scholarly journals A pair of esterases from a commensal gut bacterium remove acetylations from all positions on complex β-mannans

2020 ◽  
Vol 117 (13) ◽  
pp. 7122-7130 ◽  
Author(s):  
Leszek Michalak ◽  
Sabina Leanti La Rosa ◽  
Shaun Leivers ◽  
Lars Jordhøy Lindstad ◽  
Åsmund Kjendseth Røhr ◽  
...  
Keyword(s):  
High Performance ◽  
Plant Cell Wall ◽  
3D Structure ◽  
Three Dimensional ◽  
Catalytic Triad ◽  
Glycoside Hydrolases ◽  
Time Resolved ◽  
Mannose Residue ◽  
Insight Into

β-mannans and xylans are important components of the plant cell wall and they are acetylated to be protected from degradation by glycoside hydrolases. β-mannans are widely present in human and animal diets as fiber from leguminous plants and as thickeners and stabilizers in processed foods. There are many fully characterized acetylxylan esterases (AcXEs); however, the enzymes deacetylating mannans are less understood. Here we present two carbohydrate esterases, RiCE2 and RiCE17, from the Firmicute Roseburia intestinalis, which together deacetylate complex galactoglucomannan (GGM). The three-dimensional (3D) structure of RiCE17 with a mannopentaose in the active site shows that the CBM35 domain of RiCE17 forms a confined complex, where the axially oriented C2-hydroxyl of a mannose residue points toward the Ser41 of the catalytic triad. Cavities on the RiCE17 surface may accept galactosylations at the C6 positions of mannose adjacent to the mannose residue being deacetylated (subsite −1 and +1). In-depth characterization of the two enzymes using time-resolved NMR, high-performance liquid chromatography (HPLC), and mass spectrometry demonstrates that they work in a complementary manner. RiCE17 exclusively removes the axially oriented 2-O-acetylations on any mannose residue in an oligosaccharide, including double acetylated mannoses, while the RiCE2 is active on 3-O-, 4-O-, and 6-O-acetylations. Activity of RiCE2 is dependent on RiCE17 removing 2-O-acetylations from double acetylated mannose. Furthermore, transacetylation of oligosaccharides with the 2-O-specific RiCE17 provided insight into how temperature and pH affects acetyl migration on manno-oligosaccharides.

scholarly journals A pair of esterases from a commensal gut bacterium remove acetylations from all positions on complex β-mannans

2019 ◽  
Author(s):  
Leszek Michalak ◽  
Sabina Leanti La Rosa ◽  
Shaun Allan Leivers ◽  
Lars Jordhøy Lindstad ◽  
Åsmund Røhr Kjendseth ◽  
...  
Keyword(s):  
Cell Wall ◽  
Plant Cell ◽  
Active Site ◽  
Plant Cell Wall ◽  
3D Structure ◽  
Domain Architecture ◽  
Catalytic Triad ◽  
Glycoside Hydrolases ◽  
Time Resolved ◽  
Mannose Residue

