scholarly journals Inhibition and Crystal Structure of the Human DHTKD1-Thiamin Diphosphate Complex

2020 ◽  
Author(s):  
João Leandro ◽  
Susmita Khamrui ◽  
Hui Wang ◽  
Chalada Suebsuwong ◽  
Natalia S. Nemeria ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Thermal Stability ◽  
High Throughput Screening ◽  
Catalytic Efficiency ◽  
Degradation Pathway ◽  
Structural Basis ◽  
Missense Mutations ◽  
Thiamin Diphosphate ◽  
Starting Point ◽  
The Impact

AbstractDHTKD1 is the E1 component of the 2-oxoadipic acid dehydrogenase complex (OADHc), which functions in the L-lysine degradation pathway. Mutations in DHTKD1 have been associated with 2-aminoadipic and 2-oxoadipic aciduria, Charcot-Marie-Tooth disease type 2Q (CMT2Q) and eosinophilic esophagitis (EoE). A crystal structure and inhibitors of DHTKD1 could improve the understanding of these clinically distinct disorders, but are currently not available. Here we report the identification of adipoylphosphonic acid and tenatoprazole as DHTKD1 inhibitors using targeted and high throughput screening, respectively. We furthermore elucidate the DHTKD1 crystal structure with thiamin diphosphate bound at 2.1 Å. The protein assembles as a dimer with residues from both monomers contributing to cofactor binding. We also report the impact of ten DHTKD1 missense mutations on the encoded proteins by enzyme kinetics, thermal stability and structural modeling. Some DHTKD1 variants displayed impaired folding (S777P and S862I), whereas other substitutions rendered the enzyme inactive (L234G, R715C and R455Q) or affected the thermal stability and catalytic efficiency (V360A and P773L). Three variants (R163Q, Q305H and G729R) surprisingly showed wild type like properties. Our work provides a structural basis for further understanding of the function of DHTKD1 and a starting point for selective small molecule inhibitors of the enzyme, which could help tease apart the role of this enzyme in several human pathologies.

scholarly journals Efficient Preparation and Performance Characterization of the HMX/F2602 Microspheres by One-Step Granulation Process

2017 ◽  
Vol 2017 ◽  
pp. 1-7 ◽  
Author(s):  
Conghua Hou ◽  
Xinlei Jia ◽  
Jingyu Wang ◽  
Yingxin Tan ◽  
Yuanping Zhang ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Thermal Stability ◽  
Particle Size ◽  
Particle Morphology ◽  
Xrd Analysis ◽  
Impact Sensitivity ◽  
Scanning Calorimetry ◽  
Granulation Process ◽  
One Step ◽  
The Impact

A new one-step granulation process for preparing high melting explosive- (HMX-) based PBX was developed. HMX/F2602 microspheres were successfully prepared by using HMX and F2602 as the main explosive and binder, respectively. The particle morphology, particle size, crystal structure, thermal stability, and impact sensitivity of the as-prepared HMX/F2602 microspheres were characterized by scanning electron microscopy (SEM), X-ray diffraction (XRD), laser particle size analyzer, differential scanning calorimetry (DSC), and impact sensitivity test, respectively. The SEM analysis indicated successful coating of F2602 on the surface of HMX, and the resulting particles are ellipsoidal or spherical with a median particle size of 940 nm; the XRD analysis did not show any change in the crystal structure after the coating and still has β-HNX crystal structure; according to the DSC analysis, HMX/F2602 prepared by the new method has better thermal stability compared to that prepared by the water suspension process. The impact sensitivity of HMX/F2602 prepared by this one-step granulation process decreased, and its characteristic height H50 increased from 37.62 to 40.13 cm, thus significantly improving the safety performance. More importantly, this method does not need the freeze-drying process after recrystallization, thus increasing the efficiency by 2 to 3 times.

scholarly journals Biochemical and Structural Characterization of the Subclass B1 Metallo-β-Lactamase VIM-4

