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During de novo emergence, new protein coding genes emerge from previously nongenic sequences. The de novo proteins they encode are dissimilar in composition and predicted biochemical properties to conserved proteins. However, functional de novo proteins indeed exist. Both identification of functional de novo proteins and their structural characterization are experimentally laborious. To identify functional and structured de novo proteins in silico, we applied recently developed machine learning based tools and found that most de novo proteins are indeed different from conserved proteins both in their structure and sequence. However, some de novo proteins are predicted to adopt known protein folds, participate in cellular reactions, and to form biomolecular condensates. Apart from broadening our understanding of de novo protein evolution, our study also provides a large set of testable hypotheses for focused experimental studies on structure and function of de novo proteins in Drosophila. [ABSTRACT FROM AUTHOR]

Currently, the main α-amylase family GH13 has been divided into 47 subfamilies in CAZy, with new subfamilies regularly emerging. The present in silico study was performed to highlight the groups, represented by the maltogenic amylase from Thermotoga neapolitana and the α-amylase from Haloarcula japonica, which are worth of creating their own new GH13 subfamilies. This enlarges functional annotation and thus allows more precise prediction of the function of putative proteins. Interestingly, those two share certain sequence features, e.g. the highly conserved cysteine in the second conserved sequence region (CSR-II) directly preceding the catalytic nucleophile, or the well-preserved GQ character of the end of CSR-VII. On the other hand, the two groups bear also specific and highly conserved positions that distinguish them not only from each other but also from representatives of remaining GH13 subfamilies established so far. For the T. neapolitana maltogenic amylase group, it is the stretch of residues at the end of CSR-V highly conserved as L-[DN]. The H. japonica α-amylase group can be characterized by a highly conserved [WY]-[GA] sequence at the end of CSR-II. Other specific sequence features include an almost fully conserved aspartic acid located directly preceding the general acid/base in CSR-III or well-preserved glutamic acid in CSR-IV. The assumption that these two groups represent two mutually related, but simultaneously independent GH13 subfamilies has been supported by phylogenetic analysis as well as by comparison of tertiary structures. The main α-amylase family GH13 has thus been expanded by two novel subfamilies GH13_48 and GH13_49. Key points: • In silico analysis of two groups of family GH13 members with characterized representatives • Identification of certain common, but also some specific sequence features in seven CSRs • Creation of two novel subfamilies—GH13_48 and GH13_49 within the CAZy database [ABSTRACT FROM AUTHOR]

Ribonucleic acid is a crucial biomolecule in living organisms, with various types. To promote the research process of ribonucleic acid function, this study is for analyzing the utilization of heuristic algorithms on the ground of fusion dynamic programming in predicting the secondary structure of ribonucleic acid. Research on novel use of tree models for RNA secondary structure comparison, and use heuristic algorithms to optimize the multi branch structure comparison of tree models. Firstly, this study utilized dynamic programming algorithms to construct a comparison matrix and successfully found the backtracking path in the matrix. Meanwhile, for ensuring that the structural information of ribonucleic acid is not lost during the comparative analysis process, the study applies the idea of heuristic algorithms to calculate the optimal comparison between multi branched loops. Finally, the weights are adjusted using neural network algorithms to predict the optimal alignment structure. The results showed that the fusion dynamic programming heuristic algorithm achieved generalization performance of 0.928, 0.856, 0.842, and 0.793 on the target base data test sets of humans, mice, yeast, and spotted fish, respectively. Compared with the SimTree algorithm, the generalization performance has been improved by 15.13 %, 27.38 %, 27.77 %, and 38.88 %, respectively. In summary, the application of heuristic algorithms integrating dynamic programming in predicting the secondary structure of ribonucleic acid has good predictive performance. This has reference value for a deeper understanding of the structure and function relationship of ribonucleic acid.

The title compound, ammonium trinickel(II) hydrogen arsenate arsenate dihydroxide, was synthesized under hydrothermal conditions. Its crystal structure is isotypic with that of K[Cu3(HAsO4)(AsO4)(OH)2] and is characterized by pseudo-hexagonal (001) 2∞[Ni3As2O18/3(OH)6/3O1/1(OH)1/1]− layers formed from vertex- and edge-sharing [NiO4(OH)2] octahedra and [AsO3.5(OH)0.5] tetrahedra as the building units. The hydrogen atom of the OH group shows occupational disorder and was refined with a site occupation factor of 1/2, indicating the equal presence of [HAsO4]2– and [AsO4]3– groups. Strong asymmetric hydrogen bonds between symmetry-related (O,OH) groups of the arsenate units [O...O = 2.588 (18) Å] as well as hydrogen bonds accepted by these (O,OH) groups from OH groups bonded to the NiII atoms [O...O = 2.848 (12) Å] link adjacent layers. Additional consolidation of the packing is achieved through N—H...O hydrogen bonds from the ammonium ion, which is sandwiched between adjacent layers [N...O = 2.930 (7) Å] although the H atoms could not be located in the present study. The presence of the pseudo-hexagonal 2∞[Ni3As2O18/3(OH)6/3O1/1(OH)1/1]− layers may be the reason for the systematic threefold twinning of (NH4)[Ni3(HAsO4)(AsO4)(OH)2] crystals. Significant overlaps of the reflections of the respective twin domains complicated the structure solution and refinement.

Abstract Background While the size of chloroplast genomes (cpDNAs) is often influenced by the expansion and contraction of inverted repeat regions and the enrichment of repeats, it is the intergenic spacers (IGSs) that appear to play a pivotal role in determining the size of Pteridaceae cpDNAs. This provides an opportunity to delve into the evolution of chloroplast genomic structures of the Pteridaceae family. This study added five Pteridaceae species, comparing them with 36 published counterparts. Results Poor alignment in the non-coding regions of the Pteridaceae family was observed, and this was attributed to the widespread presence of overlong IGSs in Pteridaceae cpDNAs. These overlong IGSs were identified as a major factor influencing variations in cpDNA size. In comparison to non-expanded IGSs, overlong IGSs exhibited significantly higher GC content and were rich in repetitive sequences. Species divergence time estimations suggest that these overlong IGSs may have already existed during the early radiation of the Pteridaceae family. Conclusions This study reveals new insights into the genetic variation, evolutionary history, and dynamic changes in the cpDNA structure of the Pteridaceae family, providing a fundamental resource for further exploring its evolutionary research.

