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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]

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]

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]

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]

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]

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]

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]

Purpose: This paper aims to propose a study on the static behavior of prismatic tensegrity structures and an innovative form for determining the effect of mechanical properties and geometric parameters on the minimal mass design of these structures. Design/methodology/approach: The minimal mass design in this paper considers a stable class-two tensegrity tower built through stable models. Using the proposed structures, comprehensive parametric studies are performed to examine the mass (in which the masses of joints are ignored), the mass ratio between a class-two tensegrity tower and a single element, both having the same diameter and length and afterward determine a reliable mass saving structure under various circumstances. Findings: The simulations show that the mass ratio versus the number of units is a nonlinear regressive curve and predicts that the proposed model outperforms the standard model when the variation parameter considered is a vertical force. The difference in mass between these structures is visible when the gap gradually decreases while the number of units increases. On the geometrical aspect, the gap between the masses is not significant. Originality/value: This paper helps to understand the influences of geometric parameters and the mechanical properties on the design of cylinder tensegrity structures dealing with a compressive force. [ABSTRACT FROM AUTHOR]

• 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]

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]

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]

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]

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]

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]

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]

Aspartate-semialdehyde dehydrogenase (ASADH) functions at a critical junction in the aspartate biosynthetic pathway and represents a validated target for antimicrobial drug design. This enzyme catalyzes the NADPH-dependent reductive dephosphorylation of β-aspartyl phosphate to produce the key intermediate aspartate semialdehyde. The absence of this entire pathway in humans and other mammals will allow the selective targeting of pathogenic microorganisms for antimicrobial development. Here, the X-ray structure of a new form of ASADH from the pathogenic fungal species Aspergillus fumigatus has been determined. The overall structure of this enzyme is similar to those of its bacterial orthologs, but there are some critical differences both in biological assembly and in secondary-structural features that can potentially be exploited for the development of species-selective drugs with selective toxicity against infectious fungal organisms. [ABSTRACT FROM AUTHOR]

Background: Structural alignment of proteins is one of the most challenging problems in molecular biology. The tertiary structure of a protein strictly correlates with its function and computationally predicted structures are nowadays a main premise for understanding the latter. However, computationally derived 3D models often exhibit deviations from the native structure. A way to confirm a model is a comparison with other structures. The structural alignment of a pair of proteins can be defined with the use of a concept of protein descriptors. The protein descriptors are local substructures of protein molecules, which allow us to divide the original problem into a set of subproblems and, consequently, to propose a more efficient algorithmic solution. In the literature, one can find many applications of the descriptors concept that prove its usefulness for insight into protein 3D structures, but the proposed approaches are presented rather from the biological perspective than from the computational or algorithmic point of view. Efficient algorithms for identification and structural comparison of descriptors can become crucial components of methods for structural quality assessment as well as tertiary structure prediction. Results: In this paper, we propose a new combinatorial model and new polynomial-time algorithms for the structural alignment of descriptors. The model is based on the maximum-size assignment problem, which we define here and prove that it can be solved in polynomial time. We demonstrate suitability of this approach by comparison with an exact backtracking algorithm. Besides a simplification coming from the combinatorial modeling, both on the conceptual and complexity level, we gain with this approach high quality of obtained results, in terms of 3D alignment accuracy and processing efficiency. Conclusions: All the proposed algorithms were developed and integrated in a computationally efficient tool descs-standalone, which allows the user to identify and structurally compare descriptors of biological molecules, such as proteins and RNAs. Both PDB (Protein Data Bank) and mmCIF (macromolecular Crystallographic Information File) formats are supported. The proposed tool is available as an open source project stored on GitHub (https://github.com/mantczak/descs-standalone). [ABSTRACT FROM AUTHOR]

Serine racemase (SR) is a pyridoxal 5′-phosphate (PLP)-dependent enzyme that is responsible for d-serine biosynthesis in vivo. The first X-ray crystal structure of maize SR was determined to 2.1 Å resolution and PLP binding was confirmed in solution by UV-Vis absorption spectrometry. Maize SR belongs to the type II PLP-dependent enzymes and differs from the SR of a vancomycin-resistant bacterium. The PLP is bound to each monomer by forming a Schiff base with Lys67. Structural comparison with rat and fission yeast SRs reveals a similar arrangement of active-site residues but a different orientation of the C-terminal helix. [ABSTRACT FROM AUTHOR]

