scholarly journals Functional Characterization of 21 Rare Allelic CYP1A2 Variants Identified in a Population of 4773 Japanese Individuals by Assessing Phenacetin O-Deethylation

2021 ◽  
Vol 11 (8) ◽  
pp. 690
Author(s):  
Masaki Kumondai ◽  
Evelyn Marie Gutiérrez Rico ◽  
Eiji Hishinuma ◽  
Yuya Nakanishi ◽  
Shuki Yamazaki ◽  
...  
Keyword(s):  
Enzymatic Activity ◽  
Protein Function ◽  
Rare Variants ◽  
Functional Characterization ◽  
Three Dimensional ◽  
Additional Information ◽  
Metabolic Reactions ◽  
Underlying Mechanisms ◽  
Cytochrome Content

Cytochrome P450 1A2 (CYP1A2), which accounts for approximately 13% of the total hepatic cytochrome content, catalyzes the metabolic reactions of approximately 9% of frequently used drugs, including theophylline and olanzapine. Substantial inter-individual differences in enzymatic activity have been observed among patients, which could be caused by genetic polymorphisms. Therefore, we functionally characterized 21 novel CYP1A2 variants identified in 4773 Japanese individuals by determining the kinetic parameters of phenacetin O-deethylation. Our results showed that most of the evaluated variants exhibited decreased or no enzymatic activity, which may be attributed to potential structural alterations. Notably, the Leu98Gln, Gly233Arg, Ser380del Gly454Asp, and Arg457Trp variants did not exhibit quantifiable enzymatic activity. Additionally, three-dimensional (3D) docking analyses were performed to further understand the underlying mechanisms behind variant pharmacokinetics. Our data further suggest that despite mutations occurring on the protein surface, accumulating interactions could result in the impairment of protein function through the destabilization of binding regions and changes in protein folding. Therefore, our findings provide additional information regarding rare CYP1A2 genetic variants and how their underlying effects could clarify discrepancies noted in previous phenotypical studies. This would allow the improvement of personalized therapeutics and highlight the importance of identifying and characterizing rare variants.

scholarly journals Identification and functional characterization of NODAL rare variants in heterotaxy and isolated cardiovascular malformations

2008 ◽  
Vol 18 (5) ◽  
pp. 861-871 ◽  
Author(s):  
Bhagyalaxmi Mohapatra ◽  
Brett Casey ◽  
Hua Li ◽  
Trang Ho-Dawson ◽  
Liana Smith ◽  
...  
Keyword(s):  
Rare Variants ◽  
Functional Characterization ◽  
Cardiovascular Malformations

scholarly journals Effect of Surface Topography Parameters on Friction and Wear of Random Rough Surface

Materials ◽  
2019 ◽  
Vol 12 (17) ◽  
pp. 2762 ◽  
Author(s):  
Ruimin Shi ◽  
Bukang Wang ◽  
Zhiwei Yan ◽  
Zongyan Wang ◽  
Lei Dong
Keyword(s):  
Surface Topography ◽  
Fluid Dynamic ◽  
Dynamic Pressure ◽  
Functional Characterization ◽  
Three Dimensional ◽  
Measuring System ◽  
Height Distribution ◽  
Worn Surface ◽  
The Relationship

In order to explore the relationship between the surface topography parameters and friction properties of a rough contact interface under fluid dynamic pressure lubrication conditions, friction experiments were carried out. The three-dimensional surface topography of specimens was measured and characterized with a profile microscopy measuring system and scanning electron microscope. The friction coefficient showed a trend of decreasing first and then increasing with the increase in some surface topography parameters at lower pressure, such as the surface height arithmetic mean Sa, surface height distribution kurtosis Sku, surface volume average volume Vvv, and surface center area average void volume Vvc, which are the ISO 25178 international standard parameters. The effects of surface topographic parameters on friction were analyzed and the wear mechanism of the worn surface was presented. The wear characteristics of the samples were mainly characterized as strain fatigue, grinding, and scraping. The results provide a theoretical basis for the functional characterization of surface topography.

scholarly journals Functional Characterization of TNNC1 Rare Variants Identified in Dilated Cardiomyopathy

