Molecular dynamics simulations of a double unit cell in a protein crystal: Volume relaxation at constant pressure and correlation of motions between the two unit cells

2002 ◽  
Vol 48 (2) ◽  
pp. 327-340 ◽  
Author(s):  
Regula Walser ◽  
Philippe H. Hünenberger ◽  
Wilfred F. van Gunsteren
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Constant Pressure ◽  
Unit Cell ◽  
Protein Crystal ◽  
Volume Relaxation ◽  
Unit Cells ◽  
Dynamics Simulations ◽  
Crystal Volume

scholarly journals 4094 Structural Determinants of Immunogenicity for Peptide-Based Immunotherapy

2020 ◽  
Vol 4 (s1) ◽  
pp. 16-16
Author(s):  
Jason Devlin ◽  
Jesus Alonso ◽  
Grant Keller ◽  
Sara Bobisse ◽  
Alexandre Harari ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
T Cell ◽  
Molecular Dynamics Simulations ◽  
Crystal Structures ◽  
T Cell Receptor ◽  
Tumor Regression ◽  
Recombinant Expression ◽  
Cell Receptor ◽  
Protein Crystal ◽  
Dynamics Simulations

OBJECTIVES/GOALS: Neoantigen vaccine immunotherapies have shown promise in clinical trials, but identifying which peptides to include in a vaccine remains a challenge. We aim to establish that molecular structural features can help predict which neoantigens to target to achieve tumor regression. METHODS/STUDY POPULATION: Proteins were prepared by recombinant expression in E. coli followed by in vitro refolding. Correctly folded proteins were purified by chromatography. Affinities of protein-protein interactions were measured by surface plasmon resonance (SPR) and thermal stabilities of proteins were determined by differential scanning fluorimetry. All experiments were performed at least in triplicate. Protein crystals were obtained by hanging drop vapor diffusion. The protein crystal structures were solved by molecular replacement and underwent several rounds of automated refinement. Molecular dynamics simulations were performed using the AMBER molecular dynamics package. RESULTS/ANTICIPATED RESULTS: A T cell receptor (TCR) expressed by tumor-infiltrating T cells exhibited a 20-fold stronger binding affinity to the neoantigen peptide compared to the self-peptide. X-ray crystal structures of the peptides with the major histocompatibility complex (MHC) protein demonstrated that a non-mutated residue in the peptide samples different positions with the mutation. The difference in conformations of the non-mutated residue was supported by molecular dynamics simulations. Crystal structures of the TCR engaging both peptide/MHCs suggested that the conformation favored by the mutant peptide was crucial for TCR binding. The TCR bound the neoantigen/MHC with faster binding kinetics. DISCUSSION/SIGNIFICANCE OF IMPACT: Our results suggest that the mutation impacts the conformation of another residue in the peptide, and this alteration allows for more favorable T cell receptor binding to the neoantigen. This highlights the potential of non-mutated residues in contributing to neoantigen recognition.

Molecular Dynamics Simulations of Low-Energy Ion/Surface Interactions During Vapor Phase Crystal Growth: 10 eV Si Incident on Si(001)2×1

1989 ◽  
Vol 157 ◽  
Author(s):  
M. Kitabatake ◽  
P. Fons ◽  
J. E. Greene
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Unit Cell ◽  
Many Body ◽  
Energy Redistribution ◽  
Surface Unit ◽  
Phase Crystal ◽  
Dynamics Simulations ◽  
Body Potential ◽  
Surface Unit Cell

ABSTRACTMolecular dynamics simulations, utilizing the Tersoff many-body potential, were used to investigate the effects of 10 eV Si atom bombardment of a (001)2×1 terminated Si lattice. The irradiation events were initiated at an array of points in the primitive surface unit cell. Each event was followed to determine kinetic energy redistribution in the lattice as a function of time, projectile and lattice atom trajectories, and the nature, number, and depth of residual defects. Dimer breaking, epitaxial growth, position exchange, and the formation of residual hexagonal and split interstitials were observed. There were no residual vacancies. Impact points leading to each of the above results clustered in distinctly different regions of the surface unit cell. Bulk interstitials were annealed out over time scales corresponding to monolayer deposition during Si MBE.

scholarly journals Microfocus diffraction from different regions of a protein crystal: structural variations and unit-cell polymorphism

2018 ◽  
Vol 74 (5) ◽  
pp. 411-421 ◽  
Author(s):  
Michael C. Thompson ◽  
Duilio Cascio ◽  
Todd O. Yeates
Keyword(s):  
Principal Component ◽  
Unit Cell ◽  
Protein Crystal ◽  
Data Sets ◽  
Structural Variations ◽  
Data Set ◽  
X Ray ◽  
Unit Cells ◽  
Factor Data ◽  
Dynamics Simulations

Real macromolecular crystals can be non-ideal in a myriad of ways. This often creates challenges for structure determination, while also offering opportunities for greater insight into the crystalline state and the dynamic behavior of macromolecules. To evaluate whether different parts of a single crystal of a dynamic protein, EutL, might be informative about crystal and protein polymorphism, a microfocus X-ray synchrotron beam was used to collect a series of 18 separate data sets from non-overlapping regions of the same crystal specimen. A principal component analysis (PCA) approach was employed to compare the structure factors and unit cells across the data sets, and it was found that the 18 data sets separated into two distinct groups, with largeRvalues (in the 40% range) and significant unit-cell variations between the members of the two groups. This categorization mapped the different data-set types to distinct regions of the crystal specimen. Atomic models of EutL were then refined against two different data sets obtained by separately merging data from the two distinct groups. A comparison of the two resulting models revealed minor but discernable differences in certain segments of the protein structure, and regions of higher deviation were found to correlate with regions where larger dynamic motions were predicted to occur by normal-mode molecular-dynamics simulations. The findings emphasize that large spatially dependent variations may be present across individual macromolecular crystals. This information can be uncovered by simultaneous analysis of multiple partial data sets and can be exploited to reveal new insights about protein dynamics, while also improving the accuracy of the structure-factor data ultimately obtained in X-ray diffraction experiments.

Novel molecular dynamics simulations at constant pressure

1992 ◽  
Vol 75 (3) ◽  
pp. 669-688 ◽  
Author(s):  
R.G. Winkler ◽  
H. Morawitz ◽  
D.Y. Yoon
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Constant Pressure ◽  
Dynamics Simulations
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