2010 ◽  
Vol 55 (3) ◽  
pp. 1248-1255 ◽  
Author(s):  
Patricia Lassaux ◽  
Daouda A. K. Traoré ◽  
Elodie Loisel ◽  
Adrien Favier ◽  
Jean-Denis Docquier ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Escherichia Coli ◽  
Thermal Stability ◽  
Pseudomonas Aeruginosa ◽  
Structural Characterization ◽  
Catalytic Efficiency ◽  
X Ray ◽  
Stabilizing Effect ◽  
Loop 2

ABSTRACTThe metallo-β-lactamase VIM-4, mainly found inPseudomonas aeruginosaorAcinetobacter baumannii, was produced inEscherichia coliand characterized by biochemical and X-ray techniques. A detailed kinetic study performed in the presence of Zn2+at concentrations ranging from 0.4 to 100 μM showed that VIM-4 exhibits a kinetic profile similar to the profiles of VIM-2 and VIM-1. However, VIM-4 is more active than VIM-1 against benzylpenicillin, cephalothin, nitrocefin, and imipenem and is less active than VIM-2 against ampicillin and meropenem. The crystal structure of the dizinc form of VIM-4 was solved at 1.9 Å. The sole difference between VIM-4 and VIM-1 is found at residue 228, which is Ser in VIM-1 and Arg in VIM-4. This substitution has a major impact on the VIM-4 catalytic efficiency compared to that of VIM-1. In contrast, the differences between VIM-2 and VIM-4 seem to be due to a different position of the flapping loop and two substitutions in loop 2. Study of the thermal stability and the activity of the holo- and apo-VIM-4 enzymes revealed that Zn2+ions have a pronounced stabilizing effect on the enzyme and are necessary for preserving the structure.

scholarly journals Crystal structure and interaction studies of human DHTKD1 provide insight into a mitochondrial megacomplex in lysine catabolism

2020 ◽  
Author(s):  
Gustavo A. Bezerra ◽  
William R. Foster ◽  
Henry J. Bailey ◽  
Kevin G. Hicks ◽  
Sven W. Sauer ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Protein Interactions ◽  
Inner Core ◽  
Missense Variant ◽  
Oxidative Decarboxylation ◽  
Evolutionary Divergence ◽  
Binary Complex ◽  
Missense Mutations ◽  
Mitochondrial Energy Metabolism ◽  
Starting Point

ABSTRACTDHTKD1 is a lesser-studied E1 enzyme belonging to the family of 2-oxoacid dehydrogenases. DHTKD1, in complex with the E2 (dihydrolipoamide succinyltransferase, DLST) and E3 (lipoamide dehydrogenase, DLD) components, is implicated in lysine and tryptophan catabolism by catalysing the oxidative decarboxylation of 2-oxoadipate (2OA) in the mitochondria. Here, we solved the crystal structure of human DHTKD1 at 1.9 Å resolution in binary complex with the thiamine diphosphate (ThDP) cofactor. Our structure explains the evolutionary divergence of DHTKD1 from the well-characterized homologue 2-oxoglutarate (2OG) dehydrogenase, in its preference for the larger 2OA substrate than 2OG. Inherited DHTKD1 missense mutations cause the lysine metabolic condition 2-aminoadipic and 2-oxoadipic aciduria. Reconstruction of the missense variant proteins reveal their underlying molecular defects, which include protein destabilisation, disruption of protein-protein interactions, and alterations in the protein surface. We further generated a 5.0 Å reconstruction of the human DLST inner core by single-particle electron microscopy, revealing a 24-mer cubic architecture that serves as a scaffold for assembly of DHTKD1 and DLD. This structural study provides a starting point to develop small molecule DHTKD1 inhibitors for probing mitochondrial energy metabolism.

scholarly journals Analysis of Integrin αIIb Subunit Dynamics Reveals Long-Range Effects of Missense Mutations on Calf Domains

2022 ◽  
Vol 23 (2) ◽  
pp. 858
Author(s):  
Sali Anies ◽  
Vincent Jallu ◽  
Julien Diharce ◽  
Tarun J. Narwani ◽  
Alexandre G. de Brevern
Keyword(s):  
Amino Acid ◽  
Conformational Changes ◽  
3D Structure ◽  
Single Amino Acid ◽  
Structural Basis ◽  
Missense Mutations ◽  
Structural Alphabet ◽  
Platelet Surface ◽  
Integrin Αiibβ3 ◽  
The Impact

