Multiscale Models of the Antimicrobial Peptide Protegrin-1 on Gram-Negative Bacteria Membranes

Antimicrobial peptides (AMPs) are naturally-occurring molecules that exhibit strong antibiotic properties against numerous infectious bacterial strains. Because of their unique mechanism of action, they have been touted as a potential source for novel antibiotic drugs. We present a summary of computational investigations in our lab aimed at understanding this unique mechanism of action, in particular the development of models that provide a quantitative connection between molecular-level biophysical phenomena and relevant biological effects. Our work is focused on protegrins, a potent class of AMPs that attack bacteria by associating with the bacterial membrane and forming transmembrane pores that facilitate the unrestricted transport of ions. Using fully atomistic molecular dynamics simulations, we have computed the thermodynamics of peptide-membrane association and insertion, as well as peptide aggregation. We also present a multi-scale analysis of the ion transport properties of protegrin pores, ranging from atomistic molecular dynamics simulations to mesoscale continuum models of single-pore electrodiffusion to models of transient ion transport from bacterial cells. Overall, this work provides a quantitative mechanistic description of the mechanism of action of protegrin antimicrobial peptides across multiple length and time scales

Controlling Binder Adhesion to Impact Electrode Mesostructures and Transport

The complex three-phase composition of lithium-ion battery electrodes, containing an ion-conducting pore phase, a nanoporous electron-conducting carbon binder domain (CBD) phase, and an active material (AM) phase, provides several avenues of mesostructural engineering to enhance battery performance. We demonstrate a promising strategy for engineering electrode mesostructures by controlling the strength of adhesion between the AM and CBD phases. Using high-fidelity, physics-based colloidal and granular dynamics simulations, we predict that this strategy can provide significant control over electrochemical transport-relevant properties such as ionic conductivity, electronic conductivity, and available AM-electrolyte interface area. Importantly, the proposed strategy could be experimentally realized through surface functionalization of the AM and CBD phases and would be compatible with traditional electrode manufacturing methods

Poisson-Nernst-Planck models of nonequilibrium ion electrodiffusion through a protegrin transmembrane pore.

Protegrin peptides are potent antimicrobial agents believed to act against a variety of pathogens by forming nonselective transmembrane pores in the bacterial cell membrane. We have employed 3D Poisson-Nernst-Planck (PNP) calculations to determine the steady-state ion conduction characteristics of such pores at applied voltages in the range of -100 to +100 mV in 0.1 M KCl bath solutions. We have tested a variety of pore structures extracted from molecular dynamics (MD) simulations based on an experimentally proposed octomeric pore structure. The computed single-channel conductance values were in the range of 290-680 pS. Better agreement with the experimental range of 40-360 pS was obtained using structures from the last 40 ns of the MD simulation, where conductance values range from 280 to 430 pS. We observed no significant variation of the conductance with applied voltage in any of the structures that we tested, suggesting that the voltage dependence observed experimentally is a result of voltage-dependent channel formation rather than an inherent feature of the open pore structure. We have found the pore to be highly selective for anions, with anionic to cationic current ratios (I(Cl-)/I(K+)) on the order of 10(3). This is consistent with the highly cationic nature of the pore but surprisingly in disagreement with the experimental finding of only slight anionic selectivity. We have additionally tested the sensitivity of our PNP model to several parameters and found the ion diffusion coefficients to have a significant influence on conductance characteristics. The best agreement with experimental data was obtained using a diffusion coefficient for each ion set to 10% of the bulk literature value everywhere inside the channel, a scaling used by several other studies employing PNP calculations. Overall, this work presents a useful link between previous work focused on the structure of protegrin pores and experimental efforts aimed at investigating their conductance characteristics

Effects of Functional Groups and Ionization on the Structure of Alkanethiol-Coated Gold Nanoparticles

We report classical atomistic molecular dynamics simulations of alkanethiol-coated gold nanoparticles solvated in water and decane, as well as at water/vapor interfaces. The structure of the coatings is analyzed as a function of various functional end groups, including amine and carboxyl groups in various ionization states. We study both neutral and charged end groups for two different chain lengths (9 and 17 carbons). For the charged end groups, we simulated both mono- and divalent counterions. For the longer alkanes, we find significant local bundling of chains on the nanoparticle surface, which results in highly asymmetric coatings. In general, the charged end groups attenuate this effect by enhancing the water solubility of the nanoparticles. On the basis of the coating structures and density profiles, we can qualitatively infer the overall solubility of the nanoparticles. This asymmetry in the alkanethiol coatings is likely to have a significant effect on aggregation behavior. Our simulations elucidate the mechanism by which modulating the end group charge state can be used to control coating structure and therefore nanoparticle solubility and aggregation behavior