Biophysics

Water Permeation Through the Sodium-Dependent Galactose Cotransporter vSGLT

It is well accepted that cotransporters facilitate water movement by two independent mechanisms: osmotic flow through a water channel in the protein and flow driven by ion/substrate cotransport. However, the molecular mechanism of transport-linked …

The mechanism of sodium and substrate release from the binding pocket of vSGLT

Membrane co-transport proteins that use a five-helix inverted repeat motif have recently emerged as one of the largest structural classes of secondary active transporters1,2. However, despite many structural advances there is no clear evidence of how …

Water permeation through the sodium-dependent galactose cotransporter vSGLT

It is well accepted that cotransporters facilitate water movement by two independent mechanisms: osmotic flow through a water channel in the protein and flow driven by ion/substrate cotransport. However, the molecular mechanism of transport-linked …

Computational Approaches to Understanding the Mechanism of Transport in the Na+/Galactose Co-Transporter vSGLT

A number of recent high resolution structures suggest that a larger family of cation coupled substrate transporters share a common core architecture. At the molecular level, it is not known how this architecture enables them to harness the energy …

Conformational dynamics of the inner pore helix of voltage-gated potassium channels

Voltage-gated potassium (Kv) channels control the electrical excitability of neurons and muscles. Despite this key role, how these channels open and close or gate is not fully understood. Gating is usually attributed to the bending and straightening …

Molecular dynamics simulation study of a pulmonary surfactant film interacting with a carbonaceous nanoparticle

This article reports an all-atom molecular dynamics simulation to study a model pulmonary surfactant film interacting with a carbonaceous nanoparticle. The pulmonary surfactant is modeled as a dipalmitoylphosphatidylcholine monolayer with a peptide …

A continuum method for determining membrane protein insertion energies and the problem of charged residues

Continuum electrostatic approaches have been extremely successful at describing the charged nature of soluble proteins and how they interact with binding partners. However, it is unclear whether continuum methods can be used to quantitatively …

Bending Elasticity of Anti-Parallel β-Sheets

Using a coarse-grained elastic model, we examine the bending properties of anti-parallel β-sheets comprised of uniform amino-acid residues in vacuum as well as in explicit solvent. By comparing the conformational probability of the β-sheet from …

The elasticity of α-helices

The elasticity of α-helices is examined using equilibrium molecular-dynamics simulations. From the statistics of curvatures and twists, we compute the elastic moduli of several representative α-helices, both in the presence and absence of aqueous …