The complex of ferric-enterobactin with its transporter from Pseudomonas aeruginosa suggests a two-site model

L Moynié, S Milenkovic, GLA Mislin, V Gasser… - Nature …, 2019‏ - nature.com
Bacteria use small molecules called siderophores to scavenge iron. Siderophore-Fe3+
complexes are recognised by outer-membrane transporters and imported into the periplasm …

Ligand diffusion in globins: simulations versus experiment

R Elber - Current opinion in structural biology, 2010‏ - Elsevier
Computer simulations in molecular biophysics describe in atomic detail the structure,
dynamics, and function of biological macromolecules. To assess the quality of these models …

Map** the network of pathways of CO diffusion in myoglobin

L Maragliano, G Cottone, G Ciccotti… - Journal of the …, 2010‏ - ACS Publications
The pathways of diffusion of a CO molecule inside a myoglobin protein and toward the
solvent are investigated. Specifically, the three-dimensional potential of mean force (PMF or …

The gating mechanism of the human aquaporin 5 revealed by molecular dynamics simulations

L Janosi, M Ceccarelli - PLoS One, 2013‏ - journals.plos.org
Aquaporins are protein channels located across the cell membrane with the role of
conducting water or other small sugar alcohol molecules (aquaglyceroporins). The high …

Role of enzyme flexibility in ligand access and egress to active site: bias-exchange metadynamics study of 1, 3, 7-trimethyluric acid in cytochrome P450 3A4

M Paloncýová, V Navrátilová, K Berka… - Journal of Chemical …, 2016‏ - ACS Publications
Although the majority of enzymes have buried active sites, very little is known about the
energetics and mechanisms associated with substrate and product channeling in and out …

Control of the position of oxygen delivery in soybean lipoxygenase-1 by amino acid side chains within a gas migration channel

L Collazo, JP Klinman - Journal of Biological Chemistry, 2016‏ - jbc.org
Understanding gas migration pathways is critical to unraveling structure-function
relationships in enzymes that process gaseous substrates such as O 2, H 2, and N 2. This …

[HTML][HTML] Principal Component Analysis reveals correlation of cavities evolution and functional motions in proteins

N Desdouits, M Nilges, A Blondel - Journal of Molecular Graphics and …, 2015‏ - Elsevier
Protein conformation has been recognized as the key feature determining biological
function, as it determines the position of the essential groups specifically interacting with …

Full kinetics of CO entry, internal diffusion, and exit in myoglobin from transition-path theory simulations

TQ Yu, M Lapelosa, E Vanden-Eijnden… - Journal of the …, 2015‏ - ACS Publications
We use Markovian milestoning molecular dynamics (MD) simulations on a tessellation of the
collective variable space for CO localization in myoglobin to estimate the kinetics of entry …

Internal water and microsecond dynamics in myoglobin

S Kaieda, B Halle - The Journal of Physical Chemistry B, 2013‏ - ACS Publications
Myoglobin (Mb) binds diatomic ligands, like O2, CO, and NO, in a cavity that is only
transiently accessible. Crystallography and molecular simulations show that the ligands can …

The mechanism and energetics of a ligand-controlled hydrophobic gate in a mammalian two pore channel

S Milenkovic, IV Bodrenko, L Lagostena… - Physical Chemistry …, 2020‏ - pubs.rsc.org
In the last decade two-pore intracellular channels (TPCs) attracted the interest of
researchers, still some key questions remain open. Their importance for vacuolar (plants) …