FAD-dependent C-glycoside–metabolizing enzymes in microorganisms: Screening, characterization, and crystal structure analysis

2021 ◽  
Vol 118 (40) ◽  
pp. e2106580118
Author(s):  
Takuto Kumano ◽  
Sanae Hori ◽  
Satomi Watanabe ◽  
Yuzu Terashita ◽  
Hong Yang Yu ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Biochemical Analysis ◽  
Biochemical Properties ◽  
Crystal Structure Analysis ◽  
Local Alignment ◽  
Carminic Acid ◽  
Metabolizing Enzymes ◽  
Search Tool ◽  
Anomeric Carbon ◽  
Pharmaceutical Industries

C-glycosides have a unique structure, in which an anomeric carbon of a sugar is directly bonded to the carbon of an aglycone skeleton. One of the natural C-glycosides, carminic acid, is utilized by the food, cosmetic, and pharmaceutical industries, for a total of more than 200 tons/y worldwide. However, a metabolic pathway of carminic acid has never been identified. In this study, we isolated the previously unknown carminic acid-catabolizing microorganism and discovered a flavoenzyme “C-glycoside 3-oxidase” named CarA that catalyzes oxidation of the sugar moiety of carminic acid. A Basic Local Alignment Search Tool (BLAST) search demonstrated that CarA homologs were distributed in soil microorganisms but not intestinal ones. In addition to CarA, two CarA homologs were cloned and heterologously expressed, and their biochemical properties were determined. Furthermore, a crystal structure of one homolog was determined. Together with the biochemical analysis, the crystal structure and a mutagenesis analysis of CarA revealed the mechanisms underlying their substrate specificity and catalytic reaction. Our study suggests that CarA and its homologs play a crucial role in the metabolism of C-glycosides in nature.

scholarly journals Molecular identification of Bradyrhizobium japonicum strains isolated from root nodules of soybean (Glycine max L.)

2017 ◽  
pp. 49-56
Author(s):  
Jelena Marinkovic ◽  
Dragana Bjelic ◽  
Branislava Tintor ◽  
Maja Ignjatov ◽  
Zorica Nikolic ◽  
...  
Keyword(s):  
Molecular Identification ◽  
Bradyrhizobium Japonicum ◽  
Root Nodules ◽  
Biochemical Properties ◽  
Universal Primers ◽  
Local Alignment ◽  
Molecular Characteristics ◽  
Bradyrhizobium Sp ◽  
Search Tool ◽  
Glycine Max L

The aim of this study was to isolate and identify Bradyrhizobium japonicum strains on the basis of molecular characteristics. From root nodules of different soybean cultivars were obtained 56 isolates, characterized according to morphological, cultural, and biochemical properties. Among these isolates, 33 isolates showing resemblance with Bradyrhizobium sp. were further subjected to molecular identification. Following DNA extraction, a partial 16S rDNA gene sequence from the isolates was amplified by PCR using universal primers fD1 (27F) and rP3 (1492R). Purification and sequencing of the amplified fragments were done in the bio?technology company Macrogen, Seoul, South Korea. Sequences were analyzed using the pro?gram FinchTV and BLAST (Basic Local Alignment Search Tool) and compared to sequences in GenBank and the Bradyrhizobium ID-database for identification. Comparison of the se?quences with the Bradyrhizobium ID-database showed that all tested isolates were identified as Bradyrhizobium japonicum. Each isolate was deposited in the NCBI GenBank database under a unique accession number. Identification of Bradyrhizobium species from root nodules of soybean is of great importance because the symbiosis between rhizobia and legumes are a cheaper and usually more effective agronomic practice for ensuring an adequate supply of nitrogen for legumes, while preserving and improving fertility and productivity of soils.

