An introduction to classical molecular dynamics simulation for experimental scattering users

Classical molecular dynamics simulations are a common component of multi-modal analyses from scattering measurements, such as small-angle scattering and diffraction. Users of these experimental techniques often have no formal training in the theory and practice of molecular dynamics simulation, leading to the possibility of these simulations being treated as a "black box" analysis technique. In this article, we describe an open educational resource (OER) designed to introduce classical molecular dynamics to users of scattering methods. This resource is available as a series of interactive web pages, which can be easily accessed by students, and as an open source software repository, which can be freely copied, modified, and redistributed by educators. The topic covered in this OER includes classical atomistic modelling, parameterising interatomic potentials, molecular dynamics simulations, typical sources of error, and some of the approaches to using simulations in the analysis of scattering data.Comment: Electronic Supplementary Information (ESI) available: All analysis/plotting scripts and figure files, allowing for a fully reproducible, and automated, analysis workflow for the work presented is available at \url{https://github.com/arm61/sim_and_scat_paper} (DOI: 10.5281/zenodo.2556826) under a CC BY-SA 4.0 licens

The effect of polymer end-group on the formation of styrene – maleic acid lipid particles (SMALPs)

A series of block copolymers comprising styrene and maleic acid (SMA) has been prepared using RAFT polymerisation. RAFT often results in a large hydrophobic alkylthiocarbonylthio end group and this work examines its effect on the solution behaviour of the copolymers. SMA variants with, and without, this end group were synthesised and their behaviour compared with a commercially-available random copolymer of similar molecular weight. Dynamic light scattering and surface tension measurements found the RAFT-copolymers preferentially self-assembled into higher-order aggregates in aqueous solution. Small angle neutron scattering using deuterated styrene varients add support to the accepted model that these agreggates comprise a solvent-protected styrenic core with an acid-rich shell. Replacing the hydrophobic RAFT end group with a more hydrophilic nitrile caused differences in the resulting surface activity, attributed to the ability of the adjoining styrene homoblock to drive aggregation. Each of the copolymers formed SMALP nanodiscs with DMPC lipids, which were found to encapsulate a model membrane protein, gramicidin. However, end group variation affected solubilisition of DPPC, a lipid with a higher phase transition temperature. When using RAFT-copolymers terminated with a hydrophobic group, swelling of the bilayer and greater penetration of the homoblock into the nanodisc core occurred with increasing homoblock length. Conversely, commercial and nitrile-terminated RAFT-copolymers produced nanodisc sizes that stayed constant, instead indicating interaction at the edge of the lipid patch. The results highlight how even minor changes to the copolymer can modify the amphiphilic balance between regions, knowledge useful towards optimising copolymer structure to enhance and control nanodisc formation

Coupling Lipid Nanoparticle Structure and Automated Single Particle Composition Analysis to Design Phospholipase Responsive Nanocarriers

Lipid nanoparticles (LNPs) are versatile structures with tunable physicochemical properties that are ideally suited as a platform for vaccine delivery and RNA therapeutics. A key barrier to LNP rational design is the inability to relate composition and structure to intracellular processing and function. Here we combine Single Particle Automated Raman Trapping Analysis (SPARTA®) with small angle scattering (SAXS / SANS) techniques to link LNP composition with internal structure and morphology and to monitor dynamic LNP - phospholipase D (PLD) interactions. Our analysis demonstrates that phospholipase D, a key intracellular trafficking mediator, can access the entire LNP lipid membrane to generate stable, anionic LNPs. PLD activity on vesicles with matched amounts of enzyme substrate was an order of magnitude lower, indicating that the LNP lipid membrane structure can be used to control enzyme interactions. This represents an opportunity to design enzyme-responsive LNP solutions for stimuli-responsive delivery and diseases where PLD is dysregulated

Tuneable peptide cross-linked nanogels for enzyme-triggered protein delivery

Many diseases are associated with the dysregulated activity of enzymes, such as matrix metalloproteinases (MMPs). This dysregulation can be leveraged in drug delivery to achieve disease- or site-specific cargo release. Self-assembled polymeric nanoparticles are versatile drug carrier materials due to the accessible diversity of polymer chemistry. However, efficient loading of sensitive cargo, such as proteins, and introducing functional enzyme-responsive behaviour remain challenging. Herein, peptide-crosslinked, temperature-sensitive nanogels for protein delivery were designed to respond to MMP-7, which is overexpressed in many pathologies including cancer and inflammatory diseases. The incorporation of N-cyclopropylacrylamide (NCPAM) into N-isopropylacrylamide (NIPAM)-based copolymers enabled us to tune the polymer lower critical solution temperature from 33 to 44 °C, allowing the encapsulation of protein cargo and nanogel-crosslinking at slightly elevated temperatures. This approach resulted in nanogels that were held together by MMP-sensitive peptides for enzyme-specific protein delivery. We employed a combination of cryogenic transmission electron microscopy (cryo-TEM), dynamic light scattering (DLS), small angle neutron scattering (SANS), and fluorescence correlation spectroscopy (FCS) to precisely decipher the morphology, self-assembly mechanism, enzyme-responsiveness, and model protein loading/release properties of our nanogel platform. Simple variation of the peptide linker sequence and combining multiple different crosslinkers will enable us to adjust our platform to target specific diseases in the future