Integrin αIIbβ3, a glycoprotein complex expressed at the platelet surface, is involved in platelet aggregation and contributes to primary haemostasis. Several integrin αIIbβ3 polymorphisms prevent the aggregation that causes haemorrhagic syndromes, such as Glanzmann thrombasthenia (GT). Access to 3D structure allows understanding the structural effects of polymorphisms related to GT. In a previous analysis using Molecular Dynamics (MD) simulations of αIIb Calf-1 domain structure, it was observed that GT associated with single amino acid variation affects distant loops, but not the mutated position. In this study, experiments are extended to Calf-1, Thigh, and Calf-2 domains. Two loops in Calf-2 are unstructured and therefore are modelled expertly using biophysical restraints. Surprisingly, MD revealed the presence of rigid zones in these loops. Detailed analysis with structural alphabet, the Proteins Blocks (PBs), allowed observing local changes in highly flexible regions. The variant P741R located at C-terminal of Calf-1 revealed that the Calf-2 presence did not affect the results obtained with isolated Calf-1 domain. Simulations for Calf- 1+ Calf-2, and Thigh + Calf-1 variant systems are designed to comprehend the impact of five single amino acid variations in these domains. Distant conformational changes are observed, thus highlighting the potential role of allostery in the structural basis of GT.

scholarly journals Effect of Different Synthesis Approaches on Structural and Thermal Properties of Lanthanide(III) Metal–Organic Frameworks Based on the 1H-Pyrazole-3,5-Dicarboxylate Linker

2021 ◽  
Author(s):  
Dmytro Vlasyuk ◽  
Renata Łyszczek
Keyword(s):  
Crystal Structure ◽  
Thermal Stability ◽  
Thermal Properties ◽  
Coordination Polymers ◽  
Lanthanide Ions ◽  
X Ray Diffraction ◽  
Hydrothermal Conditions ◽  
X Ray ◽  
Synthesis Conditions ◽  
The Impact

AbstractThe impact of different synthetic procedures such as: hydrothermal, mechanochemical and precipitation on the structure and thermal properties of coordination polymers of 1H-pyrazole-3,5-dicarboxylic acid (H3pdca) with selected lanthanide ions was determined. The prepared complexes of the general formula: Ln2(Hpdca)3⋅nH2O, where Ln = Eu(III), Nd(III), Tb(III) and Er(III); n = 6 or 7 were fully investigated by: elemental analysis, Energy-Dispersive X-Ray (ED-XRF) and infrared (ATR-FTIR) spectroscopy, powder as well as single-crystal X-ray diffraction methods and thermal analysis (TG-DSC and TG-FTIR) in various atmospheres. It was proved that all used strategies offer high yields of reactions along with crystallinity of the obtained products. The X-ray diffraction methods allowed to conclude that the complexes with the same metal ions exhibit the same crystal structure despite different synthesis routes. On the other hand, the coordination polymers of Eu(III), Tb(III) and Er(III) prepared under different conditions are isomorphous. Only neodymium(III) compounds have a different crystal structure. Thermal stability of the produced complexes was correlated with the synthesis conditions, in particular with the way of energy supply. It was found that the highest thermal stability was exhibited by the complexes prepared under the hydrothermal conditions. Additionally, based on the volatile products of metal complexes decomposition, the mechanism of their pyrolysis was proposed in relation to their structures.

scholarly journals Structural Characterization and Directed Evolution of a Novel Acetyl Xylan Esterase Reveals Thermostability Determinants of the Carbohydrate Esterase 7 Family

2018 ◽  
Vol 84 (8) ◽  
Author(s):  
Fiyinfoluwa A. Adesioye ◽  
Thulani P. Makhalanyane ◽  
Surendra Vikram ◽  
Bryan T. Sewell ◽  
Wolf-Dieter Schubert ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Thermal Stability ◽  
Directed Evolution ◽  
Specific Activity ◽  
Catalytic Efficiency ◽  
Site Directed Mutagenesis ◽  
Single Point Mutation ◽  
Data Set ◽  
Carbohydrate Esterase ◽  
Thermal Stability Of

