapid step changes in power flow and frequency sweep, are provided. Finally, the features of the proposed algorithm are briefly discussed. Full article

Type III Secretion Systems (T3SSs) are multicomponent nanomachines located at the cell envelope of Gram-negative bacteria. Their main function is to transport bacterial proteins either extracellularly or directly into the eukaryotic host cell cytoplasm. Type III Secretion effectors (T3SEs), latest to be secreted T3S substrates, are destined to act at the eukaryotic host cell cytoplasm and occasionally at the nucleus, hijacking cellular processes through mimicking eukaryotic proteins. A broad range of functions is attributed to T3SEs, ranging from the manipulation of the host cell’s metabolism for the benefit of the bacterium to bypassing the host’s defense mechanisms. To perform this broad range of manipulations, T3SEs have evolved numerous novel folds that are compatible with some basic requirements: they should be able to easily unfold, pass through the narrow T3SS channel, and refold to an active form when on the other side. In this review, the various folds of T3SEs are presented with the emphasis placed on the functional and structural importance of α-helices and helical domains. Full article

Dengue virus is a serious public health issue in tropical and subtropical regions. The global incidence of dengue necessitates the potent antiviral medication for the prevention of proliferation of the virus inside the human body. The DEN2 NS2B/NS3 protease, present in the dengue virus, is an attractive drug target due to its essential role in viral replication, survival, and other cellular activities. In traditional medicine, Carica papaya leaves have been used for the treatment of dengue fever in Sri Lanka, Pakistan, and Malaysia. Therefore, phytochemicals present in Carica papaya leaves have a potential anti-viral activity, and could be used as strong drug candidates against the dengue virus. In this investigation, two phytochemical compounds in Carica papaya leaves, 5,7-dimethoxycoumarin and p-coumaric acid, were selected from the literature and then docked against the DEN2 NS2B/NS3 protease. The compounds showed strong interactions with favorable binding energies in the active site of DEN2 NS2B/NS3 protease. To validate the molecular docking results, the docked ligand–protein complexes were subjected to molecular dynamic simulation along with the apo form of the protein for 30 ns. The molecular dynamic simulation analysis comprising root mean square deviation and fluctuation, the radius of gyration, hydrogen bonding, the Dictionary of Secondary Structure of Proteins (DSSP), and MM/PBSA, revealed the stability of the apo and complex systems. Interactions formed by these compounds with residues Leu149 and Asn152 were found to be essential for the stability of the ligand–protein complex. The findings revealed that these phytochemical compounds depict the promising results against the DEN2 serotype of the dengue virus and the potential for therapeutic drugs. Further experimentation on the proposed compounds is necessary to validate the results and could lead to the development of strong inhibitors with improved activity. Full article

Brain positron emission tomography imaging with 18Fluorine-fluorodeoxyglucose (FDG-PET) has demonstrated utility in suspected autoimmune encephalitis. Visual and/or assisted image reading is not well established to evaluate hypometabolism/hypermetabolism. We retrospectively evaluated patients with autoimmune encephalitis between 2003 and 2018. Patients underwent EEG, brain magnetic resonance imaging (MRI), cerebrospinal fluid (CSF) sampling and autoantibodies testing. Individual FDG-PET images were evaluated by standard visual reading and assisted by voxel-based analyses, compared to a normal database. For the latter, three different methods were performed: two based on statistical surface projections (Siemens syngo.via Database Comparison, and 3D-SSP Neurostat) and one based on statistical parametric mapping (SPM12). Hypometabolic and hypermetabolic findings were grouped to identify specific patterns. We found six cases with definite diagnosis of autoimmune encephalitis. Two cases had anti-LGI1, one had anti-NMDA-R and two anti-CASPR2 antibodies, and one was seronegative. ¹⁸F-FDG-PET metabolic abnormalities were present in all cases, regardless of the method of analysis. Medial–temporal and extra-limbic hypermetabolism were more clearly depicted by voxel-based analyses. We found autoantibody-specific patterns in line with the literature. Statistical surface projection (SSP) methods (Neurostat and syngo.via Database Comparison) were more sensitive and localized larger hypermetabolic areas. As it may lead to comparable and accurate results, visual analysis of FDG-PET studies for the diagnosis of autoimmune encephalitis benefits from voxel-based analysis, beyond the approach based on MRI, CSF sample and EEG. Full article

The assignment of secondary structure elements in proteins is a key step in the analysis of their structures and functions. We have developed an algorithm, SACF (secondary structure assignment based on C_α fragments), for secondary structure element (SSE) assignment based on the alignment of C_α backbone fragments with central poses derived by clustering known SSE fragments. The assignment algorithm consists of three steps: First, the outlier fragments on known SSEs are detected. Next, the remaining fragments are clustered to obtain the central fragments for each cluster. Finally, the central fragments are used as a template to make assignments. Following a large-scale comparison of 11 secondary structure assignment methods, SACF, KAKSI and PROSS are found to have similar agreement with DSSP, while PCASSO agrees with DSSP best. SACF and PCASSO show preference to reducing residues in N and C cap regions, whereas KAKSI, P-SEA and SEGNO tend to add residues to the terminals when DSSP assignment is taken as standard. Moreover, our algorithm is able to assign subtle helices (3₁₀-helix, π-helix and left-handed helix) and make uniform assignments, as well as to detect rare SSEs in β-sheets or long helices as outlier fragments from other programs. The structural uniformity should be useful for protein structure classification and prediction, while outlier fragments underlie the structure–function relationship. Full article