scholarly journals Anti-Idiotype scFv Localizes an Autoepitope in the Globular Domain of C1q

2021 ◽  
Vol 22 (15) ◽  
pp. 8288
Author(s):  
Nadezhda Todorova ◽  
Miroslav Rangelov ◽  
Vanya Bogoeva ◽  
Vishnya Stoyanova ◽  
Anna Yordanova ◽  
...  
Keyword(s):  
3D Model ◽  
Potent Inhibitor ◽  
3D Structure ◽  
Recombinant Antibodies ◽  
Structural Features ◽  
Phage Library ◽  
Apical Region ◽  
Globular Domain ◽  
Potential Inhibitors ◽  
First Time

We addressed the issue of C1q autoantigenicity by studying the structural features of the autoepitopes recognized by the polyclonal anti-C1q antibodies present in Lupus Nephritis (LN) sera. We used six fractions of anti-C1q as antigens and selected anti-idiotypic scFv antibodies from the phage library “Griffin.1”. The monoclonal scFv A1 was the most potent inhibitor of the recognition of C1q and its fragments ghA, ghB and ghC, comprising the globular domain gC1q, by the lupus autoantibodies. It was sequenced and in silico folded by molecular dynamics into a 3D structure. The generated 3D model of A1 elucidated CDR similarity to the apical region of gC1q, thus mapping indirectly for the first time a globular autoepitope of C1q. The VH CDR2 of A1 mimicked the ghA sequence GSEAD suggested as a cross-epitope between anti-DNA and anti-C1q antibodies. Other potential inhibitors of the recognition of C1q by the LN autoantibodies among the selected recombinant antibodies were the monoclonal scFv F6, F9 and A12.

Homology Modeling of Mus Musculus CDK5 and Molecular Docking Studies with Flavonoids

2017 ◽  
Vol 9 (6) ◽  
Author(s):  
Sowmya Suri ◽  
Rumana Waseem ◽  
Seshagiri Bandi ◽  
Sania Shaik
Keyword(s):  
Molecular Docking ◽  
3D Model ◽  
Structural Features ◽  
Docking Studies ◽  
Amino Acid Residues ◽  
Cyclin Dependent Kinase ◽  
Ligand Complex ◽  
Ligand Interaction ◽  
Molecular Docking Studies ◽  
Cyclin Dependent Kinase 5

A 3D model of Cyclin-dependent kinase 5 (CDK5) (Accession Number: Q543f6) is generated based on crystal structure of P. falciparum PFPK5-indirubin-5-sulphonate ligand complex (PDB ID: 1V0O) at 2.30 Å resolution was used as template. Protein-ligand interaction studies were performed with flavonoids to explore structural features and binding mechanism of flavonoids as CDK5 (Cyclin-dependent kinase 5) inhibitors. The modelled structure was selected on the basis of least modeler objective function. The model was validated by PROCHECK. The predicted 3D model is reliable with 93.0% of amino acid residues in core region of the Ramachandran plot. Molecular docking studies with flavonoids viz., Diosmetin, Eriodictyol, Fortuneletin, Apigenin, Ayanin, Baicalein, Chrysoeriol and Chrysosplenol-D with modelled protein indicate that Diosmetin is the best inhibitor containing docking score of -8.23 kcal/mol. Cys83, Lys89, Asp84. The compound Diosmetin shows interactions with Cys83, Lys89, and Asp84.

Experimental and numerical investigations on novel models for mechanical behaviors of the elastic ring in aero-engine

2021 ◽  
pp. 095440622110130
Author(s):  
Zhong Luo ◽  
Lei Li ◽  
Yang Yang ◽  
Xiaojie Hou ◽  
Jiaxi Liu ◽  
...  
Keyword(s):  
3D Model ◽  
Maximum Stress ◽  
Simple Structure ◽  
Experimental Testing ◽  
Axial Direction ◽  
Elastic Ring ◽  
Load Range ◽  
Aero Engine ◽  
Stiffness Characteristics ◽  
First Time

The elastic ring is widely used in elastic support structures of aero-engine because of its simple structure and convenient manufacturing. In this paper, two elastic ring models, 3D and 2D models, are proposed, where the fillets between the bulges and ring are considered. The 2D model is more efficient for the calculation of stiffness characteristics. The 3D model can be used to obtain the maximum stress position in the axial direction. Then the experimental testing is carried out to verify the accuracy and effectiveness of the proposed models. Based on the proposed models, the stiffness nonlinearity and critical load of the elastic ring are found for the first time, which can be used to determine the normal working load range. Moreover, the elastic ring models with and without fillets are developed, and the effect of the fillets on stress is discussed. The results show that the stress is reduced by considering the fillets, which are not considered in the existing literature.