Viral capsids exhibit elaborate and symmetrical architectures of defined sizes and remarkable mechanical properties not seen with cellular macromolecular complexes. Given the uniqueness of the higher-order organization of viral capsid proteins in the virosphere, we explored the question of whether the patterns of protein–protein interactions within viral capsids are distinct from those in generic protein complexes. Our comparative analysis involving a non-redundant set of 551 inter-subunit interfaces in viral capsids from VIPERdb and 20,014 protein–protein interfaces in non-capsid protein complexes from the Protein Data Bank found 418 generic protein–protein interfaces that share similar physicochemical patterns with some protein–protein interfaces in the capsid set, using the program PCalign we developed for comparing protein–protein interfaces. This overlap in the structural space of protein–protein interfaces is significantly small, with a p -value < 0.0001, based on a permutation test on the total set of protein–protein interfaces. Furthermore, the generic protein–protein interfaces that bear similarity in their spatial and chemical arrangement with capsid ones are mostly small in size with fewer than 20 interfacial residues, which results from the relatively limited choices of natural design for small interfaces rather than having significant biological implications in terms of functional relationships. We conclude based on this study that protein–protein interfaces in viral capsids are non-representative of patterns in the smaller, more compact cellular protein complexes. Our finding highlights the design principle of building large biological containers from repeated, self-assembling units and provides insights into specific targets for antiviral drug design for improved efficacy. [ABSTRACT FROM AUTHOR]

Background: In structural bioinformatics, there is an increasing interest in identifying and understanding the evolution of local protein structures regarded as key structural or functional protein building blocks. A central need is then to compare these, possibly short, fragments by measuring efficiently and accurately their (dis)similarity. Progress towards this goal has given rise to scores enabling to assess the strong similarity of fragments. Yet, there is still a lack of more progressive scores, with meaningful intermediate values, for the comparison, retrieval or clustering of distantly related fragments. Results: We introduce here the Amplitude Spectrum Distance (ASD), a novel way of comparing protein fragments based on the discrete Fourier transform of their Cα distance matrix. Defined as the distance between their amplitude spectra, ASD can be computed efficiently and provides a parameter-free measure of the global shape dissimilarity of two fragments. ASD inherits from nice theoretical properties, making it tolerant to shifts, insertions, deletions, circular permutations or sequence reversals while satisfying the triangle inequality. The practical interest of ASD with respect to RMSD, RMSDd, BC and TM scores is illustrated through zinc finger retrieval experiments and concrete structure examples. The benefits of ASD are also illustrated by two additional clustering experiments: domain linkers fragments and complementarity-determining regions of antibodies. Conclusions: Taking advantage of the Fourier transform to compare fragments at a global shape level, ASD is an objective and progressive measure taking into account the whole fragments. Its practical computation time and its properties make ASD particularly relevant for applications requiring meaningful measures on distantly related protein fragments, such as similar fragments retrieval asking for high recalls as shown in the experiments, or for any application taking also advantage of triangle inequality, such as fragments clustering. ASD program and source code are freely available at: http://www.irisa.fr/dyliss/public/ASD/. [ABSTRACT FROM AUTHOR]

Background and Aims Automatic acquisition of plant architecture is a major challenge for the construction of quantitative models of plant development. Recently, 3-D laser scanners have made it possible to acquire 3-D images representing a sampling of an object's surface. A number of specific methods have been proposed to reconstruct plausible branching structures from this new type of data, but critical questions remain regarding their suitability and accuracy before they can be fully exploited for use in biological applications. Methods In this paper, an evaluation framework to assess the accuracy of tree reconstructions is presented. The use of this framework is illustrated on a selection of laser scans of trees. Scanned data were manipulated by experienced researchers to produce reference tree reconstructions against which comparisons could be made. The evaluation framework is given two tree structures and compares both their elements and their topological organization. Similar elements are identified based on geometric criteria using an optimization algorithm. The organization of these elements is then compared and their similarity quantified. From these analyses, two indices of geometrical and structural similarities are defined, and the automatic reconstructions can thus be compared with the reference structures in order to assess their accuracy. Key Results The evaluation framework that was developed was successful at capturing the variation in similarities between two structures as different levels of noise were introduced. The framework was used to compare three different reconstruction methods taken from the literature, and allowed sensitive parameters of each one to be determined. The framework was also generalized for the evaluation of root reconstruction from 2-D images and demonstrated its sensitivity to higher architectural complexity of structure which was not detected with a global evaluation criterion. Conclusions The evaluation framework presented quantifies geometric and structural similarities between two structures. It can be applied to the characterization and comparison of automatic reconstructions of plant structures from laser scanner data and 2-D images. As such, it can be used as a reference test for comparing and assessing reconstruction procedures. [ABSTRACT FROM AUTHOR]