Background: While the size of chloroplast genomes (cpDNAs) is often influenced by the expansion and contraction of inverted repeat regions and the enrichment of repeats, it is the intergenic spacers (IGSs) that appear to play a pivotal role in determining the size of Pteridaceae cpDNAs. This provides an opportunity to delve into the evolution of chloroplast genomic structures of the Pteridaceae family. This study added five Pteridaceae species, comparing them with 36 published counterparts. Results: Poor alignment in the non-coding regions of the Pteridaceae family was observed, and this was attributed to the widespread presence of overlong IGSs in Pteridaceae cpDNAs. These overlong IGSs were identified as a major factor influencing variations in cpDNA size. In comparison to non-expanded IGSs, overlong IGSs exhibited significantly higher GC content and were rich in repetitive sequences. Species divergence time estimations suggest that these overlong IGSs may have already existed during the early radiation of the Pteridaceae family. Conclusions: This study reveals new insights into the genetic variation, evolutionary history, and dynamic changes in the cpDNA structure of the Pteridaceae family, providing a fundamental resource for further exploring its evolutionary research. [ABSTRACT FROM AUTHOR]

The title compound, ammonium trinickel(II) hydrogen arsenate arsenate dihydroxide, was synthesized under hydrothermal conditions. Its crystal structure is isotypic with that of K[Cu3(HAsO4)(AsO4)(OH)2] and is characterized by pseudo-hexagonal (001) 2∞[Ni3As2O18/3(OH)6/3O1/1(OH)1/1]- layers formed from vertex- and edge-sharing [NiO4(OH)2] octahedra and [AsO3.5(OH)0.5] tetrahedra as the building units. The hydrogen atom of the OH group shows occupational disorder and was refined with a site occupation factor of 1/2, indicating the equal presence of [HAsO4]2- and [AsO4]3- groups. Strong asymmetric hydrogen bonds between symmetry-related (O,OH) groups of the arsenate units [O...O = 2.588 (18) Å] as well as hydrogen bonds accepted by these (O,OH) groups from OH groups bonded to the NiII atoms [O...O = 2.848 (12) Å] link adjacent layers. Additional consolidation of the packing is achieved through N--H...O hydrogen bonds from the ammonium ion, which is sandwiched between adjacent layers [N...O = 2.930 (7) Å] although the H atoms could not be located in the present study. The presence of the pseudo-hexagonal 2∞[Ni3As2O18/3(OH)6/3O1/1(OH)1/1 ]- layers may be the reason for the systematic threefold twinning of (NH4)[Ni3(HAsO4)(AsO4)(OH)2] crystals. Significant overlaps of the reflections of the respective twin domains complicated the structure solution and refinement. [ABSTRACT FROM AUTHOR]

Abstract Background Ulmus mianzhuensis is an endemic tree species in China with high ornamental and economic value. Currently, little is known regarding its genomic architecture, phylogenetic position, or adaptive evolution. Here, we sequenced the complete chloroplast genome (cp genome) of U. mianzhuensis and further compared the variations in gene organization and structure within Ulmus species to define their genomic evolution, then reconstructed the phylogenomic relationship of 31 related Ulmus species to explore the systematic position of U. mianzhuensis and the utility of cp genome for resolving phylogenetics among Ulmus species. Results Our results revealed that all the Ulmus species exhibited a typical quadripartite structure, with a large single copy (LSC) region of 87,170 − 88,408 bp, a small single copy (SSC) region of 18,650 − 19,038 bp and an inverted repeat (IR) region of 26,288 − 26,546 bp. Within Ulmus species, gene structure and content of cp genomes were highly conserved, although slight variations were found in the boundary of SC/IR regions. Moreover, genome-wide sliding window analysis uncovered the variability of ndhC-trnV-UAC, ndhF-rpl32, and psbI-trnS-GCU were higher among 31 Ulmus that may be useful for the population genetics and potential DNA barcodes. Two genes (rps15 and atpF) were further detected under a positive selection of Ulmus species. Comparative phylogenetic analysis based on the cp genome and protein-coding genes revealed consistent topology that U. mianzhuensis is a sister group to U. parvifolia (sect. Microptelea) with a relatively low-level nucleotide variation of the cp genome. Additionally, our analyses also found that the traditional taxonomic system of five sections in Ulmus is not supported by the current phylogenomic topology with a nested evolutionary relationship between sections. Conclusions Features of the cp genome length, GC content, organization, and gene order were highly conserved within Ulmus. Furthermore, molecular evidence from the low variation of the cp genome suggested that U. mianzhuensis should be merged into U. parvifolia and regarded as a subspecies of U. parvifolia. Overall, we demonstrated that the cp genome provides valuable information for understanding the genetic variation and phylogenetic relationship in Ulmus.

Two new tin(II) phosphates, SnIISnIV(PO4)2 and SrSn(PO4)PO2(OH)2, were synthesized by the high‐temperature solution method and hydrothermal method, respectively. Theoretical study indicates that by introducing tin(II) with stereochemical activity lone pairs (SCALP) in metal phosphates, the birefringence was enhanced, 0.048@1064 nm for SnIISnIV(PO4)2 and 0.080@1064 nm for SrSn(PO4)PO2(OH)2. [ABSTRACT FROM AUTHOR]

Two new tin(II) phosphates, SnIISnIV(PO4)2 and SrSn(PO4)PO2(OH)2, were synthesized by the high‐temperature solution method and hydrothermal method, respectively. Theoretical study indicates that by introducing tin(II) with stereochemical activity lone pairs (SCALP) in metal phosphates, the birefringence was enhanced, 0.048@1064 nm for SnIISnIV(PO4)2 and 0.080@1064 nm for SrSn(PO4)PO2(OH)2. [ABSTRACT FROM AUTHOR]