scholarly journals Modeling and Molecular Dynamics of the 3D Structure of the HPV16 E7 Protein and Its Variants

2021 ◽  
Vol 22 (3) ◽  
pp. 1400
Author(s):  
Ciresthel Bello-Rios ◽  
Sarita Montaño ◽  
Olga Lilia Garibay-Cerdenares ◽  
Lilian Esmeralda Araujo-Arcos ◽  
Marco Antonio Leyva-Vázquez ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
3D Structure ◽  
Epidemiological Studies ◽  
Dynamics Simulation ◽  
Structural Refinement ◽  
Oncogenic Potential ◽  
Structural Differences ◽  
Reference Protein ◽  
E6 And E7 ◽  
First Time

The oncogenic potential of high-risk human papillomavirus (HPV) is predicated on the production of the E6 and E7 oncoproteins, which are responsible for disrupting the control of the cell cycle. Epidemiological studies have proposed that the presence of the N29S and H51N variants of the HPV16 E7 protein is significantly associated with cervical cancer. It has been suggested that changes in the amino acid sequence of E7 variants may affect the oncoprotein 3D structure; however, this remains uncertain. An analysis of the structural differences of the HPV16 E7 protein and its variants (N29S and H51N) was performed through homology modeling and structural refinement by molecular dynamics simulation. We propose, for the first time, a 3D structure of the E7 reference protein and two of Its variants (N29S and H51N), and conclude that the mutations induced by the variants in N29S and H51N have a significant influence on the 3D structure of the E7 protein of HPV16, which could be related to the oncogenic capacity of this protein.

Sequence analysis, structure prediction of receptor proteins and In silico study of potential inhibitors for management of life threatening COVID-19

2021 ◽  
Vol 18 ◽  
Author(s):  
Hriday K. Basak ◽  
Soumen Saha ◽  
Joydeep Ghosh ◽  
Uttam Paswan ◽  
Sujoy Karmakar ◽  
...  
Keyword(s):  
Binding Site ◽  
Ursolic Acid ◽  
Density Functional ◽  
Actinomycin D ◽  
3D Structure ◽  
Natural Compounds ◽  
Surface Glycoprotein ◽  
Basis Set ◽  
3D Structures ◽  
Potential Inhibitors

Background: Treatment of the Covid-19 pandemic caused by the highly contagious and pathogenic SARS-CoV-2 is a global menace. Day by day this pandemic is getting worse. Doctors, Scientists and Researchers across the world are urgently scrambling for a cure for novel corona virus and continuously working at break neck speed to develop vaccine or drugs. But to date, there are no specific drugs or vaccine available in the market to cope up the virus. Objective: The present study helps us to elucidate 3D structures of SARS-CoV-2 proteins and also to identify best natural compounds as potential inhibitors against COVID-19. Methods: The 3D structures of the proteins were constructed using Modeller 9.16 modeling tool. Modelled proteins were validated with PROCHECK by Ramachandran plot analysis. In this study a small library of natural compounds (fifty compounds) was docked to the ACE2 binding site of the modelled surface glycoprotein of SARS-CoV-2 using Auto Dock Vina to repurpose these inhibitors for SARS-CoV-2. Conceptual density functional theory calculations of best eight compounds had been performed by Gaussian-09. Geometry optimizations for these molecules were done at M06-2X/ def2-TZVP level of theory. ADME parameters, pharmacokinetic properties and drug likeliness of the compounds were analyzed in the swissADME website. Results: In this study we analysed the sequences of surface glycoprotein, nucleocapsid phosphoprotein and envelope protein obtained from different parts of the globe. We have modelled all the different sequences of surface glycoprotein and envelop protein in order to derive 3D structure of a molecular target which is essential for the development of therapeutics. Different electronic properties of the inhibitors have been calculated using DFT through M06-2X functional with def2-TZVP basis set. Docking result at the hACE2 binding site of all modelled surface glycoproteins of SARS-CoV-2 showed that all the eight inhibitors (Actinomycin D, avellanin C, ichangin, kanglemycin A, obacunone, ursolic acid, ansamiotocin P-3 and isomitomycin A) studied here many folds better compared to hydroxychloroquine which has been found to be effective to treat patients suffering fromCOVID-19 pandemic. All the inhibitors meet most of criteria of drug likeness assessment. Conclusion: We will expect that eight compounds (Actinomycin D, avellanin C, ichangin, kanglemycin A, obacunone, ursolic acid, ansamiotocin P-3 and isomitomycin A) can be used as potential inhibitors against SARS-CoV-2.