Crystal Structure Analysis of Cu-Zr Alloys by Convergent Beam Diffraction

1981 ◽  
Vol 39 ◽  
pp. 354-355
Author(s):  
A. F. Marshall ◽  
J. W. Steeds ◽  
D. Bouchet ◽  
S. L. Shinde ◽  
R. G. Walmsley
Keyword(s):  
Crystal Structure ◽  
Point Group ◽  
Intermetallic Phase ◽  
Three Dimensional ◽  
Crystal Structure Analysis ◽  
Ion Milling ◽  
Composition And Structure ◽  
Unit Cells ◽  
Sputter Deposited ◽  
Convergent Beam

Convergent beam electron diffraction is a powerful technique for determining the crystal structure of a material in TEM. In this paper we have applied it to the study of the intermetallic phases in the Cu-rich end of the Cu-Zr system. These phases are highly ordered. Their composition and structure has been previously studied by microprobe and x-ray diffraction with sometimes conflicting results.The crystalline phases were obtained by annealing amorphous sputter-deposited Cu-Zr. Specimens were thinned for TEM by ion milling and observed in a Philips EM 400. Due to the large unit cells involved, a small convergence angle of diffraction was used; however, the three-dimensional lattice and symmetry information of convergent beam microdiffraction patterns is still present. The results are as follows:1) 21 at% Zr in Cu: annealed at 500°C for 5 hours. An intermetallic phase, Cu3.6Zr (21.7% Zr), space group P6/m has been proposed near this composition (2). The major phase of our annealed material was hexagonal with a point group determined as 6/m.

The Influence of Memory-Aware Computation on Distributed BLAST

2019 ◽  
Vol 14 (2) ◽  
pp. 157-163
Author(s):  
Majid Hajibaba ◽  
Mohsen Sharifi ◽  
Saeid Gorgin
Keyword(s):  
Search Time ◽  
Genomic Research ◽  
Local Alignment ◽  
Negative Effects ◽  
Sequencing Technologies ◽  
Percent Improvement ◽  
Fast Processing ◽  
Search Tool ◽  
Memory Awareness ◽  
Generation Sequencing

Background: One of the pivotal challenges in nowadays genomic research domain is the fast processing of voluminous data such as the ones engendered by high-throughput Next-Generation Sequencing technologies. On the other hand, BLAST (Basic Local Alignment Search Tool), a longestablished and renowned tool in Bioinformatics, has shown to be incredibly slow in this regard. Objective: To improve the performance of BLAST in the processing of voluminous data, we have applied a novel memory-aware technique to BLAST for faster parallel processing of voluminous data. Method: We have used a master-worker model for the processing of voluminous data alongside a memory-aware technique in which the master partitions the whole data in equal chunks, one chunk for each worker, and consequently each worker further splits and formats its allocated data chunk according to the size of its memory. Each worker searches every split data one-by-one through a list of queries. Results: We have chosen a list of queries with different lengths to run insensitive searches in a huge database called UniProtKB/TrEMBL. Our experiments show 20 percent improvement in performance when workers used our proposed memory-aware technique compared to when they were not memory aware. Comparatively, experiments show even higher performance improvement, approximately 50 percent, when we applied our memory-aware technique to mpiBLAST. Conclusion: We have shown that memory-awareness in formatting bulky database, when running BLAST, can improve performance significantly, while preventing unexpected crashes in low-memory environments. Even though distributed computing attempts to mitigate search time by partitioning and distributing database portions, our memory-aware technique alleviates negative effects of page-faults on performance.

Crystal structure analysis of 4-R-phenyl-2,6-dimethyl-3,5-N-(dimethylcarbamoyl)-1,4-dihydropyridines [R=2-nitro (1), 4-methoxy (2) and 3,4-dichloro (3)]

1998 ◽  
Vol 213 (3) ◽  
Author(s):  
M. Bidya Sagar ◽  
K. Ravikumar ◽  
Y. S. Sadanandam
Keyword(s):  
Crystal Structure ◽  
Calcium Channel ◽  
Structure Analysis ◽  
Crystal Structure Analysis ◽  
Calcium Channel Antagonists

AbstractThe crystallographic characterization of the following three calcium channel antagonists is reported here: 2,6-dimethyl-3,5-dicarbamoyl-4-[2-nitro]-1,4-dihydropyridine (

scholarly journals Combined Use of Structure Analysis, Studies of Molecular Association in Solution, and Molecular Modelling to Understand the Different Propensities of Dihydroxybenzoic Acids to Form Solid Phases

Pharmaceutics ◽  
2021 ◽  
Vol 13 (5) ◽  
pp. 734
Author(s):  
Aija Trimdale ◽  
Anatoly Mishnev ◽  
Agris Bērziņš
Keyword(s):  
Crystal Structure ◽  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Structure Analysis ◽  
Crystal Structure Analysis ◽  
Molecular Association ◽  
Hydroxyl Groups ◽  
Solid Phases ◽  
Solvent Molecules ◽  
Dynamics Simulations

