Conformational Changes and Slow Dynamics through Microsecond Polarized Atomistic Molecular Simulation of an Integral Kv1.2 Ion Channel

Structure and dynamics of voltage-gated ion channels, in particular the motion of the S4 helix, is a highly interesting and hotly debated topic in current membrane protein research. It has critical implications for insertion and stabilization of membrane proteins as well as for finding how transitions occur in membrane proteins—not to mention numerous applications in drug design. Here, we present a full 1 µs atomic-detail molecular dynamics simulation of an integral Kv1.2 ion channel, comprising 120,000 atoms. By applying 0.052 V/nm of hyperpolarization, we observe structural rearrangements, including up to 120° rotation of the S4 segment, changes in hydrogen-bonding patterns, but only low amounts of translation. A smaller rotation (∼35°) of the extracellular end of all S4 segments is present also in a reference 0.5 µs simulation without applied field, which indicates that the crystal structure might be slightly different from the natural state of the voltage sensor. The conformation change upon hyperpolarization is closely coupled to an increase in 310 helix contents in S4, starting from the intracellular side. This could support a model for transition from the crystal structure where the hyperpolarization destabilizes S4–lipid hydrogen bonds, which leads to the helix rotating to keep the arginine side chains away from the hydrophobic phase, and the driving force for final relaxation by downward translation is partly entropic, which would explain the slow process. The coordinates of the transmembrane part of the simulated channel actually stay closer to the recently determined higher-resolution Kv1.2 chimera channel than the starting structure for the entire second half of the simulation (0.5–1 µs). Together with lipids binding in matching positions and significant thinning of the membrane also observed in experiments, this provides additional support for the predictive power of microsecond-scale membrane protein simulations

Artificial Modulation of the Gating Behavior of a K+ Channel in a KvAP-DNA Chimera

We present experiments where the gating behavior of a voltage-gated ion channel is modulated by artificial ligand binding. We construct a channel-DNA chimera with the KvAP potassium channel reconstituted in an artificial membrane. The channel is functional and the single channel ion conductivity unperturbed by the presence of the DNA. However, the channel opening probability vs. bias voltage, i.e., the gating, can be shifted considerably by the electrostatic force between the charges on the DNA and the voltage sensing domain of the protein. Different hybridization states of the chimera DNA thus lead to different response curves of the channel

PIP2-Binding Site in Kir Channels: Definition by Multiscale Biomolecular Simulations†

Phosphatidylinositol bisphosphate (PIP(2)) is an activator of mammalian inwardly rectifying potassium (Kir) channels. Multiscale simulations, via a sequential combination of coarse-grained and atomistic molecular dynamics, enabled exploration of the interactions of PIP(2) molecules within the inner leaflet of a lipid bilayer membrane with possible binding sites on Kir channels. Three Kir channel structures were investigated: X-ray structures of KirBac1.1 and of a Kir3.1-KirBac1.3 chimera and a homology model of Kir6.2. Coarse-grained simulations of the Kir channels in PIP(2)-containing lipid bilayers identified the PIP(2)-binding site on each channel. These models of the PIP(2)-channel complexes were refined by conversion to an atomistic representation followed by molecular dynamics simulation in a lipid bilayer. All three channels were revealed to contain a conserved binding site at the N-terminal end of the slide (M0) helix, at the interface between adjacent subunits of the channel. This binding site agrees with mutagenesis data and is in the proximity of the site occupied by a detergent molecule in the Kir chimera channel crystal. Polar contacts in the coarse-grained simulations corresponded to long-lived electrostatic and H-bonding interactions between the channel and PIP(2) in the atomistic simulations, enabling identification of key side chains

Test stand for the Silicon Vertex Detector of the Collider Detector Facility

A test stand for the next generation of the Silicon Vertex Detector (SVX-II) of the Collider Detector Facility (CDF) at Fermilab has been developed. It is capable of performing cosmic ray, beam, and laser pulsing tests on silicon strip detectors using the new generation of SVX chips. The test stand is composed of a SGI workstation, a VME CPU, the Silicon Test Acquisition and Readout (STAR) board, the Test Fiber Interface Board (TFIB), and the Test Port Card (TPC). The STAR mediates between external stimuli for the different tests and produces appropriate high level commands which are sent to the TFIB. The TFIB, in conjunction with the TPC, translates these commands into the correct logic levels to control the SVX chips. The four modes of operation of the SVX chips are configuration, data acquisition, digitization, and data readout. The data read out from the SVX chips is transferred to the STAR. The STAR can then be accessed by the VME CPU and the SGI workstation for future analyses. The detailed description of this test stand is given

Albania and the Ottoman invasion of Italy, 1480-1881

Donated by Klaus Kreise

Self assembly of peptides near or within membranes using coarse grained MD simulations

International audienceCoarse grain modeling has recently emerged as an alternative to classical atomistic simulations in the study of spontaneous self assembly and structural organization of complex molecular systems. For surfactant and lipid systems, it was shown to allow, under appropriate conditions, in-silico self assembly of a variety of architectures. Recently, this approach has been extended to peptides for which force fields allowing self assembly of mixed peptides–lipid systems were proposed. Here we introduce elements of a coarse grained force field that accurately describe self assembly of hydrophobic cyclic peptides [Trp–Leu]4 and their reorganization within lipid membranes to form transmembrane channels in agreement with experiments. Extension to hydrophobic helical transmembrane, and amphipatic helical antimicrobial peptides show that the model is robust enough to constitute a building block for more complete and appropriate force field describing peptide interactions with membranes