scholarly journals Deformation twinning and the role of amino acids and magnesium in calcite hardness from molecular simulation

2015 ◽  
Vol 17 (31) ◽  
pp. 20178-20184 ◽  
Author(s):  
A. S. Côté ◽  
R. Darkins ◽  
D. M. Duffy
Keyword(s):  
Molecular Dynamics ◽  
Amino Acids ◽  
Molecular Simulation ◽  
Elastic Properties ◽  
Deformation Twinning ◽  
Pure Crystal ◽  
Classical Molecular Dynamics ◽  
Deformation Twins

We employ classical molecular dynamics to calculate elastic properties and to model the nucleation and propagation of deformation twins in calcite, both as a pure crystal and with magnesium and aspartate inclusions.

Deterministic role of structural flexibility on catalytic activity of conductive 2D layered metal–organic frameworks

2021 ◽  
Author(s):  
Mohammad R. Momeni ◽  
Zeyu Zhang ◽  
Farnaz A. Shakib
Keyword(s):  
Molecular Dynamics ◽  
Quantum Mechanics ◽  
Catalytic Activity ◽  
Metal Organic Frameworks ◽  
Structural Flexibility ◽  
Classical Molecular Dynamics ◽  
Structural Deformations ◽  
Metal Organic

A combined quantum mechanics and classical molecular dynamics approach is used to unravel the effects of structural deformations and heterogeneity on catalytic activity of 2D π-stacked layered metal–organic frameworks.

scholarly journals Residues within the Foot-and-Mouth Disease Virus 3Dpol Nuclear Localization Signal Affect Polymerase Fidelity

2020 ◽  
Vol 94 (17) ◽  
Author(s):  
Anna Kloc ◽  
Devendra K. Rai ◽  
Douglas P. Gladue ◽  
Elizabeth Schafer ◽  
Mary Kenney ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Amino Acids ◽  
Molecular Dynamics Simulation ◽  
Nuclear Localization ◽  
Nuclear Localization Signal ◽  
Foot And Mouth Disease ◽  
Dynamics Simulation ◽  
Mouth Disease Virus ◽  
Localization Signal

ABSTRACT Many RNA viruses encode a proof-reading deficient, low-fidelity RNA-dependent polymerase (RdRp), which generates genetically diverse populations that can adapt to changing environments and thwart antiviral therapies. 3Dpol, the RdRp of the foot-and-mouth disease virus (FMDV), is responsible for replication of viral genomes. The 3Dpol N terminus encodes a nuclear localization signal (NLS) sequence,MRKTKLAPT, important for import of the protein to host nucleus. Previous studies showed that substitutions at residues 18 and 20 of the NLS are defective in proper incorporation of nucleotides and RNA binding. Here, we use a systematic alanine scanning mutagenesis approach to understand the role of individual residues of the NLS in nuclear localization and nucleotide incorporation activities of 3Dpol. We identify two residues of 3Dpol NLS, T19 and L21, that are important for the maintenance of enzyme fidelity. The 3Dpol NLS alanine substitutions of T19 and L21 results in aberrant incorporation of nucleoside analogs, conferring a low fidelity phenotype of the enzyme. A molecular dynamics simulation of RNA- and mutagen (RTP)-bound 3Dpol revealed that the T19 residue participates in a hydrogen bond network, including D165 in motif F and R416 at the C terminus of the FMDV 3Dpol and RNA template-primer. Based on these findings and previous studies, we conclude that at least the first six residues of theMRKTKLAPT sequence motif play a vital role in the maintenance of faithful RNA synthesis activity (fidelity) of FMDV 3Dpol, suggesting that the role of the NLS motif in similar viral polymerases needs to be revisited. IMPORTANCE In this study, we employed genetic and molecular dynamics approaches to analyze the role of individual amino acids of the FMDV 3Dpol nuclear localization signal (NLS). The NLS residues were mutated to alanine using a type A full-genome cDNA clone, and the virus progeny was analyzed for defects in growth and in competition with the parental virus. We identified two mutants in 3Dpol, T19A and L21A, that exhibited high rate of mutation, were sensitive to nucleotide analogs, and displayed reduced replicative fitness compared to the parental virus. Using molecular dynamics simulation, we demonstrated that residues T19 and L21 played a role in the structural configuration of the interaction network at the 3Dpol palm subdomain. Cumulatively, our data suggest that the T19 and L21 3Dpol amino acids are important for maintaining the fidelity of the FMDV polymerase and ensuring faithful replication of the FMDV genome.

Evidence for the role of the α-helix in the xylosylation reactions involving the glycosaminoglycan-bearing serine of decorin/DS-PGII as shown by 1H NMR, CD, and molecular modeling studies

1996 ◽  
Vol 74 (3) ◽  
pp. 389-401 ◽  
Author(s):  
Yunjun Wang ◽  
Jan Sejbal ◽  
George Kotovych ◽  
Paul G. Scott
Keyword(s):  
Molecular Dynamics ◽  
Amino Acids ◽  
Water Mixture ◽  
Terminal Sequence ◽  
Trans Isomers ◽  
Methionine Residue ◽  
Nmr Techniques ◽  
Molecular Modeling Studies ◽  
Α Helix