scholarly journals Description of the larva of Bromeliagrion rehni (Odonata: Coenagrionidae) with bionomic notes concerning its phytotelmic habitat in central Amazonas, Brazil

2008 ◽  
Vol 25 (3) ◽  
pp. 479-486 ◽  
Author(s):  
Sharlene R. da S. Torreias ◽  
Ulisses G. Neiss ◽  
Neusa Hamada ◽  
Ruth L. Ferreira-Keppler ◽  
Frederico A.A. Lencioni
Keyword(s):  
Rainy Season ◽  
Environmental Parameters ◽  
Dry Season ◽  
Stage Larva ◽  
Water Volume ◽  
Apical Region ◽  
Last Stage ◽  
First Time ◽  
The Relationship

The last-stage larva of Bromeliagrion rehni Garrison in De Marmels & Garrison, 2005 is described and illustrated and bionomics and habitat information on this species are provided. The study was conducted in the Reserva Florestal Adolpho Ducke, located near Manaus, state of Amazonas, Brazil.Twelve samplings were done between April, 2003 and April, 2005: six in the rainy season and six in the dry season. In each sampling month, 12 bromeliads (Guzmania brasiliensis Ule, 1907, Bromeliaceae) were collected, six of which were terrestrial and six epiphytic, yielding144 samples. A total of 75 specimens of B. rehni were collected. The relationship between larval B. rehni abundance and the measured environmental parameters (volume (ml), pH, season and stratum) was significant (ANCOVA, F = 5.296, d.f. = 130, p < 0.001). Larvae were most abundant in the rainy season (p < 0.01) and water volume was positively related to the abundance of B. rehni. Larvae of B. rehni can be distinguished from those of B. fernandezianum (the only species in the genus with described larvae) by the number of setae in the prementum and by the color of the apical region of the femur. The association of this species with phytotelmata of G. brasiliensis is reported here for the first time.

How Crystals Form from a Cloud of Atoms

2011 ◽  
Vol 675-677 ◽  
pp. 3-7
Author(s):  
Peter Häussler ◽  
Martin Stiehler
Keyword(s):  
Structure Formation ◽  
Fundamental Equation ◽  
Structural Features ◽  
Local Order ◽  
Total System ◽  
Angular Momenta ◽  
General Dynamics ◽  
Bloch’S Theorem ◽  
The Given ◽  
First Time

Structure formation, the condensation of a cloud of atoms to a crystal is still not well understood. Disordered sytems (amorphous/liquid) should be in the center of this research, they are the precursors of any crystal. We consider elementary systems, as well as binary, or ternary amorphous alloys, irrespective whether they are metallically, covalently or ionically bonded and describe the process of structure formation in the formal language of thermodynamics but, as far as we know for the first time, by an extended version (general dynamics), based on the complete Gibbs fundamental equation, applied to internal subsystems. Major structural features evolve from global resonances between formerly independent internal subsystems by exchanging momenta and angular momenta, both accompanied by energy. By this they adjust mutually their internal features and create spherical-periodic structural order at medium-range distances. Under the given external constraints the resonances get optimized by selforganization. Global resonances of the type considered have clearly to be distinguished from local resonances between individual ions (described by quantum chemistry) forming local order. The global resonances cause anti-bonding (non-equilibrium) as well as bonding (equilibrium) states of the coupled total system, occupying the latter to form new structurally extended order. The transition to equilibrium creates entropy which itself leaves the system together with energy. At resonance the energetical splitting between the bonding and anti-bonding state is largest, the creation of entropy and the decrease of the total energy therefore, too. The crystal, finally, evolves by additionally optimizing a resonance based on angular momentum, and the additional adjustments of the local resonances to the global ones, theoretically done by applying Bloch’s theorem.

scholarly journals UNDERWATER PHOTOGRAMMETRY DIGITAL SURFACE MODEL (DSM) OF THE SUBMERGED SITE OF THE ANCIENT LIGHTHOUSE NEAR QAITBAY FORT IN ALEXANDRIA, EGYPT

2019 ◽  
Vol XLII-2/W10 ◽  
pp. 1-8 ◽  
Author(s):  
M. Abdelaziz ◽  
M. Elsayed
Keyword(s):  
3D Model ◽  
Low Cost ◽  
Data Gathering ◽  
Archaeological Site ◽  
3D Models ◽  
Surface Model ◽  
Digital Surface Model ◽  
Architectural Elements ◽  
3D Photogrammetry ◽  
First Time

