Predict the Strong Binding Ability Polypeptide of Human α-Enolase with the HLA-DRB1 * 0401

2013 ◽  
Vol 380-384 ◽  
pp. 4353-4358
Author(s):  
Rui Jie ◽  
Quan Zhou ◽  
Jin Song Wang ◽  
Yun He Liang ◽  
Ting Ting Liao ◽  
...  
Keyword(s):  
Rheumatoid Arthritis ◽  
Molecular Dynamics ◽  
Mhc Class Ii ◽  
Structural Model ◽  
Three Dimensional ◽  
Prediction Method ◽  
T Cell Epitopes ◽  
Binding Ability ◽  
Strong Binding ◽  
Chain Conformations

Human α-enolase (ENO1), an evolutionarily conserved and multifunctional protein, is a target self-antigen of rheumatoid arthritis (RA). Rheumatoid arthritis (RA) is genetically associated with MHC class II molecules, such as DRB1*0101, DRB1*0401 and DRB1*0404 allele. Among these DRB1 alleles, DRB1*0401 show the most correlation with RA. However, strong binding ability polypeptide of ENO1 with HLA-DRB1*0401 is still largely unknown. In this study, we used NetMHCII prediction method to predict the strong binding ability polypeptide with HLA-DRB1*0401. Among the 434 predicted fragment peptide, ENO1129-141: PLYRHIADLAGNS showed strong binding with HLA-DR4 and peptide ENO1281-293 KSFIKDYPVVSIE is the second candidate peptide. Based on these result, we choosed EON1129-141 and EON1281-293 polypeptides to do the molecular modeling, and used the molecular dynamics to optimize the three-dimensional structural model. The molecular dynamics results showed that ENO1129-141: PLYRHIADLAGNS and ENO1281-293: KSFIKDYPVVSIE have strong binding ability with HLA-DR4* 0401. In the shared epitope, both ENO1129-141and ENO1281-293 have the very near distance 3.15Å and 3.10Å with K71 of the β1 chain. The main-chain conformations of ENO1129-141 sit more deeply with β1 chain. All together, results indicated that ENO1129-141 and ENO1281-293 bind strong with HLA-DR4 and would be potential T cell epitopes of human α-enolase that induced RA.

scholarly journals Molecular Dynamics Investigation of Phenolic Oxidative Coupling Protein Hyp-1 Derived from Hypericum perforatum

Crystals ◽  
2021 ◽  
Vol 11 (1) ◽  
pp. 43
Author(s):  
Joanna Smietanska ◽  
Tomasz Kozik ◽  
Radoslaw Strzalka ◽  
Ireneusz Buganski ◽  
Janusz Wolny
Keyword(s):  
Molecular Dynamics ◽  
Md Simulation ◽  
Hypericum Perforatum ◽  
Structural Model ◽  
Md Simulations ◽  
Atomic Displacement ◽  
Experimental Models ◽  
Coupling Protein ◽  
Atomic Displacement Parameters ◽  
Chain Conformations

Molecular dynamics (MD) simulations provide a physics-based approach to understanding protein structure and dynamics. Here, we used this intriguing tool to validate the experimental structural model of Hyp-1, a pathogenesis-related class 10 (PR-10) protein from the medicinal herb Hypericum perforatum, with potential application in various pharmaceutical therapies. A nanosecond MD simulation using the all-atom optimized potentials for liquid simulations (OPLS–AA) force field was performed to reveal that experimental atomic displacement parameters (ADPs) underestimate their values calculated from the simulation. The average structure factors obtained from the simulation confirmed to some extent the relatively high compliance of experimental and simulated Hyp-1 models. We found, however, many outliers between the experimental and simulated side-chain conformations within the Hyp-1 model, which prompted us to propose more reasonable energetically preferred rotameric forms. Therefore, we confirmed that MD simulation may be applicable for the verification of refined, experimental models and the explanation of their structural intricacies.

scholarly journals Protection of mice against experimental cryptococcosis by synthesized peptides delivered in glucan particles

2021 ◽  
Author(s):  
Charles Specht ◽  
E. Jane Homan ◽  
Chrono K Lee ◽  
Zhongming Mou ◽  
Christina L Gomez ◽  
...  
Keyword(s):  
Mhc Class Ii ◽  
Peptide Sequence ◽  
T Cell Epitopes ◽  
Binding Region ◽  
Chitin Deacetylase ◽  
Lethal Challenge ◽  
Amino Acid Peptide ◽  
Mhc Ii ◽  
Strong Binding ◽  
Experimental Cryptococcosis

The high global burden of cryptococcosis has made development of a protective vaccine a public health priority. We previously demonstrated that a vaccine composed of recombinant Cryptococcus neoformans chitin deacetylase 2 (Cda2) delivered in glucan particles (GPs) protects BALB/c and C57BL/6 mice from an otherwise lethal challenge with a highly virulent C. neoformans strain. An immunoinformatic analysis of Cda2 revealed a peptide sequence predicted to have strong binding to the MHC Class II (MHC II) H2-IAd allele found in BALB/c mice. BALB/c mice vaccinated with GPs containing a 32 amino acid peptide (Cda2-Pep1) that included this strong binding region were protected from cryptococcosis. Protection was lost with GP-based vaccines containing versions of recombinant Cda2 protein and Cda2-Pep1 with mutations predicted to greatly diminish MHC II binding. Cda2 has homology to the three other C. neoformans chitin deacetylases, Cda1, Cda3 and Fpd1, in the high MHC II binding region. GPs loaded with homologous peptides of Cda1, Cda3 and Fpd1 protected BALB/c mice from experimental cryptococcosis, albeit not as robustly as the Cda2-Pep1 vaccine. Finally, seven other peptides were synthesized based on regions in Cda2 predicted to contain promising CD4+ T cell epitopes in BALB/c or C57BL/6 mice. While five peptide vaccines significantly protected BALB/c mice, only one protected C57BL/6 mice. Thus, GP-based vaccines containing a single peptide can protect mice against cryptococcosis. However, given the diversity of human MHC II alleles, a peptide-based Cryptococcus vaccine for use in humans would be challenging and likely need to contain multiple peptide sequences.

