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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]

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]

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]

The title compound, ammonium trinickel(II) hydrogen arsenate arsenate di-hydroxide, was synthesized under hydro-thermal conditions. Its crystal structure is isotypic with that of K[Cu 3 (HAsO 4 )(AsO 4 )(OH) 2 ] and is characterized by pseudo-hexa-gonal (001) 2 ∞ [Ni 3 As 2 O 18/3 (OH) 6/3 O 1/1 (OH) 1/1 ] - layers formed from vertex- and edge-sharing [NiO 4 (OH) 2 ] octa-hedra and [AsO 3.5 (OH) 0.5 ] tetra-hedra 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 [HAsO 4 ] 2- and [AsO 4 ] 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 Ni II 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-hexa-gonal 2 ∞ [Ni 3 As 2 O 18/3 (OH) 6/3 O 1/1 (OH) 1/1 ] - layers may be the reason for the systematic threefold twinning of (NH 4 )[Ni 3 (HAsO 4 )(AsO 4 )(OH) 2 ] crystals. Significant overlaps of the reflections of the respective twin domains complicated the structure solution and refinement., (© Eder and Weil 2024.)