Secondary Structure Parameters Research Articles

In silico Structural and Functional Annotation of Tomato Chocolate spot Virus

Aims: The study aims to predict in-silico the structural and functional annotation of Tomato Chocolate Spot Virus (TCSV) retrieved from Uniprotkb with the accession number C7EXM3.
 Study design: To use the In-silico approach for the structural and functional annotation of the Tomato Chocolate Spot Virus.
 Place and Duration of Study: The research was conducted at the Bioinformatics Unit, Chevron Biotechnology Centre, Modibbo Adama University Yola, Nigeria. Between August 2021 to September 2021.
 Methodology: The sequence of the Tomato Chocolate Spot Virus was retrieved from Uniprotkb with accession number C7EXM3, Physicochemical characteristics were computed using the ProtParam tool. The sever SOPMA was used for secondary structure analysis (Helix, Sheets and Coils). The tool CELLO v2.5 was used to predict the subcellular localization of the protein. Four different Homology Modelling tools (trRosetta, Lomet, RaptorX and IntFOLD5) were used to predict the 3D structure of the protein, the quality of the predicted proteins was assessed used PROCHECK. Three tools (InterProScan, NCBI conserved domains and Phobius) were used to get the possible function(s) of the protein.
 Results: ProtParam tool computed various Physical and Chemical properties such as Molecular weight (MW) 20396.96 Daltons, isoelectric point (pI) of 6.92. Instability Index 41.94, and Grand Average Hydropathy (GRAVY) -0.503. SOPMA was used for calculating the secondary structure parameters of the protein as Helices (Hh) 43.48%, Extended strands (Ee) 18.48%, Random coils (Cc) 38.04%. CELLO v2.5 was used for subcellular localization of the protein, it predicted that the protein can be both Nuclear and Cytoplasmic with the reliability of 1.653 and 1.504 respectively. Different Homology modelling tools were used to obtain the best 3D structure of the protein. Furthermore, PROCHECK was used to assess the quality of the models obtained. Model from trRosetta was found to be the best because of the quality of the Ramachandran Plot obtained from PROCHECK which has more than 90% of amino acid in the most favourable regions. NCBI-CDD and interproScan predicted that protein is a DNA double-strand break repair Rad50 ATPase, which is involved in the early steps of DNA double-strand break (DSB) repair. Furthermore, the Phobius server predicted the protein to be non-cytoplasmic in its domain, which means they help target proteins to their final destinations.
 Conclusion: The study has helped in obtaining the 3D structure of the protein Tomato Chocolate Spot Virus from different Modelling tools, as well as the possible function of the protein.

Post‐agriculture rain forest succession on a tropical Pacific island

AbstractQuestionsThe effects of agriculture on forest biodiversity and ecosystem properties can persist decades or centuries after abandonment. Many Pacific island nations are experiencing declines in traditional agriculture. Seed dispersal and seedling recruitment are critical to forest regeneration, and this is particularly relevant for Polynesia where native seed disperser diversity is low and species have been extirpated to crisis levels. In this study we asked: are secondary lowland tropical forests converging to mature forest, and are there seedling recruitment and survival differences between forest types?LocationThe Polynesian island of Tutuila, American Samoa, where traditional agriculture has been on the decline since the 1940s and secondary forests comprise 70% of all forest area.MethodsWe surveyed 34 vegetation plots (containing 2,232 adult trees and 6,579 tree seedlings) across mature forest and >50 years old secondary lowland rain forest. We quantitatively compared forest diversity, structure and the 3‐year seedling regeneration dynamics of the tree community.ResultsAlthough species richness and stem densities were similar between mature and secondary forest, most diversity and structure parameters remained distinguishable between the two forest types. Basal area remained significantly higher in mature forest; the diagnostic tree species of mature and secondary forest differed; and community composition (as indicated by NMDS) remained significantly different. However, seedling survivorship did not differ between forest types and seedling recruitment patterns indicated that there remained a suite of effective seed dispersers on Tutuila.ConclusionsWe conclude that (a) community differences between mature and secondary lowland rainforest were driven by the abundance of diagnostic species rather than exclusion of species from a forest type, and (b) there was no evidence of biophysical or ecological barriers to forest recovery of lowland secondary rain forest, or its convergence towards mature lowland rain forest. Nevertheless, more than 50 years after agricultural abandonment, secondary forest remains distinct from mature forest, highlighting that land use legacies are long‐term drivers of forest composition and successional trajectory in post‐agricultural landscapes of Polynesia.

