Molecular Dynamics Simulations of Scorpion Toxin Recognition by the Ca²⁺-Activated Potassium Channel KCa3.1

The Ca²⁺-activated channel of intermediate-conductance (KCa3.1) is a target for antisickling and immunosuppressant agents. Many small peptides isolated from animal venoms inhibit KCa3.1 with nanomolar affinities and are promising drug scaffolds. Although the inhibitory effect of peptide toxins on KCa3.1 has been examined extensively, the structural basis of toxin-channel recognition has not been understood in detail. Here, the binding modes of two selected scorpion toxins, charybdotoxin (ChTx) and OSK1, to human KCa3.1 are examined in atomic detail using molecular dynamics (MD) simulations. Employing a homology model of KCa3.1, we first determine conduction properties of the channel using Brownian dynamics and ascertain that the simulated results are in accord with experiment. The model structures of ChTx-KCa3.1 and OSK1-KCa3.1 complexes are then constructed using MD simulations biased with distance restraints. The ChTx-KCa3.1 complex predicted from biased MD is consistent with the crystal structure of ChTx bound to a voltage-gated K(+) channel. The dissociation constants (Kd) for the binding of both ChTx and OSK1 to KCa3.1 determined experimentally are reproduced within fivefold using potential of mean force calculations. Making use of the knowledge we gained by studying the ChTx-KCa3.1 complex, we attempt to enhance the binding affinity of the toxin by carrying out a theoretical mutagenesis. A mutant toxin, in which the positions of two amino acid residues are interchanged, exhibits a 35-fold lower Kd value for KCa3.1 than that of the wild-type. This study provides insight into the key molecular determinants for the high-affinity binding of peptide toxins to KCa3.1, and demonstrates the power of computational methods in the design of novel toxins.This work was supported by the National Health and Medical Research Council of Australia and The Medical Advances Without Animals Trust (MAWA)

Structural Basis of the Selective Block of Kv1.2 by Maurotoxin from Computer Simulations

The 34-residue polypeptide maurotoxin (MTx) isolated from scorpion venoms selectively inhibits the current of the voltage-gated potassium channel Kv1.2 by occluding the ion conduction pathway. Here using molecular dynamics simulation as a docking method, the binding modes of MTx to three closely related channels (Kv1.1, Kv1.2 and Kv1.3) are examined. We show that MTx forms more favorable electrostatic interactions with the outer vestibule of Kv1.2 compared to Kv1.1 and Kv1.3, consistent with the selectivity of MTx for Kv1.2 over Kv1.1 and Kv1.3 observed experimentally. One salt bridge in the bound complex of MTx-Kv1.2 forms and breaks in a simulation period of 20 ns, suggesting the dynamic nature of toxin-channel interactions. The toxin selectivity likely arises from the differences in the shape of the channel outer vestibule, giving rise to distinct orientations of MTx on block. Potential of mean force calculations show that MTx blocks Kv1.1, Kv1.2 and Kv1.3 with an IC(50) value of 6 µM, 0.6 nM and 18 µM, respectively.This work was supported by the National Health and Medical Research Council of Australia (http://www.nhmrc.gov.au). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript

Generalized Langevin models of molecular dynamics simulations with applications to ion channels

We present a new methodology, which combines molecular dynamics and stochastic dynamics, for modeling the permeation of ions across biological ion channels. Using molecular dynamics, a free energy profile is determined for the ion(s) in the channel, and the distribution of random and frictional forces is measured over discrete segments of the ion channel. The parameters thus determined are used in stochastic dynamics simulations based on the nonlinear generalized Langevin equation. We first provide the theoretical basis of this procedure, which we refer to as "distributional molecular dynamics," and detail the methods for estimating the parameters from molecular dynamics to be used in stochastic dynamics. We test the technique by applying it to study the dynamics of ion permeation across the gramicidin pore. Given the known difficulty in modeling the conduction of ions in gramicidin using classical molecular dynamics, there is a degree of uncertainty regarding the validity of the MD-derived potential of mean force (PMF) for gramicidin. Using our techniques and systematically changing the PMF, we are able to reverse engineer a modified PMF which gives a current-voltage curve closely matching experimental results.This work was supported by grants from the National Health and Medical Research Council of Australia. The calculations upon which this work is based were carried out using the SGI Altix cluster of the Australian National University Supercomputer Facility. NAMD was developed by the Theoretical and Computational Biophysics Group in the Beckman Institute for Advanced Science and Technology at the University of Illinois at Urbana-Champaign

The effect of hydrophobic and hydrophilic channel walls on the structure and diffusion of water and ions

Molecular dynamics simulations are carried out to determine the effects of channel wall structure on water and ion properties. We compare hydrophobic (Lennard-Jones 5-3 and atomic) and molecular-hydrophilic cylindrical pores of 2-6 Å in effective radius