The identification and exploration of (dis)similarities between macromolecular structures can help to gain biological insight, for instance when visualizing or quantifying the response of a protein to ligand binding. Obtaining a residue alignment between compared structures is often a prerequisite for such comparative analysis. If the conformational change of the protein is dramatic, conventional alignment methods may struggle to provide an intuitive solution for straightforward analysis. To make such analyses more accessible, the Procrustes Structural Matching Alignment and Restraints Tool ( ProSMART) has been developed, which achieves a conformation-independent structural alignment, as well as providing such additional functionalities as the generation of restraints for use in the refinement of macromolecular models. Sensible comparison of protein (or DNA/RNA) structures in the presence of conformational changes is achieved by enforcing neither chain nor domain rigidity. The visualization of results is facilitated by popular molecular-graphics software such as CCP4 mg and PyMOL, providing intuitive feedback regarding structural conservation and subtle dissimilarities between close homologues that can otherwise be hard to identify. Automatically generated colour schemes corresponding to various residue-based scores are provided, which allow the assessment of the conservation of backbone and side-chain conformations relative to the local coordinate frame. Structural comparison tools such as ProSMART can help to break the complexity that accompanies the constantly growing pool of structural data into a more readily accessible form, potentially offering biological insight or influencing subsequent experiments. [ABSTRACT FROM AUTHOR]

Abstract: The synthesis of two new bicyclic hypervalent iodine(III) reagents 5 and 6 is described along with their corresponding X-ray crystal structures for the first time. A detailed comparison in the bond lengths and bond angles of reported bicyclic hypervalent iodine(III) reagents is also presented. Furthermore, an initial study shows that these two hypervalent iodine(III) reagents could promote the dipeptide coupling reaction. [Copyright &y& Elsevier]

In this study, we have made homology models of mouse, rat, and monkey vascular adhesion protein-1 (VAP-1) to reveal basis for the species-specific ligand recognition of VAP-1. Based on the structural comparisons, rodent VAP-1s have a narrower active site channel than primate VAP-1s. The variable residues in mouse and rat VAP-1, Phe447 from arm I and the polar residues from the first α-helix of the D3 domain together with C-terminal residues are likely to affect ligand recognition and binding. [ABSTRACT FROM AUTHOR]

We present the crystal structures of two universal stress proteins (USP) from Archaeoglobus fulgidus and Nitrosomonas europaea in both apo- and ligand-bound forms. This work is the first complete synthesis of the structural properties of 26 USP available in the Protein Data Bank, over 75% of which were determined by structure genomics centers with no additional information provided. The results of bioinformatic analyses of all available USP structures and their sequence homologs revealed that these two new USP structures share overall structural similarity with structures of USPs previously determined. Clustering and cladogram analyses, however, show how they diverge from other members of the USP superfamily and show greater similarity to USPs from organisms inhabiting extreme environments. We compared them with other archaeal and bacterial USPs and discuss their similarities and differences in context of structure, sequential motifs, and potential function. We also attempted to group all analyzed USPs into families, so that assignment of the potential function to those with no experimental data available would be possible by extrapolation. [ABSTRACT FROM AUTHOR]