1H, 13C, 15N backbone and side-chain NMR assignments of the C-terminal domain of Mycobacterium Tuberculosisribosome maturation factor RimM.

Tuberculosis (TB), a lethal disease caused by Mycobacterium tuberculosis (Mtb) infection, develops multidrug-resistance and needs new drugs for effective treatment. As a ribosome maturation factor protein, RimM plays an essential role in the bacterial ribosome assembly and is a potential target for antibiotics against TB. RimM is involved in the incorporation of ribosomal protein S19 into the 30S ribosomal subunit, where the C-terminal domain of RimM is speculated to bind S19. However, the structure and dynamics features of MtbRimM remain unclear to date. Herein, we report the NMR assignments for the 1H, 13C, 15N backbone and side-chain resonances of the C-terminal domain of MtbRimM. We also provide the prediction of its secondary structure and order parameters. Our work lays the basis for solution structure, dynamics and functional studies on MtbRimM in future, and provides clues for the anti-tuberculosis drug development.

Numerical study on flow and heat transfer performance of serpentine parallel flow channels in a high voltage heater system

In this study, a high voltage heater system with a size of 310 mm ? 210 mm ? 60 mm has been numerically studied and experimentally verified to explore the influence of the cavity structure on the flow and heat transfer performance. The response surface model and analysis of variance are used to determine the influence of the length of the mainstream area of the inlet, Lin, the length of the mainstream area of the outlet, Lout, the length of the parallel flow channel, Lch, and the single channel width, W, on the flow heat transfer, and ultimately find the best structural plan. The results show that the structural parameters of the parallel flow channel are significantly more important than those of the mainstream area, with the width and length of the parallel single channel being the primary and secondary structural parameters, respectively. The optimization scheme obtained by the NGSA-II algorithm can simultaneously meet the requirements of heat transfer and flow uniformity. Specifically, compared with the original model, the flow distribution uniformity coefficient, S, and the inlet/outlet pressure drop, Ptotal, decreased by 53.49% and 19.52%, respectively, while the average heat transfer coefficient increased by 28.05%.

1H, 13C, 15N backbone and side-chain resonance assignments of the pathogenic G131V mutant of human prion protein (91-231).

Human prion disease, also known as transmissible spongiform encephalopathy (TSEs), is caused by the conformational conversion of the normal cellular prion protein (PrPC) into the scrapie form (PrPSc). Pathogenic point mutations of prion proteins typically facilitate conformational conversion and lead to inherited prion diseases. A previous study has demonstrated that the pathogenic G131V mutation of human prion protein (HuPrP) brings in Gerstmann-Sträussler-Scheinker syndrome. However, the three-dimensional structure and dynamic features of the HuPrP(G131V) mutant remain unclear. It is expected that the determination of these structural bases will be beneficial to the pathogenic mechanistic understanding of G131V-related prion diseases. Here, we performed 1H, 15N, 13C backbone and side-chain resonance assignments of the G131V mutant of HuPrP(91-231) by using heteronuclear multi-dimensional NMR spectroscopy, and predicted the secondary structural elements and order parameters of the protein based on the assigned backbone chemical shifts. Our work lays the necessary foundation for further structural determination, dynamics characterization, and intermolecular interaction assay for the G131V mutant.

Variations in Orf3a protein of SARS-CoV-2 alter its structure and function

Severe acquired respiratory syndrome coronavirus 2 (SARS-CoV-2) rapidly spread worldwide and acquired multiple mutations in its genome. Orf3a, an accessory protein encoded by the genome of SARS-CoV-2, plays a significant role in viral infection and pathogenesis. In the present in-silico study, 15,928 sequences of Orf3a reported worldwide were compared to identify variations in this protein. Our analysis revealed the occurrence of mutations at 173 residues of Orf3a protein. Subsequently, protein modelling was performed that revealed twelve mutations which can considerably affect the stability of Orf3a. Among the 12 mutations, three mutations (Y160H, D210Y and S171L) also lead to alterations in secondary structure and protein disorder parameters of the Orf3a protein. Further, we used predictive tools to identify five promising epitopes of B-cells, which resides in the mutated regions of Orf3a. Altogether, our study sheds light on the variations occurring in Orf3a that might contribute to alteration in protein structure and function.

