scholarly journals Does pixel/voxel-size limit the measurement of distances in CBCT-tomography?

2018 ◽  
Author(s):  
Roland Köberle ◽  
Deusdedit Lineu Spavieri ◽  
Jonas Bianchi ◽  
Jaquelilne Ignácio ◽  
João Roberto Gonçalves
Keyword(s):  
Structural Information ◽  
Imaging Modality ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Bovine Bone ◽  
Experimental Conditions ◽  
Geometrical Structures ◽  
Voxel Size ◽  
Free Region ◽  
Confocal Spectroscopy

The necessity to obtain relevant structural information from tomographic images is an all-pervasive step in a host of clinical and research-areas. Cone Beam Computed Tomography (CBCT) is the imaging modality often used among the many available. Currently approaches to extract structural properties from raw CBCT-images, involve some manual intervention by experts to measure their properties, such as size and displacements of their geometrical structures. Regarding the factors limiting the precision of these measurements, such as voxel-size and image contrast, we find conflicting statements in the literature. It is therefore useful to provide accurate data under well-defined experimental conditions. Here we present a method and associated software to measure displacements of geometrical structures. We also determined the minimum measureable displacement and minimum detectable defect in terms of voxel size. We select as our geometrical structure a sample of bovine bone and to provide a set of defects, we drilled a pattern of holes into it. We determined the hole's three-dimensional structures using confocal spectroscopy. In order to obtain the minimum measurable displacement, we acquired CBCT-radiographies containing a stationary reference and micro-metrically cnc controlled displacements of the sample. We then process these images with our software to extract the distances and compare them with the cnc displacements. All our processing includes a computational interpolation from the voxel-size of $0.35$ mm corresponding to our CBCT-radiographies, down to $0.05$ mm. We find that sample-displacements can be measured with a precision of $\sim 20 \mu$, 17 times smaller than the voxel-size of $0.35$ mm. To measure the size of the holes using our CBCT-radiographies, we first register the holes onto a hole-free region of the sample with our software, then overlay the result with the three-dimensional structure obtained from confocal spectroscopy. We find the minimum detectable hole-size to be $0.7$ mm, twice the voxel-size.

scholarly journals SphereCon—a method for precise estimation of residue relative solvent accessible area from limited structural information

2020 ◽  
Vol 36 (11) ◽  
pp. 3372-3378
Author(s):  
Alexander Gress ◽  
Olga V Kalinina
Keyword(s):  
Protein Function ◽  
Structural Information ◽  
Solvent Accessibility ◽  
Three Dimensional ◽  
Structural Data ◽  
Supplementary Information ◽  
Dimensional Structure ◽  
Relative Solvent Accessibility ◽  
Precise Measure ◽  
The Impact

Abstract Motivation In proteins, solvent accessibility of individual residues is a factor contributing to their importance for protein function and stability. Hence one might wish to calculate solvent accessibility in order to predict the impact of mutations, their pathogenicity and for other biomedical applications. A direct computation of solvent accessibility is only possible if all atoms of a protein three-dimensional structure are reliably resolved. Results We present SphereCon, a new precise measure that can estimate residue relative solvent accessibility (RSA) from limited data. The measure is based on calculating the volume of intersection of a sphere with a cone cut out in the direction opposite of the residue with surrounding atoms. We propose a method for estimating the position and volume of residue atoms in cases when they are not known from the structure, or when the structural data are unreliable or missing. We show that in cases of reliable input structures, SphereCon correlates almost perfectly with the directly computed RSA, and outperforms other previously suggested indirect methods. Moreover, SphereCon is the only measure that yields accurate results when the identities of amino acids are unknown. A significant novel feature of SphereCon is that it can estimate RSA from inter-residue distance and contact matrices, without any information about the actual atom coordinates. Availability and implementation https://github.com/kalininalab/spherecon. Contact [email protected] Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals Crystallization and preliminary X-ray diffraction analysis of a single variable domain of the immunoglobulin superfamily in amphioxus,Amphi-IgSF-V

2014 ◽  
Vol 70 (8) ◽  
pp. 1072-1075 ◽  
Author(s):  
Bo Jiang ◽  
Yanjie Liu ◽  
Rong Chen ◽  
Zhenbao Wang ◽  
Mansoor Tariq ◽  
...  
Keyword(s):  
Immune System ◽  
Structural Information ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Immunoglobulin Superfamily ◽  
X Ray Diffraction ◽  
X Ray ◽  
Cell Parameters ◽  
System A ◽  
Human Immunoglobulins

