Effects of oscillating electric fields on conotoxin peptide conformation: A molecular dynamic simulation study.

Molecular Dynamics (MD) simulation is a computational method frequently used in biological and material sciences to efficiently model atomic and molecular interactions occurring in biological systems and effects of external stimuli on molecules and cells. In this study, M - 1 conotoxin protein was simulated under the oscillating (time-varying) electric fields of strengths 2e, 6e and 4.7e V/nm at the frequency of 1800 MHz.

Structural effects of divalent calcium cations on the α7 nicotinic acetylcholine receptor: A molecular dynamics simulation study.

The α7 subtype of neuronal nicotinic acetylcholine receptor (nAChR) is a ligand-gated ion channel protein that is vital to various neurological functions, including modulation of neurotransmitter release. A relatively high concentration of extracellular Ca in the neuronal environment is likely to exert substantial structural and functional influence on nAChRs, which may affect their interactions with agonists and antagonists. In this work, we employed atomistic molecular dynamics (MD) simulations to examine the effects of elevated Ca on the structure and dynamics of α7 nAChR embedded in a model phospholipid bilayer.

Molecular simulation study of the unbinding of α-conotoxin [ϒ4E]GID at the α7 and α4β2 neuronal nicotinic acetylcholine receptors.

The α7 and α4β2 neuronal nicotinic receptors belonging to the family of ligand-gated ion channels are most prevalent in the brain, and are implicated in various neurodegenerative disorders. α-conotoxin GID (and its analogue [ϒ4E]GID) specifically inhibits these subtypes, with more affinity towards the human α7 (hα7) subtype, and is valuable in understanding the physiological roles of these receptors. In this study, we use umbrella-sampling molecular dynamics simulations to understand the mechanism of interaction between [ϒ4E]GID and the agonist binding pockets of the α4β2 and the hα7 receptors, and to estimate their relative binding affinities (ΔG).

Structural features for homodimer folding mechanism.

The homodimers have essential role in catalysis and regulation. The homodimer folding mechanism through 2-state without stable intermediate (2S), 3-state with monomer intermediate (3SMI) and 3-state with dimer intermediate (3SDI) is fascinating. 23MI and 3SDI constitute 3-state (3S).

A decision tree model for the prediction of homodimer folding mechanism.

The formation of protein homodimer complexes for molecular catalysis and regulation is fascinating. The homodimer formation through 2S (2 state), 3SMI (3 state with monomer intermediate) and 3SDI (3 state with dimer intermediate) folding mechanism is known for 47 homodimer structures. Our dataset of forty-seven homodimers consists of twenty-eight 2S, twelve 3SMI and seven 3SDI.

Types of interfaces for homodimer folding and binding.

Homodimers have a role in catalysis and regulation through the formation of stable interfaces. These interfaces are formed through different folding mechanisms such as 2-state without stable intermediate (2S), 3-state with monomer intermediate (3SMI) and 3-state with dimer intermediate (3SDI). Therefore, it is of interest to understand folding mechanism using structural features at the interfaces.