scholarly journals Assessment of Amyloid Forming Tendency of Peptide Sequences from Amyloid Beta and Tau Proteins Using Force-Field, Semi-Empirical, and Density Functional Theory Calculations

2021 ◽  
Vol 22 (6) ◽  
pp. 3244
Author(s):  
Charuvaka Muvva ◽  
Natarajan Arul Murugan ◽  
Venkatesan Subramanian

A wide variety of neurodegenerative diseases are characterized by the accumulation of protein aggregates in intraneuronal or extraneuronal brain regions. In Alzheimer’s disease (AD), the extracellular aggregates originate from amyloid-β proteins, while the intracellular aggregates are formed from microtubule-binding tau proteins. The amyloid forming peptide sequences in the amyloid-β peptides and tau proteins are responsible for aggregate formation. Experimental studies have until the date reported many of such amyloid forming peptide sequences in different proteins, however, there is still limited molecular level understanding about their tendency to form aggregates. In this study, we employed umbrella sampling simulations and subsequent electronic structure theory calculations in order to estimate the energy profiles for interconversion of the helix to β-sheet like secondary structures of sequences from amyloid-β protein (KLVFFA) and tau protein (QVEVKSEKLD and VQIVYKPVD). The study also included a poly-alanine sequence as a reference system. The calculated force-field based free energy profiles predicted a flat minimum for monomers of sequences from amyloid and tau proteins corresponding to an α-helix like secondary structure. For the parallel and anti-parallel dimer of KLVFFA, double well potentials were obtained with the minima corresponding to α-helix and β-sheet like secondary structures. A similar double well-like potential has been found for dimeric forms for the sequences from tau fibril. Complementary semi-empirical and density functional theory calculations displayed similar trends, validating the force-field based free energy profiles obtained for these systems.

Minerals ◽  
2018 ◽  
Vol 8 (5) ◽  
pp. 205 ◽  
Author(s):  
Ragnhild Hånde ◽  
Vivien Ramothe ◽  
Stéphane Tesson ◽  
Baptiste Dazas ◽  
Eric Ferrage ◽  
...  

Following our previous works on dioctahedral clays, we extend the classical Polarizable Ion Model (PIM) to trioctahedral clays, by considering dry Na-, Cs-, Ca- and Sr-hectorites as well as hydrated Na-hectorite. The parameters of the force field are determined by optimizing the atomic forces and dipoles on density functional theory calculations. The simulation results are validated by comparison with experimental X-ray diffraction (XRD) data. The XRD patterns calculated from classical molecular dynamics simulations performed with the PIM force field are in very good agreement with experimental results. In the bihydrated state, the less structured electronic density profile obtained with PIM compared to the one from the state-of-the-art non-polarizable force field clayFF explains the slightly better agreement between the PIM results and experiments.


Author(s):  
Michael Fischer ◽  
Robert G. Bell

AbstractDensity-functional theory calculations including a semi-empirical dispersion correction (DFT-D) are employed to study the interaction of small guest molecules (CH


Molecules ◽  
2018 ◽  
Vol 23 (10) ◽  
pp. 2466 ◽  
Author(s):  
Junming Ho ◽  
Yihan Shao ◽  
Jin Kato

This study examines whether the use of more accurate embedding potentials improves the convergence of quantum mechanics/molecular mechanics (QM/MM) models with respect to the size of the QM region. In conjunction with density functional theory calculations using the ωB97X-D functional, various embedding potentials including the TIP3P water model, the effective fragment potential (EFP), and semi-empirical methods (PM6, PM7, and DFTB) were used to simulate the deprotonation energies of solvated acid clusters. The calculations were performed on solvated neutral (HA) and cationic (HB+) acids clusters containing 160 and 480 water molecules using configurations sampled from molecular dynamics simulations. Consistently, the ωB97X-D/EFP model performed the best when using a minimal QM region size. The performance for the other potentials appears to be highly sensitive to the charge character of the acid/base pair. Neutral acids display the expected trend that semi-empirical methods generally perform better than TIP3P; however, an opposite trend was observed for the cationic acids. Additionally, electronic embedding provided an improvement over mechanical embedding for the cationic systems, but not the neutral acids. For the best performing ωB97X-D/EFP model, a QM region containing about 6% of the total number of solvent molecules is needed to approach within 10 kJ mol−1 of the pure QM result if the QM region was chosen based on the distance from the reaction centre.


2006 ◽  
Vol 17 (08) ◽  
pp. 1179-1190 ◽  
Author(s):  
EMİNE DENİZ ÇALIŞIR ◽  
ŞAKİR ERKOÇ

The structural, vibrational, electronic and QSAR properties of the dipropyl sulfide (DPS) molecule in gas phase have been investigated theoretically by performing semi-empirical molecular orbital (AM1 and PM3), ab initio (RHF) and density functional theory calculations. The geometry of the molecule has been optimized, infrared spectrum (vibrational modes and intensities) and the electronic properties of the molecule have been calculated in its ground state. It has been found that DPS molecule kinetically may not be stable however it is thermodynamically stable.


Life ◽  
2021 ◽  
Vol 11 (12) ◽  
pp. 1343
Author(s):  
Tolga Yaman ◽  
Jeremy N. Harvey

Novel density functional theory calculations are presented regarding a mechanism for prebiotic amino acid synthesis from alpha-keto acids that was suggested to happen via catalysis by dinucleotide species. Our results were analysed with comparison to the original hypothesis (Copley et al., PNAS, 2005, 102, 4442–4447). It was shown that the keto acid–dinucleotide hypothesis for possible prebiotic amino acid synthesis was plausible based on an initial computational analysis, and details of the structures for the intermediates and transition states showed that there was wide scope for interactions between the keto acid and dinucleotide moieties that could affect the free energy profiles and lead to the required proto-metabolic selectivity.


Author(s):  
So-Jin Ahn ◽  
Du-Hyeon Kim ◽  
Eung-Gun Kim ◽  
Yong-Kul Lee

The reaction mechanism of the carboxylation of K-2-naphthoxide was investigated by density functional theory calculations and spectroscopic studies. The reaction intermediates and products were confirmed by CO2 adsorbed-FTIR and 1H-NMR measurements. Four steps of the reaction pathway were identified: CO2 activation, electrophilic substitution, CO2-K complex rearrangement, and H-shift, producing 2-hydroxy-1-naphthoic acid (2,1-HNA), 2-hydroxy-3-naphthoic acid (2,3-HNA), and 2-hydroxy-6-naphthoic acid (2,6-HNA). The occurrence of CO2-K complex rearrangement was also confirmed. These energy profiles of reaction pathways for the reaction intermediates were well consistent the experimental results on the carboxylation of K-2-naphthoxide.


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