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The complex of ferric-enterobactin with its transporter from Pseudomonas aeruginosa suggests a two-site model
Bacteria use small molecules called siderophores to scavenge iron. Siderophore-Fe3+
complexes are recognised by outer-membrane transporters and imported into the periplasm …
complexes are recognised by outer-membrane transporters and imported into the periplasm …
Ligand diffusion in globins: simulations versus experiment
Computer simulations in molecular biophysics describe in atomic detail the structure,
dynamics, and function of biological macromolecules. To assess the quality of these models …
dynamics, and function of biological macromolecules. To assess the quality of these models …
Map** the network of pathways of CO diffusion in myoglobin
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 …
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
Aquaporins are protein channels located across the cell membrane with the role of
conducting water or other small sugar alcohol molecules (aquaglyceroporins). The high …
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
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 …
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
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 …
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
Protein conformation has been recognized as the key feature determining biological
function, as it determines the position of the essential groups specifically interacting with …
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
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 …
collective variable space for CO localization in myoglobin to estimate the kinetics of entry …
Internal water and microsecond dynamics in myoglobin
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 …
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
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) …
researchers, still some key questions remain open. Their importance for vacuolar (plants) …