Abstract: Embedded systems are widely used in several applications nowadays. As they integrate hard- and software elements, their functionality and reliability are often tested by hardware-in-the-loop methods, in which the system under test runs in a simulated environment. Due to the rising complexity of the embedded functions, performance limitations and practicability reasons, the simulations are often specialized to test specific aspects of the embedded system and develop a high diversity by themselves. This diversity is difficult to manage for a user and results in erroneously selected test components and compatibility problems in the test configuration. This paper presents a generative programming approach that handles the diversity of test libraries. Compatibility issues are explicitly evaluated by a new interface concept. Furthermore, a novel model analyzer facilitates the efficient application in practice by migrating existing libraries. The approach is evaluated for an example from the automotive domain using MATLAB/Simulink. [Copyright &y& Elsevier]

Abstract: The three dimensional structure of a protein provides major insights into its function. Protein structure comparison has implications in functional and evolutionary studies. A structural alphabet (SA) is a library of local protein structure prototypes that can abstract every part of protein main chain conformation. Protein Blocks (PBs) is a widely used SA, composed of 16 prototypes, each representing a pentapeptide backbone conformation defined in terms of dihedral angles. Through this description, the 3D structural information can be translated into a 1D sequence of PBs. In a previous study, we have used this approach to compare protein structures encoded in terms of PBs. A classical sequence alignment procedure based on dynamic programming was used, with a dedicated PB Substitution Matrix (SM). PB-based pairwise structural alignment method gave an excellent performance, when compared to other established methods for mining. In this study, we have (i) refined the SMs and (ii) improved the Protein Block Alignment methodology (named as iPBA). The SM was normalized in regards to sequence and structural similarity. Alignment of protein structures often involves similar structural regions separated by dissimilar stretches. A dynamic programming algorithm that weighs these local similar stretches has been designed. Amino acid substitutions scores were also coupled linearly with the PB substitutions. iPBA improves (i) the mining efficiency rate by 6.8% and (ii) more than 82% of the alignments have a better quality. A higher efficiency in aligning multi-domain proteins could be also demonstrated. The quality of alignment is better than DALI and MUSTANG in 81.3% of the cases. Thus our study has resulted in an impressive improvement in the quality of protein structural alignment. [Copyright &y& Elsevier]

Abstract: Core protein of hepatitis B virus (HBV) with various C-terminal lengths (residue 154, 164, 167 and 183) can self-assemble into recombinant hepatitis B core antigen (HBcAg) particles. To understand the RNA encapsidation mechanism of HBV, the three-dimensional structures of these particles were reconstructed by cryo-electron microscopy (cryoEM). Detailed structural comparisons showed that their capsid structures are highly similar, while the RNA content is increased upon the retention of more amino acid residues at the C-terminus of core protein, suggesting the crucial role of the basic C-terminal tail on determining the genome size. [Copyright &y& Elsevier]

The ever increasing number of protein structures determined by structural genomic projects has spurred much interest in the development of methods for structure-based function prediction. Existing methods can be roughly classified in two groups: some use a comparative approach looking for the presence of structural motifs possibly associated with a known biochemical function. Other methods try to identify functional patches on the surface of a protein using only its physicochemical characteristics. This review will cover both kinds of approaches to structure-based function prediction as well as their use in real-world cases. The main issues and limitations in using protein structure to predict function will also be discussed. These are mainly: the assessment of the statistical significance of structural similarities and the extent to which these methods depend on the accuracy and availability of structural data. [ABSTRACT FROM AUTHOR]

Orotidine 5′-monophoshate decarboxylase (OMPDC) catalyses the decarboxylation of orotidine 5′-monophosphate (OMP) to uridine 5′-monophosphate (UMP). Here, we report the X-ray analysis of apo, substrate or product-complex forms of OMPDC from Plasmodium falciparum (PfOMPDC) at 2.7, 2.65 and 2.65 Å, respectively. The structural analysis provides the substrate recognition mechanism with dynamic structural changes, as well as the rearrangement of the hydrogen bond array at the active site. The structural basis of substrate or product binding to PfOMPDC will help to uncover the decarboxylation mechanism and facilitate structure-based optimization of antimalarial drugs. [ABSTRACT FROM PUBLISHER]