In the sequence-based classification of glycoside hydrolases (GHs) of the CAZy database, the family GH119 represents one of the four α-amylase GH families. The family GH119 was established based on a study describing the α-amylase from Bacillus circulans (currently re-classified as Niallia circulans), a product of the igtZ gene. This family with ~ 40 members belongs to the smallest GH families. In addition to a partial biochemical characterization of the α-amylase from N. circulans, nothing has been found in GH119 until now. There was only a single in silico study predicting the catalytic domain structure, catalytic machinery and conserved sequence regions (CSRs) as shared with those well-established in the second α-amylase family GH57. The present bioinformatics study was undertaken in an effort to deliver a detailed analysis of all family GH119 members with regard to their domain arrangement, exact location of all five CSRs and potentially unique sequence features. In order to perform a relevant comparison, the studied set of actual GH119 members was completed by all characterized family GH57 members, i.e. 80 sequences were compared in total. Taking into account the experimentally determined tertiary structure of the GH57 Thermococcus litoralis 4-α-glucanotransferase and the AlphaFold database model of the GH119 N. circulans α-amylase, the position of the CSR-5 in the family GH119 has been precisely re-defined. Phylogenetic trees constructed separately for the N-terminal and C-terminal parts of sequences demonstrated that taxonomy was most probably the main driving factor governing the evolution of the family GH119. [ABSTRACT FROM AUTHOR]

Copyright of Journal of Railway Science & Engineering is the property of Journal of Railway Science & Engineering Editorial Office and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Background: Ulmus mianzhuensis is an endemic tree species in China with high ornamental and economic value. Currently, little is known regarding its genomic architecture, phylogenetic position, or adaptive evolution. Here, we sequenced the complete chloroplast genome (cp genome) of U. mianzhuensis and further compared the variations in gene organization and structure within Ulmus species to define their genomic evolution, then reconstructed the phylogenomic relationship of 31 related Ulmus species to explore the systematic position of U. mianzhuensis and the utility of cp genome for resolving phylogenetics among Ulmus species. Results: Our results revealed that all the Ulmus species exhibited a typical quadripartite structure, with a large single copy (LSC) region of 87,170 − 88,408 bp, a small single copy (SSC) region of 18,650 − 19,038 bp and an inverted repeat (IR) region of 26,288 − 26,546 bp. Within Ulmus species, gene structure and content of cp genomes were highly conserved, although slight variations were found in the boundary of SC/IR regions. Moreover, genome-wide sliding window analysis uncovered the variability of ndhC-trnV-UAC, ndhF-rpl32, and psbI-trnS-GCU were higher among 31 Ulmus that may be useful for the population genetics and potential DNA barcodes. Two genes (rps15 and atpF) were further detected under a positive selection of Ulmus species. Comparative phylogenetic analysis based on the cp genome and protein-coding genes revealed consistent topology that U. mianzhuensis is a sister group to U. parvifolia (sect. Microptelea) with a relatively low-level nucleotide variation of the cp genome. Additionally, our analyses also found that the traditional taxonomic system of five sections in Ulmus is not supported by the current phylogenomic topology with a nested evolutionary relationship between sections. Conclusions: Features of the cp genome length, GC content, organization, and gene order were highly conserved within Ulmus. Furthermore, molecular evidence from the low variation of the cp genome suggested that U. mianzhuensis should be merged into U. parvifolia and regarded as a subspecies of U. parvifolia. Overall, we demonstrated that the cp genome provides valuable information for understanding the genetic variation and phylogenetic relationship in Ulmus. [ABSTRACT FROM AUTHOR]

In late 2019, a new coronaviridae family member officially designated as “Severe Acute Respiratory Syndrome Coronavirus-2” (SARS-CoV-2) emerged and began to spread intensely, worldwide. Its rapid spread was declared as a pandemic by the World Health Organization (WHO) in March 2020. Within the coronaviridae family, SARS-CoV-2 is the third highly pathogenic virus that infects human beings, following the Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV) and the Middle East Respiratory Syndrome Coronavirus (MERS-CoV). In this review, the molecular basis for the origin, mode of action, invasion, and organization of these viruses are discussed by using various models. Moreover, the transmission pathways, replication mechanisms, and diagnostic strategies of these viruses are also discussed. The molecular basis of SARS and MERS helps to understand their infection patterns, pathogenic mechanisms with anecdotes on their diagnosis, and future directions. Expectedly, this study would serve the purpose of being a reliable source of information to scientists, clinicians, as well as the general public.

Copyright of Seljuk University Journal of Seljuk Studies is the property of Selcuk University Journal of Seljuk Studies and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Abstract Background Colocasia gigantea, Caladium bicolor and Xanthosoma sagittifolium are three worldwide famous ornamental and/or vegetable plants in the Araceae family, these species in the subfamily Aroideae are phylogenetically perplexing due to shared interspecific morphological traits and variation. Result This study, for the first time ever, assembled and analyzed complete chloroplast genomes of C. gigantea, C. bicolor and X. sagittifolium with genome sizes of 165,906 bp, 153,149 bp and 165,169 bp in length, respectively. The genomes were composed of conserved quadripartite circular structures with a total of 131 annotated genes, including 8 rRNA, 37 tRNA and 86 protein-coding genes. A comparison within Aroideae showed seven protein-coding genes (accD, ndhF, ndhK, rbcL, rpoC1, rpoC2 and matK) linked to environmental adaptation. Phylogenetic analysis confirmed a close relationship of C. gigantea with C. esculenta and S. colocasiifolia, and the C. bicolor with X. sagittifolium. Furthermore, three DNA barcodes (atpH-atpI + psaC-ndhE, atpH-atpI + trnS-trnG, atpH-atpI + psaC-ndhE + trnS-trnG) harbored highly variable regions to distinguish species in Aroideae subfamily. Conclusion These results would be beneficial for species identification, phylogenetic relationship, genetic diversity, and potential of germplasm resources in Aroideae.

