scholarly journals Immunoinformatics-Based Designing of a Multi-Epitope Chimeric Vaccine From Multi-Domain Outer Surface Antigens of Leptospira

2021 ◽  
Vol 12 ◽  
Author(s):  
Pankaj Kumar ◽  
Surabhi Lata ◽  
Umate Nachiket Shankar ◽  
Mohd. Akif
Keyword(s):  
Outer Surface ◽  
Cytotoxic T Lymphocyte ◽  
Three Dimensional ◽  
Dynamics Simulation ◽  
Effective Vaccine ◽  
Accurate Information ◽  
Cell Mediated Immunity ◽  
Heparin Binding ◽  
The Stability ◽  
Chimeric Vaccine

Accurate information on antigenic epitopes within a multi-domain antigen would provide insights into vaccine design and immunotherapy. The multi-domain outer surface Leptospira immunoglobulin-like (Lig) proteins LigA and LigB, consisting of 12–13 homologous bacterial Ig (Big)-like domains, are potential antigens of Leptospira interrogans. Currently, no effective vaccine is available against pathogenic Leptospira. Both the humoral immunity and cell-mediated immunity of the host play critical roles in defending against Leptospira infection. Here, we used immunoinformatics approaches to evaluate antigenic B-cell lymphocyte (BCL) and cytotoxic T-lymphocyte (CTL) epitopes from Lig proteins. Based on certain crucial parameters, potential epitopes that can stimulate both types of adaptive immune responses were selected to design a chimeric vaccine construct. Additionally, an adjuvant, the mycobacterial heparin-binding hemagglutinin adhesin (HBHA), was incorporated into the final multi-epitope vaccine construct with a suitable linker. The final construct was further scored for its antigenicity, allergenicity, and physicochemical parameters. A three-dimensional (3D) modeled construct of the vaccine was implied to interact with Toll-like receptor 4 (TLR4) using molecular docking. The stability of the vaccine construct with TLR4 was predicted with molecular dynamics simulation. Our results demonstrate the application of immunoinformatics and structure biology strategies to develop an epitope-specific chimeric vaccine from multi-domain proteins. The current findings will be useful for future experimental validation to ratify the immunogenicity of the chimera.

scholarly journals Structural Analysis of Avian Encephalomyelitis Virus Polyprotein for Development of Multi Epitopes Vaccine Using Immunoinformatics Approach

2021 ◽  
Vol 15 (1) ◽  
pp. 262-278
Author(s):  
Fatima Khalid Elhassan ◽  
Yassir A. Almofti ◽  
Khoubieb Ali Abd-elrahman ◽  
Mashair AA Nouri ◽  
Elsideeq EM Eltilib
Keyword(s):  
T Cells ◽  
Disulfide Bonds ◽  
Tertiary Structure ◽  
High Mobility ◽  
Dynamics Simulation ◽  
High Morbidity ◽  
E Coli ◽  
Encephalomyelitis Virus ◽  
The Stability ◽  
Chimeric Vaccine

Avian Encephalomyelitis (AE) is the disease caused by avian encephalomyelitis virus (AEV). The disease mainly affects young birds nervous system worldwide causing high morbidity and variable mortality rate in chicks and noticed egg dropping and hatchability in mature hens. Vaccination is the only way to control AEV infection since there is no treatment yet to the avian encephalomyelitis. This study aimed to use immunoinformatics approaches to predict multi epitopes vaccine from the AEV polyprotein that could elicit both B and T cells. The vaccine construct comprises 482 amino acids obtained from epitopes predicted against B and T cells by IEDB server, adjuvant, linkers and 6-His-tag. The chimeric vaccine was potentially antigenic and nonallergic and demonstrated thermostability and hydrophilicity in protparam server. The solubility of the vaccine was measured in comparison to E. coli proteins. The stability was also assessed by disulfide bonds engineering to reduce the high mobility regions in the designed vaccine. Furthermore molecular dynamics simulation further strengthen stability of the predicted vaccine. Tertiary structure of the vaccine construct after prediction, refinement was used for molecular docking with chicken alleles BF2*2101 and BF2*0401 and the docking process demonstrated favourable binding energy score of -337.47 kcal/mol and -326.87 kcal/mol, respectively. Molecular cloning demonstrated the potential clonability of the chimeric vaccine in pET28a(+) vector. This could guarantee the efficient translation and expression of the vaccine within suitable expression vector.