Amphioxus is regarded as an essential animal model for the study of immune evolution. Discovery of new molecules with the immunoglobulin superfamily (IgSF) variable (V) domain in amphioxus would help in studying the evolution of IgSF V molecules in the immune system. A protein was found which just contains only one IgSF V domain in amphioxus, termedAmphi-IgSF-V; it has over 30% sequence identity to the V domains of human immunoglobulins and mammalian T-cell receptors. In order to clarify the three-dimensional structure of this new molecule in amphioxus,Amphi-IgSF-V was expressed, purified and crystallized, and diffraction data were collected to a resolution of 1.95 Å. The crystal belonged to space groupP3221, with unit-cell parametersa=b= 53.9,c= 135.5 Å. The Matthews coefficient and solvent content were calculated to be 2.58 Å3 Da−1and 52.38%, respectively. The results will provide structural information to study the evolution of IgSF V molecules in the immune system.

scholarly journals Prediction and Analysis of Surface Hydrophobic Residues in Tertiary Structure of Proteins

2014 ◽  
Vol 2014 ◽  
pp. 1-7 ◽  
Author(s):  
Shambhu Malleshappa Gowder ◽  
Jhinuk Chatterjee ◽  
Tanusree Chaudhuri ◽  
Kusum Paul
Keyword(s):  
Tertiary Structure ◽  
Structural Information ◽  
Solvent Accessibility ◽  
Conservation Score ◽  
Protein Structures ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Data Set ◽  
Hydrophobic Residues ◽  
Monomeric Proteins

The analysis of protein structures provides plenty of information about the factors governing the folding and stability of proteins, the preferred amino acids in the protein environment, the location of the residues in the interior/surface of a protein and so forth. In general, hydrophobic residues such as Val, Leu, Ile, Phe, and Met tend to be buried in the interior and polar side chains exposed to solvent. The present work depends on sequence as well as structural information of the protein and aims to understand nature of hydrophobic residues on the protein surfaces. It is based on the nonredundant data set of 218 monomeric proteins. Solvent accessibility of each protein was determined using NACCESS software and then obtained the homologous sequences to understand how well solvent exposed and buried hydrophobic residues are evolutionarily conserved and assigned the confidence scores to hydrophobic residues to be buried or solvent exposed based on the information obtained from conservation score and knowledge of flanking regions of hydrophobic residues. In the absence of a three-dimensional structure, the ability to predict surface accessibility of hydrophobic residues directly from the sequence is of great help in choosing the sites of chemical modification or specific mutations and in the studies of protein stability and molecular interactions.

Structure of nanocrystalline MgFe2O4from X-ray diffraction, Rietveld and atomic pair distribution function analysis

2005 ◽  
Vol 38 (5) ◽  
pp. 772-779 ◽  
Author(s):  
Milen Gateshki ◽  
Valeri Petkov ◽  
Swapan K. Pradhan ◽  
Tom Vogt
Keyword(s):  
Distribution Function ◽  
Pair Distribution Function ◽  
Structural Information ◽  
Function Analysis ◽  
Three Dimensional ◽  
Structural Disorder ◽  
Dimensional Structure ◽  
Spinel Type ◽  
Atomic Pair Distribution Function ◽  
Atomic Pair

The three-dimensional structure of nanocrystalline magnesium ferrite, MgFe2O4, prepared by ball milling, has been determined using synchrotron radiation powder diffraction and employing both Rietveld and atomic pair distribution function (PDF) analysis. The nanocrystalline ferrite exhibits a very limited structural coherence length and a high degree of structural disorder. Nevertheless, the nanoferrite possesses a very well defined local atomic ordering that may be described in terms of a spinel-type structure with Mg2+and Fe3+ions almost randomly distributed over its tetrahedral and octahedral sites. The new structural information helps explain the material's unusual magnetic properties.

scholarly journals Structural Model for 12-Helix Transporters Belonging to the Major Facilitator Superfamily

2003 ◽  
Vol 185 (5) ◽  
pp. 1712-1718 ◽  
Author(s):  
Teruhisa Hirai ◽  
Jürgen A. W. Heymann ◽  
Peter C. Maloney ◽  
Sriram Subramaniam
Keyword(s):  
Structural Model ◽  
Structural Information ◽  
Three Dimensional ◽  
Spatial Arrangement ◽  
Bound State ◽  
Major Facilitator Superfamily ◽  
Dimensional Structure ◽  
Sequence Information ◽  
Major Facilitator ◽  
Related Proteins

ABSTRACT The major facilitator superfamily includes a large collection of evolutionarily related proteins that have been implicated in the transport of a variety of solutes and metabolites across the membranes of organisms ranging from bacteria to humans. We have recently reported the three-dimensional structure, at 6.5 Å resolution, of the oxalate transporter, OxlT, a representative member of this superfamily. In the oxalate-bound state, 12 helices surround a central cavity to form a remarkably symmetrical structure that displays a well-defined pseudo twofold axis perpendicular to the plane of the membrane as well as two less pronounced, mutually perpendicular pseudo twofold axes in the plane of the membrane. Here, we combined this structural information with sequence information from other members of this protein family to arrive at models for the arrangement of helices in this superfamily of transport proteins. Our analysis narrows down the number of helix arrangements from about a billion starting possibilities to a single probable model for the relative spatial arrangement for the 12 helices, consistent both with our structural findings and with the majority of previous biochemical studies on members of this superfamily.