Synthetic cation-selective nanotube: Permeant cations chaperoned by anions

The ability to design ion-selective, synthetic nanotubes which mimic biological ion channels may have significant implications for the future treatment of bacteria, diseases, and as ultrasensitive biosensors. We present the design of a synthetic nanotube made from carbon atoms that selectively allows monovalent cations to move across and rejects all anions. The cation-selective nanotube mimics some of the salient properties of biological ion channels. Before practical nanodevices are successfully fabricated it is vital that proof-of-concept computational studies are performed. With this in mind we use molecular and stochastic dynamics simulations to characterize the dynamics of ion permeation across a single-walled (10, 10), 36 Å long, carbon nanotube terminated with carboxylic acid with an effective radius of 5.08 Å. Although cations encounter a high energy barrier of 7 kT, its height is drastically reduced by a chloride ion in the nanotube. The presence of a chloride ion near the pore entrance thus enables a cation to enter the pore and, once in the pore, it is chaperoned by the resident counterion across the narrow pore. The moment the chaperoned cation transits the pore, the counterion moves back to the entrance to ferry another ion. The synthetic nanotube has a high sodium conductance of 124 pS and shows linear current-voltage and current-concentration profiles. The cation-anion selectivity ratio ranges from 8 to 25, depending on the ionic concentrations in the reservoirs.We acknowledge the support from the National Health and Medical Research Council and the MAWA Trust

Binding of fullerenes and nanotubes to MscL

Multi-drug resistance is becoming an increasing problem in the treatment of bacterial infections and diseases. The mechanosensitive channel of large conductance (MscL) is highly conserved among prokaryotes. Evidence suggests that a pharmacological agent that can affect the gating of, or block the current through, MscL has significant potential as a new class of antimicrobial compound capable of targeting a range of pathogenic bacteria with minimal side-effects to infected patients. Using molecular dynamics we examine the binding of fullerenes and nanotubes to MscL and demonstrate that both are stable within the MscL pore. We predict that fullerenes will attenuate the flow of ions through MscL by reducing the pore volume available to water and ions, but nanotubes will prevent pore closure resulting in a permanently open pore. Moreover, we confirm experimentally that it is possible to attenuate the flow of ions through MscL using a C60-γ 3 cyclodextrin complex

Alpha-Linolenic Acid-Enriched Butter Promotes Fatty Acid Remodeling and Thermogenic Activation in the Brown Adipose Tissue

Supplementation with n-3 long-chain (LC) polyunsaturated fatty acids (PUFA) is known to promote thermogenesis via the activation of brown adipose tissue (BAT). Agricultural products that are biofortified with α-linolenic acid (ALA), the precursor of n-3 LC PUFA, have been launched to the market, but their impact on BAT function is unknown. This study aimed to evaluate the effects of ALA-biofortified butter on lipid metabolism and thermogenic functions in the BAT. C57BL/6 mice were fed a high-fat diet containing ALA-biofortified butter (n3Bu, 45% calorie from fat) for ten weeks in comparison with the isocaloric high-fat diets prepared from conventional butter or margarine. The intake of n3Bu significantly reduced the whitening of BAT and increased the thermogenesis in response to acute-cold treatment. Also, n3Bu supplementation is linked with the remodeling of BAT by promoting bioconversion into n-3 LC PUFA, FA elongation and desaturation, and mitochondrial biogenesis. Taken together, our results support that ALA-biofortified butter is a novel source of n-3 PUFA, which potentiates the BAT thermogenic function

Impacts of Two Types of El Niño and La Niña Events on Typhoon Activity

The HadISST (Hadley Centre Sea Ice and Sea Surface Temperature) dataset is used to define the years of El Niño, El Niño Modoki, and La Niña events and to find out the impacts of these events on typhoon activity. The results show that the formation positions of typhoon are farther eastward moving in El Niño years than in La Niña years and much further eastward in El Niño Modoki years. The lifetime and the distance of movement are longer, and the intensity of typhoons is stronger in El Niño and in El Niño Modoki years than in La Niña years. The Accumulated Cyclone Energy of typhoon is highly correlated with the Oceanic Niño Index with a correlation coefficient of 0.79. We also find that the typhoons anomalously decrease during El Niño years but increase during El Niño Modoki years. Besides, there are two types of El Niño Modoki, I and II. The intensity of typhoon in El Niño Modoki I years is stronger than in El Niño Modoki II years. Furthermore, the centroid position of the Western Pacific Warm Pool is strongly related to the area of typhoon formation with a correlation coefficient of 0.95

Trapping a Free-propagating Single-photon into an Atomic Ensemble as a Quantum Stationary Light Pulse

Efficient photon-photon interaction is one of the key elements for realizing quantum information processing. The interaction, however, must often be mediated through an atomic medium due to the bosonic nature of photons, and the interaction time, which is critically linked to the efficiency, depends on the properties of the atom-photon interaction. While the electromagnetically induced transparency effect does offer the possibility of photonic quantum memory, it does not enhance the interaction time as it fully maps the photonic state to an atomic state. The stationary light pulse (SLP) effect, on the contrary, traps the photonic state inside an atomic medium with zero group velocity, opening up the possibility of the enhanced interaction time. In this work, we report the first experimental demonstration of trapping a free-propagating single-photon into a cold atomic ensemble via the quantum SLP (QSLP) process. We conclusively show that the quantum properties of the single-photon state are preserved well during the QSLP process. Our work paves the way to new approaches for efficient photon-photon interactions, exotic photonic states, and many-body simulations in photonic systems