scholarly journals Immunoinformatic based identification of cytotoxic T lymphocyte epitopes from the Indian isolate of SARS-CoV-2

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Viswajit Mulpuru ◽  
Nidhi Mishra
Keyword(s):  
T Lymphocyte ◽  
Cytotoxic T Lymphocyte ◽  
Human Leukocyte ◽  
Docking Studies ◽  
Indian Isolate ◽  
Dynamics Simulation ◽  
Effective Vaccine ◽  
Ctl Epitopes ◽  
Hla System ◽  
Epitope Candidate

AbstractThe Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has turned into a pandemic with about thirty million confirmed cases worldwide as of September 2020. Being an airborne infection, it can be catastrophic to populous countries like India. This study sets to identify potential cytotoxic T lymphocyte (CTL) epitopes in the SARS-CoV-2 Indian isolate which can act as an effective vaccine epitope candidate for the majority of the Indian population. The immunogenicity and the foreignness of the epitopes towards the human body have to be studied to further confirm their candidacy. The top-scoring epitopes were subjected to molecular docking studies to study their interactions with the corresponding human leukocyte antigen (HLA) system. The CTL epitopes were observed to bind at the peptide-binding groove of the corresponding HLA system, indicating their potency as an epitope candidate. The candidacy was further analyzed using sequence conservation studies and molecular dynamics simulation. The identified epitopes can be subjected to further studies for the development of the SARS-CoV-2 vaccine.

scholarly journals Structure elucidation and docking analysis of 5M mutant of T1 lipase Geobacillus zalihae

PLoS ONE ◽  
2021 ◽  
Vol 16 (6) ◽  
pp. e0251751
Author(s):  
Siti Nor Hasmah Ishak ◽  
Nor Hafizah Ahmad Kamarudin ◽  
Mohd Shukuri Mohamad Ali ◽  
Adam Thean Chor Leow ◽  
Fairolniza Mohd Shariff ◽  
...  
Keyword(s):  
Amino Acids ◽  
Hydrogen Bonds ◽  
Three Dimensional ◽  
Substrate Preference ◽  
Dynamics Simulation ◽  
Dimensional Structure ◽  
Docking Analysis ◽  
Three Dimensional Structure ◽  
Ion Interactions ◽  
The Stability

5M mutant lipase was derived through cumulative mutagenesis of amino acid residues (D43E/T118N/E226D/E250L/N304E) of T1 lipase from Geobacillus zalihae. A previous study revealed that cumulative mutations in 5M mutant lipase resulted in decreased thermostability compared to wild-type T1 lipase. Multiple amino acids substitution might cause structural destabilization due to negative cooperation. Hence, the three-dimensional structure of 5M mutant lipase was elucidated to determine the evolution in structural elements caused by amino acids substitution. A suitable crystal for X-ray diffraction was obtained from an optimized formulation containing 0.5 M sodium cacodylate trihydrate, 0.4 M sodium citrate tribasic pH 6.4 and 0.2 M sodium chloride with 2.5 mg/mL protein concentration. The three-dimensional structure of 5M mutant lipase was solved at 2.64 Å with two molecules per asymmetric unit. The detailed analysis of the structure revealed that there was a decrease in the number of molecular interactions, including hydrogen bonds and ion interactions, which are important in maintaining the stability of lipase. This study facilitates understanding of and highlights the importance of hydrogen bonds and ion interactions towards protein stability. Substrate specificity and docking analysis on the open structure of 5M mutant lipase revealed changes in substrate preference. The molecular dynamics simulation of 5M-substrates complexes validated the substrate preference of 5M lipase towards long-chain p-nitrophenyl–esters.