Abstract: Since convergent evolution of enzyme active sites was first identified in serine proteases, other individual instances of this phenomenon have been documented. However, a systematic analysis assessing the frequency of this phenomenon across enzyme space is still lacking. This work uses the Query3d structural comparison algorithm to integrate for the first time detailed knowledge about catalytic residues, available through the Catalytic Site Atlas (CSA), with the evolutionary information provided by the Structural Classification of Proteins (SCOP) database. This study considers two modes of convergent evolution: (i) mechanistic analogues which are enzymes that use the same mechanism to perform related, but possibly different, reactions (considered here as sharing the first three digits of the EC number); and (ii) transformational analogues which catalyse exactly the same reaction (identical EC numbers), but may use different mechanisms. Mechanistic analogues were identified in 15% (26 out of 169) of the three-digit EC groups considered, showing that this phenomenon is not rare. Furthermore 11 of these groups also contain transformational analogues. The catalytic triad is the most widespread active site; the results of the structural comparison show that this mechanism, or variations thereof, is present in 23 superfamilies. Transformational analogues were identified for 45 of the 951 four-digit EC numbers present within the CSA and about half of these were also mechanistic analogues exhibiting convergence of their active sites. This analysis has also been extended to the whole Protein Data Bank to provide a complete and manually curated list of the all the transformational analogues whose structure is classified in SCOP. The results of this work show that the phenomenon of convergent evolution is not rare, especially when considering large enzymatic families. [Copyright &y& Elsevier]

Several studies based on the known three-dimensional (3-D) structures of proteins show that two homologous proteins with insignificant sequence similarity could adopt a common fold and may perform same or similar biochemical functions. Hence, it is appropriate to use similarities in 3-D structure of proteins rather than the amino acid sequence similarities in modelling evolution of distantly related proteins. Here we present an assessment of using 3-D structures in modelling evolution of homologous proteins. Using a dataset of 108 protein domain families of known structures with at least 10 members per family we present a comparison of extent of structural and sequence dissimilarities among pairs of proteins which are inputs into the construction of phylogenetic trees. We find that correlation between the structure-based dissimilarity measures and the sequence-based dissimilarity measures is usually good if the sequence similarity among the homologues is about 30% or more. For protein families with low sequence similarity among the members, the correlation coefficient between the sequence-based and the structure-based dissimilarities are poor. In these cases the structure-based dendrogram clusters proteins with most similar biochemical functional properties better than the sequence-similarity based dendrogram. In multi-domain protein families and disulphide-rich protein families the correlation coefficient for the match of sequence-based and structure-based dissimilarity (SDM) measures can be poor though the sequence identity could be higher than 30%. Hence it is suggested that protein evolution is best modelled using 3-D structures if the sequence similarities (SSM) of the homologues are very low. [ABSTRACT FROM AUTHOR]

Abstract: The nature of the factors leading to the conversion of the cellular prion protein (PrPC) into its amyloidogenic isoform (PrPSc) is still matter of debate in the field of structural biology. The NMR structures of non-mammalian PrPC (non-mPrP) from frog, chicken and turtle [Calzolai, L., Lysek, D.A., Perez, D.R., Guntert, P. and Wuthrich, K. (2005) Prion protein NMR structures of chickens, turtles, and frogs. Proc. Natl. Acad. Sci. USA 102, 651–655] have provided some new and valuable information on the scaffolding elements that preserve the PrPC folding, despite their low sequence identity with the mammalian prions (mPrP). The present molecular dynamics study of non-mPrPC focuses on the hydration properties of these proteins in comparison with the mammalian ones. The data reveal new insights in the PrP hydration and focus on the implications for PrPC folding stability and its propensity for interactions. In addition, for the first time, a role in disfavoring the PrPC aggregation is suggested for a conserved β-bulge which is stabilized by the local hydration. [Copyright &y& Elsevier]

Self-similarity of plants has attracted the attention of biologists for at least 50 years, yet its formal treatment is rare, and no measure for quantifying the degree of self-similarity currently exists. We propose a formal definition and measures of self-similarity, tailored to branching plant structures. To evaluate self-similarity, we make use of an algorithm for computing topological distances between branching systems, developed in computer science. The formalism is illustrated using theoretical branching systems, and applied to analyze self-similarity in two sample plant structures: inflorescences of Syringa vulgaris (lilac) and shoots of Oryza sativa (rice). [ABSTRACT FROM AUTHOR]