Foveal macular pigment dip in offspring of age-related macular degeneration patients is inversely associated with omega-3 index

BackgroundOffspring of parent(s) with age-related macular degeneration (AMD) have a 45% lifetime risk of developing the disease. High foveal macular pigment optical density (MPOD) is protective, whereas individuals with a “foveal macular pigment dip” (FMPD) are at increased risk. Shortage of the dietary carotenoids lutein, zeaxanthin as well as fish consumption are reported AMD risk factors. This Early Biomarkers of AMD (EBAMD) study evaluates serum factors that protect foveal MPOD architecture in Caucasian offspring of parent(s) with AMD.MethodsN = 130 subjects [mean (SD) age 62.8 (8.6) years; 36/94 male/female] were recruited from Scripps Health/ Scripps Memorial Hospital/ Scripps Mericos Eye Institute between 2012 and 2017. Macula pigment 3D topography was evaluated using specular reflectance. Buccal genetic cheek swab, circulating serum dietary carotenoids and long-term RBC omega-3 fatty acid status, as well as common secondary clinical structural and vision function parameters were obtained.Results41 % of offspring of AMD parent(s) presented with FMPD. These offspring were about 4 years younger than those without FMPD (controls; P = 0.012) and had thinner foveas (P = 0.010). There were no differences in gender, BMI, % body fat, visual acuity or contrast sensitivity between those with and without FMPD. % RBC membrane docosahexaenoic acid (DHA) was reduced in FMPD offspring vs. control offspring (P = 0.04). The Omega-3 Index was significantly decreased in the FMPD group (P = 0.03).ConclusionsThe percentage of FMPD in AMD offspring is nearly twice that reported for the general population in the scientific literature. Offspring presenting FMPD had similar AMD genetic risk, but significantly reduced % RBC membrane omega-3 fatty acids and thinner foveas compared with those without FMPD. Our data supports the importance of ‘essential fatty’ acids as an independent AMD risk factor.

Using the Chou’s Pseudo Component to Predict the ncRNA Locations Based on the Improved K-Nearest Neighbor (iKNN) Classifier

Background: The non-coding RNA identification at the organelle genome level is a challenging task. In our previous work, an ncRNA dataset with less than 80% sequence identity was built, and a method incorporating an increment of diversity combining with support vector machine method was proposed. Objective: Based on the ncRNA_361 dataset, a novel decision-making method-an improved KNN (iKNN) classifier was proposed. Methods: In this paper, based on the iKNN algorithm, the physicochemical features of nucleotides, the degeneracy of genetic codons, and topological secondary structure were selected to represent the effective ncRNA characters. Then, the incremental feature selection method was utilized to optimize the feature set. Results: The results of iKNN indicated that the decision-making method of mean value is distinctly superior to the traditional decision-making method of majority vote the Increment of Diversity Combining Support Vector Machine (ID-SVM). The iKNN algorithm achieved an overall accuracy of 97.368% in the jackknife test, when k=3. Conclusion: It should be noted that the triplets of the structure-sequence mode under reading frames not only contains the entire sequence information but also reflects whether the base was paired or not, and the secondary structural topological parameters further describe the ncRNA secondary structure on the spatial level. The ncRNA dataset and the iKNN classifier are freely available at http://202.207.14.87:8032/fuwu/iKNN/index.asp.

Backbone assignments and conformational dynamics in the S. typhimurium tryptophan synthase α-subunit from solution-state NMR.

Backbone assignments for the isolated α-subunit of Salmonella typhimurium tryptophan synthase (TS) are reported based on triple resonance solution-state NMR experiments on a uniformly 2H,13C,15N-labeled sample. From the backbone chemical shifts, secondary structure and random coil index order parameters (RCI-S2) are predicted. Titration with the 3-indole-D-glycerol 3'-phosphate analog, N-(4'-trifluoromethoxybenzenesulfonyl)-2-aminoethyl phosphate (F9), leads to chemical shift perturbations indicative of conformational changes from which an estimate of the dissociation constant is obtained. Comparisons of the backbone chemical-shifts, RCI-S2 values, and site-specific relaxation times with and without F9 reveal allosteric changes including modulation in secondary structures and loop rigidity induced upon ligand binding. A comparison is made to the X-ray crystal structure of the α-subunit in the full TS αββα bi-enzyme complex and to two new X-ray crystal structures of the isolated TS α-subunit reported in this work.