Abstractβ-Mannans and xylans are important components of the plant cell wall and they are acetylated to be protected from degradation by glycoside hydrolases. β-Mannans are widely present in human and animal diets as fiber from leguminous plants and as thickeners and stabilizers in processed foods. There are many fully characterized acetylxylan esterases (AcXEs), however, the enzymes deacetylating mannans are less understood. Here we present two carbohydrate esterases, RiCE2 and RiCEX, from the Firmicute Roseburia intestinalis, which together deacetylate complex galactoglucomannan (GGM). The 3D-structure of RiCEX with a mannopentaose in the active site shows that the CBM35 domain of RiCEX forms a confined complex, where the axially oriented C2-hydroxyl of a mannose residue points towards the Ser41 of the catalytic triad. Cavities on the RiCEX surface may accept galactosylations at the C6 positions of mannose adjacent to the mannose residue being deacetylated (subsite −1 and +1). In depth characterization of the two enzymes using time-resolved NMR, HPLC and mass spectrometry demonstrates that they work in a complementary manner. RiCEX exclusively removes the axially oriented 2-O-acetylations on any mannose residue in an oligosaccharide, including double acetylated mannoses, while the RiCE2 is active on 3-O-, 4-O- and 6-O-acetylations. Activity of RiCE2 is dependent on RiCEX removing 2-O-acetylations from double acetylated mannose. Furthermore, transacetylation of oligosaccharides with the 2-O specific RiCEX provided new insight to how temperature and pH affects acetyl migration on mannooligosaccharides.Significance statementAcetylations are an important feature of hemicellulose, altering the physical properties of the plant cell wall, and limiting enzyme accessibility. Removal of acetyl groups from beta-mannan is a key step towards efficient utilization of mannans as a carbon source for gut microbiota and in biorefineries. We present detailed insight into mannan deacetylation by two highly substrate-specific acetyl-mannan esterases (AcMEs) from a prevalent gut commensal Firmicute, which cooperatively deacetylate complex galactoglucomannan. The 3D structure of RiCEX with mannopentaose in the active site has a unique two-domain architecture including a CBM35 and an SGNH superfamily hydrolytic domain. Discovery of mannan specific esterases improves the understanding of an important step in dietary fiber utilization by gut commensal Firmicutes.

Three-Dimensional Graphite Filled Poly(Vinylidene Fluoride) Composites with Enhanced Strength and Thermal Conductivity

2020 ◽  
Vol 842 ◽  
pp. 63-68
Author(s):  
Xiao Zhang ◽  
Jian Zheng ◽  
Yong Qiang Du ◽  
Chun Ming Zhang
Keyword(s):  
Mechanical Properties ◽  
Thermal Conductivity ◽  
Energetic Materials ◽  
High Performance ◽  
Vinylidene Fluoride ◽  
3D Structure ◽  
Three Dimensional ◽  
3D Network ◽  
Poly Vinylidene Fluoride ◽  
Polymer Bonded Explosives

Three-dimensional (3D) network structure has been recognized as an efficient approach to enhance the mechanical and thermal conductive properties of polymeric composites. However, it has not been applied in energetic materials. In this work, a fluoropolymer based composite with vertically oriented and interconnected 3D graphite network was fabricated for polymer bonded explosives (PBXs). Here, the graphite and graphene oxide platelets were mixed, and self-assembled via rapid freezing and using crystallized ice as the template. The 3D structure was finally obtained by freezing-dry, and infiltrating with polymer. With the increasing of filler fraction and cooling rate, the thermal conductivity of the polymer composite was significantly improved to 2.15 W m-1 K-1 by 919% than that of pure polymer. Moreover, the mechanical properties, such as tensile strength and elastic modulus, were enhanced by 117% and 563%, respectively, when the highly ordered structure was embedded in the polymer. We attribute the increased thermal and mechanical properties to this 3D network, which is beneficial to the effective heat conduction and force transfer. This study supports a desirable way to fabricate the strong and thermal conductive fluoropolymer composites used for the high-performance polymer bonded explosives (PBXs).

scholarly journals Electrostatics of Tau Protein by Molecular Dynamics

Biomolecules ◽  
2019 ◽  
Vol 9 (3) ◽  
pp. 116 ◽  
Author(s):  
Tarsila Castro ◽  
Florentina-Daniela Munteanu ◽  
Artur Cavaco-Paulo
Keyword(s):  
Molecular Dynamics ◽  
3D Structure ◽  
Three Dimensional ◽  
Dynamics Simulation ◽  
Microtubule Assembly ◽  
Interaction Sites ◽  
Disordered Protein ◽  
Fluid Environment ◽  
Function Relationship ◽  
Insight Into

