scholarly journals Three-Dimensional Models of Wild-Type and Mutated Forms of Cytochrome P450 14α-Sterol Demethylases from Aspergillus fumigatus and Candida albicans Provide Insights into Posaconazole Binding

2004 ◽  
Vol 48 (2) ◽  
pp. 568-574 ◽  
Author(s):  
Li Xiao ◽  
Vincent Madison ◽  
Andrew S. Chau ◽  
David Loebenberg ◽  
Robert E. Palermo ◽  
...  
Keyword(s):  
Cytochrome P450 ◽  
Candida Albicans ◽  
Aspergillus Fumigatus ◽  
Active Site ◽  
Three Dimensional ◽  
Fungal Growth ◽  
Binding Modes ◽  
Ergosterol Synthesis ◽  
Three Dimensional Models ◽  
Heme Cofactor

ABSTRACT The cytochrome P450 sterol 14α-demethylase enzyme (CYP51) is the target of azole antifungals. Azoles block ergosterol synthesis, and thereby fungal growth, by binding in the active-site cavity of the enzyme and ligating the iron atom of the heme cofactor through a nitrogen atom of the azole. Mutations in and around the CYP51 active site have resulted in azole resistance. In this work, homology models of the CYP51 enzymes from Aspergillus fumigatus and Candida albicans were constructed based on the X-ray crystal structure of CYP51 from Mycobacterium tuberculosis. Using these models, binding modes for voriconazole (VOR), fluconazole (FLZ), itraconazole (ITZ), and posaconazole (POS) were predicted from docking calculations. Previous work had demonstrated that mutations in the vicinity of the heme cofactor had a greater impact on the binding of FLZ and VOR than on the binding of POS and ITZ. Our modeling data suggest that the long side chains of POS and ITZ occupy a specific channel within CYP51 and that this additional interaction, which is not available to VOR and FLZ, serves to stabilize the binding of these azoles to the mutated CYP51 proteins. The model also predicts that mutations that were previously shown to specifically impact POS susceptibility in A. fumigatus and C. albicans act by interfering with the binding of the long side chain.

scholarly journals Cholesterol Ester Oxidation by Mycobacterial Cytochrome P450

2014 ◽  
Vol 289 (44) ◽  
pp. 30417-30425 ◽  
Author(s):  
Daniel J. Frank ◽  
Yarrow Madrona ◽  
Paul R. Ortiz de Montellano
Keyword(s):  
Cytochrome P450 ◽  
Active Site ◽  
Cholesterol Ester ◽  
Degradation Pathway ◽  
Binding Modes ◽  
Sequence Comparisons ◽  
Multiple Binding ◽  
Enzyme Families ◽  
Mycobacterial Growth ◽  
Cholesteryl Sulfate

Mycobacteria share a common cholesterol degradation pathway initiated by oxidation of the alkyl side chain by enzymes of cytochrome P450 (CYP) families 125 and 142. Structural and sequence comparisons of the two enzyme families revealed two insertions into the N-terminal region of the CYP125 family (residues 58–67 and 100–109 in the CYP125A1 sequence) that could potentially sterically block the oxidation of the longer cholesterol ester molecules. Catalytic assays revealed that only CYP142 enzymes are able to oxidize cholesteryl propionate, and although CYP125 enzymes could oxidize cholesteryl sulfate, they were much less efficient at doing so than the CYP142 enzymes. The crystal structure of CYP142A2 in complex with cholesteryl sulfate revealed a substrate tightly fit into a smaller active site than was previously observed for the complex of CYP125A1 with 4-cholesten-3-one. We propose that the larger CYP125 active site allows for multiple binding modes of cholesteryl sulfate, the majority of which trigger the P450 catalytic cycle, but in an uncoupled mode rather than one that oxidizes the sterol. In contrast, the more unhindered and compact CYP142 structure enables enzymes of this family to readily oxidize cholesteryl esters, thus providing an additional source of carbon for mycobacterial growth.

scholarly journals Virulence of the Fungal Pathogen Candida albicans Requires the Five Isoforms of Protein Mannosyltransferases

2005 ◽  
Vol 73 (8) ◽  
pp. 4571-4580 ◽  
Author(s):  
Mahmoud Rouabhia ◽  
Martin Schaller ◽  
Cristina Corbucci ◽  
Anna Vecchiarelli ◽  
Stephan K.-H. Prill ◽  
...  
Keyword(s):  
Candida Albicans ◽  
Mouse Model ◽  
Fungal Pathogen ◽  
Antifungal Agents ◽  
Three Dimensional ◽  
Secretory Proteins ◽  
In Vitro Growth ◽  
Specific Host ◽  
Three Dimensional Models