Hydrophobic pore space constituted in macroporous ZIF-8 for lipase immobilization greatly improving lipase catalytic performance in biodiesel preparation

BackgroundDuring lipase-mediated biodiesel production, by-product glycerol adsorbing on immobilized lipase is a common trouble that hinders enzymatic catalytic activity in biodiesel production process. In this work, we built a hydrophobic pore space in macroporous ZIF-8 (named as M-ZIF-8) to accommodate lipase so that the generated glycerol would be hard to be adsorbed in such hydrophobic environment. The performance of the immobilized lipase in biodiesel production as well as its characteristics for glycerol adsorption were systematically studied. The PDMS (polydimethylsiloxane) CVD (chemical vapor deposition) method was utilized to get hydrophobic M-ZIF-8-PDMS with hydrophobic macropore space and then ANL (Aspergillus niger lipase) was immobilized on M-ZIF-8 and M-ZIF-8-PDMS by diffusion into the macropores.ResultsANL@M-ZIF-8-PDMS presented higher enzymatic activity recovery and better biodiesel production catalytic performance compared to ANL@M-ZIF-8. Further study revealed that less glycerol adsorption was observed through the hydrophobic modification, which may attribute to the improved immobilized lipase performance during biodiesel production and ANL@M-ZIF-8-PDMS remained more than 96% activity after five cycles’ reuse. Through secondary structure and kinetic parameters’ analysis, we found that ANL@M-ZIF-8-PDMS had lower extent of protein aggregation and twice catalytic efficiency (Vmax/Km) than ANL@M-ZIF-8.ConclusionsHydrophobic pore space constituted in macroporous ZIF-8 for lipase immobilization greatly improved lipase catalytic performance in biodiesel preparation. The hydrophobic modification time showed negligible influence on the reusability of the immobilized lipase. This work broadened the prospect of immobilization of enzyme on MOFs with some inspiration.

Design Optimization and Performance Investigation of Novel Linear Induction Motors With Two Kinds of Secondaries

In order to reduce the transverse edge effect of a single-sided linear induction motors (SLIMs) for a low-speed Maglev train, this article proposes novel SLIMs with symmetry/asymmetry double-slit secondary. First, the end effects of the conventional SLIMs with flat-solid and cap-solid secondaries are investigated based on three-dimensional (3-D) finite-element model. For the latter one, the influences of slip frequency and secondary structure parameters are obtained as well. Second, the structures of the proposed double-slit secondaries are introduced, and the topology parameters are investigated by a single-variable optimization method. Third, the force performances of SLIMs with proposed two kinds of double-slit secondaries are compared with those of the SLIMs with the traditional cap-solid secondary. Finally, a prototype of SLIM with asymmetry double-slit secondary is manufactured and tested to validate the predictions. The results show that the SLIM with the proposed asymmetry double-slit secondary can improve the force performances due to reduction in the transverse end effect.

Peptide-Enhanced Cargo Transport across 2D and 3D Epithelial Barriers: A Structure-Function Investigation

There is a great need to enhance the delivery of therapeutics across biological barriers, such as the blood-brain barrier. We have identified a cationic peptide, called the CL peptide, which can deliver a small-molecule cargo across a 2D epithelial barrier model at a moderately high rate. In this study, we measure cargo delivery in a novel 3D microvessel platform. Furthermore, we investigate the effect of arginine spacing, number of arginines, secondary structure, stereochemistry, and other parameters on the cargo permeability. These studies can help provide design rules for developing novel peptides for transcellular cargo delivery.