Four new MI/CuII/TeIV/O phases were obtained under hydrothermal conditions or with water as a mineralizer, and their crystal structures determined by single‐crystal X‐ray diffraction. Li2Cu2Te3O9 comprises trigonal‐pyramidal [TeO3], distorted tetrahedral [LiO4] and distorted square‐pyramidal [CuO5] units, forming a framework penetrated by channels into which the electron lone pairs of the TeIV atoms are directed. Li2Cu3Te4O12 contains isolated trigonal‐pyramidal [TeO3] units, tetrahedral [LiO4] groups forming [Li2O6] dimers by sharing an edge, as well as square‐planar [CuO4] and square‐pyramidal [CuO5] units, forming ∞1 ${_\infty ^1 }$ [Cu3O10] chains oriented parallel to [100]. These units also form a framework structure with channels where the electron lone pairs reside. Rb2Cu3Te6O16 and Cs2Cu3Te6O16 have isopointal crystal structures containing isolated [TeO3] groups and ∞1 ${_\infty ^1 }$ [Te4O10] chains oriented parallel to [010]. While in Rb2Cu3Te6O16 both Cu sites are 4‐coordinate in form of nearly square‐planar [CuO4] units, in Cs2Cu3Te6O16 one Cu site has a fifth oxygen contact resulting in a distorted square‐pyramidal [CuO5] polyhedron. Both crystal structures are made up from two alternating layer types stacked along [100]. The differences between Rb2Cu3Te6O16 and Cs2Cu3Te6O16 originate almost exclusively from the layer type consisting of the 5‐coordinate Cu site in Cs2Cu3Te6O16, while the other layer type shows almost no difference. A quantitative comparison between the two crystal structures is given. [ABSTRACT FROM AUTHOR]

Small and medium enterprises (SMEs) are undeniably the backbone of many developing economies, considering their sizeable share of business establishments and contribution to employment creation. Nevertheless, they have fallen short of policymakers' expectations because of the weak interlinkage issue that limits their ability to create wealth. The issue stems from SMEs' excessive reliance on non-SMEs as their primary input sources, while non-SMEs are more dependent on their cluster and imports. This paper seeks to assess the magnitude of the issue in Malaysia and Thailand by comparing the productive structures of SMEs in both economies using the cascaded input-output modelling technique. The findings validated the weak interlinkage issue in Malaysia and Thailand, with the latter suffering from it to a greater extent. Overall, SMEs remain integral to the growth drivers of developing economies. Therefore, development policies should continue to support them by considering their value-added multiplier impacts. Considering all facts and figures, strengthening existing linkage programmes and establishing an SME content requirement policy are this study's two recommendations for improving the interlinkage situation. [ABSTRACT FROM AUTHOR]

Background: Colocasia gigantea, Caladium bicolor and Xanthosoma sagittifolium are three worldwide famous ornamental and/or vegetable plants in the Araceae family, these species in the subfamily Aroideae are phylogenetically perplexing due to shared interspecific morphological traits and variation. Result: This study, for the first time ever, assembled and analyzed complete chloroplast genomes of C. gigantea, C. bicolor and X. sagittifolium with genome sizes of 165,906 bp, 153,149 bp and 165,169 bp in length, respectively. The genomes were composed of conserved quadripartite circular structures with a total of 131 annotated genes, including 8 rRNA, 37 tRNA and 86 protein-coding genes. A comparison within Aroideae showed seven protein-coding genes (accD, ndhF, ndhK, rbcL, rpoC1, rpoC2 and matK) linked to environmental adaptation. Phylogenetic analysis confirmed a close relationship of C. gigantea with C. esculenta and S. colocasiifolia, and the C. bicolor with X. sagittifolium. Furthermore, three DNA barcodes (atpH-atpI + psaC-ndhE, atpH-atpI + trnS-trnG, atpH-atpI + psaC-ndhE + trnS-trnG) harbored highly variable regions to distinguish species in Aroideae subfamily. Conclusion: These results would be beneficial for species identification, phylogenetic relationship, genetic diversity, and potential of germplasm resources in Aroideae. [ABSTRACT FROM AUTHOR]

Rituximab, a murine–human chimera, is the first monoclonal antibody (mAb) developed as a therapeutic agent to target CD20 protein. Its Fab domain and its interaction with CD20 have been extensively studied and high-resolution atomic models obtained by X-ray diffraction or cryo-electron microscopy are available. However, the structure of the full-length antibody is still missing as the inherent protein flexibility hampers the formation of well-diffracting crystals and the reconstruction of 3D microscope images. The global structure of rituximab from its dilute solution is here elucidated by small-angle X-ray scattering (SAXS). The limited data resolution achievable by this technique has been compensated by intensive computational modelling that led to develop a new and effective procedure to characterize the average mAb conformation as well as that of the single domains. SAXS data indicated that rituximab adopts an asymmetric average conformation in solution, with a radius of gyration and a maximum linear dimension of 52 Å and 197 Å, respectively. The asymmetry is mainly due to an uneven arrangement of the two Fab units with respect to the central stem (the Fc domain) and reflects in a different conformation of the individual units. As a result, the Fab elbow angle, which is a crucial determinant for antigen recognition and binding, was found to be larger (169°) in the more distant Fab unit than that in the less distant one (143°). The whole flexibility of the antibody has been found to strongly depend on the relative inter-domain orientations, with one of the Fab arms playing a major role. The average structure and the amount of flexibility has been studied in the presence of different buffers and additives, and monitored at increasing temperature, up to the complete unfolding of the antibody. Overall, the structural characterization of rituximab can help in designing next-generation anti-CD20 antibodies and finding more efficient routes for rituximab production at industrial level.

