Transport of ions through pores in membranes is a process of fundamental importance to
cell biology. In living organisms, such transport is facilitated by ion channels that utilize the …

In this chapter, practical concepts and guidelines are provided for the use of molecular
dynamics (MD) simulation for the refinement of homology models. First, an overview of the …

Opening of ion channels directly by tension in the surrounding membrane appears to be the
most ancient and simple mechanism of gating. Bacterial mechanosensitive channels MscL …

Many large biological macromolecules have inherent structural symmetry, being composed
of a few distinct subunits, repeated in a symmetric array. These complexes are often not …

Life, as we know it, is inseparable from water. Solvation sets chemical potentials for all
soluble components inside and outside the cell, affects intermolecular interactions, drives …

The anesthetic propofol inhibits the currents of the homopentameric ligand-gated ion
channel GLIC, yet the crystal structure of GLIC with five propofol molecules bound …

The bacterial potassium channel KcsA, which has been crystallized in several
conformations, offers an ideal model to investigate activation gating of ion channels. In this …

Transient receptor potential vanilloid 4 (TRPV4) is a Ca 2+-permeable channel activated by
diverse physical and chemical stimuli, including mechanical stress and endogenous lipid …

We derive a formulation of molecular dynamics that generates only symmetric
configurations. We implement it for all 2D planar and 3D space groups. An atlas of 2D …

Animals need to sense and react to potentially dangerous environments. TRP ion channels
participate in nociception, presumably via Ca2+ influx, in most animal species. However, the …