2011 ◽  
Vol 286 (39) ◽  
pp. 34404-34412 ◽  
Author(s):  
Jose Renato Pinto ◽  
Jill D. Siegfried ◽  
Michelle S. Parvatiyar ◽  
Duanxiang Li ◽  
Nadine Norton ◽  
...  
Keyword(s):  
Dilated Cardiomyopathy ◽  
Rare Variants ◽  
Functional Characterization

scholarly journals Protein function prediction in genomes: Critical assessment of coiled-coil predictions based on protein structure data

2019 ◽  
Author(s):  
Dominic Simm ◽  
Klas Hatje ◽  
Stephan Waack ◽  
Martin Kollmar
Keyword(s):  
Protein Function ◽  
Protein Function Prediction ◽  
Functional Characterization ◽  
Coiled Coil ◽  
Imbalanced Data ◽  
Large Data ◽  
Data Sets ◽  
Data Set ◽  
Protein Motifs ◽  
Additional Information

AbstractCoiled-coil regions were among the first protein motifs described structurally and theoretically. The beauty and simplicity of the motif gives hope to detecting coiled-coil regions with reasonable accuracy and precision in any protein sequence. Here, we re-evaluated the most commonly used coiled-coil prediction tools with respect to the most comprehensive reference data set available, the entire Protein Data Base (PDB), down to each amino acid and its secondary structure. Apart from the thirtyfold difference in number of predicted coiled-coils the tools strongly vary in their predictions, across structures and within structures. The evaluation of the false discovery rate and Matthews correlation coefficient, a widely used performance metric for imbalanced data sets, suggests that the tested tools have only limited applicability for large data sets. Coiled-coil predictions strongly impact the functional characterization of proteins, are used for functional genome annotation, and should therefore be supported and validated by additional information.

Self-Contained Three-Dimensional Bioprinter for Applications in Cardiovascular Research

2019 ◽  
Vol 13 (3) ◽  
Author(s):  
Prabhuti Kharel ◽  
Likitha Somasekhar ◽  
Amy Vecheck ◽  
Kunal Mitra
Keyword(s):  
Functional Characterization ◽  
Three Dimensional ◽  
Environmental Parameters ◽  
3D Bioprinting ◽  
Cardiovascular Research ◽  
Form Complex ◽  
Tissue Constructs ◽  
Long Duration ◽  
Selection Of

Bioprinting is a technique of creating 3D cell-laden structures by accurately dispensing biomaterial to form complex synthetic tissue. The printed constructs aim to mimic the native tissue by preserving the cell functionality and viability within the printed structure. The 3D bioprinting system presented in this paper aims to facilitate the process of 3D bioprinting through its ability to control the environmental parameters within an enclosed printing chamber. This design of the bioprinter targets to eliminate the need for a laminar flow hood, by regulating the necessary environmental conditions important for cell survival, especially during long duration prints. A syringe-based extrusion (SBE) deposition method comprising multiple nozzles is integrated into the system. This allows for a wider selection of biomaterials that can be used for the formation of the extracellular matrix (ECM). Tissue constructs composed of alginate-gelatin hydrogels were mixed with fibrinogen and human endothelial cells which were then characterized and compared using two methodologies: casted and bioprinted. Furthermore, vasculature was incorporated in the bioprinted constructs using sacrificial printing. Structural and functional characterization of the constructs were performed by assessing rheological, mechanical properties, and analyzing live-dead assay measurements.

scholarly journals Functional Characterization of Three-Dimensional Cortical Cultures for In Vitro Modeling of Brain Networks

iScience ◽  
2020 ◽  
Vol 23 (8) ◽  
pp. 101434
Author(s):  
Yu-Ting L. Dingle ◽  
Volha Liaudanskaya ◽  
Liam T. Finnegan ◽  
Kyler C. Berlind ◽  
Craig Mizzoni ◽  
...  
Keyword(s):  
Functional Characterization ◽  
Brain Networks ◽  
Three Dimensional ◽  
In Vitro Modeling ◽  
Cortical Cultures

scholarly journals GlcNAc De-N-Acetylase from the Hyperthermophilic ArchaeonSulfolobus solfataricus

2018 ◽  
Vol 85 (2) ◽  
Author(s):  
Roberta Iacono ◽  
Andrea Strazzulli ◽  
Luisa Maurelli ◽  
Nicola Curci ◽  
Angela Casillo ◽  
...  
Keyword(s):  
Functional Characterization ◽  
Recombinant Enzyme ◽  
Mass Spectrometry Analysis ◽  
Genomic Context ◽  
Content Type ◽  
Spectrometry Analysis ◽  
Additional Information ◽  
The One ◽  
Hydrolysis Of

