Multiscale simulations of biological membranes: the challenge to understand biological phenomena in a living substance
Biological membranes are tricky to investigate. They are complex in terms of molecular
composition and structure, functional over a wide range of time scales, and characterized by …
composition and structure, functional over a wide range of time scales, and characterized by …
An expandable, modular de novo protein platform for precision redox engineering
The electron-conducting circuitry of life represents an as-yet untapped resource of exquisite,
nanoscale biomolecular engineering. Here, we report the characterization and structure of a …
nanoscale biomolecular engineering. Here, we report the characterization and structure of a …
The impact of using single atomistic long-range cutoff schemes with the GROMOS 54A7 force field
With the recent increase in computing power, the molecular modeling community is now
more focused on improving the accuracy and overall quality of biomolecular simulations. For …
more focused on improving the accuracy and overall quality of biomolecular simulations. For …
Computational methods used to explore transport events in biological systems
T Pienko, J Trylska - Journal of Chemical Information and …, 2019 - ACS Publications
Transport of various molecules facilitated with membrane proteins is necessary for
maintaining homeostasis in living cells. In humans, dysfunction of these proteins leads to …
maintaining homeostasis in living cells. In humans, dysfunction of these proteins leads to …
Identification of the initial steps in signal transduction in the α4β2 nicotinic receptor: insights from equilibrium and nonequilibrium simulations
ASF Oliveira, DK Shoemark, HR Campello… - Structure, 2019 - cell.com
Nicotinic acetylcholine receptors (nAChRs) modulate synaptic transmission in the nervous
system. These receptors have emerged as therapeutic targets in drug discovery for treating …
system. These receptors have emerged as therapeutic targets in drug discovery for treating …
[HTML][HTML] Coupling between protonation and conformation in cytochrome c oxidase: Insights from constant-pH MD simulations
Cytochrome c oxidases (CcOs) are the terminal enzymes of the respiratory chain in
mitochondria and most bacteria. These enzymes reduce dioxygen (O 2) to water and …
mitochondria and most bacteria. These enzymes reduce dioxygen (O 2) to water and …
On atomistic models for molecular oxygen
M Javanainen, I Vattulainen… - The Journal of Physical …, 2017 - ACS Publications
Molecular oxygen (O2) is key to all life on earth, as it is constantly cycled via photosynthesis
and cellular respiration. Substantial scientific effort has been devoted to understanding …
and cellular respiration. Substantial scientific effort has been devoted to understanding …
Bacterial denitrifying nitric oxide reductases and aerobic respiratory terminal oxidases use similar delivery pathways for their molecular substrates
P Mahinthichaichan, RB Gennis… - Biochimica et Biophysica …, 2018 - Elsevier
The superfamily of heme‑copper oxidoreductases (HCOs) include both NO and O 2
reductases. Nitric oxide reductases (NORs) are bacterial membrane enzymes that catalyze …
reductases. Nitric oxide reductases (NORs) are bacterial membrane enzymes that catalyze …
Molecular dynamics simulation of diffusion and O2 dissolution in water using four water molecular models
This work evaluates four popular 3-site water models, TIP3P, SPC/E, SPC, and F3C, in
predicting temperature-dependent O 2 diffusion and dissolution and self-diffusion in liquid …
predicting temperature-dependent O 2 diffusion and dissolution and self-diffusion in liquid …
Studying O2 pathways in [NiFe]- and [NiFeSe]-hydrogenases
Hydrogenases are efficient biocatalysts for H2 production and oxidation with various
potential biotechnological applications.[NiFe]-class hydrogenases are highly active in both …
potential biotechnological applications.[NiFe]-class hydrogenases are highly active in both …