Computational Fluid Dynamics Simulation of a Single-Phase Rectangular Thermosiphon

2020 ◽  
Author(s):  
Tri Nguyen ◽  
Elia Merzari
Keyword(s):  
Single Phase ◽  
Fluid Dynamic ◽  
Three Dimensional ◽  
Heat Removal ◽  
Spectral Element ◽  
Dynamics Simulation ◽  
Velocity Measurements ◽  
Buoyancy Driven Flows ◽  
The Stability ◽  
Flow Reversals

Abstract Buoyancy-driven flows are widespread in diverse engineering applications. Such flows have been studied in great detail theoretically, experimentally, and numerically. However, the fluid-dynamic instabilities and flow reversals of thermosiphon are still actively investigated. The presence of such instabilities limits the effectiveness of such devices for decay heat removal. Traditionally the stability analysis of natural convection loops has been confined to one-dimensional calculations, on the argument that the flow would be mono-dimensional when the ratio between the radius of the loop and the radius of the pipe is much larger than 1. Nevertheless, accurate velocity measurements of the flow in toroidal loops have shown that the flow presents three-dimensional effects. Previous works of the authors have shown that these structures can be seen in thermosiphons. In this paper, we aim to use modern CFD methods to investigate the three-dimensional flow in thermosiphons. This paper focuses on rectangular thermosiphons. In particular, we perform a series of high-fidelity simulations using the spectral element code Nek5000 to investigate the stability behavior of the flow in a rectangular thermosiphon. We compare the results with available existing experimental data from the L2 facility in Genoa. We examine in detail the flow structures generated. Moreover, in the past various authors have demonstrated that the overall behavior of the thermosiphon depends strongly on the boundary conditions (BCs). The simulation campaign was carried out with different BCs to investigate and confirm this effect. In particular, simulations with Dirichlet, Neumann and Robin BCs for heater and sink were performed.

scholarly journals Multivalent Display of SARS-CoV-2 Spike (RBD Domain) of COVID-19 to Nanomaterial, Protein Ferritin Nanocages

Biomolecules ◽  
2021 ◽  
Vol 11 (2) ◽  
pp. 297
Author(s):  
Umesh Kalathiya ◽  
Monikaben Padariya ◽  
Robin Fahraeus ◽  
Soumyananda Chakraborti ◽  
Ted R. Hupp
Keyword(s):  
Vaccine Development ◽  
Protein A ◽  
Virus Transmission ◽  
Surface Glycoprotein ◽  
Dynamics Simulation ◽  
Spike Protein ◽  
Effective Vaccine ◽  
Protein Protein Interaction ◽  
Multivalent Display ◽  
The Stability

SARS-CoV-2, or COVID-19, has a devastating effect on our society, both in terms of quality of life and death rates; hence, there is an urgent need for developing safe and effective therapeutics against SARS-CoV-2. The most promising strategy to fight against this deadly virus is to develop an effective vaccine. Internalization of SARS-CoV-2 into the human host cell mainly occurs through the binding of the coronavirus spike protein (a trimeric surface glycoprotein) to the human angiotensin-converting enzyme 2 (ACE2) receptor. The spike-ACE2 protein–protein interaction is mediated through the receptor-binding domain (RBD) of the spike protein. Mutations in the spike RBD can significantly alter interactions with the ACE2 host receptor. Due to its important role in virus transmission, the spike RBD is considered to be one of the key molecular targets for vaccine development. In this study, a spike RBD-based subunit vaccine was designed by utilizing a ferritin protein nanocage as a scaffold. Several fusion protein constructs were designed in silico by connecting the spike RBD via a synthetic linker (different sizes) to different ferritin subunits (H-ferritin and L-ferritin). The stability and the dynamics of the engineered nanocage constructs were tested by extensive molecular dynamics simulation (MDS). Based on our MDS analysis, a five amino acid-based short linker (S-Linker) was the most effective for displaying the spike RBD over the surface of ferritin. The behavior of the spike RBD binding regions from the designed chimeric nanocages with the ACE2 receptor was highlighted. These data propose an effective multivalent synthetic nanocage, which might form the basis for new vaccine therapeutics designed against viruses such as SARS-CoV-2.

A Liquid Metal Flow Between Two Coaxial Cylinders System

2019 ◽  
Vol 11 (1) ◽  
pp. 79-86
Author(s):  
Abdelkrim Merah ◽  
Ridha Kelaiaia ◽  
Faiza Mokhtari
Keyword(s):  
Couette Flow ◽  
Metal Flow ◽  
Three Dimensional ◽  
Liquid Sodium ◽  
Taylor Vortex ◽  
Turbulent Regime ◽  
Coaxial Cylinders ◽  
Concentric Cylinders ◽  
Ideal Tool ◽  
The Stability

Abstract The Taylor-Couette flow between two rotating coaxial cylinders remains an ideal tool for understanding the mechanism of the transition from laminar to turbulent regime in rotating flow for the scientific community. We present for different Taylor numbers a set of three-dimensional numerical investigations of the stability and transition from Couette flow to Taylor vortex regime of a viscous incompressible fluid (liquid sodium) between two concentric cylinders with the inner one rotating and the outer one at rest. We seek the onset of the first instability and we compare the obtained results for different velocity rates. We calculate the corresponding Taylor number in order to show its effect on flow patterns and pressure field.