ABSTRACTA hot desert hypolith metagenomic DNA sequence data set was screenedin silicofor genes annotated as acetyl xylan esterases (AcXEs). One of the genes identified encoded an ∼36-kDa protein (Axe1NaM1). The synthesized gene was cloned and expressed, and the resulting protein was purified. NaM1 was optimally active at pH 8.5 and 30°C and functionally stable at salt concentrations of up to 5 M. The specific activity and catalytic efficiency were 488.9 U mg−1and 3.26 × 106M−1s−1, respectively. The crystal structure of wild-type NaM1 was solved at a resolution of 2.03 Å, and a comparison with the structures and models of more thermostable carbohydrate esterase 7 (CE7) family enzymes and variants of NaM1 from a directed evolution experiment suggests that reduced side-chain volume of protein core residues is relevant to the thermal stability of NaM1. Surprisingly, a single point mutation (N96S) not only resulted in a simultaneous improvement in thermal stability and catalytic efficiency but also increased the acyl moiety substrate range of NaM1.IMPORTANCEAcXEs belong to nine carbohydrate esterase families (CE1 to CE7, CE12, and CE16), of which CE7 enzymes possess a unique and narrow specificity for acetylated substrates. All structurally characterized members of this family are moderately to highly thermostable. The crystal structure of a novel, mesophilic CE7 AcXE (Axe1NaM1), from a soil metagenome, provides a basis for comparisons with thermostable CE7 enzymes. Using error-prone PCR and site-directed mutagenesis, we enhanced both the stability and activity of the mesophilic AcXE. With comparative structural analyses, we have also identified possible thermal stability determinants. These are valuable for understanding the thermal stability of enzymes within this family and as a guide for future protein engineering of CE7 and other α/β hydrolase enzymes.

Crystal structure images of large gold clusters and growing crystals by HRTEM

1984 ◽  
Vol 42 ◽  
pp. 428-429
Author(s):  
L.R. Wallenberg ◽  
J.-O. Bovin ◽  
G. Schmid
Keyword(s):  
Crystal Structure ◽  
Nucleation And Growth ◽  
Close Packing ◽  
Gold Clusters ◽  
Molecular Weight Determination ◽  
Growth Mechanisms ◽  
Starting Point ◽  
Different Types ◽  
Nucleation And Growth Mechanisms ◽  
Points Of View

Metallic clusters are interesting from various points of view, e.g. as a mean of spreading expensive catalysts on a support, or following heterogeneous and homogeneous catalytic events. It is also possible to study nucleation and growth mechanisms for crystals with the cluster as known starting point.Gold-clusters containing 55 atoms were manufactured by reducing (C6H5)3PAuCl with B2H6 in benzene. The chemical composition was found to be Au9.2[P(C6H5)3]2Cl. Molecular-weight determination by means of an ultracentrifuge gave the formula Au55[P(C6H5)3]Cl6 A model was proposed from Mössbauer spectra by Schmid et al. with cubic close-packing of the 55 gold atoms in a cubeoctahedron as shown in Fig 1. The cluster is almost completely isolated from the surroundings by the twelve triphenylphosphane groups situated in each corner, and the chlorine atoms on the centre of the 3x3 square surfaces. This gives four groups of gold atoms, depending on the different types of surrounding.

Computer simulation study about the dependence of amorphous silicon photonic waveguides efficiency on the material quality

2020 ◽  
Vol 90 (3) ◽  
pp. 30502
Author(s):  
Alessandro Fantoni ◽  
João Costa ◽  
Paulo Lourenço ◽  
Manuela Vieira
Keyword(s):  
Amorphous Silicon ◽  
High Throughput Screening ◽  
Simulation Analysis ◽  
Low Cost ◽  
Deposition Process ◽  
Large Area ◽  
Sidewall Roughness ◽  
Sensing Applications ◽  
Fabrication Defects ◽  
The Impact

