scholarly journals Elucidation of the Molecular Basis for Arabinoxylan-Debranching Activity of a Thermostable Family GH62 α-l-Arabinofuranosidase from Streptomyces thermoviolaceus

2014 ◽  
Vol 80 (17) ◽  
pp. 5317-5329 ◽  
Author(s):  
Weijun Wang ◽  
Galina Mai-Gisondi ◽  
Peter J. Stogios ◽  
Amrit Kaur ◽  
Xiaohui Xu ◽  
...  
Keyword(s):  
Hydrophobic Interactions ◽  
Complex Structure ◽  
Three Dimensional ◽  
Binding Pocket ◽  
Content Type ◽  
Wheat Arabinoxylan ◽  
Debranching Enzymes ◽  
The Family ◽  
Multiple Binding ◽  
Hydrolysis Of

ABSTRACTXylan-debranching enzymes facilitate the complete hydrolysis of xylan and can be used to alter xylan chemistry. Here, the family GH62 α-l-arabinofuranosidase fromStreptomyces thermoviolaceus(SthAbf62A) was shown to have a half-life of 60 min at 60°C and the ability to cleave α-1,3l-arabinofuranose (l-Araf) from singly substituted xylopyranosyl (Xylp) backbone residues in wheat arabinoxylan; low levels of activity on arabinan as well as 4-nitrophenyl α-l-arabinofuranoside were also detected. After selective removal of α-1,3l-Arafsubstituents from disubstituted Xylpresidues present in wheat arabinoxylan, SthAbf62A could also cleave the remaining α-1,2l-Arafsubstituents, confirming the ability of SthAbf62A to remove α-l-Arafresidues that are (1→2) and (1→3) linked to monosubstituted β-d-Xylpsugars. Three-dimensional structures of SthAbf62A and its complex with xylotetraose andl-arabinose confirmed a five-bladed β-propeller fold and revealed a molecular Velcro in blade V between the β1 and β21 strands, a disulfide bond between Cys27 and Cys297, and a calcium ion coordinated in the central channel of the fold. The enzyme-arabinose complex structure further revealed a narrow and seemingly rigidl-arabinose binding pocket situated at the center of one side of the β propeller, which stabilized the arabinofuranosyl substituent through several hydrogen-bonding and hydrophobic interactions. The predicted catalytic amino acids were oriented toward this binding pocket, and the catalytic essentiality of Asp53 and Glu213 was confirmed by site-specific mutagenesis. Complex structures with xylotetraose revealed a shallow cleft for xylan backbone binding that is open at both ends and comprises multiple binding subsites above and flanking thel-arabinose binding pocket.

Synthesis and properties of modified PBT for FDM

2017 ◽  
Vol 23 (4) ◽  
pp. 804-810 ◽  
Author(s):  
Shiqing Cao ◽  
Dandan Yu ◽  
Weilan Xue ◽  
Zuoxiang Zeng ◽  
Wanyu Zhu
Keyword(s):  
Mechanical Properties ◽  
Impact Strength ◽  
Fused Deposition Modeling ◽  
Complex Structure ◽  
Three Dimensional ◽  
Sebacic Acid ◽  
Wire Drawing ◽  
Content Type ◽  
Fused Deposition ◽  
Deposition Modeling

Purpose The purpose of this paper is to prepare a new modified polybutylene terephalate (MPBT) for fused deposition modeling (FDM) to increase the variety of materials compatible with printing. And the printing materials can be used to print components with a complex structure and functional mechanical parts. Design/methodology/approach The MPBT, poly(butylene terephalate-co-isophthalate-co-sebacate) (PBTIS), was prepared for FDM by direct esterification and subsequent polycondensation using terephthalic acid (PTA), isophthalic acid (PIA), sebacic acid (SA) and 1,4-butanediol (BDO). The effects of the content of PIA (20-40 mol%) on the mechanical properties of PBTIS were investigated when the mole per cent of SA (αSA) is zero. The effects of αSA (0-7mol%) on the thermal, rheological and mechanical properties of PBTIS were investigated at nPTA/nPIA = 7/3. A desktop wire drawing and extruding machine was used to fabricate the filaments, whose printability and anisotropy were tested by three-dimensional (3D) printing experiments. Findings A candidate content of PIA introducing into PBT was obtained to be about 30 per cent, and the Izod notched impact strength of PBTIS increased with the increase of αSA. The results showed that the PBTIS (nPTA/nPIA = 7/3, αSA = 3-5mol%) is suitable for FDM. Originality/value New printing materials with good Izod notched impact strength were obtained by introducing PIA and SA (nPTA/nPIA = 7/3, αSA = 3-5 mol%) into PBT and their anisotropy are better than that of ABS.

