Recent advances of studies on cell-penetrating peptides based on molecular dynamics simulations
J Ouyang, Y Sheng, W Wang - Cells, 2022 - mdpi.com
With the ability to transport cargo molecules across cell membranes with low toxicity, cell-
penetrating peptides (CPPs) have become promising candidates for next generation peptide …
penetrating peptides (CPPs) have become promising candidates for next generation peptide …
Revealing thermodynamics and kinetics of lipid self-assembly by Markov state model analysis
Self-assembly is ubiquitous in the realm of biology and has become an elegant bottom-up
approach to fabricate new materials. Although molecular dynamics (MD) simulations can …
approach to fabricate new materials. Although molecular dynamics (MD) simulations can …
Glycerol transport through the aquaglyceroporin GlpF: bridging dynamics and kinetics with atomic simulation
The aquaglyceroporin GlpF is a member of the aquaporin family. It selectively conducts
small molecules, such as glycerol, across the cell membrane under a concentration gradient …
small molecules, such as glycerol, across the cell membrane under a concentration gradient …
Conformational changes and binding property of the periplasmic binding protein BtuF during vitamin B12 transport revealed by collision-induced unfolding, hydrogen …
L Zhou, D Wang, M Iftikhar, Y Lu, M Zhou - International Journal of …, 2021 - Elsevier
The periplasmic binding protein (PBP) BtuF plays a key role in transporting vitamin B 12
from periplasm to the ATP-binding cassette (ABC) transporter BtuCD. Conformational …
from periplasm to the ATP-binding cassette (ABC) transporter BtuCD. Conformational …
Studying noncovalent or covalent bond problem between smoothened and cholesterol by molecular dynamics simulation and Markov state model
L Feng, H Pérez-Sánchez, Q Bai - Physical Chemistry Chemical …, 2022 - pubs.rsc.org
Smoothened (SMO) is an attractive therapeutic target for the treatment and prevention of
several malignant tumors of the nervous system. The crystal structure of SMO shows …
several malignant tumors of the nervous system. The crystal structure of SMO shows …
The Role of Calcium in Regulating the Conformational Dynamics of d-Galactose/d-Glucose-Binding Protein Revealed by Markov State Model Analysis
M Yang, Y Tang, J Weng, Z Liu… - Journal of Chemical …, 2021 - ACS Publications
The d-glucose/d-galactose-binding protein (GGBP) from Escherichia coli is a substrate-
binding protein (SBP) associated with sugar transport and chemotaxis. It is also a calcium …
binding protein (SBP) associated with sugar transport and chemotaxis. It is also a calcium …
Prediction of large conformational changes of a protein binding pocket associated with ligand binding
T Ishida - 2024 - chemrxiv.org
Docking simulation, a key technique in virtual screening, typically treats proteins as rigid
bodies. However, proteins are inherently flexible, and ligand binding can induce significant …
bodies. However, proteins are inherently flexible, and ligand binding can induce significant …