New tricks for old dogs: improving the accuracy of biomolecular force fields by pair-specific corrections to non-bonded interactions
J Yoo, A Aksimentiev - Physical Chemistry Chemical Physics, 2018 - pubs.rsc.org
In contrast to ordinary polymers, the vast majority of biological macromolecules adopt highly
ordered three-dimensional structures that define their functions. The key to folding of a …
ordered three-dimensional structures that define their functions. The key to folding of a …
CHARMM-GUI Membrane Builder: Past, Current, and Future Developments and Applications
Molecular dynamics simulations of membranes and membrane proteins serve as
computational microscopes, revealing coordinated events at the membrane interface. As G …
computational microscopes, revealing coordinated events at the membrane interface. As G …
CHARMM-GUI input generator for NAMD, GROMACS, AMBER, OpenMM, and CHARMM/OpenMM simulations using the CHARMM36 additive force field
Proper treatment of nonbonded interactions is essential for the accuracy of molecular
dynamics (MD) simulations, especially in studies of lipid mono-and bilayers. The use of the …
dynamics (MD) simulations, especially in studies of lipid mono-and bilayers. The use of the …
CHARMM‐GUI Membrane Builder toward realistic biological membrane simulations
CHARMM‐GUI Membrane Builder, http://www. charmm‐gui. org/input/membrane, is a web‐
based user interface designed to interactively build all‐atom protein/membrane or …
based user interface designed to interactively build all‐atom protein/membrane or …
All-atom molecular dynamics simulations of Synaptotagmin-SNARE-complexin complexes bridging a vesicle and a flat lipid bilayer
Synaptic vesicles are primed into a state that is ready for fast neurotransmitter release upon
Ca 2+-binding to Synaptotagmin-1. This state likely includes trans-SNARE complexes …
Ca 2+-binding to Synaptotagmin-1. This state likely includes trans-SNARE complexes …
Comparative molecular dynamics simulation studies of realistic eukaryotic, prokaryotic, and archaeal membranes
ID Pogozheva, GA Armstrong, L Kong… - Journal of chemical …, 2022 - ACS Publications
We present a comparative all-atom molecular dynamics simulation study of 18
biomembrane systems with lipid compositions corresponding to eukaryotic, bacterial, and …
biomembrane systems with lipid compositions corresponding to eukaryotic, bacterial, and …
Molecular basis of PIP2-dependent regulation of the Ca2+-activated chloride channel TMEM16A
The calcium-activated chloride channel (CaCC) TMEM16A plays crucial roles in regulating
neuronal excitability, smooth muscle contraction, fluid secretion and gut motility. While …
neuronal excitability, smooth muscle contraction, fluid secretion and gut motility. While …
Developing and testing of lipid force fields with applications to modeling cellular membranes
The amphipathic nature of the lipid molecule (hydrophilic head and hydrophobic tails)
enables it to act as a barrier between fluids with various properties and to sustain an …
enables it to act as a barrier between fluids with various properties and to sustain an …
Mechanistic understanding from molecular dynamics in pharmaceutical research 2: lipid membrane in drug design
We review the use of molecular dynamics (MD) simulation as a drug design tool in the
context of the role that the lipid membrane can play in drug action, ie, the interaction …
context of the role that the lipid membrane can play in drug action, ie, the interaction …
Calcium directly regulates phosphatidylinositol 4, 5-bisphosphate headgroup conformation and recognition
The orchestrated recognition of phosphoinositides and concomitant intracellular release of
Ca2+ is pivotal to almost every aspect of cellular processes, including membrane …
Ca2+ is pivotal to almost every aspect of cellular processes, including membrane …