The arrangement of hydroxyl groups in the benzene ring has a significant effect on the propensity of dihydroxybenzoic acids (diOHBAs) to form different solid phases when crystallized from solution. All six diOHBAs were categorized into distinctive groups according to the solid phases obtained when crystallized from selected solvents. A combined study using crystal structure and molecule electrostatic potential surface analysis, as well as an exploration of molecular association in solution using spectroscopic methods and molecular dynamics simulations were used to determine the possible mechanism of how the location of the phenolic hydroxyl groups affect the diversity of solid phases formed by the diOHBAs. The crystal structure analysis showed that classical carboxylic acid homodimers and ring-like hydrogen bond motifs consisting of six diOHBA molecules are prominently present in almost all analyzed crystal structures. Both experimental spectroscopic investigations and molecular dynamics simulations indicated that the extent of intramolecular bonding between carboxyl and hydroxyl groups in solution has the most significant impact on the solid phases formed by the diOHBAs. Additionally, the extent of hydrogen bonding with solvent molecules and the mean lifetime of solute–solvent associates formed by diOHBAs and 2-propanol were also investigated.

scholarly journals Preparative-scale HPLC Resolution of Metallacyclic η3-Allyltricarbonyliron Complexes and Determination of the Absolute Configuration by X-Ray Crystal Structure Analysis

1999 ◽  
Vol 23 (9) ◽  
pp. 578-579
Author(s):  
Rainer Schobert ◽  
Hermann Pfab ◽  
Jutta Böhmer ◽  
Frank Hampel ◽  
Andreas Werner
Keyword(s):  
Crystal Structure ◽  
Silica Gel ◽  
Structure Analysis ◽  
Absolute Configuration ◽  
Crystal Structure Analysis ◽  
Preparative Scale ◽  
X Ray ◽  
The Absolute

Racemates of (η3-allyl)tricarbonyliron lactone complex Fe(CO)3{η1:η3-C(O)XCH2CHCMeCH2} 1a (X = O) and (η3-allyl)tricarbonyliron lactam complex 2a (X = NMe) are resolved on a preparative scale by HPLC on cellulose tris(3,5-dimethylphenyl)carbamate/silica gel RP-8 and the absolute configuration of (-)-2a is determined by X-ray crystal structure analysis.

scholarly journals Predicting bacteriophage hosts based on sequences of annotated receptor-binding proteins

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Dimitri Boeckaerts ◽  
Michiel Stock ◽  
Bjorn Criel ◽  
Hans Gerstmans ◽  
Bernard De Baets ◽  
...  
Keyword(s):  
Machine Learning ◽  
Predictive Model ◽  
Receptor Binding ◽  
Bacterial Infections ◽  
Sequence Data ◽  
Sequence Similarity ◽  
Area Under The Curve ◽  
Local Alignment ◽  
Search Tool ◽  
Different Levels

AbstractNowadays, bacteriophages are increasingly considered as an alternative treatment for a variety of bacterial infections in cases where classical antibiotics have become ineffective. However, characterizing the host specificity of phages remains a labor- and time-intensive process. In order to alleviate this burden, we have developed a new machine-learning-based pipeline to predict bacteriophage hosts based on annotated receptor-binding protein (RBP) sequence data. We focus on predicting bacterial hosts from the ESKAPE group, Escherichia coli, Salmonella enterica and Clostridium difficile. We compare the performance of our predictive model with that of the widely used Basic Local Alignment Search Tool (BLAST). Our best-performing predictive model reaches Precision-Recall Area Under the Curve (PR-AUC) scores between 73.6 and 93.8% for different levels of sequence similarity in the collected data. Our model reaches a performance comparable to that of BLASTp when sequence similarity in the data is high and starts outperforming BLASTp when sequence similarity drops below 75%. Therefore, our machine learning methods can be especially useful in settings in which sequence similarity to other known sequences is low. Predicting the hosts of novel metagenomic RBP sequences could extend our toolbox to tune the host spectrum of phages or phage tail-like bacteriocins by swapping RBPs.

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