ABSTRACT The PMT gene family in Candida albicans encodes five isoforms of protein mannosyltransferases (Pmt proteins Pmt1p, Pmt2p, Pmt4p, Pmt5p, and Pmt6p) that initiate O mannosylation of secretory proteins. We compared virulence characteristics of pmt mutants in two complex, three-dimensional models of localized candidiasis, using reconstituted human epithelium (RHE) and engineered human oral mucosa (EHOM); in addition, mutants were tested in a mouse model of hematogenously disseminated candidiasis (HDC). All pmt mutants showed attenuated virulence in the HDC model and at least one model of localized candidiasis. The pmt5 mutant, which lacks in vitro growth phenotypes, was less virulent in the EHOM and HDC assays but had no consistent phenotype in the RHE assay. In contrast, the pmt4 and pmt6 mutants were less virulent in the RHE and HDC assays but not in the EHOM assay. The results stress the contribution of all Pmt isoforms to the virulence of C. albicans and suggest that the importance of individual Pmt isoforms may differ in specific host niches. We propose that Pmt proteins may be suitable targets for future novel classes of antifungal agents.

Plastic replicas as three-dimensional models of pulps

1975 ◽  
Vol 39 (8) ◽  
pp. 544-546
Author(s):  
HL Wakkerman ◽  
GS The ◽  
AJ Spanauf
Keyword(s):  
Three Dimensional ◽  
Dimensional Models ◽  
Three Dimensional Models

Validation of a Belt Model for Prediction of Hub Forces from a Rolling Tire4

2009 ◽  
Vol 37 (2) ◽  
pp. 62-102 ◽  
Author(s):  
C. Lecomte ◽  
W. R. Graham ◽  
D. J. O’Boy
Keyword(s):  
Internal Pressure ◽  
Equations Of Motion ◽  
Three Dimensional ◽  
Prediction Method ◽  
Analytical Models ◽  
Beam Model ◽  
Impedance Boundary ◽  
Bending Waves ◽  
Tire Rotation ◽  
Three Dimensional Models

Abstract An integrated model is under development which will be able to predict the interior noise due to the vibrations of a rolling tire structurally transmitted to the hub of a vehicle. Here, the tire belt model used as part of this prediction method is first briefly presented and discussed, and it is then compared to other models available in the literature. This component will be linked to the tread blocks through normal and tangential forces and to the sidewalls through impedance boundary conditions. The tire belt is modeled as an orthotropic cylindrical ring of negligible thickness with rotational effects, internal pressure, and prestresses included. The associated equations of motion are derived by a variational approach and are investigated for both unforced and forced motions. The model supports extensional and bending waves, which are believed to be the important features to correctly predict the hub forces in the midfrequency (50–500 Hz) range of interest. The predicted waves and forced responses of a benchmark structure are compared to the predictions of several alternative analytical models: two three dimensional models that can support multiple isotropic layers, one of these models include curvature and the other one is flat; a one-dimensional beam model which does not consider axial variations; and several shell models. Finally, the effects of internal pressure, prestress, curvature, and tire rotation on free waves are discussed.

In Silico Identification and Molecular Characterization of Extracellular Cathepsin L Proteases from Giardia duodenalis

2020 ◽  
Vol 17 (4) ◽  
pp. 342-351
Author(s):  
Sergio A. Durán-Pérez ◽  
José G. Rendón-Maldonado ◽  
Lucio de Jesús Hernandez-Diaz ◽  
Annete I. Apodaca-Medina ◽  
Maribel Jiménez-Edeza ◽  
...  
Keyword(s):  
In Silico ◽  
Cathepsin L ◽  
Three Dimensional ◽  
Giardia Duodenalis ◽  
Evolutionary Genetics ◽  
Extracellular Proteins ◽  
In Silico Identification ◽  
Dimensional Models ◽  
Three Dimensional Models

