scholarly journals Integrative Approach for Computationally Inferring Interactions between the Alpha and Beta Subunits of the Calcium-Activated Potassium Channel (BK): A Docking Study

2013 ◽  
Vol 7 ◽  
pp. BBI.S10077 ◽  
Author(s):  
Janneth González ◽  
Angela Gálvez ◽  
Ludis Morales ◽  
George E. Barreto ◽  
Francisco Capani ◽  
...  
Keyword(s):  
Potassium Channel ◽  
Model Building ◽  
Three Dimensional ◽  
Docking Study ◽  
3D Models ◽  
Accessible Surface Area ◽  
Potential Interaction ◽  
Integrative Approach ◽  
Interaction Sites ◽  
Calcium Activated Potassium Channel

Three-dimensional models of the alpha- and beta-1 subunits of the calcium-activated potassium channel (BK) were predicted by threading modeling. A recursive approach comprising of sequence alignment and model building based on three templates was used to build these models, with the refinement of non-conserved regions carried out using threading techniques. The complex formed by the subunits was studied by means of docking techniques, using 3D models of the two subunits, and an approach based on rigid-body structures. Structural effects of the complex were analyzed with respect to hydrogen-bond interactions and binding-energy calculations. Potential interaction sites of the complex were determined by referencing a study of the difference accessible surface area (DASA) of the protein subunits in the complex.

scholarly journals Structural Landscape of the Transition from an ssDNA Dumbbell Plus Its Complementary Hairpin to a dsDNA Microcircle Via a Kissing Loop Intermediate

Molecules ◽  
2021 ◽  
Vol 26 (10) ◽  
pp. 3017
Author(s):  
Alberto Mills ◽  
Federico Gago
Keyword(s):  
Model Building ◽  
Three Dimensional ◽  
3D Models ◽  
Base Pairs ◽  
T4 Dna Ligase ◽  
Double Stranded Dna ◽  
Explicit Solvent ◽  
Dynamics Simulations ◽  
Enzyme Recognition ◽  
Kissing Loop

The experimental construction of a double-stranded DNA microcircle of only 42 base pairs entailed a great deal of ingenuity and hard work. However, figuring out the three-dimensional structures of intermediates and the final product can be particularly baffling. Using a combination of model building and unrestrained molecular dynamics simulations in explicit solvent we have characterized the different DNA structures involved along the process. Our 3D models of the single-stranded DNA molecules provide atomic insight into the recognition event that must take place for the DNA bases in the cohesive tail of the hairpin to pair with their complementary bases in the single-stranded loops of the dumbbell. We propose that a kissing loop involving six base pairs makes up the core of the nascent dsDNA microcircle. We also suggest a feasible pathway for the hybridization of the remaining complementary bases and characterize the final covalently closed dsDNA microcircle as possessing two well-defined U-turns. Additional models of the pre-ligation complex of T4 DNA ligase with the DNA dumbbell and the post-ligation pre-release complex involving the same enzyme and the covalently closed DNA microcircle are shown to be compatible with enzyme recognition and gap ligation.

scholarly journals Recognition of Errors in the Refinement and Validation of Three-Dimensional Structures of AC1 Proteins of Begomovirus Strains by Using ProSA-Web

2014 ◽  
Vol 2014 ◽  
pp. 1-6 ◽  
Author(s):  
Rajneesh Prajapat ◽  
Avinash Marwal ◽  
R. K. Gaur
Keyword(s):  
Structure Prediction ◽  
Structural Model ◽  
Protein Structures ◽  
Three Dimensional ◽  
Docking Study ◽  
3D Models ◽  
Analysis Tool ◽  
Protein Structure Analysis ◽  
Potential Problems ◽  
Potential Ligand

The structural model of begomovirus AC1 protein is useful for understanding biological function at molecular level and docking study. For this study we have used the ProSA program (Protein Structure Analysis) tool to establish the structure prediction and modeling of protein. This tool was used for refinement and validation of experimental protein structures. Potential problems of protein structures based on energy plots are easily seen by ProSA and are displayed in a three-dimensional manner. In the present study we have selected different AC1 proteins of begomovirus strains (YP_003288785, YP_002004579, and YP_003288773) for structural analysis and display of energy plots that highlight potential problems spotted in protein structures. The 3D models of Rep proteins with recognized errors can be effectively used for in silico docking study for development of potential ligand molecules against begomovirus infection.