scholarly journals Luminescent Nanosensors for Ratiometric Monitoring of Three-Dimensional Oxygen Gradients in Laboratory and Clinical Pseudomonas aeruginosa Biofilms

2019 ◽  
Vol 85 (20) ◽  
Author(s):  
Megan P. Jewell ◽  
Anne A. Galyean ◽  
J. Kirk Harris ◽  
Edith T. Zemanick ◽  
Kevin J. Cash
Keyword(s):  
Cystic Fibrosis ◽  
Pseudomonas Aeruginosa ◽  
Temporal Variation ◽  
Complex Structure ◽  
Three Dimensional ◽  
Spatial And Temporal Variation ◽  
Content Type ◽  
Oxygen Penetration ◽  
Oxygen Gradients ◽  
Oxygen Sensitive

ABSTRACT Bacterial biofilms can form persistent infections on wounds and implanted medical devices and are associated with many chronic diseases, such as cystic fibrosis. These infections are medically difficult to treat, as biofilms are more resistant to antibiotic attack than their planktonic counterparts. An understanding of the spatial and temporal variation in the metabolism of biofilms is a critical component toward improved biofilm treatments. To this end, we developed oxygen-sensitive luminescent nanosensors to measure three-dimensional (3D) oxygen gradients, an application of which is demonstrated here with Pseudomonas aeruginosa biofilms. The method was applied here and improves on traditional one-dimensional (1D) methods of measuring oxygen profiles by investigating the spatial and temporal variation of oxygen concentration when biofilms are challenged with antibiotic attack. We observed an increased oxygenation of biofilms that was consistent with cell death from comparisons with antibiotic kill curves for PAO1. Due to the spatial and temporal nature of our approach, we also identified spatial and temporal inhomogeneities in the biofilm metabolism that are consistent with previous observations. Clinical strains of P. aeruginosa subjected to similar interrogation showed variations in resistance to colistin and tobramycin, which are two antibiotics commonly used to treat P. aeruginosa infections in cystic fibrosis patients. IMPORTANCE Biofilm infections are more difficult to treat than planktonic infections for a variety of reasons, such as decreased antibiotic penetration. Their complex structure makes biofilms challenging to study without disruption. To address this limitation, we developed and demonstrated oxygen-sensitive luminescent nanosensors that can be incorporated into biofilms for studying oxygen penetration, distribution, and antibiotic efficacy—demonstrated here with our sensors monitoring antibiotic impacts on metabolism in biofilms formed from clinical isolates. The significance of our research is in demonstrating not only a nondisruptive method for imaging and measuring oxygen in biofilms but also that this nanoparticle-based sensing platform can be modified to measure many different ions and small molecule analytes.

scholarly journals Alkaloids as Inhibitors of Malate Synthase from Paracoccidioides spp.: Receptor-Ligand Interaction-Based Virtual Screening and Molecular Docking Studies, Antifungal Activity, and the Adhesion Process

2015 ◽  
Vol 59 (9) ◽  
pp. 5581-5594 ◽  
Author(s):  
Fausto Guimaraes Costa ◽  
Benedito Rodrigues da Silva Neto ◽  
Ricardo Lemes Gonçalves ◽  
Roosevelt Alves da Silva ◽  
Cecília Maria Alves de Oliveira ◽  
...  
Keyword(s):  
3D Structure ◽  
Three Dimensional ◽  
Binding Pocket ◽  
Docking Studies ◽  
Malate Synthase ◽  
Human Pathogens ◽  
Ligand Interaction ◽  
Content Type ◽  
Extracellular Matrix Components ◽  
Paracoccidioides Spp

