Simulating ion channel activation mechanisms using swarms of trajectories

Abstract

Atomic-level studies of protein activity represent a significant challenge as a result of the complexity of conformational changes occurring on wide-ranging timescales, often greatly exceeding that of even the longest simulations. A prime example is the elucidation of protein allosteric mechanisms, where localized perturbations transmit throughout a large macromolecule to generate a response signal. For example, the conversion of chemical to electrical signals during synaptic neurotransmission in the brain is achieved by specialized membrane proteins called pentameric ligand-gated ion channels. Here, the binding of a neurotransmitter results in a global conformational change to open an ion-conducting pore across the nerve cell membrane. X-ray crystallography has produced static structures of the open and closed states of the proton-gated GLIC pentameric ligand-gated ion channel protein, allowing for atomistic simulations that can uncover changes related to activation. We discuss a range of enhanced sampling approaches that could be used to explore activation mechanisms. In particular, we describe recent application of an atomistic string method, based on Roux's "swarms of trajectories" approach, to elucidate the sequence and interdependence of conformational changes during activation. We illustrate how this can be combined with transition analysis and Brownian dynamics to extract thermodynamic and kinetic information, leading to understanding of what controls ion channel function.

Mechanistic Understanding from Molecular Dynamics in Pharmaceutical Research 2: Lipid Membrane in Drug Design

“…A modified version of RAMD, known as τRAMD allows for the study of the residence time of ligands in the binding pocket [107]. Two additional methods have been developed to find the optimal pathway in complex multidimensional space that bear mentioning: the first is based on the combined use of metadynamics and a path-searching algorithm [108] and the second is based on what is known as a "string method" involving a swarm of trajectories [109,110].…”

“…binding pocket [107]. Two additional methods have been developed to find the optimal pathway in complex multidimensional space that bear mentioning: the first is based on the combined use of metadynamics and a path-searching algorithm [108] and the second is based on what is known as a "string method" involving a swarm of trajectories [109,110]. All of the above methods to determine the free energy between two regions of conformation space, usually two different local minima, involved moving the system through a path in conformation space.…”

Water in Nanopores and Biological Channels: A Molecular Simulation Perspective

“… 460 Comparable studies have also been performed for the entire GLIC channel. 461 , 462 For the isolated transmembrane domain, the free-energy cost of hydrating the hydrophobic gate (with TIP3P water) was estimated. 463 The hydration state at such a region was suggested to be a principal determinant of the functional (ion conduction) state of the channel based on calculations from the latter study, whereby pore hydration was associated with an increase in free energy of ∼46 kJ mol –1 , compared with the smaller energetic cost (∼5 kJ mol –1 ) of transferring a sodium ion into a hydrated gate.…”

Molecular Simulations of Hydrophobic Gating of Pentameric Ligand Gated Ion Channels: Insights into Water and Ions

“…The main challenge is the time scale of conformational transitions associated with channel gating (i.e., msec , ), which is currently difficult to address directly via MD simulations. A range of approaches have been applied including direct (long) simulations of 5-HT 3 R , and other pLGICs, e.g., GluCl, and the use of a range of enhanced sampling approaches, including, e.g., the use of strings and swarms of simulations , and of extensive cloud-based nonequilibrium simulations . A promising approach is to combine extended MD simulations initiated from multiple starting states as determined by, e.g., cryo-EM (seen, e.g, in a recent study of the bacterial channel GLIC) or NMR (as has recently been applied to gating modes of potassium channels).…”