New Insights on KCa3.1 Channel Modulation

2020 ◽  
Vol 26 (18) ◽  
pp. 2096-2101
Author(s):  
Giuseppe Manfroni ◽  
Francesco Ragonese ◽  
Lorenzo Monarca ◽  
Andrea Astolfi ◽  
Loretta Mancinelli ◽  
...  
Keyword(s):  
Potassium Channel ◽  
Critical Role ◽  
Calcium Signalling ◽  
Typical Feature ◽  
Open Probability ◽  
Pharmacological Agents ◽  
Channel Modulation ◽  
Calcium Dependent ◽  
Modelling Techniques ◽  
Calcium Activated Potassium Channel

The human intermediate conductance calcium-activated potassium channel, KCa3.1, is involved in several pathophysiological conditions playing a critical role in cell secretory machinery and calcium signalling. The recent cryo-EM analysis provides new insights for understanding the modulation by both endogenous and pharmacological agents. A typical feature of this channel is the low open probability in saturating calcium concentrations and its modulation by potassium channel openers (KCOs), such as benzo imidazolone 1-EBIO, without changing calcium-dependent activation. In this paper, we proposed a model of KCOs action in the modulation of channel activity. The KCa3.1 channel has a very rich pharmacological profile with several classes of molecules that selectively interact with different binding sites of the channel. Among them, benzo imidazolones can be openers (positive modulators such as 1-EBIO, DC-EBIO) or blockers (negative modulators such as NS1619). Through computation modelling techniques, we identified the 1,4-benzothiazin-3-one as a promising scaffold to develop new KCa3.1 channel modulators. Further studies are needed to explore the potential use of 1-4 benzothiazine- 3-one in KCa3.1 modulation and its pharmacological application.

Towards further Understanding the Structural Requirements of Combretastatin- like Chalcones as Inhibitors of Microtubule Polymerization

2020 ◽  
Vol 16 (2) ◽  
pp. 155-166
Author(s):  
Naveen Dhingra ◽  
Anand Kar ◽  
Rajesh Sharma
Keyword(s):  
Three Dimensional ◽  
3D Qsar ◽  
Docking Study ◽  
Structure Activity Relationship ◽  
Docking Studies ◽  
Activity Relationship ◽  
Structural Requirement ◽  
Ligand Interaction ◽  
Microtubule Polymerization ◽  
Structure Activity

Background: Microtubules are dynamic filamentous cytoskeletal structures which play several key roles in cell proliferation and trafficking. They are supposed to contribute in the development of important therapeutic targeting tumor cells. Chalcones are important group of natural compounds abundantly found in fruits & vegetables that are known to possess anticancer activity. We have used QSAR and docking studies to understand the structural requirement of chalcones for understanding the mechanism of microtubule polymerization inhibition. Methods: Three dimensional (3D) QSAR (CoMFA and CoMSIA), pharmacophore mapping and molecular docking studies were performed for the generation of structure activity relationship of combretastatin-like chalcones through statistical models and contour maps. Results: Structure activity relationship revealed that substitution of electrostatic, steric and donor groups may enhance the biological activity of compounds as inhibitors of microtubule polymerization. From the docking study, it was clear that compounds bind at the active site of tubulin protein. Conclusion: The given strategies of modelling could be an encouraging way for designing more potent compounds as well as for the elucidation of protein-ligand interaction.

scholarly journals Structured-light 3D scanning of exhibited historical clothing—a first-ever methodical trial and its results

2021 ◽  
Vol 9 (1) ◽  
Author(s):  
Jerzy Montusiewicz ◽  
Marek Miłosz ◽  
Jacek Kęsik ◽  
Kamil Żyła
Keyword(s):  
Cultural Heritage ◽  
Information Technologies ◽  
Structured Light ◽  
Three Dimensional ◽  
3D Models ◽  
3D Scanning ◽  
Dimensional Representation ◽  
3D Scanner ◽  
Three Dimensional Representation ◽  
3D Scanners

AbstractHistorical costumes are part of cultural heritage. Unlike architectural monuments, they are very fragile, which exacerbates the problems of their protection and popularisation. A big help in this can be the digitisation of their appearance, preferably using modern techniques of three-dimensional representation (3D). The article presents the results of the search for examples and methodologies of implementing 3D scanning of exhibited historical clothes as well as the attendant problems. From a review of scientific literature it turns out that so far practically no one in the world has made any methodical attempts at scanning historical clothes using structured-light 3D scanners (SLS) and developing an appropriate methodology. The vast majority of methods for creating 3D models of clothes used photogrammetry and 3D modelling software. Therefore, an innovative approach was proposed to the problem of creating 3D models of exhibited historical clothes through their digitalisation by means of a 3D scanner using structural light technology. A proposal for the methodology of this process and concrete examples of its implementation and results are presented. The problems related to the scanning of 3D historical clothes are also described, as well as a proposal how to solve them or minimise their impact. The implementation of the methodology is presented on the example of scanning elements of the Emir of Bukhara's costume (Uzbekistan) from the end of the nineteenth century, consisting of the gown, turban and shoes. Moreover, the way of using 3D models and information technologies to popularise cultural heritage in the space of digital resources is also discussed.

scholarly journals Comparative Analysis of Digital Models of Objects of Cultural Heritage Obtained by the “3D SLS” and “SfM” Methods