ABSTRACTParacoccidioidesis the agent of paracoccidioidomycosis. Malate synthase plays a crucial role in the pathogenicity and virulence of various fungi, such as those that are human pathogens. Thus, an inhibitor of this enzyme may be used as a powerful antifungal without side effects in patients once these enzymes are absent in humans. Here, we searched for compounds with inhibitory capacity against the malate synthase ofParacoccidioidesspecies (PbMLS). The three-dimensional (3D) structure ofPbMLS was determined using the I-TASSER server. Compounds were selected from the ZINC database. Based on the mechanism underlying the interaction of the compounds withPbMLS, it was possible to identify β-carboline moiety as a standard key structure. The compounds with β-carboline moiety that are available in our laboratories were investigated. A total of nine alkaloid compounds were selected. The primary mechanisms of interaction of the alkaloid compounds in the binding pocket ofPbMLS were identified and compared with the mechanism of interaction of acetyl coenzyme A (acetyl-CoA). We discovered that the amphipathic nature of the compounds, concomitant with the presence of β-carboline moiety, was crucial for their stability in the binding pocket ofPbMLS. In addition, the importance of a critical balance of the polar and nonpolar contacts of the compounds in this region was observed. Four β-carboline alkaloid compounds showed the ability to inhibit recombinantPbMLS (PbMLSr) activity,Paracoccidioidesspecies growth, and adhesion of the fungus andPbMLSr to the extracellular matrix components. The cytotoxicity of the alkaloids was also evaluated.

Digital description model of a three-dimensional arrangement structure of conductive fiber of electromagnetic shielding fabric

2017 ◽  
Vol 29 (1) ◽  
pp. 14-24 ◽  
Author(s):  
Xiuchen Wang ◽  
Yaping Li ◽  
Ying Su ◽  
Zhen Pan ◽  
Zhe Liu
Keyword(s):  
Feature Extraction ◽  
Complex Structure ◽  
Three Dimensional ◽  
Electromagnetic Shielding ◽  
Electromagnetic Properties ◽  
Shielding Effectiveness ◽  
Content Type ◽  
Conductive Fiber ◽  
Feature Parameters ◽  
Conductive Fibers

Purpose The three-dimensional arrangement structure of the conductive fiber is an important factor of the shielding effectiveness of the electromagnetic shielding fabric (EMSF). However, until now, the three-dimensional arrangement structure has not been described because of the complex structure, which leads to many difficulties for the subsequent analysis of the electromagnetic characteristics. Therefore, the purpose of this paper is to propose a feature extraction method to describe the arrangement structure of the conductive fiber based on the three-dimensional calibration and image processing technology, providing a new idea for the above problem. Design/methodology/approach First, the three-dimensional positions of the conductive fibers in the EMSF are calibrated using the VHX-600 3D digital microscope and the MATLAB7.5 software. The arrangement characteristics of the conductive fibers are analyzed, and equivalent twist, cross-sectional content, and average angle of a single fiber are proposed to describe the arrangement characteristic of the conductive fiber. Then, a digital description model of the conductive fiber is constructed according to the feature parameters and its three-dimensional structures are reproduced using CATIA. Finally, the reliability of the model is verified by an FDTD example, and the significance and application of the model are given. Findings The proposed method can provide the feature extraction and description for the complex spatial three-dimensional arrangement structure of conductive fibers. The feature parameters can reflect different micro arrangement features of the conductive fiber. The proposed idea and method can provide a solid foundation for subsequent studies of the electromagnetic properties of the EMSF. Originality/value The study in this paper is of great significance and academic value. This paper provides a new three-dimensional calibration method and constructs multiple feature parameters to describe the complex three-dimensional arrangement structure, providing a new effective method to overcome the problem of the conductive fiber description. The proposed method provides an important basis for the shielding mechanism, transmission characteristics, electromagnetic calculation and product design, and woven technology of the EMSF.

scholarly journals In Silico Screening of Novel α1-GABAA Receptor PAMs towards Schizophrenia Based on Combined Modeling Studies of Imidazo [1,2-a]-Pyridines