Tau is a microtubule-associated protein that promotes microtubule assembly and stability. This protein is implicated in several neurodegenerative diseases, including Alzheimer’s. To date, the three-dimensional (3D) structure of tau has not been fully solved, experimentally. Even the most recent information is sometimes controversial in regard to how this protein folds, interacts, and behaves. Predicting the tau structure and its profile sheds light on the knowledge about its properties and biological function, such as the binding to microtubules (MT) and, for instance, the effect on ionic conductivity. Our findings on the tau structure suggest a disordered protein, with discrete portions of well-defined secondary structure, mostly at the microtubule binding region. In addition, the first molecular dynamics simulation of full-length tau along with an MT section was performed, unveiling tau structure when associated with MT and interaction sites. Electrostatics and conductivity were also examined to understand how tau affects the ions in the intracellular fluid environment. Our results bring a new insight into tau and tubulin MT proteins, their characteristics, and the structure–function relationship.

Solving the 3D structure of metal nanoparticles

2007 ◽  
Vol 222 (11/2007) ◽  
Author(s):  
Anatoly Frenkel
Keyword(s):  
Metal Nanoparticles ◽  
Short Range ◽  
Short Range Order ◽  
3D Structure ◽  
Three Dimensional ◽  
X Ray ◽  
Particle Distributions ◽  
Structure Of Metal ◽  
X Ray Absorption

We discuss methods of Extended X-ray Absorption Fine-Structure (EXAFS) analysis that provide three-dimensional structural characterization of metal nanoparticles, both mono- and bi-metallic. For the bimetallic alloys, we use short range order measurements to discriminate between random and non-random inter-particle distributions of atoms. We also discuss the application of EXAFS to heterogeneous nanoparticle systems.

scholarly journals An in silico structural insights into Plasmodium LytB protein and its inhibition

2014 ◽  
Vol 70 (a1) ◽  
pp. C1791-C1791
Author(s):  
Rajabrata Bhunya ◽  
Suman Nandy ◽  
Alpana Seal
Keyword(s):  
In Silico ◽  
3D Structure ◽  
Three Dimensional ◽  
Comparative Modeling ◽  
Binding Energies ◽  
E Coli ◽  
Dimethylallyl Diphosphate ◽  
In Silico Study ◽  
Structural Insights ◽  
Insight Into

In most of the pathogenic organisms including Plasmodium falciparum, isoprenoids are synthesized via MEP (MethylErythritol 4-Phosphate) pathway. LytB is the last enzyme of this pathway which catalyzes the conversion of (E)-4-hydroxy-3-methylbut-2-en-1-yl diphosphate (HMBPP) into the two isoprenoid precursors: isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP). Since the MEP pathway is not used by humans, it represents an attractive target for the development of new antimalarial compounds or inhibitors. Here a systematic in-silico study has been conducted to get an insight into the structure of Plasmodium lytB as well as its affinities towards different inhibitors. We used comparative modeling technique to predict the three dimensional (3D) structure of Plasmodium LytB taking E. Coli LytB protein (PDB ID: 3KE8) as template and the model was subsequently refined through molecular dynamics (MD) simulation. A large ligand dataset containing diphospate group was subjected for virtual screening against the target using GOLD 5.2 program. Considering the mode of binding and affinities, 17 leads were selected on basis of binding energies in comparison to its substrate HMBPP (Gold.Chemscore.DG: -20.9734 kcal/mol). Among them, 5 were discarded because of their inhibitory activity towards other human enzymes. The rest 12 potential leads carry all the properties of any "drug like" molecule and the knowledge of Plasmodium LytB inhibitory mechanism which can provide valuable support for the antimalarial inhibitor design in future.

scholarly journals The three-dimensional structure of the cellobiohydrolase Cel7A fromAspergillus fumigatusat 1.5 Å resolution

2015 ◽  
Vol 71 (1) ◽  
pp. 114-120 ◽  
Author(s):  
Olga V. Moroz ◽  
Michelle Maranta ◽  
Tarana Shaghasi ◽  
Paul V. Harris ◽  
Keith S. Wilson ◽  
...  
Keyword(s):  
Enzymatic Degradation ◽  
Plant Cell Wall ◽  
Three Dimensional ◽  
Biofuel Production ◽  
Industrial Processes ◽  
Dimensional Structure ◽  
Carbohydrate Active Enzymes ◽  
Cazy Database ◽  
Generation Biofuel ◽  
Insight Into