<p><strong>Abstract.</strong> Underwater photogrammetry in archaeology in Egypt is a completely new experience applied for the first time on the submerged archaeological site of the lighthouse of Alexandria situated on the eastern extremity of the ancient island of Pharos at the foot of Qaitbay Fort at a depth of 2 to 9 metres. In 2009/2010, the CEAlex launched a 3D photogrammetry data-gathering programme for the virtual reassembly of broken artefacts. In 2013 and the beginning of 2014, with the support of the Honor Frost Foundation, methods were developed and refined to acquire manual photographic data of the entire underwater site of Qaitbay using a DSLR camera, simple and low cost materials to obtain a digital surface model (DSM) of the submerged site of the lighthouse, and also to create 3D models of the objects themselves, such as statues, bases of statues and architectural elements. In this paper we present the methodology used for underwater data acquisition, data processing and modelling in order to generate a DSM of the submerged site of Alexandria’s ancient lighthouse. Until 2016, only about 7200&amp;thinsp;m<sup>2</sup> of the submerged site, which exceeds more than 13000&amp;thinsp;m<sup>2</sup>, was covered. One of our main objectives in this project is to georeference the site since this would allow for a very precise 3D model and for correcting the orientation of the site as regards the real-world space.</p>

scholarly journals Earthquake-induced debris flows at Popocatépetl Volcano, Mexico

2020 ◽  
Author(s):  
Velio Coviello ◽  
Lucia Capra ◽  
Gianluca Norini ◽  
Norma Dávila ◽  
Dolores Ferrés ◽  
...  
Keyword(s):  
Debris Flows ◽  
Horizontal Stress ◽  
Structural Features ◽  
Volcanic Edifice ◽  
Western Slope ◽  
Slope Failures ◽  
Ground Shaking ◽  
Seismic Records ◽  
Maximum Horizontal Stress ◽  
First Time

Abstract. The M7.1 Puebla-Morelos earthquake that occurred on 19 September 2017, with epicenter located ∼ 70 km SW from Popocatépetl volcano, severely hit central Mexico. Seismic shaking of the volcanic edifice induced by the earthquake triggered hundreds of shallow landslides on the volcanic flanks, remobilizing loose pyroclastic deposits and saturated soils. The largest landslides occurred on the slopes of aligned ENE-WSW-trending ravines on opposite sides of the volcanic cone, roughly parallel to the regional maximum horizontal stress and local volcanotectonic structural features. This configuration may suggest transient reactivation of local faults and extensional fractures as one of the mechanisms that has weakened the volcanic edifice and promoted the largest slope failures. The seismic records from a broadband station located at few kilometers from the main landslides are used to infer the intensity of ground shaking that triggered the slope failures. The material involved in the larger landslides, mainly ash and pumice fall deposits from late Holocene eruptions with a total volume of about 106 cubic meters, transformed into two large debris flows on the western slope of the volcano and one on its eastern side. The debris flows were highly viscous and contained abundant large woods (about 105 cubic meter). Their peculiar rheology is reconstructed by field evidences and analyzing the grain size distribution of samples from both landslide scars and deposits. This is the first time that such flows were observed at this volcano. Our work provides new insights to constrain a multi-hazard risk assessment for Popocatépetl and other continental active volcanoes.

Observations on the structure of the small intestine on foetal, neo-natal and sucklings pigs

1971 ◽  
Vol 259 (834) ◽  
pp. 517-531 ◽  
Keyword(s):  
Small Intestine ◽  
Structural Features ◽  
Surface Pattern ◽  
Apical Region ◽  
Intercellular Spaces ◽  
Large Numbers ◽  
Newborn Pigs ◽  
Dilated Intercellular Spaces ◽  
Vacuolated Cells ◽  
Newborn Animals

Light and electronmicroscopic observations of changes throughout the small intestine of foetal, and both suckled and unsuckled newborn pigs are reported. Foetal animals between 73 days gestation and term showed vacuolation in the terminal ileum. This was most extensive between 90 and 100 days when the terminal 30% of the small intestine contained vacuolated cells. The apical region of such cells contained a system of smooth tubes and vesicles, some of which showed evidence of a characteristic surface pattern. The vacuoles contained material of variable electron density and were sometimes seen apparently discharging their contents into the dilated intercellular spaces. Unsuckled newborn animals showed most of the features described above, but, in addition, the vacuolated cells contained large numbers of electron dense inclusions. In suckled animals from birth to 70 h of age there were considerable variations in cellular structure, which could be related to the position in the small intestine, the position on the villus and the age of the animal. The structural features described are discussed in relation to the transfer of colostrum immunoglobulins into the circulation. Keywords: swine, foetus, newborn, small intestine, structure.

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