Seismic control of modularized suspended structures with optimal vertical distributions of the secondary structure parameters

Suspended building systems with vibration control features dissipate seismic energy by the interaction between their main parts and the suspended parts; they are also architecturally appealing. A modularized suspended structure has been previously proposed to overcome the fragility of its secondary structure and to enhance overall attenuation. However, the full potential of modularization is yet to be achieved via the previous configuration, especially in terms of multi-mode control. In this study, the protection effect of prefabricated modules is further harnessed in such a way that drastic vertical-irregularities of inter-story stiffness and dampers within the suspended segment are allowed. Vertical distribution vectors of structural parameters were set as the variables in genetic-algorithm optimizations, with the maximum mean square moment of the primary structure being the main objective. The results show considerably improved attenuation of responses in multiple modes instead of only the fundamental mode. In the optimized distributions, peaks of damping coefficient occur at the troughs of inter-story stiffness, but without a highly concentrated pattern. Models with different irregularity levels have well-separated Pareto fronts; this indicates that comprehensive improvement can be obtained at compromised choices. The main mechanism is that, with the well-designed irregularities, the secondary structure provides satisfactory dissipation and tuning to the primary structure in the major modes. The analysis with non-stationary excitations reveals that optimized vertical distributions further quicken the vibration decay. The time-history performance verifications and the structural uncertainty analysis are also carried out.

Investigating the affinity of BDE154 and 3OH-BDE154 with HSA: Experimental and simulation validation.

The physicochemical properties of polybrominated diphenyl ethers are important for modeling their transport, but these data are often missing. Here, satisfactory bioactivity results were obtained using human serum albumin as the carrier, 2,2',4,4',5,6'-hexabromodiphenyl ether (BDE154) and 3-hydroxy-2,2',4,4', 5,6'-hexabromodiphenyl ether (3OH-BDE154) as the ligands, using UV-visible absorbance, fluorescence, circular dichroism, molecular docking, and molecular dynamics methods. The interactions between human serum albumin and BDE154 or 3OH-BDE154 were verified, consistent with the static quenching procedure. At pH 7.4, the binding constants of the complexes for site I were relatively comparable and increased in the order BDE154<3OH-BDE154. Then, the secondary structure and kinetic parameters of albumin were analyzed using the circular dichroism spectra and GROMACS software. The data obtained from these simulations indicate that hydrophobic attraction might be the key factor for the stability of complexes. The docking experiments provided further insight into the hydrophobic pocket and showed that 3OH-BDE154 has a stronger binding affinity to human serum albumin than BDE154. The experimental spectral data were obtained and compared with the simulation results, showing good agreement. A detailed analysis of PBDEs-HSA interactions would provide valuable information to better understand the interaction on this class of compounds.

Magnetostructural phase transitions in NiO and MnO: Neutron diffraction data

Structural and magnetic phase transitions in NiO and MnO antiferromagnets have been studied by high-precision neutron diffraction. The experiments have been performed on a high-resolution Fourier diffractometer (pulsed reactor IBR-2), which has the record resolution for the interplanar distance and a high intensity in the region of large interplanar distances; as a result, the characteristics of both transitions have been determined simultaneously. It has been shown that the structural and magnetic transitions in MnO occur synchronously and their temperatures coincide within the experimental errors: Tstr ≈ Tmag ≈ (119 ± 1) K. The measurements for NiO have been performed with powders with different average sizes of crystallites (~1500 nm and ~138 nm). It has been found that the transition temperatures differ by ~50 K: Tstr = (471 ± 3) K, Tmag = (523 ± 2) K. It has been argued that a unified mechanism of the “unsplit” magnetic and structural phase transition at a temperature of Tmag is implemented in MnO and NiO. Deviation from this scenario in the behavior of NiO is explained by the quantitative difference—a weak coupling between the magnetic and secondary structural order parameters.

Plant-PrAS: a database of physicochemical and structural properties and novel functional regions in plant proteomes.