ABC block copolymer micelles driving the thermogelation:Scattering, imaging and spectroscopy

Thermoresponsive polymers have attracted much scientific attention due to their capacity for temperature-driven hydrogel formation. For biomedical applications, such as drug delivery, this transition should be tuned below body temperature to facilitate controlled and targeted drug release. We have recently developed a thermoresponsive polymer that forms gel at low concentrations (2 w/w%) in aqueous media and offers a cost-effective alternative to thermoresponsive systems currently being applied in clinics. This polymer is an ABC triblock terpolymer, where A, B, and C correspond to oligo(ethylene glycol) methyl ether methacrylate with average Mn 300 g mol−1 (OEGMA300), n-butyl methacrylate (BuMA), and di(ethylene glycol) methyl ether methacrylate (DEGMA). To investigate the self-assembly and the gelation mechanism in diluted solutions, we used small-angle neutron scattering (SANS) on 1 w/w% (below the gelation concentration) and 5 w/w% solutions (above the gelation concentration). As a comparison, we also investigated the solutions of the most studied thermoresponsive polymer, namely, Pluronic F127, an ABA triblock bipolymer made of ethylene glycol (A) and propylene glycol (B) blocks. SANS revealed that the in-house synthesised polymer forms elliptical cylinders, whose length increases significantly with temperature. In contrast, Pluronic F127 solutions form core-shell spherical micelles, which slightly elongate with temperature. Transmission electron microscopy images support the SANS findings, with tubular/worm structures being present. Variable-temperature circular dichroism (CD) and proton nuclear magnetic resonance (1H NMR) spectroscopy experiments reveal insights on the tacticity, structural changes, and molecular origin of the self-assembly

Investigating multigelator systems across multiple length scales

No abstract available

Atomic structures of naphthalene dipeptide micelles unravel mechanisms of assembly and gelation

Peptide-based biopolymers have gained increasing attention due to their versatile applications. A naphthalene dipeptide (2NapFF) can form chirality-dependent tubular micelles, leading to supramolecular gels. The precise molecular arrangement within these micelles and the mechanism governing gelation have remained enigmatic. We determined, at near-atomic resolution, cryoelectron microscopy structures of the 2NapFF micelles LL-tube and LD-tube, generated by the stereoisomers (ʟ,ʟ)-2NapFF and (ʟ,ᴅ)-2NapFF, respectively. The structures reveal that the fundamental packing of dipeptides is driven by the systematic π-π stacking of aromatic rings and that same-charge repulsion between the carbonyl groups is responsible for the stiffness of both tubes. The structural analysis elucidates how a single residue’s altered chirality gives rise to markedly distinct tubular structures and sheds light on the mechanisms underlying the pH-dependent gelation of LL- and LD-tubes. The understanding of dipeptide packing and gelation mechanisms provides insights for the rational design of 2NapFF derivatives, enabling the modulation of micellar dimensions

Gelation enabled charge separation following visible light excitation using self-assembled perylene bisimides

Perylene bisimides (PBIs) can be functionalised to enable controlled aggregation into complex supramolecular structures and are promising materials for photovoltaic and solar fuel applications. Amino acid appended PBIs such as PBI-alanine (PBI-A) have been found to form photoconductive films containing worm-like structures that enable charge transport. However, despite being strong chromophores in the visible region, when PBI-A films are prepared by drying down solutions, activity only occurs under UV illumination. This limits potential applications. The requirement for UV illumination has previously been suggested to be due to the large ion-pair energy in the low dielectric environment of the dried samples. Hydrogel films, rehydrated xerogels and dry xerogels of PBI-A can also be prepared offering an ideal sample set to examine the influence of hydration on charge-separation. Using transient absorption (TA) spectroscopy, we demonstrate a correlation between water content and efficiency of generation of long-lived charge separated states within the PBI-A materials, highlighting their potential, particularly for light-driven water splitting

On the syneresis of an OPV functionalised dipeptide hydrogel

We describe a new dipeptide hydrogel based on an oligophenylene vinylene core. After gelation, the initial network evolves, expelling solvent and resulting in syneresis. We describe this process and the effects in the bulk properties of the material

Elongation rate and average length of amyloid fibrils in solution using isotope-labelled small-angle neutron scattering.

Funder: Boehringer Ingelheim FondsFunder: University of BathWe demonstrate a solution method that allows both elongation rate and average fibril length of assembling amyloid fibrils to be estimated. The approach involves acquisition of real-time neutron scattering data during the initial stages of seeded growth, using contrast matched buffer to make the seeds effectively invisible to neutrons. As deuterated monomers add on to the seeds, the labelled growing ends give rise to scattering patterns that we model as cylinders whose increase in length with time gives an elongation rate. In addition, the absolute intensity of the signal can be used to determine the number of growing ends per unit volume, which in turn provides an estimate of seed length. The number of ends did not change significantly during elongation, demonstrating that any spontaneous or secondary nucleation was not significant compared with growth on the ends of pre-existing fibrils, and in addition providing a method of internal validation for the technique. Our experiments on initial growth of alpha synuclein fibrils using 1.2 mg ml-1 seeds in 2.5 mg ml-1 deuterated monomer at room temperature gave an elongation rate of 6.3 ± 0.5 Å min-1, and an average seed length estimate of 4.2 ± 1.3 μm