2021 ◽  
Vol 22 (17) ◽  
pp. 9645
Author(s):  
Xiaojiao Zheng ◽  
Chenchen Wang ◽  
Na Zhai ◽  
Xiaogang Luo ◽  
Genyan Liu ◽  
...  
Keyword(s):  
Gabaa Receptor ◽  
Rational Design ◽  
Hydrophobic Interactions ◽  
Three Dimensional ◽  
Pharmacophore Model ◽  
3D Qsar ◽  
Md Simulations ◽  
Binding Pocket ◽  
Pharmacophore Modeling ◽  
Topomer Search

The ionotropic GABAA receptor (GABAAR) has been proven to be an important target of atypical antipsychotics. A novel series of imidazo [1,2-a]-pyridine derivatives, as selective positive allosteric modulators (PAMs) of α1-containing GABAARs with potent antipsychotic activities, have been reported recently. To better clarify the pharmacological essentiality of these PAMs and explore novel antipsychotics hits, three-dimensional quantitative structure–activity relationships (3D-QSAR), molecular docking, pharmacophore modeling, and molecular dynamics (MD) were performed on 33 imidazo [1,2-a]-pyridines. The constructed 3D-QSAR models exhibited good predictive abilities. The dockings results and MD simulations demonstrated that hydrogen bonds, π–π stackings, and hydrophobic interactions play essential roles in the binding of these novel PAMs in the GABAAR binding pocket. Four hit compounds (DS01–04) were then screened out by the combination of the constructed models and computations, including the pharmacophore model, Topomer Search, molecular dockings, ADME/T predictions, and MD simulations. The compounds DS03 and DS04, with higher docking scores and better predicted activities, were also found to be relatively stable in the binding pocket by MD simulations. These results might provide a significant theoretical direction or information for the rational design and development of novel α1-GABAAR PAMs with antipsychotic activities.

scholarly journals Heterodimers as the Structural Unit of the T=1 Capsid of the Fungal Double-Stranded RNA Rosellinia necatrix Quadrivirus 1

2016 ◽  
Vol 90 (24) ◽  
pp. 11220-11230 ◽  
Author(s):  
Daniel Luque ◽  
Carlos P. Mata ◽  
Fernando González-Camacho ◽  
José M. González ◽  
Josué Gómez-Blanco ◽  
...  
Keyword(s):  
Electron Microscopy ◽  
Molecular Sieves ◽  
Three Dimensional ◽  
Rosellinia Necatrix ◽  
Double Stranded Rna ◽  
Content Type ◽  
Cryo Electron Microscopy ◽  
Wide Range ◽  
The Family ◽  
Dsrna Viruses

ABSTRACTMost double-stranded RNA (dsRNA) viruses are transcribed and replicated in a specialized icosahedral capsid with a T=1 lattice consisting of 60 asymmetric capsid protein (CP) dimers. These capsids help to organize the viral genome and replicative complex(es). They also act as molecular sieves that isolate the virus genome from host defense mechanisms and allow the passage of nucleotides and viral transcripts. Rosellinia necatrix quadrivirus 1 (RnQV1), the type species of the familyQuadriviridae, is a dsRNA fungal virus with a multipartite genome consisting of four monocistronic segments (segments 1 to 4). dsRNA-2 and dsRNA-4 encode two CPs (P2 and P4, respectively), which coassemble into ∼450-Å-diameter capsids. We used three-dimensional cryo-electron microscopy combined with complementary biophysical techniques to determine the structures of RnQV1 virion strains W1075 and W1118. RnQV1 has a quadripartite genome, and the capsid is based on a single-shelled T=1 lattice built of P2-P4 dimers. Whereas the RnQV1-W1118 capsid is built of full-length CP, P2 and P4 of RnQV1-W1075 are cleaved into several polypeptides, maintaining the capsid structural organization. RnQV1 heterodimers have a quaternary organization similar to that of homodimers of reoviruses and other dsRNA mycoviruses. The RnQV1 capsid is the first T=1 capsid with a heterodimer as an asymmetric unit reported to date and follows the architectural principle for dsRNA viruses that a 120-subunit capsid is a conserved assembly that supports dsRNA replication and organization.IMPORTANCEGiven their importance to health, members of the familyReoviridaeare the basis of most structural and functional studies and provide much of our knowledge of dsRNA viruses. Analysis of bacterial, protozoal, and fungal dsRNA viruses has improved our understanding of their structure, function, and evolution, as well. Here, we studied a dsRNA virus that infects the fungusRosellinia necatrix, an ascomycete that is pathogenic to a wide range of plants. Using three-dimensional cryo-electron microscopy and analytical ultracentrifugation analysis, we determined the structure and stoichiometry of Rosellinia necatrix quadrivirus 1 (RnQV1). The RnQV1 capsid is a T=1 capsid with 60 heterodimers as the asymmetric units. The large amount of genetic information used by RnQV1 to construct a simple T=1 capsid is probably related to the numerous virus-host and virus-virus interactions that it must face in its life cycle, which lacks an extracellular phase.