2021 ◽  
Vol 11 (12) ◽  
pp. 5321
Author(s):  
Marcin Barszcz ◽  
Jerzy Montusiewicz ◽  
Magdalena Paśnikowska-Łukaszuk ◽  
Anna Sałamacha
Keyword(s):  
Cultural Heritage ◽  
Low Cost ◽  
Three Dimensional ◽  
3D Models ◽  
Silk Road ◽  
Digital Models ◽  
Global Pandemic ◽  
University Of Technology ◽  
Three Dimensional Models ◽  
3D Digitisation

In the era of the global pandemic caused by the COVID-19 virus, 3D digitisation of selected museum artefacts is becoming more and more frequent practice, but the vast majority is performed by specialised teams. The paper presents the results of comparative studies of 3D digital models of the same museum artefacts from the Silk Road area generated by two completely different technologies: Structure from Motion (SfM)—a method belonging to the so-called low-cost technologies—and by Structured-light 3D Scanning (3D SLS). Moreover, procedural differences in data acquisition and their processing to generate three-dimensional models are presented. Models built using a point cloud were created from data collected in the Afrasiyab museum in Samarkand (Uzbekistan) during “The 1st Scientific Expedition of the Lublin University of Technology to Central Asia” in 2017. Photos for creating 3D models in SfM technology were taken during a virtual expedition carried out under the “3D Digital Silk Road” program in 2021. The obtained results show that the quality of the 3D models generated with SfM differs from the models from the technology (3D SLS), but they may be placed in the galleries of the vitrual museum. The obtained models from SfM do not have information about their size, which means that they are not fully suitable for archiving purposes of cultural heritage, unlike the models from SLS.

scholarly journals 3D-Volume Rendering of the Pelvis with Emphasis on Paraurethral Structures Based on MRI Scans and Comparisons between 3D Slicer and OsiriX®

2021 ◽  
Vol 45 (3) ◽  
Author(s):  
C. M. Durnea ◽  
S. Siddiqi ◽  
D. Nazarian ◽  
G. Munneke ◽  
P. M. Sedgwick ◽  
...  
Keyword(s):  
Image Processing ◽  
Secondary Analysis ◽  
Three Dimensional ◽  
3D Models ◽  
Clinical Role ◽  
Cross Sectional ◽  
3D Slicer ◽  
Mri Scans ◽  
3D Volume ◽  
Good Agreement

AbstractThe feasibility of rendering three dimensional (3D) pelvic models of vaginal, urethral and paraurethral lesions from 2D MRI has been demonstrated previously. To quantitatively compare 3D models using two different image processing applications: 3D Slicer and OsiriX. Secondary analysis and processing of five MRI scan based image sets from female patients aged 29–43 years old with vaginal or paraurethral lesions. Cross sectional image sets were used to create 3D models of the pelvic structures with 3D Slicer and OsiriX image processing applications. The linear dimensions of the models created using the two different methods were compared using Bland-Altman plots. The comparisons demonstrated good agreement between measurements from the two applications. The two data sets obtained from different image processing methods demonstrated good agreement. Both 3D Slicer and OsiriX can be used interchangeably and produce almost similar results. The clinical role of this investigation modality remains to be further evaluated.

scholarly journals Improving 3D-3D facial registration methods: potential role of three-dimensional models in personal identification of the living

2021 ◽  
Author(s):  
Daniele Gibelli ◽  
Andrea Palamenghi ◽  
Pasquale Poppa ◽  
Chiarella Sforza ◽  
Cristina Cattaneo ◽  
...  
Keyword(s):  
Three Dimensional ◽  
3D Models ◽  
Personal Identification ◽  
Surveillance Systems ◽  
3D Registration ◽  
Three Dimensional Models ◽  
Point To Point ◽  
Point Distance ◽  
Male Subjects

AbstractPersonal identification of the living from video surveillance systems usually involves 2D images. However, the potentiality of three-dimensional facial models in gaining personal identification through 3D-3D comparison still needs to be verified. This study aims at testing the reliability of a protocol for 3D-3D registration of facial models, potentially useful for personal identification. Fifty male subjects aged between 18 and 45 years were randomly chosen from a database of 3D facial models acquired through stereophotogrammetry. For each subject, two acquisitions were available; the 3D models of faces were then registered onto other models belonging to the same and different individuals according to the least point-to-point distance on the entire facial surface, for a total of 50 matches and 50 mismatches. RMS value (root mean square) of point-to-point distance between the two models was then calculated through the VAM® software. Intra- and inter-observer errors were assessed through calculation of relative technical error of measurement (rTEM). Possible statistically significant differences between matches and mismatches were assessed through Mann–Whitney test (p < 0.05). Both for intra- and inter-observer repeatability rTEM was between 2.2 and 5.2%. Average RMS point-to-point distance was 0.50 ± 0.28 mm in matches, 2.62 ± 0.56 mm in mismatches (p < 0.01). An RMS threshold of 1.50 mm could distinguish matches and mismatches in 100% of cases. This study provides an improvement to existing 3D-3D superimposition methods and confirms the great advantages which may derive to personal identification of the living from 3D facial analysis.

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