In the present study, chitin was extracted from marine crustacean shell waste (shrimp, crab, squilla and lobster) using traditional chemical methods (deproteinisation and demineralization) and its physicochemical and structural properties were characterized. The chitin content of crustacean shell waste ranged from 17.50% to 23.75% on a dry weight basis. The molecular weight analyses revealed that the crustacean chitin showed low molecular weight. The results of X-ray diffraction analysis (XRD), Fourier transform infrared spectroscopy (FT-IR), Energy dispersive X-ray analysis (EDAX), scanning electron microscopy (SEM) and thermogravimetry/differential thermal analysis (TG/DTA) confirmed that the α-chitins isolated from crustacean shell waste were similar to commercial crustacean chitin. The crystalline index value of the extracted chitin varied from 80.3% to 80.8%. The infrared spectroscopy analysis of the crustacean chitin exhibited two bands at around 1660 and 1620 cm−1. SEM analysis of the extracted chitin showed the nanofibre and nanopore structures. Additionally, thermal stability of the crustacean chitin was close to that of the commercial chitin. Therefore, the results of this study confirmed that the extracted chitin is in α-form.

Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) catalyzes the oxidative phosphorylation of d-glyceraldehyde 3-phosphate (G3P) into 1,3-diphosphoglycerate (BGP) in the presence of the NAD cofactor. GAPDH is an important drug target because of its central role in glycolysis, and nonglycolytic processes such as nuclear RNA transport, DNA replication/repair, membrane fusion and cellular apoptosis. Recent studies found that GAPDH participates in the development of diabetic retinopathy and its progression after the cessation of hyperglycemia. Here, we report two structures for native bovine photoreceptor GAPDH as a homotetramer with differing occupancy by NAD, bGAPDH(NAD)4 , and bGAPDH(NAD)3 . The bGAPDH(NAD)4 was solved at 1.52 Å, the highest resolution for GAPDH. Structural comparison of the bGAPDH(NAD)4 and bGAPDH(NAD)3 models revealed novel details of conformational changes induced by cofactor binding, including a loop region (residues 54-56). Structure analysis of bGAPDH confirmed the importance of Phe34 in NAD binding, and demonstrated that Phe34 was stabilized in the presence of NAD but displayed greater mobility in its absence. The oxidative state of the active site Cys149 residue is regulated by NAD binding, because this residue was found oxidized in the absence of dinucleotide. The distance between Cys149 and His176 decreased upon NAD binding and Cys149 remained in a reduced state when NAD was bound. These findings provide an important structural step for understanding the mechanism of GAPDH activity in vision and its pathological role in retinopathies.

Snake venom phospholipases B (SVPLBs) are the least studied enzymes. They constitute about 1% of Bothrops crude venoms, however, in other snake venoms, it is present in less than 1%. These enzymes are considered the most potent hemolytic agent in the venom. Currently, no structural information is available about these enzymes from snake venom. To better understand its three-dimensional structure and mechanisms of envenomation, the current work describes the first model-based structure report of this enzyme from Bothrops moojeni venom named as B. moojeni phospholipase B (PLB_Bm). The structure model of PLB_Bm was generated using model building software like I-TESSER, MODELLER 9v19, and Swiss-Model. The build PLB_Bm model was validated using validation tools (PROCHECK, ERRAT, and Verif3D). The analysis of the PLB_Bm modeled structure indicates that it contains 491 amino acid residues that form a well-defined four-layer αββα sandwich core and has a typical fold of the N-terminal nucleophile aminohydrolase (Ntn-hydrolase). The overall structure of PLB_Bm contains 18 β-strands and 17 α-helices with many connecting loops. The structure divides into two chains (A and B) after maturation. The A chain is smaller and contains 207 amino acid residues, whereas the B chain is larger and contains 266 amino acid residues. The sequence and structural comparison among homologous snake venom, bacterial, and mammals PLBs indicate that differences in the length and sequence composition may confer variable substrate specificity to these enzymes. Moreover, the surface charge distribution, average volume, and depth of the active site cavity also vary in these enzymes. The present work will provide more information about the structure–function relationship and mechanism of action of these enzymes in snakebite envenomation.

The subfamily GH13_16 trehalose synthase (TreS) converts maltose to trehalose and vice versa. Typically, it consists of three domains, but it may contain a C-terminal extension exhibiting clear sequence features of a maltokinase (MaK). The present in silico study was focused on collection of naturally fused TreS-MaKs and their subsequent detailed bioinformatics analysis. Hence a set of total 3354 unique sequences was compared consisting of 1900 single TreSs, 1426 fused TreS-MaKs and 28 single MaKs. Fused TreS-MaKs were divided into five groups, namely with a standard MaK, with mutations in the maltose-binding site, of the catalytic nucleophile, of the general acid/base and of both catalytic residues. Sequence logos bearing the best conserved sequence regions were prepared for both TreSs and MaKs in an effort to find unique sequence features. In addition, linkers connecting the TreS and MaK parts in the fused enzymes were analysed. This analysis revealed that MaKs in fused enzymes have an extended N-terminal regions compared to single MaKs. Finally, the evolutionary relationships were demonstrated by phylogenetic trees of TreS parts from single TreSs and fused TreS-MaKs from the same organism as well as of single TreSs existing in multiple isoforms in the same organism. [ABSTRACT FROM AUTHOR]

Recognized as a high-quality biomass resource, bamboo presents challenges in its effective utilization owing to its complex cellular structure and diverse cell types. Thus, identifying differences in the recalcitrant structures within distinct cells is of paramount importance for bamboo chemical processing. In this study, alkaline treatment was employed to extract hemicellulose and lignin-carbohydrate complexes (LCC) separately from bamboo fibers (BF) and parenchyma cells (PC), and the chemical composition, structural characteristics, and distribution of LCC were analyzed. The results revealed that the LCC in alkali-soluble hemicellulose was primarily derived from the secondary cell wall (S-layer) and cell corner middle lamella (CCML) regions of BF, as well as the S-layer of PC. Compared to LCC A-F , a higher content of condensed lignin structures and a greater abundance of Syringyl (S) structural units were observed in LCC A-P. Furthermore, an increased proportion of lignin-arabinose and lignin-glucan linkage structures was detected in the phenyl glycosidic (PhGlc) bonds of LCC A-P. These findings provide valuable insights into the disparities between the chemical compositions and structural characteristics of LCCs within the alkali-soluble hemicelluloses of different bamboo cell types, thereby providing essential guidance for the preparation of functional materials from BF and PC substrates. [Display omitted] • The LCC structures in fibers (BF) and parenchyma cells (PC) have been elucidated. • PC LCC contains a higher proportion of lignin-arabinose and lignin-glucose linkage. • BF LCC has a higher proportion of FA and PCA linkages. • The first comparative of Bambusa chungii BF and PC in was conducted. [ABSTRACT FROM AUTHOR]