Type I interferon structures: Possible scaffolds for the interferon-alpha receptor complex

2002 ◽  
Vol 80 (8) ◽  
pp. 1166-1173 ◽  
Author(s):  
Tattanahalli L Nagabhushan ◽  
Paul Reichert ◽  
Mark R Walter ◽  
Nicholas J Murgolo
Keyword(s):  
Structural Model ◽  
Structural Information ◽  
Three Dimensional ◽  
Cell Receptor ◽  
Type I Interferons ◽  
Dimensional Structure ◽  
Type I ◽  
Receptor Complex ◽  
X Ray Crystallography ◽  
Receptor Complexes

The structures of several type I interferons (IFNs) are known. We review the structural information known for IFN alphas and compare them to other interferons and cytokines. We also review the structural information known or proposed for IFN–cell receptor complexes. However, the structure of the IFN – cell receptor – IFN receptor2 (IFNAR2) and IFN receptor1 (IFNAR1) complex has not yet been determined. This paper describes a structural model of human IFN-IFNAR2/IFNAR1 complex using human IFN-α2b dimer as the ligand. Both the structures of recombinant human IFN-α2b and IFN-β were determined by X-ray crystallography as zinc-mediated dimers. Our proposed model was generated using human IFN-α2b dimer docked with IFNAR2/IFNAR1. We compare our model with the receptor complex models proposed for IFN-β and IFN-γ to contrast similarities and differences. The mutual binding sites of human IFN-α2b and IFNAR2/IFNAR1 complex are consistent with available mutagenesis studies.Key words: three dimensional structure, antiviral activity, receptor, interferon.

scholarly journals Homology Modeling and Docking Studies of TMPRSS2 with Experimentally Known Inhibitors Camostat Mesylate, Nafamostat and Bromhexine Hydrochloride to Control SARS-Coronavirus-2

2020 ◽  
Author(s):  
Kailas Sonawane ◽  
Sagar S. Barale ◽  
Maruti J. Dhanavade ◽  
Shailesh R. Waghmare ◽  
Naiem H. Nadaf ◽  
...  
Keyword(s):  
Host Cell ◽  
Human Cell ◽  
Structural Information ◽  
Three Dimensional ◽  
Catalytic Triad ◽  
New Drugs ◽  
Dimensional Structure ◽  
Inhibition Mechanism ◽  
Global Public Health ◽  
Sars Coronavirus

The rapid outbreak of SARS-Coronavirus 2 (SARS-CoV-2) caused a serious global public health threat. The spike ‘S’ protein of SARS-CoV-2 and ACE2 of the host cell are being targeted to design and discover new drugs to control Covid-19 disease. Similarly, a transmembrane serine protease, TMPRSS2 of the host cell has been found to play a significant role in proteolytic cleavage of viral spike protein priming to the receptor ACE2 present in human cell. However, three dimensional structure and inhibition mechanism of TMPRSS2 is yet to be explored experimentally. Hence, in the present study we have generated a homology model of TMPRSS2 and studied its binding properties with experimentally studied inhibitors <i>viz.</i> Camostat mesylate, Nafamostat and Bromhexine hydrochloride (BHH) using molecular docking technique. Docking analysis revealed that the Camostat mesylate and its structural analogue Nafamostat interacts strongly with residues His296, Ser441 and Asp435 present in catalytic triad of TMPRSS2. However, BHH interacts with Gln438 and other residues present in the active site pocket of TMPRSS2 through hydrophobic contacts effectively. Thus, these results revealed the inhibition mechanism of TMPRSS2 by known inhibitors Camostat mesylate, Nafamostat and Bromhexine hydrochloride in detail at the molecular level. However, Camostat mesylate shows strong binding as compared to other two inhibitors. This structural information could also be useful to design and discover new inhibitors of TMPRSS2, which may be helpful to prevent the entry to SARS-Coronavirus 2 in human cell.