ABSTRACTSulfolobus solfataricusis an aerobic crenarchaeal hyperthermophile with optimum growth at temperatures greater than 80°C and pH 2 to 4. Within the crenarchaeal group ofSulfolobales,N-acetylglucosamine (GlcNAc) has been shown to be a component of exopolysaccharides, forming their biofilms, and of theN-glycan decorating some proteins. The metabolism of GlcNAc is still poorly understood inArchaea, and one approach to gaining additional information is through the identification and functional characterization of carbohydrate active enzymes (CAZymes) involved in the modification of GlcNAc. The screening ofS. solfataricusextracts allowed the detection of a novel α-N-acetylglucosaminidase (α-GlcNAcase) activity, which has never been identified inArchaea. Mass spectrometry analysis of the purified activity showed a protein encoded by thesso2901gene. Interestingly, the purified recombinant enzyme, which was characterized in detail, revealed a novel de-N-acetylase activity specific for GlcNAc and derivatives. Thus, assays to identify an α-GlcNAcase found a GlcNAc de-N-acetylase instead. The α-GlcNAcase activity observed inS. solfataricusextracts did occur when SSO2901 was used in combination with an α-glucosidase. Furthermore, the inspection of the genomic context and the preliminary characterization of a putative glycosyltransferase immediately upstream ofsso2901(sso2900) suggest the involvement of these enzymes in the GlcNAc metabolism inS. solfataricus.IMPORTANCEIn this study, a preliminary screening of cellular extracts ofS. solfataricusallowed the identification of an α-N-acetylglucosaminidase activity. However, the characterization of the corresponding recombinant enzyme revealed a novel GlcNAc de-N-acetylase, which, in cooperation with the α-glucosidase, catalyzed the hydrolysis of O-α-GlcNAc glycosides. In addition, we show that the product of a gene flanking the one encoding the de-N-acetylase is a putative glycosyltransferase, suggesting the involvement of the two enzymes in the metabolism of GlcNAc. The discovery and functional analysis of novel enzymatic activities involved in the modification of this essential sugar represent a powerful strategy to shed light on the physiology and metabolism ofArchaea.

scholarly journals Functional Characterization of Clinically-Relevant Rare Variants in ABCG2 Identified in a Gout and Hyperuricemia Cohort

Cells ◽  
2019 ◽  
Vol 8 (4) ◽  
pp. 363 ◽  
Author(s):  
Toyoda ◽  
Mančíková ◽  
Krylov ◽  
Morimoto ◽  
Pavelcová ◽  
...  
Keyword(s):  
Genetic Risk ◽  
Rare Variants ◽  
Direct Sequencing ◽  
Functional Characterization ◽  
Cellular Proteins ◽  
European Descent ◽  
Primary Gout ◽  
Abcg2 Protein ◽  
Functional Analyses

ATP-binding cassette subfamily G member 2 (ABCG2) is a physiologically important urate transporter. Accumulating evidence demonstrates that congenital dysfunction of ABCG2 is an important genetic risk factor in gout and hyperuricemia; recent studies suggest the clinical significance of both common and rare variants of ABCG2. However, the effects of rare variants of ABCG2 on the risk of such diseases are not fully understood. Here, using a cohort of 250 Czech individuals of European descent (68 primary hyperuricemia patients and 182 primary gout patients), we examined exonic non-synonymous variants of ABCG2. Based on the results of direct sequencing and database information, we experimentally characterized nine rare variants of ABCG2: R147W (rs372192400), T153M (rs753759474), F373C (rs752626614), T421A (rs199854112), T434M (rs769734146), S476P (not annotated), S572R (rs200894058), D620N (rs34783571), and a three-base deletion K360del (rs750972998). Functional analyses of these rare variants revealed a deficiency in the plasma membrane localization of R147W and S572R, lower levels of cellular proteins of T153M and F373C, and null urate uptake function of T434M and S476P. Accordingly, we newly identified six rare variants of ABCG2 that showed lower or null function. Our findings contribute to deepening the understanding of ABCG2-related gout/hyperuricemia risk and the biochemical characteristics of the ABCG2 protein.

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