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A review of the coordination chemistry along with the structural features of heavy element complexes of dithiocarbimate di-anions in the form of [(R)C=NCS2]2− for R = CN, alkyl, and aryl are described. This class of compound is far less studied compared with the well-explored dithiocarbamate mono-anions formulated as [R(R’)NCS2]− for R/R’ = H, alkyl, and aryl. The coordination chemistry of dithiocarbimate di-anions is dominated by a S,S-chelating mode; rare examples of alternative modes of coordination are evident. When comparisons are available, the structural motifs adopted by metal dithiocarbimate complexes match those found for their dithiocarbamate analogs, with only small, non-systematic variations in the M–S bond lengths.

• OD matrix 'structure' is defined as its skeletal framework. • The OD flows corresponding to the skeleton is termed as mass. • A holistic comparison of OD matrices should include its structure and mass. • Normalised Levenshtein distance for OD matrices (NLOD) is proposed for the structural comparison. • NLOD satisfies the mathematical properties of a distance measure. Origin-Destination (OD) matrix is a tableau of travel demand distributed between different zonal pairs. Essentially, OD matrix provides two types of information: (a) the individual cell value represents travel demand between a specific OD pair; and (b) group of OD pairs provides insights into structural information in terms of distribution pattern of OD flows. Comparison of OD matrices should account both types of information. Limited studies in the past developed structural similarity measures, and most studies still depend on traditional measures for OD matrices comparison. Traditional performance measures are based on cell by cell comparison, and often neglect OD matrix structural information within their formulations. We propose a methodology that adopts the fundamentals of Levenshtein distance, traditionally used to compare sequences of strings, and extends it to quantify the structural comparison of OD matrices. The novel performance measure is named as normalised Levenshtein distance for OD matrices (NLOD). The results of sensitivity analysis support NLOD to be a robust statistical measure for holistic comparison of OD matrices. The study demonstrates the practicality of the approach with a case study application on real Bluetooth based OD matrices from the Brisbane City Council (BCC) region, Australia. [ABSTRACT FROM AUTHOR]

Protein kinase CK2a1 is a serine/threonine kinase that plays a crucial role in the growth, proliferation and survival of cells and is a well known target for tumour and glomerulonephritis therapies. Here, the crystal structure of the kinase domain of CK2a1 complexed with 5‐iodotubercidin (5IOD), an ATP‐mimetic inhibitor, was determined at 1.78 Å resolution. The structure shows distinct structural features and, in combination with a comparison of the crystal structures of five off‐target kinases complexed with 5IOD, provides valuable information for the development of highly selective inhibitors. [ABSTRACT FROM AUTHOR]

The root mean square deviation (RMSD) and the least RMSD are two widely used similarity measures in structural bioinformatics. Yet, they stem from global comparisons, possibly obliterating locally conserved motifs. We correct these limitations with the so‐called combined RMSD, which mixes independent lRMSD measures, each computed with its own rigid motion. The combined RMSD is relevant in two main scenarios, namely to compare (quaternary) structures based on motifs defined from the sequence (domains and SSE) and to compare structures based on structural motifs yielded by local structural alignment methods. We illustrate the benefits of combined RMSD over the usual RMSD on three problems, namely (a) the assignment of quaternary structures for hemoglobin (scenario #1), (b) the calculation of structural phylogenies (case study: class II fusion proteins; scenario #1), and (c) the analysis of conformational changes based on combined RMSD of rigid structural motifs (case study: one class II fusion protein; scenario #2). Based on these illustrations, we argue that the combined RMSD is a tool of choice to perform positive and negative discrimination of degree of freedom, with applications to the design of move sets and collective coordinates. Executables to compute combined RMSD are available within the Structural Bioinformatics Library (http://sbl.inria.fr). [ABSTRACT FROM AUTHOR]

Graphical abstract Highlights • The basis for receptor sharing among γc cytokines remains to be defined. • We obtained and compared the tertiary structures of γc cytokines. • The tertiary structure of γc cytokines dictates receptor chain sharing. • Unlike previously thought, IL‐9 is closer to IL‐2 and IL‐15 than to IL‐7. • IL-7 fold topology resembles that of long-chain 4-helix bundle cytokines. Abstract The γc family of cytokines comprising interleukin-2 (IL-2), IL-4, IL-7, IL-9, IL-15 and IL-2 is an important group of 4-helix bundle cytokines that signals through receptors incorporating the common gamma chain (γc). These cytokines are involved in lymphocyte biology and their specific functions are contingent on binding to cognate receptor chains. Here, we examined the structural relationships between γc cytokines, aiming to understand the basis for receptor chain usage and sharing. To that end, we obtained tertiary structures of human and mouse γc cytokines plus two other related cytokines, IL-13 and TSLP, which share receptors with IL-4 and IL-7, respectively. Subsequently, we compared the cytokine 3D-structures introducing a structural similarity score that grouped γc cytokines in a manner that mirrored the relationships dictated by receptor sharing. Unlike previously thought, we identified that IL-9 is more closely related to IL-2 and IL-15 than to IL-7, which is actually the most distant member of the γc family of cytokines. Moreover, we found that all the members of the γc family of cytokines share the topology of short-chain 4-helix bundle cytokines but IL-7 that with TSLP has the topology of long-chain 4-helix bundle cytokines. We also carried out Maximun-Likehood and Bayesian phylogenetic analyses that supported these results at the amino acid sequence level. Overall, our findings are of paramount relevance to understand receptor sharing among γ c cytokines and can lead to the discovery of new cytokine receptor partners. [ABSTRACT FROM AUTHOR]