Background: The protozoan Giardia duodenalis, which causes giardiasis, is an intestinal parasite that commonly affects humans, mainly pre-school children. Although there are asymptomatic cases, the main clinical features are chronic and acute diarrhea, nausea, abdominal pain, and malabsorption syndrome. Little is currently known about the virulence of the parasite, but some cases of chronic gastrointestinal alterations post-infection have been reported even when the infection was asymptomatic, suggesting that the cathepsin L proteases of the parasite may be involved in the damage at the level of the gastrointestinal mucosa. Objective: The aim of this study was the in silico identification and characterization of extracellular cathepsin L proteases in the proteome of G. duodenalis. Methods: The NP_001903 sequence of cathepsin L protease from Homo sapienswas searched against the Giardia duodenalisproteome. The subcellular localization of Giardia duodenaliscathepsin L proteases was performed in the DeepLoc-1.0 server. The construction of a phylogenetic tree of the extracellular proteins was carried out using the Molecular Evolutionary Genetics Analysis software (MEGA X). The Robetta server was used for the construction of the three-dimensional models. The search for possible inhibitors of the extracellular cathepsin L proteases of Giardia duodenaliswas performed by entering the three-dimensional structures in the FINDSITEcomb drug discovery tool. Results: Based on the amino acid sequence of cathepsin L from Homo sapiens, 8 protein sequences were identified that have in their modular structure the Pept_C1A domain characteristic of cathepsins and two of these proteins (XP_001704423 and XP_001704424) are located extracellularly. Threedimensional models were designed for both extracellular proteins and several inhibitory ligands with a score greater than 0.9 were identified. In vitrostudies are required to corroborate if these two extracellular proteins play a role in the virulence of Giardia duodenalisand to discover ligands that may be useful as therapeutic targets that interfere in the mechanism of pathogenesis generated by the parasite. Conclusion: In silicoanalysis identified two proteins in the Giardia duodenalisprotein repertoire whose characteristics allowed them to be classified as cathepsin L proteases, which may be secreted into the extracellular medium to act as virulence factors. Three-dimensional models of both proteins allowed the identification of inhibitory ligands with a high score. The results suggest that administration of those compounds might be used to block the endopeptidase activity of the extracellular cathepsin L proteases, interfering with the mechanisms of pathogenesis of the protozoan parasite Giardia duodenalis.

The Molecular and Enzyme Kinetic Basis for Altered Activity of Three Cytochrome P450 2C19 Variants Found in the Chinese Population

2020 ◽  
Vol 13 (3) ◽  
pp. 233-244
Author(s):  
Amelia Nathania Dong ◽  
Nafees Ahemad ◽  
Yan Pan ◽  
Uma Devi Palanisamy ◽  
Beow Chin Yiap ◽  
...  
Keyword(s):  
Cytochrome P450 ◽  
Molecular Docking ◽  
Active Site ◽  
Chinese Population ◽  
Accessible Surface Area ◽  
Solvent Accessible Surface Area ◽  
In Vitro Assays ◽  
Access Channel ◽  
Cytochrome P450 2C19

Background: There is a large inter-individual variation in cytochrome P450 2C19 (CYP2C19) activity. The variability can be caused by the genetic polymorphism of CYP2C19 gene. This study aimed to investigate the molecular and kinetics basis for activity changes in three alleles including CYP2C19*23, CYP2C19*24 and CYP2C19*25found in the Chinese population. Methods: The three variants expressed by bacteria were investigated using substrate (omeprazole and 3- cyano-7-ethoxycoumarin[CEC]) and inhibitor (ketoconazole, fluoxetine, sertraline and loratadine) probes in enzyme assays along with molecular docking. Results: All alleles exhibited very low enzyme activity and affinity towards omeprazole and CEC (6.1% or less in intrinsic clearance). The inhibition studies with the four inhibitors, however, suggested that mutations in different variants have a tendency to cause enhanced binding (reduced IC50 values). The enhanced binding could partially be explained by the lower polar solvent accessible surface area of the inhibitors relative to the substrates. Molecular docking indicated that G91R, R335Q and F448L, the unique mutations in the alleles, have caused slight alteration in the substrate access channel morphology and a more compact active site cavity hence affecting ligand access and binding. It is likely that these structural alterations in CYP2C19 proteins have caused ligand-specific alteration in catalytic and inhibitory specificities as observed in the in vitro assays. Conclusion: This study indicates that CYP2C19 variant selectivity for ligands was not solely governed by mutation-induced modifications in the active site architecture, but the intrinsic properties of the probe compounds also played a vital role.

Handheld Laser Scanner Research

2019 ◽  
Vol 952 (10) ◽  
pp. 47-54
Author(s):  
A.V. Komissarov ◽  
A.V. Remizov ◽  
M.M. Shlyakhova ◽  
K.K. Yambaev
Keyword(s):  
Point Cloud ◽  
Three Dimensional ◽  
Laser Scanner ◽  
Test Site ◽  
Optical Systems ◽  
Advantages And Disadvantages ◽  
Site Survey ◽  
Laser Scanners ◽  
Three Dimensional Models ◽  
The Stability

The authors consider hand-held laser scanners, as a new photogrammetric tool for obtaining three-dimensional models of objects. The principle of their work and the newest optical systems based on various sensors measuring the depth of space are described in detail. The method of simultaneous navigation and mapping (SLAM) used for combining single scans into point cloud is outlined. The formulated tasks and methods for performing studies of the DotProduct (USA) hand-held laser scanner DPI?8X based on a test site survey are presented. The accuracy requirements for determining the coordinates of polygon points are given. The essence of the performed experimental research of the DPI?8X scanner is described, including scanning of a test object at various scanner distances, shooting a test polygon from various scanner positions and building point cloud, repeatedly shooting the same area of the polygon to check the stability of the scanner. The data on the assessment of accuracy and analysis of research results are given. Fields of applying hand-held laser scanners, their advantages and disadvantages are identified.

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