Structural Characteristics of Human Salivary Statherin: A Model for Boundary Lubrication at the Enamel Surface

1993 ◽  
Vol 4 (3) ◽  
pp. 363-370 ◽  
Author(s):  
Narayanan Ramasubbu ◽  
Leonard M. Thomas ◽  
Krishna K. Bhandary ◽  
Michael J. Levine
Keyword(s):  
Boundary Lubrication ◽  
Structure Prediction ◽  
Structural Model ◽  
Structural Characteristics ◽  
Three Dimensional ◽  
Structural Features ◽  
Enamel Surface ◽  
Binding Region ◽  
Binding Ability ◽  
Oriented Aggregation

A three-dimensional structural model for salivary statherin in aqueous phase has been developed using structure prediction, circular dichroism, molecular modeling, and mechanics. The relevant structural features of statherin are N-terminal helix segment connected to a long poly-L-proline type II segment, which is followed by a short extended structure. Using this model, the hydroxyapatite binding ability of statherin has been explained. The hydroxyapatite binding region is comprised of the N-terminal acidic residues (Asp-pSer-pSer-Glu-Glu) and Glu-26, which are clustered together in space. Partial conformational unfolding and oriented aggregation of several statherin molecules at the enamel surface provides an amphipathic film that is responsible for the boundary lubrication exhibited by statherin.

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.

scholarly journals A Numerical Study of Sub-Millisecond Integrated Mix-and-Inject Microfluidic Devices for Sample Delivery at Synchrotron and XFELs

2021 ◽  
Vol 11 (8) ◽  
pp. 3404
Author(s):  
Majid Hejazian ◽  
Eugeniu Balaur ◽  
Brian Abbey
Keyword(s):  
Molecular Dynamics ◽  
Flow Rate ◽  
Numerical Study ◽  
Three Dimensional ◽  
Microfluidic Devices ◽  
Liquid Jets ◽  
Mixing Efficiency ◽  
X Ray Diffraction ◽  
Cross Sectional ◽  
Time Required

Microfluidic devices which integrate both rapid mixing and liquid jetting for sample delivery are an emerging solution for studying molecular dynamics via X-ray diffraction. Here we use finite element modelling to investigate the efficiency and time-resolution achievable using microfluidic mixers within the parameter range required for producing stable liquid jets. Three-dimensional simulations, validated by experimental data, are used to determine the velocity and concentration distribution within these devices. The results show that by adopting a serpentine geometry, it is possible to induce chaotic mixing, which effectively reduces the time required to achieve a homogeneous mixture for sample delivery. Further, we investigate the effect of flow rate and the mixer microchannel size on the mixing efficiency and minimum time required for complete mixing of the two solutions whilst maintaining a stable jet. In general, we find that the smaller the cross-sectional area of the mixer microchannel, the shorter the time needed to achieve homogeneous mixing for a given flow rate. The results of these simulations will form the basis for optimised designs enabling the study of molecular dynamics occurring on millisecond timescales using integrated mix-and-inject microfluidic devices.

Color Reproduction Accuracy Promotion of 3D-Printed Surfaces Based on Microscopic Image Analysis

2019 ◽  
Vol 34 (01) ◽  
pp. 2054004 ◽  
Author(s):  
Xiaochun Wang ◽  
Chen Chen ◽  
Jiangping Yuan ◽  
Guangxue Chen
Keyword(s):  
Surface Roughness ◽  
Image Analysis ◽  
Three Dimensional ◽  
Prediction Method ◽  
Chromatic Aberration ◽  
Optimization Methods ◽  
Experimental Models ◽  
Microscopic Image ◽  
Color Reproduction ◽  
Microscopic Image Analysis

Full-color three-dimensional (3D) printing technology is a powerful process to manufacture intelligent customized colorful objects with improved surface qualities; however, poor surface color optimization methods are the main impeding factors for its commercialization. As such, the paper explored the correlation between microstructure and color reproduction, then an assessment and prediction method of color optimization based on microscopic image analysis was proposed. The experimental models were divided into 24-color plates and 4-color cubes printed by ProJet 860 3D printer, then impregnated according to preset parameters, at last measured by a spectrophotometer and observed using both a digital microscope and a scanning electron microscope. The results revealed that the samples manifested higher saturation and smaller chromatic aberration ([Formula: see text]) after postprocessing. Moreover, the brightness of the same color surface increased with the increasing soaked surface roughness. Further, reduction in surface roughness, impregnation into surface pores, and enhancement of coating transparency effectively improved the accuracy of color reproduction, which could be verified by the measured values. Finally, the chromatic aberration caused by positioning errors on different faces of the samples was optimized, and the value of [Formula: see text] for a black cube was reduced from 8.12 to 0.82, which is undetectable to human eyes.

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