scholarly journals Actinomarinicola tropica gen. nov. sp. nov., a new marine actinobacterium of the family Iamiaceae, isolated from South China Sea sediment environments

2020 ◽  
Vol 70 (6) ◽  
pp. 3852-3858 ◽  
Author(s):  
Yuan-Qiu He ◽  
Rou-Wen Chen ◽  
Cun Li ◽  
Song-Biao Shi ◽  
Lin-Qing Cui ◽  
...  
Keyword(s):  
South China Sea ◽  
South China ◽  
Rrna Gene ◽  
16S Rrna Gene Sequences ◽  
Content Type ◽  
China Sea ◽  
Link Type ◽  
The Family ◽  
Hydrolysis Of ◽  
The 16S Rrna Gene

A novel marine actinobacterium, strain SCSIO 58843T, was isolated from the sediment sample collected from the South China Sea. Strain SCSIO 58843T was Gram-stain-positive, aerobic and rod shaped. The whole-cell hydrolysis of amino acids contained dd-DAP, alanine, glutamic acid, glycine and aspartic acid. The main menaquinone was MK-9(H8). The major fatty acids were C17 : 1  ω8c and C17 : 0. The major phospholipids were diphosphatidylglycerol (DPG), phosphatidylinositol (PI), phospatidylcholine (PC) and phosphatidylinositolmannoside (PIM). The G+C content of the genomic DNA was 72.5 %. Phylogenetic analysis of the 16S rRNA gene sequences showed that strain SCSIO 58843T formed a new lineage in the family Iamiaceae and had the highest similarity of 93.8 % with Iamia majanohamensis DSM 19957T. Strain SCSIO 58843T can be distinguished from these known genera in the family Iamiaceae by polyphasic data analyses, and represents a novel genus and novel species, for which Actinomarinicola tropica gen. nov., sp. nov is proposed with the type strain SCSIO 58843T(=KCTC 49408T=CGMCC 1.17503T).

Characterization of sintered hydroxyapatite samples produced by 3D printing

2014 ◽  
Vol 20 (5) ◽  
pp. 413-421 ◽  
Author(s):  
I. Pires ◽  
B. Gouveia ◽  
J. Rodrigues ◽  
R. Fonte
Keyword(s):  
Phase Stability ◽  
Mechanical Stability ◽  
Sintering Temperature ◽  
Calcium Phosphates ◽  
Complex Structure ◽  
Three Dimensional ◽  
Dimensional Accuracy ◽  
Compression Tests ◽  
Powder Morphology ◽  
Content Type

Purpose – The purpose of this study is to characterize sintered hydroxyapatite (HA) samples produced by three-dimensional printing (3DP). This study is part of a project concerned with the fabrication of calcium phosphates implants by 3DP. However, before considering a more complex structure, like scaffolds or implants, a thorough knowledge of the role played by the sintering temperature on physical and mechanical the properties of porous HA is necessary. Design/methodology/approach – The characteristics of sintered HA samples have been analyzed by means of x-ray diffraction, scanning electron microscope (SEM) and uniaxial compression tests. The 3DP parameters used to produce the HA samples were those who led to higher accuracy and mechanical stability. Findings – Sintering temperature and powder morphology are critical factors influencing densification behavior, porosity, phase stability, mechanical strength and tangent modulus of the HA samples produced by 3DP. This study allowed us to conclude about the 3DP parameters to be used to produce porous HA specimens with the required integrity and dimensional accuracy, and the optimal post-processing sintering temperature which led to the best results in terms of porosity, microstructure, phase stability of HA and mechanical properties. Originality/value – This paper provides a method to evaluate the manufacturability of calcium phosphate models produced by 3DP.