Arabidopsis thaliana is an important model species for studies of plant gene functions. Research on Arabidopsis has resulted in the generation of high-quality genome sequences, annotations and related post-genomic studies. The amount of annotation, such as gene-coding regions and structures, is steadily growing in the field of plant research. In contrast to the genomics resource of animals and microorganisms, there are still some difficulties with characterization of some gene functions in plant genomics studies. The acquisition of information on protein structure can help elucidate the corresponding gene function because proteins encoded in the genome possess highly specific structures and functions. In this study, we calculated multiple physicochemical and secondary structural parameters of protein sequences, including length, hydrophobicity, the amount of secondary structure, the number of intrinsically disordered regions (IDRs) and the predicted presence of transmembrane helices and signal peptides, using a total of 208,333 protein sequences from the genomes of six representative plant species, Arabidopsis thaliana, Glycine max (soybean), Populus trichocarpa (poplar), Oryza sativa (rice), Physcomitrella patens (moss) and Cyanidioschyzon merolae (alga). Using the PASS tool and the Rosetta Stone method, we annotated the presence of novel functional regions in 1,732 protein sequences that included unannotated sequences from the Arabidopsis and rice proteomes. These results were organized into the Plant Protein Annotation Suite database (Plant-PrAS), which can be freely accessed online at http://plant-pras.riken.jp/.

Structure-Based Prediction of Asparagine and Aspartate Degradation Sites in Antibody Variable Regions

Monoclonal antibodies (mAbs) and proteins containing antibody domains are the most prevalent class of biotherapeutics in diverse indication areas. Today, established techniques such as immunization or phage display allow for an efficient generation of new mAbs. Besides functional properties, the stability of future therapeutic mAbs is a key selection criterion which is essential for the development of a drug candidate into a marketed product. Therapeutic proteins may degrade via asparagine (Asn) deamidation and aspartate (Asp) isomerization, but the factors responsible for such degradation remain poorly understood. We studied the structural properties of a large, uniform dataset of Asn and Asp residues in the variable domains of antibodies. Their structural parameters were correlated with the degradation propensities measured by mass spectrometry. We show that degradation hotspots can be characterized by their conformational flexibility, the size of the C-terminally flanking amino acid residue, and secondary structural parameters. From these results we derive an accurate in silico prediction method for the degradation propensity of both Asn and Asp residues in the complementarity-determining regions (CDRs) of mAbs.

ChemInform Abstract: Self‐Assembled Structures from Amphiphilic Peptides

Nanotechnology and its applications are strongly influenced by structures self-assembled from a variety of different materials. This review covers nanostructures, including micelles, rod-like micelles, fibers and peptide beads, self-assembled from de novo designed amphiphilic peptides. The latter are promising candidates for the development of nanoscale carrier systems because they are completely composed of amino acids. In addition to designing primary sequences, secondary structure and external parameters are also discussed with respect to their impact on self-assembly. Moreover, the assembly process itself is examined. Potential applications range from gene and drug delivery devices to diagnostics, thereby highlighting the versatility of the system.

Self-assembled Structures from Amphiphilic Peptides

Nanotechnology and its applications are strongly influenced by structures self-assembled from a variety of different materials. This review covers nanostructures, including micelles, rod-like micelles, fibers and peptide beads, self-assembled from de novo designed amphiphilic peptides. The latter are promising candidates for the development of nanoscale carrier systems because they are completely composed of amino acids. In addition to designing primary sequences, secondary structure and external parameters are also discussed with respect to their impact on self-assembly. Moreover, the assembly process itself is examined. Potential applications range from gene and drug delivery devices to diagnostics, thereby highlighting the versatility of the system.

Ezrin mRNA target site selection for DNAzymes using secondary structure and hybridization thermodynamics

Ezrin, a membrane organizer and linker between plasma membrane and cytoskeleton, is well documented to play an important role in the metastatic capacity of cancer cells especially for osteosarcoma cells. It has provided an ideal target for cancer gene therapy. RNA-cleaving 10-23 DNAzymes, consisting of a 15-nucleotide catalytical domain flanked by two target-specific complementary arms, can cleave the target mRNA at purine-pyrimidine dinucleotide effectively. In the present study, we designed and screened the target sites for 10-23 DNAzymes against ezrin mRNA by using multiple computational methods with combination of secondary structural and hybridization thermodynamic parameters. Then, we testified the activities of the DNAzymes directed against these selected target sites in vitro. Our results show that AU1751 is the most effective target site of ezrin mRNA for DNAzymes because of its ideal secondary structure and hybridization thermodynamics. So, there is a significant correlation between the multiple computational methods and the efficacy of the corresponding DNAzymes. These provide a rational, efficient way for DNAzymes selection.