Tooth and root size as determined from 0.25- and 0.30-mm voxel size cone-beam CT imaging when contrasted to micro-CT scans (0.06 mm): An ex vivo study

2021 ◽  
pp. 146531252110661
Author(s):  
Gaston F Coutsiers Morell ◽  
Yuli Berlin-Broner ◽  
Carlos Flores-Mir ◽  
Giseon Heo
Keyword(s):  
Repeated Measures ◽  
Root Resorption ◽  
Ex Vivo ◽  
Imaging Modality ◽  
Cone Beam Ct ◽  
Three Dimensional ◽  
Cone Beam ◽  
Micro Ct ◽  
Voxel Size ◽  
Ex Vivo Study

Objective: To quantify tooth volume differences from extracted teeth when using three different three-dimensional (3D) computed tomography (CT)-based imaging modalities. Design: Ex vivo study. Setting: Laboratory and clinics of the University of Alberta. Methods: Cone-beam CT (CBCT) of 12 extracted teeth were scanned using 0.25- and 0.30-mm voxel size from CBCT and a 0.06-mm voxel size from micro-CT (reference standard). 3D reconstructions for each tooth from each imaging modality were made through the software ITK-SNAP®. The mean volume differences between each pair of scanning modalities were calculated and then compared and analysed through a repeated measures ANOVA. Results: The average overestimations of the teeth volume were 15.2% for the high-resolution CBCT and 28.1% for the low-resolution CBCT compared to micro-CT measurements. The differences in absolute volume were 81.6 mm3 and 152.8 mm3, respectively. All differences were statistically significant ( P < 0.05). Conclusions: Orthodontists and researchers who assess root resorption through CBCT imaging should be aware that the depicted volumes may likely be overestimating tooth volume and camouflaging real root volumetric treatment changes.

scholarly journals Homology Modeling and Docking Studies of TMPRSS2 with Experimentally Known Inhibitors Camostat Mesylate, Nafamostat and Bromhexine Hydrochloride to Control SARS-Coronavirus-2

2020 ◽  
Author(s):  
Kailas Sonawane ◽  
Sagar S. Barale ◽  
Maruti J. Dhanavade ◽  
Shailesh R. Waghmare ◽  
Naiem H. Nadaf ◽  
...  
Keyword(s):  
Host Cell ◽  
Human Cell ◽  
Structural Information ◽  
Three Dimensional ◽  
Catalytic Triad ◽  
New Drugs ◽  
Dimensional Structure ◽  
Inhibition Mechanism ◽  
Global Public Health ◽  
Sars Coronavirus

The rapid outbreak of SARS-Coronavirus 2 (SARS-CoV-2) caused a serious global public health threat. The spike ‘S’ protein of SARS-CoV-2 and ACE2 of the host cell are being targeted to design and discover new drugs to control Covid-19 disease. Similarly, a transmembrane serine protease, TMPRSS2 of the host cell has been found to play a significant role in proteolytic cleavage of viral spike protein priming to the receptor ACE2 present in human cell. However, three dimensional structure and inhibition mechanism of TMPRSS2 is yet to be explored experimentally. Hence, in the present study we have generated a homology model of TMPRSS2 and studied its binding properties with experimentally studied inhibitors <i>viz.</i> Camostat mesylate, Nafamostat and Bromhexine hydrochloride (BHH) using molecular docking technique. Docking analysis revealed that the Camostat mesylate and its structural analogue Nafamostat interacts strongly with residues His296, Ser441 and Asp435 present in catalytic triad of TMPRSS2. However, BHH interacts with Gln438 and other residues present in the active site pocket of TMPRSS2 through hydrophobic contacts effectively. Thus, these results revealed the inhibition mechanism of TMPRSS2 by known inhibitors Camostat mesylate, Nafamostat and Bromhexine hydrochloride in detail at the molecular level. However, Camostat mesylate shows strong binding as compared to other two inhibitors. This structural information could also be useful to design and discover new inhibitors of TMPRSS2, which may be helpful to prevent the entry to SARS-Coronavirus 2 in human cell.

ISAACS– interactive structure analysis of amorphous and crystalline systems

2010 ◽  
Vol 43 (1) ◽  
pp. 181-185 ◽  
Author(s):  
Sébastien Le Roux ◽  
Valeri Petkov
Keyword(s):  
Structure Analysis ◽  
Structural Information ◽  
Structural Characteristics ◽  
Three Dimensional ◽  
Local Symmetry ◽  
Distribution Functions ◽  
Dimensional Structure ◽  
Coordination Numbers ◽  
Structure Factors ◽  
Cross Platform

ISAACS(interactive structure analysis of amorphous and crystalline systems) is a cross-platform program developed to analyze the structural characteristics of three-dimensional structure models built by computer simulations. The models may have any degree of periodicity (i.e.crystallinity) and local symmetry. The following structural information is computed from the models: total and partial radial distribution functions and structure factors for X-ray or neutron scattering, coordination numbers, bond-angle and near atomic neighbor distributions, bond-valence sums, ring statistics, and spherical harmonics invariants. The information may be visualized conveniently and stored for further use.

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