Amorphous silicon PECVD photonic integrated devices are promising candidates for low cost sensing applications. This manuscript reports a simulation analysis about the impact on the overall efficiency caused by the lithography imperfections in the deposition process. The tolerance to the fabrication defects of a photonic sensor based on surface plasmonic resonance is analysed. The simulations are performed with FDTD and BPM algorithms. The device is a plasmonic interferometer composed by an a-Si:H waveguide covered by a thin gold layer. The sensing analysis is performed by equally splitting the input light into two arms, allowing the sensor to be calibrated by its reference arm. Two different 1 × 2 power splitter configurations are presented: a directional coupler and a multimode interference splitter. The waveguide sidewall roughness is considered as the major negative effect caused by deposition imperfections. The simulation results show that plasmonic effects can be excited in the interferometric waveguide structure, allowing a sensing device with enough sensitivity to support the functioning of a bio sensor for high throughput screening. In addition, the good tolerance to the waveguide wall roughness, points out the PECVD deposition technique as reliable method for the overall sensor system to be produced in a low-cost system. The large area deposition of photonics structures, allowed by the PECVD method, can be explored to design a multiplexed system for analysis of multiple biomarkers to further increase the tolerance to fabrication defects.

Liszt at the Piano: The Impact of Iconography on mid-Nineteenth Century Musicology

2014 ◽  
Vol 55 (1-2) ◽  
pp. 131-144
Author(s):  
Suzanne Marie Francis
Keyword(s):  
Nineteenth Century ◽  
Music History ◽  
Collective Identities ◽  
Cultural Contexts ◽  
Maximum Benefit ◽  
Starting Point ◽  
The Social ◽  
Iconic Status ◽  
The Impact

By the time of his death in 1827, the image of Beethoven as we recognise him today was firmly fixed in the minds of his contemporaries, and the career of Liszt was beginning to flower into that of the virtuosic performer he would be recognised as by the end of the 1830s. By analysing the seminal artwork Liszt at the Piano of 1840 by Josef Danhauser, we can see how a seemingly unremarkable head-and-shoulders bust of Beethoven in fact holds the key to unlocking the layers of commentary on both Liszt and Beethoven beneath the surface of the image. Taking the analysis by Alessandra Comini as a starting point, this paper will look deeper into the subtle connections discernible between the protagonists of the picture. These reveal how the collective identities of the artist and his painted assembly contribute directly to Beethoven’s already iconic status within music history around 1840 and reflect the reception of Liszt at this time. Set against the background of Romanticism predominant in the social and cultural contexts of the mid 1800s, it becomes apparent that it is no longer enough to look at a picture of a composer or performer in isolation to understand its impact on the construction of an overall identity. Each image must be viewed in relation to those that preceded and came after it to gain the maximum benefit from what it can tell us.

A Rare Low Spin Co(IV) Bis-Silyldiamide with High Thermal Stability: Exploring the Origin of an Unusual S = 1/2 Configuration

2020 ◽  
Author(s):  
David Zanders ◽  
Goran Bačić ◽  
Dominique Leckie ◽  
Oluwadamilola Odegbesan ◽  
Jeremy M. Rawson ◽  
...  
Keyword(s):  
Thermal Stability ◽  
Density Functional ◽  
Atomic Layer ◽  
Epr Spectrum ◽  
Functional Theory ◽  
Cluster Calculations ◽  
Layer Deposition ◽  
Starting Point ◽  
Higher Spin ◽  
Surface Saturation

Attempted preparation of a chelated Co(II) β-silylamide re-sulted in the unprecedented disproportionation to Co(0) and a spirocyclic cobalt(IV) bis(β-silyldiamide): [Co[(NtBu)2SiMe2]2] (1). Compound 1 exhibits a room temperature magnetic moment of 1.8 B.M and a solid state axial EPR spectrum diagnostic of a rare S = 1/2 configuration. Semicanonical coupled-cluster calculations (DLPNO-CCSD(T)) revealed the doublet state was clearly preferred (–27 kcal/mol) over higher spin configurations for which density functional theory (DFT) showed no energetic preference. Unlike other Co(IV) complexes, 1 had remarkable thermal stability, and was demonstrated to form a stable self-limiting monolayer in initial atomic layer deposition (ALD) surface saturation tests. The ease of synthesis and high-stability make 1 an attractive starting point to begin investigating otherwise inaccessible Co(IV) intermediates and synthesizing new materials.

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