Functional characterization and structural modelling of peptidoglycan degrading β-N-acetyl-glucosaminidase from a dental isolate of Serratia marcescens

2020 ◽  
Vol 23 ◽  
Author(s):  
Aditi Rathee ◽  
Anil Panwar ◽  
Seema Kumari ◽  
Sanjay Chhibber ◽  
Ashok Kumar
Keyword(s):  
Functional Characterization ◽  
Major Change ◽  
Crystal Form ◽  
Bound State ◽  
Dynamics Simulation ◽  
Gram Positive ◽  
Structural Cell ◽  
Stability Structure ◽  
Arginine Residues ◽  
The Stability

Introduction:: Enzymatic degradation of peptidoglycan, a structural cell wall component of Gram-positive bacteria, has attracted considerable attention being a specific target for many known antibiotics. Methods:: Peptidoglycan hydrolases are involved in bacterial lysis through peptidoglycan degradation. β-N-acetylglucosaminidase, a peptidoglycan hydrolase, acts on O-glycosidic bonds formed by N-acetylglucosamine and N-acetyl muramic acid residues of peptidoglycan. Aim of present study was to study the action of β-N-acetylglucosaminidase, on methicillin- resistant Staphylococcus aureus (MRSA) and other Gram-negative bacteria. Results:: We investigated its dynamic behaviour using molecular dynamics simulation and observed that serine and alanine residues are involved in catalytic reaction in addition to aspartic acid, histidine, lysine and arginine residues. When simulated in its bound state, the RMSD values were found lesser than crystal form in the time stamp of 1000 picoseconds revealing its stability. Structure remained stably folded over 1000 picoseconds without undergoing any major change further confirming the stability of complex. Conclusion:: It can be concluded that enzymes belonging to this category can serve as a tool in eradicating Gram-positive pathogens and associated infections.

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.

scholarly journals Rational thermostabilisation of four-helix bundle dimeric de novo proteins

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Shin Irumagawa ◽  
Kaito Kobayashi ◽  
Yutaka Saito ◽  
Takeshi Miyata ◽  
Mitsuo Umetsu ◽  
...  
Keyword(s):  
Protein Design ◽  
De Novo ◽  
Protein Complexes ◽  
Salt Bridge ◽  
Dynamics Simulation ◽  
Saturation Mutagenesis ◽  
Helix Bundle ◽  
Stable Mutant ◽  
Four Helix Bundle ◽  
The Stability

AbstractThe stability of proteins is an important factor for industrial and medical applications. Improving protein stability is one of the main subjects in protein engineering. In a previous study, we improved the stability of a four-helix bundle dimeric de novo protein (WA20) by five mutations. The stabilised mutant (H26L/G28S/N34L/V71L/E78L, SUWA) showed an extremely high denaturation midpoint temperature (Tm). Although SUWA is a remarkably hyperstable protein, in protein design and engineering, it is an attractive challenge to rationally explore more stable mutants. In this study, we predicted stabilising mutations of WA20 by in silico saturation mutagenesis and molecular dynamics simulation, and experimentally confirmed three stabilising mutations of WA20 (N22A, N22E, and H86K). The stability of a double mutant (N22A/H86K, rationally optimised WA20, ROWA) was greatly improved compared with WA20 (ΔTm = 10.6 °C). The model structures suggested that N22A enhances the stability of the α-helices and N22E and H86K contribute to salt-bridge formation for protein stabilisation. These mutations were also added to SUWA and improved its Tm. Remarkably, the most stable mutant of SUWA (N22E/H86K, rationally optimised SUWA, ROSA) showed the highest Tm (129.0 °C). These new thermostable mutants will be useful as a component of protein nanobuilding blocks to construct supramolecular protein complexes.

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