Bacteria synthesize fatty acids in a dissociated type pathway different from that in humans. Enoyl acyl carrier protein reductase, which catalyzes the final step of fatty acid elongation, has been validated as a potential anti-microbial drug target. Triclosan is known to inhibit this enzyme effectively. Precise characterization of the mode of triclosan binding is required to develop highly specific inhibitors. With this in view, interactions between triclosan, the cofactor NADH/NAD+ and the enzyme from five different species, one plant and four of microbial origin, have been examined in the available crystal structures. A comparison of these structures shows major structural differences at the substrate/inhibitor/cofactor-binding loop. The analysis reveals that the conformation of this flexible loop and the binding affinities of triclosan to each of these enzymes are strongly correlated. [Copyright &y& Elsevier]

Towards understanding how histamine, a vital neurotansmitter, can perform multiple physiological tasks, an analysis of the different proteins that bind histamine is reported here. Their structural comparison reveals conformational rigidity of histamine. Yet, flexibility in the modes of histamine binding has been observed, which appears to suit specific biological roles of the proteins. These results will be helpful in developing specific antihistamines and also in understanding the pharmacological and toxicological profiles of existing antihistamines. [Copyright &y& Elsevier]

We describe a graph theoretic method designed to perform efficient searches for substructural patterns in nucleic acid structural coordinate databases using a simplified vectorial representation. Two vectors represent each nucleic acid base and the relative positions of bases with respect to one another are described in terms of distances between the defined start and end points of the vectors on each base. These points comprise the nodes and the distances the edges of a graph, and a pattern search can then be performed using a subgraph isomorphism algorithm. The minimal representation was designed to facilitate searches for complex patterns but was first tested on simple, well-characterised arrangements of bases such as base pairs and GNRA-tetraloop receptor interactions. The method performed very well for these interaction types. A survey of side-by-side base interactions, of which the adenosine platform is the best known example, also locates examples of similar base rearrangements that we consider to be important in structural regulation. A number of examples were found, with GU platforms being particularly prevalent. A GC platform in the RNA of the Thermus thermophilus small ribosomal subunit is in an analogous position to an adenosine platform in other species. An unusual GG platform is also observed close to one of the substrate binding sites in Haloarcula marismortui large ribosomal subunit RNA. [ABSTRACT FROM AUTHOR]

WW domains are small protein modules composed of approximately 40 amino acids. These domains fold as a stable, triple stranded β-sheet and recognize proline-containing ligands. WW domains are found in many different signaling and structural proteins, often localized in the cytoplasm as well as in the cell nucleus. Based on analyses of seven structures of WW domains, we discuss their diverse binding preferences and sequence conservation patterns. While modeling WW domains for which structures have not been determined we uncovered a case of potential molecular and functional convergence between WW and SH3 domains. The binding surface of the modeled WW domain of Npw38 protein shows a remarkable similarity to the SH3 domain of Sem5 protein, confirming biochemical data on similar binding predilections of both domains. [Copyright &y& Elsevier]

The cloning, overexpression and characterization of a cold-adapted DNA ligase from the Antarctic sea water bacterium Pseudoalteromonas haloplanktis are described. Protein sequence analysis revealed that the cold-adapted Ph DNA ligase shows a significant level of sequence similarity to other NAD+-dependent DNA ligases and contains several previously described sequence motifs. Also, a decreased level of arginine and proline residues in Ph DNA ligase could be involved in the cold-adaptation strategy. Moreover, 3D modelling of the N-terminal domain of Ph DNA ligase clearly indicates that this domain is destabilized compared with its thermophilic homologue. The recombinant Ph DNA ligase was overexpressed in Escherichia coli and purified to homogeneity. Mass spectroscopy experiments indicated that the purified enzyme is mainly in an adenylated form with a molecular mass of 74 593 Da. Ph DNA ligase shows similar overall catalytic properties to other NAD+-dependent DNA ligases but is a cold-adapted enzyme as its catalytic efficiency (kcat/Km) at low and moderate temperatures is higher than that of its mesophilic counterpart E. coli DNA ligase. A kinetic comparison of three enzymes adapted to different temperatures (P. haloplanktis, E. coli and Thermus scotoductus DNA ligases) indicated that an increased kcat is the most important adaptive parameter for enzymatic activity at low temperatures, whereas a decreased Km for the nicked DNA substrate seems to allow T. scotoductus DNA ligase to work efficiently at high temperatures. Besides being useful for investigation of the adaptation of enzymes to extreme temperatures, P. haloplanktis DNA ligase, which is very efficient at low temperatures, offers a novel tool for biotechnology. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

