First-principles study of L-shell iron and chromium opacity at stellar interior temperatures.

Recently developed free-energy density functional theory (DFT)-based methodology for optical property calculations of warm dense matter has been applied for studying L-shell opacity of iron and chromium at T=182 eV. We use Mermin-Kohn-Sham density functional theory with a ground-state and a fully-temperature-dependent generalized gradient approximation exchange-correlation (XC) functionals. It is demonstrated that the role of XC at such a high-T is negligible due to the total free energy of interacting systems being dominated by the noninteracting free-energy term, in agreement with estimations for the homogeneous electron gas.

Atomic and optical properties of warm dense copper.

The emission of x rays from warm dense matter is of great interest for both spectroscopic diagnostics and development of intense x-ray sources. We report the results from the collisional-radiative steady-state (CRSS) modeling of atomic and optical properties of copper plasmas at near-solid and solid-state density for a range of temperatures. The CRSS model is validated against the available data on the average charge state and shifts of energy levels in aluminum and the opacity and emissivity spectra of carbon and aluminum plasmas.

Electroelastic coupling between membrane surface fluctuations and membrane-embedded charges: continuum multidielectric treatment.

The coupling of electric fields and charges with membrane-water interfacial fluctuations affects membrane electroporation, ionic conductance, and voltage gating. A modified continuum model is introduced to study charge interaction with membrane-water interfacial fluctuations in multidielectric environments. By surrounding a point charge with a low dielectric sphere, the linear Poisson-Boltzmann equation is directly solved by calculating the reaction field potential via a method that eliminates singularity contributions.

Shape-Dependent Global Deformation Modes of Large Protein Structures.

Conformational changes are central to the functioning of pore-forming proteins that open and close their molecular gates in response to external stimuli such as pH, ionic strength, membrane voltage or ligand binding. Normal mode analysis (NMA) is used to identify and characterize the slowest motions in the gA, KcsA, ClC-ec1, LacY and LeuT(Aa) proteins at the onset of gating. Global deformation modes of the essentially cylindrical gA, KcsA, LacY and LeuT(Aa) biomolecules are reminiscent of global twisting, transverse and longitudinal motions in a homogeneous elastic rod.

Antiport mechanism for Cl(-)/H(+) in ClC-ec1 from normal-mode analysis.

ClC chloride channels and transporters play major roles in cellular excitability, epithelial salt transport, volume, pH, and blood pressure regulation. One family member, ClC-ec1 from Escherichia coli, has been structurally resolved crystallographically and subjected to intensive mutagenetic, crystallographic, and electrophysiological studies. It functions as a Cl(-)/H(+) antiporter, not a Cl(-) channel; however, the molecular mechanism for Cl(-)/H(+) exchange is largely unknown.

Conformational changes in the selectivity filter of the open-state KcsA channel: an energy minimization study.

Potassium channels switch between closed and open conformations and selectively conduct K(+) ions. There are at least two gates. The TM2 bundle at the intracellular site is the primary gate of KcsA, and rearrangements at the selectivity filter (SF) act as the second gate.

Open-state conformation of the KcsA K+ channel: Monte Carlo normal mode following simulations.

Potassium channels fluctuate between closed and open states. The detailed mechanism of the conformational changes opening the intracellular pore in the K+ channel from Streptomyces lividans (KcsA) is unknown. Applying Monte Carlo normal mode following, we find that gating involves rotation and unwinding of the TM2 bundle, lateral movement of the TM2 helices away from the channel axis, and disappearance of the TM2 bundle.

The open state gating mechanism of gramicidin a requires relative opposed monomer rotation and simultaneous lateral displacement.

The gating mechanism of the open state of the gramicidin A (gA) channel is studied by using a new Monte Carlo Normal Mode Following (MC-NMF) technique, one applicable even without a target structure. The results demonstrate that the lowest-frequency normal mode (NM) at approximately 6.5 cm(-1) is the crucial mode that initiates dissociation.

Permeation and gating in proteins: kinetic Monte Carlo reaction path following.

We present a new Monte Carlo technique, kinetic Monte Carlo reaction path following (kMCRPF), for the computer simulation of permeation and large-scale gating transitions in protein channels. It combines ideas from Metropolis Monte Carlo (MMC) and kinetic Monte Carlo (kMC) algorithms, and is particularly suitable when a reaction coordinate is well defined. Evolution of transition proceeds on the reaction coordinate by small jumps (kMC technique) toward the nearest lowest-energy uphill or downhill states, with the jumps thermally activated (constrained MMC).

Water and ion permeation in bAQP1 and GlpF channels: a kinetic Monte Carlo study.

The kinetic Monte Carlo reaction-path-following technique is applied to determine the lowest-energy water pathway and the coordinating amino acids in bAQP1 and GlpF channels, both treated as rigid. In bAQP1, water molecules pass through the pore between the asparagine-proline-alanine (NPA) and selectivity filter (SF) sites one at a time. The water chain is interrupted at the SF where one water forms three stable hydrogen bonds with protein atoms.

Membrane inclusions as coupled harmonic oscillators: effects due to anisotropic membrane slope relaxation.

Membrane-mediated interaction between membrane-spanning peptides or protein segments plays an important role in their function and stability. Our rigorous "coupled harmonic oscillators" representation is extended to account for the complex boundary conditions permitting anisotropic relaxation of the membrane slope along the contours of the inclusions. Using this representation and applying a highly efficient finite-difference algorithm, we have analyzed the membrane-mediated interaction triggered by deformation of the hydrophobic tails of lipid molecules to match the lipophilic exterior of the inserted peptide.

Permeation in ion channels: the interplay of structure and theory.

Combined with high-resolution atomic-level crystal structures of channel forming peptides, theory has become a powerful tool for illuminating factors influencing permeation. Here, advantages and limitations of the more familiar continuum and molecular modeling techniques are briefly outlined. These methods are applied to issues of permeation in two different channel families: gramicidin and K(+) channels.

Anion pathway and potential energy profiles along curvilinear bacterial ClC Cl- pores: electrostatic effects of charged residues.

X-ray structures permit theoretical study of Cl(-) permeation along bacterial ClC Cl(-) pores. We determined the lowest energy curvilinear pathway, identified anion-coordinating amino acids, and calculated the electrostatic potential energy profiles. We find that all four bacterial ClC Cl(-) crystal structures correspond to closed states.

Gating gramicidin channels in lipid bilayers: reaction coordinates and the mechanism of dissociation.

The dissociation of gramicidin A (gA) channels into monomers is the simplest example of a channel gating process. The initial steps in this process are studied via a computational model that simulates the reaction coordinate for dimer-monomer dissociation. The nonbonded interaction energy between the monomers is determined, allowing for their free relative translational and rotational motion.

Permeation energetics in a model potassium channel.

Known structures of selective ion channels share a common property: a narrow constriction, presumably crucial for ionic discrimination. This region can be fairly long, imposing single file motion on waters and ion(s). We apply the semi-microscopic Monte Carlo approach to study permeation in the KcsA channel, decomposing energetics into a three-step process: cation dehydration; ion transfer into a uniform low epsilon dielectric; and transfer from the uniform dielectric into the channel.