Cucurbitaceae is the fourth most important economic plant family with creeping herbaceous species mainly distributed in tropical and subtropical regions. Here, we described and compared the complete chloroplast genome sequences of ten representative species from Cucurbitaceae. The lengths of the ten complete chloroplast genomes ranged from 155,293 bp (C. sativus) to 158,844 bp (M. charantia), and they shared the most common genomic features. 618 repeats of three categories and 813 microsatellites were found. Sequence divergence analysis showed that the coding and IR regions were highly conserved. Three protein-coding genes (accD, clpP, and matK) were under selection and their coding proteins often have functions in chloroplast protein synthesis, gene transcription, energy transformation, and plant development. An unconventional translation initiation codon of psbL gene was found and provided evidence for RNA editing. Applying BI and ML methods, phylogenetic analysis strongly supported the position of Gomphogyne, Hemsleya, and Gynostemma as the relatively original lineage in Cucurbitaceae. This study suggested that the complete chloroplast genome sequences were useful for phylogenetic studies. It would also determine potential molecular markers and candidate DNA barcodes for coming studies and enrich the valuable complete chloroplast genome resources of Cucurbitaceae. [ABSTRACT FROM AUTHOR]

Abstract: Introducing fluorine into borates indicates the direction for structural evolution. A new fluorooxoborate, NaRbB6O9F2 featuring a unique [B6O9F2]∞ layered structure and excellent optical properties has been synthesized. It is further demonstrated that incorporation of fluorine can enrich the structural chemistry of borates. [ABSTRACT FROM AUTHOR]

Snake venom thrombin-like enzymes (SVTLEs) constitute the major portion (10–24%) of snake venom and these are the second most abundant enzymes present in the crude venom. During envenomation, these enzymes had shown prominently the various pathological effects, such as disturbance in hemostatic system, fibrinogenolysis, fibrinolysis, platelet aggregation, thrombosis, neurologic disorders, activation of coagulation factors, coagulant, procoagulant etc. These enzymes also been used as a therapeutic agent for the treatment of various diseases such as congestive heart failure, ischemic stroke, thrombotic disorders etc. Although the crystal structures of five SVTLEs are available in the Protein Data Bank (PDB), there is no single article present in the literature that has described all of them. The current work describes the structural aspects, structure-based mechanism of action, processing and inhibition of these enzymes. The sequence analysis indicates that these enzymes show a high sequence identity (57–85%) with each other and low sequence identity with trypsin (36–43%), human alpha-thrombin (29–36%) and other snake venom serine proteinases (57–85%). Three-dimensional structural analysis indicates that the loops surrounding the active site are variable both in amino acids composition and length that may convey variable substrate specificity to these enzymes. The surface charge distributions also vary in these enzymes. Docking analysis with suramin shows that this inhibitor preferably binds to the C-terminal region of these enzymes and causes the destabilization of their three-dimensional structure. [ABSTRACT FROM AUTHOR]

The seismic capacity of a structure is determined by the performance index that reaches its ultimate bearing or deformation capacity first. This paper presents a multi-index seismic capacity evaluation method for accurately evaluating the seismic capacity of a structure. The normalized response curves of several indices are concurrently plotted to form a multi-index seismic capacity evaluation figure, in which the seismic capacity and demand values that correspond to various indices can be determined by vertical and horizontal threshold lines. Based on an incremental dynamic analysis (IDA), a 6-story buckling-restrained braced frame (BRBF) and a series of comparable 6-story steel frames are analyzed using the proposed method to verify the method and investigate the seismic behavior of BRBFs. The results show that the seismic performance of buckling-restrained braces is not the only factor that determines the seismic capacity of BRBFs and indicate that the multi-index seismic capacity evaluation method can effectively identify the critical index of a structure and the weakest links that restrict the structural seismic capacity. [ABSTRACT FROM AUTHOR]

In this paper, we present a novel approach to solve the labeled point cloud superpositioning problem for performing structural comparisons of protein binding sites. The solution is based on a parallel evolution strategy that operates on large populations and runs on GPU hardware. The proposed evolution strategy reduces the likelihood of getting stuck in a local optimum of the multimodal real-valued optimization problem represented by labeled point cloud superpositioning. The performance of the GPU-based parallel evolution strategy is compared to a previously proposed CPU-based sequential approach for labeled point cloud superpositioning, indicating that the GPU-based parallel evolution strategy leads to qualitatively better results and significantly shorter runtimes, with speed improvements of up to a factor of 1,500 for large populations. Binary classification tests based on the ATP, NADH, and FAD protein subsets of CavBase, a database containing putative binding sites, show average classification rate improvements from about 92 percent (CPU) to 96 percent (GPU). Further experiments indicate that the proposed GPU-based labeled point cloud superpositioning approach can be superior to traditional protein comparison approaches based on sequence alignments. [ABSTRACT FROM AUTHOR]

A recombinant Staphylococcus equorum manganese superoxide dismutase (MnSOD) with an Asp13Arg substitution displays activity over a wide range of pH, at high temperature and in the presence of chaotropic agents, and retains 50% of its activity after irradiation with UVC for up to 45 min. Interestingly, Bacillus subtilis MnSOD does not have the same stability, despite having a closely similar primary structure and thus presumably also tertiary structure. Here, the crystal structure of S. equorum MnSOD at 1.4 Å resolution is reported that may explain these differences. The crystal belonged to space group P3221, with unit‐cell parameters a = 57.36, b = 57.36, c = 105.76 Å, and contained one molecule in the asymmetric unit. The symmetry operation indicates that the enzyme has a dimeric structure, as found in nature and in B. subtilis MnSOD. As expected, their overall structures are nearly identical. However, the loop connecting the helical and α/β domains of S. equorum MnSOD is shorter than that in B. subtilis MnSOD, and adopts a conformation that allows more direct water‐mediated hydrogen‐bond interactions between the amino‐acid side chains of the first and last α‐helices in the latter domain. Furthermore, S. equorum MnSOD has a slightly larger buried area compared with the dimer surface area than that in B. subtilis MnSOD, while the residues that form the interaction in the dimer‐interface region are highly conserved. Thus, the stability of S. equorum MnSOD may not originate from the dimeric form alone. Furthermore, an additional water molecule was found in the active site. This allows an alternative geometry for the coordination of the Mn atom in the active site of the apo form. This is the first structure of MnSOD from the genus Staphylococcus and may provide a template for the structural study of other MnSODs from this genus. [ABSTRACT FROM AUTHOR]