The enzymatic degradation of plant cell-wall cellulose is central to many industrial processes, including second-generation biofuel production. Key players in this deconstruction are the fungal cellobiohydrolases (CBHs), notably those from family GH7 of the carbohydrate-active enzymes (CAZY) database, which are generally known as CBHI enzymes. Here, three-dimensional structures are reported of theAspergillus fumigatusCBHI Cel7A solved in uncomplexed and disaccharide-bound forms at resolutions of 1.8 and 1.5 Å, respectively. The product complex with a disaccharide in the +1 and +2 subsites adds to the growing three-dimensional insight into this family of industrially relevant biocatalysts.

Synthesis and Characterization of a Three-dimensional Porous Compound: [Cu(H2O)6][{Cu(H2O)2}2{Cu(H2O)4H4W12O42}] · 12H2O

2008 ◽  
Vol 63 (2) ◽  
pp. 187-192 ◽  
Author(s):  
Chun-jing Zhang ◽  
Ya-guang Chen ◽  
Dong-mei Shi ◽  
Hai-jun Pang
Keyword(s):  
Aqueous Solution ◽  
Magnetic Susceptibility ◽  
Elemental Analysis ◽  
3D Structure ◽  
Three Dimensional ◽  
Synthesis And Characterization ◽  
X Ray Diffraction ◽  
X Ray ◽  
Vis Spectroscopy

A novel transition metal polyoxotungstate, [Cu(H2O)6][{Cu(H2O)2}2{Cu(H2O)4H4W12O42}] · 12H2O (1), has been synthesized in aqueous solution and characterized by single-crystal X-ray diffraction, elemental analysis, IR and UV/vis spectroscopy, and TG analysis. The paradodecatungstate anions [H2W12O42]10− are linked by CuO6 octahedra, forming a three-dimensional (3D) structure. The magnetic susceptibility of compound 1 in the temperature range 2 - 300 K shows the presence of antiferromagnetic interactions within the uniform Cu2・ ・ ・Cu3 chains

scholarly journals Three-dimensional analysis of seminiferous tubules and spermatogenic waves in mice

Reproduction ◽  
2017 ◽  
Vol 154 (5) ◽  
pp. 569-579 ◽  
Author(s):  
Hiroki Nakata ◽  
Takahiro Sonomura ◽  
Shoichi Iseki
Keyword(s):  
High Performance ◽  
Average Length ◽  
Periodic Acid ◽  
3D Structure ◽  
Three Dimensional ◽  
Rete Testis ◽  
Seminiferous Tubules ◽  
Periodic Acid Schiff ◽  
Adult Mice ◽  
Branching Points

The aim of the present study was to reconstruct seminiferous tubules and analyze spermatogenic waves in seminiferous epithelia in developing and adult mice using serial paraffin sections and high-performance three-dimensional (3D) reconstruction software. By labeling the basement membrane of seminiferous tubules with fluorescent immunohistochemistry or periodic acid-Schiff-hematoxylin staining, all seminiferous tubules were reconstructed in 9 testes from 9 different mice, 3 each at 0, 21 and 90 days (adult) postpartum. The 3D structure of seminiferous tubules, including the number and length of tubules as well as the number of connections with the rete testis, branching points and blind ends, was assessed accurately. Although tubules showed marked variations among individual mice, their overall structure was regular and retained from newborn to adult mice. Some seminiferous tubules contained inner portions running distant from the testis surface. In a representative testis at 21 days, the sites at which spermatids initially occurred were examined by labeling acrosomes and were found to be preferentially distributed in the upper and medial portions of the testis close to the rete testis. In a representative adult testis, 76 complete waves with an average length of 16.9 mm were found and their directions were analyzed. The methods used in the present study will be useful for investigating the structure and function of seminiferous tubules in mice and humans under normal and pathological conditions, such as infertility.

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