Molecular insight into the early stage of amyloid-β (1-42) Homodimers aggregation influenced by histidine tautomerism

A Salimi, H Li, JY Lee - International Journal of Biological Macromolecules, 2021 - Elsevier
Aggregated amyloid β-peptide (Aβ) in small oligomeric forms inside the brain causes
synaptic function disruption and the development of Alzheimer's disease (AD). Histidine is …

[HTML][HTML] Validation of molecular dynamics simulations for prediction of three-dimensional structures of small proteins

K Kato, T Nakayoshi, S Fukuyoshi, E Kurimoto, A Oda - Molecules, 2017 - mdpi.com
Although various higher-order protein structure prediction methods have been developed,
almost all of them were developed based on the three-dimensional (3D) structure …

Comparison of the activation energy barrier for succinimide formation from α-and β-aspartic acid residues obtained from density functional theory calculations

T Nakayoshi, K Kato, S Fukuyoshi, O Takahashi… - … et Biophysica Acta (BBA …, 2018 - Elsevier
The l-α-Asp residues in peptides or proteins are prone to undergo nonenzymatic reactions to
form l-β-Asp, d-α-Asp, and d-β-Asp residues via a succinimide five-membered ring …

Comparison of molecular dynamics simulation methods for amyloid β1–42 monomers containing d-aspartic acid residues for predicting retention times in …

A Oda, K Kobayashi, O Takahashi - Journal of Chromatography B, 2011 - Elsevier
Molecular dynamics simulations of amyloid β1–42 containing d-aspartic acid residues were
performed using several continuous solvent models to investigate the usefulness of …

Influences of conformations of peptides on stereoinversions and/or isomerizations of aspartic acid residues

A Oda, T Nakayoshi, S Fukuyoshi, E Kurimoto… - … et Biophysica Acta (BBA …, 2018 - Elsevier
Recently, non-enzymatic stereoinversions of aspartic acid (Asp) residues in proteins and
peptides have been reported. Here, we performed replica exchange molecular dynamics …

Validation of molecular force field parameters for peptides including isomerized amino acids

A Oda, T Nakayoshi, S Fukuyoshi, E Kurimoto… - Chirality, 2018 - Wiley Online Library
Recently, stereoinversions and isomerizations of amino acid residues in the proteins of
living beings have been observed. Because isomerized amino acids cause structural …

Theoretical study on keto–enol tautomerisation of glutarimide for exploration of the isomerisation reaction pathway of glutamic acid in proteins using density functional …

S Fukuyoshi, T Nakayoshi, O Takahashi… - Molecular Physics, 2017 - Taylor & Francis
In order to elucidate the reason why glutamic acid residues have lesser racemisation
reactivity than asparaginic acid, we investigated the racemisation energy barrier of …

Computational studies on the water‐catalyzed stereoinversion mechanism of glutamic acid residues in peptides and proteins

T Nakayoshi, K Kato, S Fukuyoshi, O Takahashi… - Chirality, 2018 - Wiley Online Library
In contrast with the common belief that all the amino acid residues in higher organisms are l‐
forms, d‐amino acid residues have been recently detected in various aging tissues. Aspartic …

Lipophilicity of amyloid β-peptide 12–28 and 25–35 to unravel their ability to promote hydrophobic and electrostatic interactions

G Ermondi, F Catalano, M Vallaro, I Ermondi… - International Journal of …, 2015 - Elsevier
The growing interest for peptide therapeutics calls for new strategies to determine the
physico-chemical properties responsible for the interactions of peptides with the …

[HTML][HTML] Computational studies on water-catalyzed mechanisms for stereoinversion of glutarimide intermediates formed from glutamic acid residues in aqueous phase

T Nakayoshi, S Fukuyoshi, K Kato, E Kurimoto… - International Journal of …, 2019 - mdpi.com
Aspartic acid (Asp) residues are prone to non-enzymatic stereoinversion, and Asp-residue
stereoinversion is believed to be mediated via a succinimide (SI) intermediate. The …