Two new phosphates, KCd 2 P 3 O 10 and K 8 Cd 21 Pb 7 (P 2 O 7) 16 , have been obtained using high-temperature molten method for the first time. They show three-dimensional (3D) framework structures composed of [Cd 2 P 3 O 18 ] ∞ layers for KCd 2 P 3 O 10 and [Cd 36 P 48 O 237 ] ∞ corrugated layers for K 8 Cd 21 Pb 7 (P 2 O 7) 16. To the best of our knowledge, K 8 Cd 21 Pb 7 (P 2 O 7) 16 is the first Cd-based phosphate that is constructed by tremendous [Cd 18 P 24 O 121 ] ∞ anionic duplicate units, which contain intriguing multimember-rings (6-MR, 8-MR, 16-MR). In addition, K 8 Cd 21 Pb 7 (P 2 O 7) 16 contains coexistent Cd 2 O 10 single rings and Cd 3 O 12 twin rings, which have not been found in other Cd-based phosphates. The comparison of structures was carried out among all the relevant anhydrous Cd-based phosphates. Combining with theoretical analysis, the relationship between electronic structures and optical properties is further elaborated. For K 8 Cd 21 Pb 7 (P 2 O 7) 16 , coexistent Cd 3 O 12 twin rings and Cd 2 O 10 single rings combining with four types of P 2 O 7 groups form tremendous [Cd 18 P 24 O 121 ] unit that contains multimember-rings, which is undiscovered in Cd-based phosphates. Image 1 • K 8 Cd 21 Pb 7 (P 2 O 7) 16 is constructed by tremendous [Cd 18 P 24 O 121 ] anionic skeleton. • K 8 Cd 21 Pb 7 (P 2 O 7) 16 has two unique Cd 2 O 10 single rings and Cd 3 O 12 twin rings. • KCd 2 P 3 O 10 exhibits shorter cutoff edge (210 ​nm). [ABSTRACT FROM AUTHOR]

Alkaline soluble polysaccharide 1 (ASP1) was a polysaccharide extracted from residues remaining from the extraction of sugar beet pulp. This study aimed to separate ASP1 into five different fractions, named UP, UR, F50, F65 and F75, by using ultrafiltration membrane and stepwise alcohol-precipitation. The results showed that the fractions differed from each other regarding their chemical and macromolecular features. The Mw of these sub-fractions decreased in the order of F65 (340 kg mol−1), UR (325 kg mol−1), F75 (295 kg mol−1), F50 (278 kg mol−1) and UP (78 kg mol−1). The emulsifying properties of these fractions in oil-in-water systems containing 10% w/w MCT were compared, taking ASP1 as the reference. At concentrations of 1% of each polysaccharide, F75 showed the best emulsifying activity with the d 4,3 value of 0.35 μm, while the droplet size for UP was 10 times greater than the others. After storage at 60 °C for seven days, emulsion stability decreased in the order of F65, UR, ASP1, F75, F50 and UP, based on the d 4,3 value increment of 0.27 μm, 0.95 μm, 1.48 μm, 3.33 μm, 3.99 μm and 21.5 μm, respectively. Due to the occurrence of calcium bridge flocculation, most polysaccharides in this work could not stabilize oil-in-water systems into homogeneous emulsions, except F65 and F75, in which d 4,3 values were increased from 1.22 and 0.72 μm to 13.7 and 3.6 μm, respectively, after storage, demonstrating great resistance to calcium for F75. In conclusion, membrane filtration combined with alcohol-precipitation is feasible to separate the mother polysaccharide into sub-fractions with different emulsifying properties, among which selected fractions exhibiting superior emulsifying properties could be used as potential emulsifiers in low-calcium systems. Image 1 • ASP1 was fractioned into five components with different physicochemical properties. • The membrane permeated fraction from ASP1 showed poor emulsifying properties. • F75 showed better emulsifying activity and Ca2+ tolerance compared to the other ones. • Hydrophobic amino acid content of ethanol-fractioned samples could be regulated. [ABSTRACT FROM AUTHOR]