Pentosan polysulfate sodium (PPS) is a semi-synthetic, heparin-like polysaccharide with manifold therapeutic actions. It is approved for treatment of bladder pain syndrome / interstitial cystitis in humans and treatment of musculoskeletal diseases in animals. PPS is produced by a complex procedure using beech wood as starting material. It consists of a mixture of sulfated glucuronoxylans, whose structural composition cannot be fully characterized by physicochemical analysis. The question arises whether PPS follow-on products are identical with the original and thus meet the requirement for generic drug application. The aim of this study was to investigate whether commercially available PPS products differ in physicochemical characteristics and biological effects from the original. Ten PPS preparations from different manufactures were analyzed using orthogonal analytical techniques including, inter alia, size exclusion chromatography with triple detection, nuclear magnetic resonance spectroscopy, and high-resolution mid-infrared spectroscopy in aqueous solution with chemometric evaluation. For functional analysis, we measured the plasma kallikrein generation in human plasma and FXII activation. The study revealed significant structural and biological differences between PPS from different sources. Therefore, follow-on products cannot be considered identical but at best similar to original PPS. However, their similar efficacy and safety have still to be proven by comprehensive studies. [Display omitted] [ABSTRACT FROM AUTHOR]

• Structural analysis allows comparison across body treatments. • Distinction measures allow comparative analysis of mortuary programs. • Symbolically detached measures highlight different aspects of mortuary complexity. • Differences in horizontal structure do not necessarily materialize vertically. • Variation includes cultural preferences and differential access to exotics. Archaeologists in the Carpathian Basin are increasingly focused on social variability across the Bronze Age landscape. However, when it comes to mortuary variability, the difference in body treatments (cremation and inhumation) between populations impairs our ability to carry out regional comparisons and appreciate the range of community social organizations. In this paper, we compare mortuary assemblages from three Bronze Age culture areas on the Great Hungarian Plain. In our coarse quantitative framework, we characterize the intensity of funerary distinction as a proxy for complexity and identify structural variation across mortuary programs. We identify both horizontal and vertical differences in funerary assemblages and note horizontal differences that do not necessarily materialize vertically. The results also show that societies can represent varying values across the different measures, underlying the necessity of working with analytical frameworks which approach the question of complexity in a non-linear manner. We believe that the method offered here can be a useful addition to the toolkit of mortuary archaeologists who work in areas and/or time periods with various body treatment practices. [ABSTRACT FROM AUTHOR]

Spider venoms are complex mixtures of proteins, peptides and small organic and inorganic molecules. Among the proteins, phospholipases D (PLDs) present the major portion, and till now they are the most studied enzymes in spider venom. These PLDs have been divided into two classes, I and II, based on their primary and tertiary structure. Currently, crystal structures of both classes of these enzymes are available in the Protein Data Bank (PDB). Their three-dimensional structure is composed of eight α-helices and eight β-strands forming the ubiquitous fold called triosephosphate isomerase (TIM) barrel. These enzymes use general acid-base catalysis to hydrolyzes their substrate. In this review, we have described the structural features, structure-based mechanisms of catalysis, maturation, and inhibition of these enzymes using the synthetic inhibitor. [ABSTRACT FROM AUTHOR]

Abstract: Cephalosporins belong the largest class of antibiotics used in the treatment of a wide range of infectious diseases caused by susceptible organisms. In the present study, we chose two typical antibiotics cefalexin/cefixime based on their structure, and investigated the interaction of cephalexin/cefixime with bovine serum albumin (BSA) using UV–vis absorption spectra, fluorescence spectroscopy, circular dichroism (CD) spectroscopy and molecular modeling approaches. Spectroscopic experiments revealed the formation of a BSA − cefalexin/cefixime complex. The binding parameters calculated using a modified Stern − Volmer method and the Scatchard method reached 103–104 L·mol−1. Thermodynamic parameter studies revealed that binding characteristics by negative enthalpy and positive entropy changes, and electrostatic interactions play a major role. Site marker competitive displacement experiments and molecular modeling approaches demonstrated that cefalexin and cefixime bind with appropriate affinity to site I (subdomain IIA) of BSA. Furthermore, synchronous fluorescence spectra, CD spectra and molecular modeling results indicated that the secondary structure of BSA was changed in the presence of cefalexin and cefixime. Additionally, the effects of metal ions on the BSA − cefalexin/cefixime system were also assessed. [ABSTRACT FROM AUTHOR]

Calmodulin is a calcium binding protein that consists of four EF-hand domains. The two EF-lobes of calmodulin, called the N-lobe and the C-lobe, arose from duplication and fusion of a precursor EF-hand. The amino acid sequences and the structures of the N-lobe and of the C-lobe are quite similar to each other. The N-lobe and the C-lobe, however, have subtle differences in structure and function. We analyzed the helix positions of calmodulin lobes by the alignment with the pseudo-two fold axis of the EF-lobe. We made a map of conformational landscape of helix positions. The four states of the EF-lobe appeared on two lines in the landscape; these two lines show the trajectory of opening and closing of the EF-lobe. For the N-lobe of calmodulin, the calcium bound form and the apo-forms are on the lower line. The two apo-forms of the C-lobe of calmodulin, with target and without target, are on the upper line. The calcium bound form of the C-lobe is on the lower line. The rearrangement of helix interaction between two the EF-hands is necessary for calcium binding in the C-lobe. The hydrophobic packing in the apo-form of the N-lobe is similar to the packing of the N- and C-lobes of the calcium bound form. However, the packing of C-lobe side chains in the apo-form is different from these other three structures. Our detailed analysis should serve as an example that can be applied to other proteins that undergo changes in conformation upon binding effectors. [ABSTRACT FROM AUTHOR]