The conformation of four peptides (N-terminal acetylated and unacetylated 14-mers DEASGIGPEEHFPENH2 and 24-mers AcQKGLFDFMLEDEASGIGPEEHFPENH2 with a normal and an oxidized methionine residue) containing the sequence Asp-Glu-Ala-Ser-Gly-Ile-Gly (DEASGIG), which is known to play an important role in the xylosylation reactions involving the glycosaminoglycan-bearing serine of decorin/DS-PGII, were studied by two-dimensional proton NMR techniques, circular dichroism spectroscopy, and molecular dynamics in a methanol–water mixture. The 14-residue peptide comprises the first (i.e., N-terminal) 14 amino acids of the mature decorin protein and the 24-residue peptide incorporates an additional (N-terminal) sequence of 10 amino acids derived from the procore of decorin. The resonance heterogeneity induced by the isomerization of the two prolines (Pro8, Pro13 in the 14-mer, and Pro18, Pro23 in the 24-mer) in the peptides studied was evaluated from TOCSY and NOESY NMR spectra. The trans-trans, trans-cis, and cis-trans isomers exist in approximate 68:25:7 proportions in the methanol–water mixture. The NOE distance constraints were used as input parameters for molecular dynamics and restrained energy minimization calculations. It was demonstrated that the conformation of the DEASGIG fragment was affected by the presence of the 10 amino acids at the N-terminal end of the 24-mer, and that the serine is part of an α-helix. The results indicate that an α-helix is present in the 24-mer beginning at the N-terminal end with Lys2 and ending at Gly15, and suggest that this could be the signal for the xylosylation of serine Ser14. A type VIb β turn was observed, involving the C-terminal cis-proline in the sequence His-Phe-Pro-Glu. Key words: xylosylation, nascent helix, α-helix, csi-proline, type VIb β-turn, molecular dynamics.

Role of donor–acceptor macrocycles in sequence specific peptide recognition and their optoelectronic properties: a detailed computational insight

2016 ◽  
Vol 18 (30) ◽  
pp. 20682-20690 ◽  
Author(s):  
Arkamita Bandyopadhyay ◽  
Swapan K Pati
Keyword(s):  
Molecular Dynamics ◽  
Optoelectronic Properties ◽  
Peptide Recognition ◽  
Classical Molecular Dynamics ◽  
Donor Acceptor ◽  
Specific Peptide

We have demonstrated sequence specific peptide recognition by donor–acceptor macrocycles by performing DFT and classical molecular dynamics studies.

scholarly journals Energy dissipation to tungsten surfaces upon hot-atom and Eley–Rideal recombination of H2

2018 ◽  
Vol 20 (33) ◽  
pp. 21334-21344 ◽  
Author(s):  
Oihana Galparsoro ◽  
H. Fabio Busnengo ◽  
Alejandra E. Martinez ◽  
Joseba Iñaki Juaristi ◽  
Maite Alducin ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Energy Dissipation ◽  
Molecular Dynamics Simulations ◽  
Surface Structure ◽  
Hole Pair ◽  
Electron Hole ◽  
Classical Molecular Dynamics ◽  
Electron Hole Pair ◽  
Dynamics Simulations

Adiabatic and nonadiabatic quasi-classical molecular dynamics simulations are performed to investigate the role of electron–hole pair excitations in hot-atom and Eley–Rideal H2 recombination mechanisms on H-covered W(100). The influence of the surface structure is analyzed by comparing with previous results for W(110).

scholarly journals Delineating the role of ripples on the thermal expansion of 2D honeycomb materials: graphene, 2D h-BN and monolayer (ML)-MoS2

2017 ◽  
Vol 19 (16) ◽  
pp. 10518-10526 ◽  
Author(s):  
P. Anees ◽  
M. C. Valsakumar ◽  
B. K. Panigrahi
Keyword(s):  
Molecular Dynamics ◽  
Thermal Expansion ◽  
Molecular Dynamics Simulations ◽  
Thermophysical Properties ◽  
Classical Molecular Dynamics ◽  
Dynamics Simulations ◽  
2D Crystals

Thermally excited ripples are inevitable in 2D crystals, and they can affect the thermophysical properties of these materials significantly. We delineated the role of ripples on the thermal expansion of 2D honeycomb materials using classical molecular dynamics simulations.

scholarly journals D-Retro Inverso (DRI) Amylin and the Stability of Amylin Fibrils

2020 ◽  
Author(s):  
Preeti Pandey ◽  
Natalie Nguyen ◽  
Ulrich H.E. Hansmann
Keyword(s):  
Molecular Dynamics ◽  
Amino Acids ◽  
Type Ii Diabetes ◽  
Type Ii ◽  
Fibril Structure ◽  
Elongation Process ◽  
The Stability ◽  
Dynamics Simulations ◽  
Potential Use

AbstractMotivated by the role that amylin aggregates pay in type-II diabetes, we compare the stability of regular amylin fibrils with the stability of fibrils where L-amino acid chains are replaced by D-Retro Inverso (DRI) amylin, i.e., peptides where the sequence of amino acids is reversed, and at the same time the L-amino acids are replaced by their mirror images. Our molecular dynamics simulations show that despite leading to only marginal difference in fibril structure and stability, aggregating DRI-amylin peptides have different pattern of contacts and hydrogen bonding. Because of these differences does DRI-amylin, when interacting with regular (L) amylin, alter the elongation process and lowers the stability of hybrid amylin fibrils. Our results suggest not only a potential use of DRI-amylin as inhibitor of amylin fibril-formation, but points also to the possibility of using insertion of DRI-proteins in L-assemblies as a way to probe the role of certain kinds of hydrogen bonds in supra-molecular assemblies or aggregates.

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