[HTML][HTML] Flexible selection of the solute region in replica exchange with solute tempering: Application to protein-folding simulations

M Kamiya, Y Sugita - The Journal of chemical physics, 2018 - pubs.aip.org
Replica-exchange molecular dynamics (REMD) and their variants have been widely used in
simulations of the biomolecular structure and dynamics. Replica exchange with solute …

“Multiple partial recognitions in dynamic equilibrium” in the binding sites of proteins form the molecular basis of promiscuous recognition of structurally diverse ligands

D Kohda - Biophysical Reviews, 2018 - Springer
Promiscuous recognition of ligands by proteins is as important as strict recognition in
numerous biological processes. In living cells, many short, linear amino acid motifs function …

Molecular basis of the dynamic structure of the TIM23 complex in the mitochondrial intermembrane space

R Bajaj, Ł Jaremko, M Jaremko, S Becker… - Structure, 2014 - cell.com
The presequence translocase TIM23 is a highly dynamic complex in which its subunits can
adopt multiple conformations and undergo association-dissociation to facilitate import of …

Graphics processing unit acceleration and parallelization of GENESIS for large-scale molecular dynamics simulations

J Jung, A Naurse, C Kobayashi… - Journal of Chemical …, 2016 - ACS Publications
The graphics processing unit (GPU) has become a popular computational platform for
molecular dynamics (MD) simulations of biomolecules. A significant speedup in the …

Synthetic mitochondria-targeting peptides incorporating α-aminoisobutyric acid with a stable amphiphilic helix conformation in plant cells

K Terada, J Gimenez-Dejoz, T Kurita… - ACS Biomaterials …, 2021 - ACS Publications
In the genetic modification of plant cells, the mitochondrion is an important target in addition
to the nucleus and plastid. However, gene delivery into the mitochondria of plant cells has …

Conformational ensemble of an intrinsically flexible loop in mitochondrial import protein Tim21 studied by modeling and molecular dynamics simulations

A Srivastava, S Bala, H Motomura, D Kohda… - … et Biophysica Acta (BBA …, 2020 - Elsevier
Background Tim21, a subunit of a highly dynamic translocase of the inner mitochondrial
membrane (TIM23) complex, translocates proteins by interacting with subunits in the …

Rational design of crystal contact‐free space in protein crystals for analyzing spatial distribution of motions within protein molecules

R Matsuoka, A Shimada, Y Komuro, Y Sugita… - Protein …, 2016 - Wiley Online Library
Contacts with neighboring molecules in protein crystals inevitably restrict the internal
motions of intrinsically flexible proteins. The resultant clear electron densities permit model …

A computational study of the glycine-rich loop of mitochondrial processing peptidase

T Kučera, M Otyepka, A Matušková, A Samad… - PLoS …, 2013 - journals.plos.org
An all atomic, non-restrained molecular dynamics (MD) simulation in explicit water was used
to study in detail the structural features of the highly conserved glycine-rich loop (GRL) of the …

Computational investigation of the conformational dynamics in Tom20‐mitochondrial presequence tethered complexes

A Srivastava, F Tama, D Kohda… - … Structure, Function, and …, 2019 - Wiley Online Library
The translocase of the outer membrane (TOM) mediates the membrane permeation of
mitochondrial matrix proteins. Tom20 is a subunit of the TOM complex and binds to the N …

Diferencias fenotípicas de fibroblastos gingivales en sujetos con hiperplasia gingival idiopática frente a sujetos periodontalmente sanos: estudio piloto

VH Simancas-Escorcia… - Acta Odontológica …, 2021 - revistas.unal.edu.co
Objetivo: identificar, describir y diferenciar las características fenotípicas de los fibroblastos
gingivales (FGs) en pacientes con hiperplasia gingival idiopática (HGI) e individuos …