scholarly journals Engineering the Substrate Specificity of a Thermophilic Penicillin Acylase from Thermus thermophilus

2012 ◽  
Vol 79 (5) ◽  
pp. 1555-1562 ◽  
Author(s):  
Leticia L. Torres ◽  
Ángel Cantero ◽  
Mercedes del Valle ◽  
Anabel Marina ◽  
Fernando López-Gallego ◽  
...  
Keyword(s):  
Thermus Thermophilus ◽  
Three Dimensional ◽  
Catalytic Efficiency ◽  
Binding Pocket ◽  
Penicillin Acylase ◽  
Penicillin G ◽  
Content Type ◽  
Marked Preference ◽  
Three Dimensional Models ◽  
Phenylalanine Residue

ABSTRACTA homologue of theEscherichia colipenicillin acylase is encoded in the genomes of several thermophiles, including in differentThermus thermophilusstrains. Although the natural substrate of this enzyme is not known, this acylase shows a marked preference for penicillin K over penicillin G. Three-dimensional models were created in which the catalytic residues and the substrate binding pocket were identified. Through rational redesign, residues were replaced to mimic the aromatic binding site of theE. colipenicillin G acylase. A set of enzyme variants containing between one and four amino acid replacements was generated, with altered catalytic properties in the hydrolyses of penicillins K and G. The introduction of a single phenylalanine residue in position α188, α189, or β24 improved theKmfor penicillin G between 9- and 12-fold, and the catalytic efficiency of these variants for penicillin G was improved up to 6.6-fold. Structural models, as well as docking analyses, can predict the positioning of penicillins G and K for catalysis and can demonstrate how binding in a productive pose is compromised when more than one bulky phenylalanine residue is introduced into the active site.

scholarly journals The family 42 carbohydrate-binding module of family 54 α-L-arabinofuranosidase specifically binds the arabinofuranose side chain of hemicellulose

2006 ◽  
Vol 399 (3) ◽  
pp. 503-511 ◽  
Author(s):  
Akimasa Miyanaga ◽  
Takuya Koseki ◽  
Yozo Miwa ◽  
Yuichiro Mese ◽  
Sachiko Nakamura ◽  
...  
Keyword(s):  
Binding Pocket ◽  
Side Chain ◽  
Titration Calorimetry ◽  
Glycoside Hydrolase Family ◽  
Carbohydrate Binding ◽  
Carbohydrate Binding Module ◽  
Binding Assays ◽  
The Family ◽  
Affinity Gel Electrophoresis ◽  
Hydrolysis Of

α-L-Arabinofuranosidase catalyses the hydrolysis of the α-1,2-, α-1,3-, and α-1,5-L-arabinofuranosidic bonds in L-arabinose-containing hemicelluloses such as arabinoxylan. AkAbf54 (the glycoside hydrolase family 54 α-L-arabinofuranosidase from Aspergillus kawachii) consists of two domains, a catalytic and an arabinose-binding domain. The latter has been named AkCBM42 [family 42 CBM (carbohydrate-binding module) of AkAbf54] because homologous domains are classified into CBM family 42. In the complex between AkAbf54 and arabinofuranosyl-α-1,2-xylobiose, the arabinose moiety occupies the binding pocket of AkCBM42, whereas the xylobiose moiety is exposed to the solvent. AkCBM42 was found to facilitate the hydrolysis of insoluble arabinoxylan, because mutants at the arabinose binding site exhibited markedly decreased activity. The results of binding assays and affinity gel electrophoresis showed that AkCBM42 interacts with arabinose-substituted, but not with unsubstituted, hemicelluloses. Isothermal titration calorimetry and frontal affinity chromatography analyses showed that the association constant of AkCBM42 with the arabinose moiety is approximately 103 M−1. These results indicate that AkCBM42 binds the non-reducing-end arabinofuranosidic moiety of hemicellulose. To our knowledge, this is the first example of a CBM that can specifically recognize the side-chain monosaccharides of branched hemicelluloses.

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