pH-Dependent Conformational Plasticity of Monoclonal Antibodies at the SiO/Water Interface: Insights from Neutron Reflectivity and Molecular Dynamics.

Investigating the molecular conformations of monoclonal antibodies (mAbs) adsorbed at the solid/liquid interface is crucial for understanding mAb solution stability and advancing the development of mAb-based biosensors. This study examines the pH-dependent conformational plasticity of a human IgG1k mAb, COE-3, at the SiO/water interface under varying pH conditions (pH 5.5 and 9).

Extreme heterogeneity in the microrheology of lamellar surfactant gels analyzed with neural networks.

The heterogeneity of the viscoelasticity of a lamellar gel network based on cetyl-trimethylammonium chloride and cetostearyl alcohol was studied using particle-tracking microrheology. A recurrent neural network (RNN) architecture was used for estimating the Hurst exponent, H, on small sections of tracks of probe spheres moving with fractional Brownian motion. Thus, dynamic segmentation of tracks via neural networks was used in microrheology and it is significantly more accurate than using mean square displacements (MSDs).

Electrical signaling in three-dimensional bacterial biofilms using an agent-based fire-diffuse-fire model.

Agent-based models were used to describe electrical signaling in bacterial biofilms in three dimensions. Specifically, wavefronts of potassium ions in Escherichia coli biofilms subjected to stress from blue light were modeled from experimental data. Electrical signaling occurs only when the biofilms grow beyond a threshold size, which we have shown to vary with the K^{+} ion diffusivity, and the K^{+} ion threshold concentration, which triggered firing in the fire-diffuse-fire model.

The viscoelasticity of high concentration monoclonal antibodies using particle tracking microrheology.

The viscoelasticity of monoclonal antibodies (mAbs) is important during their production, formulation, and drug delivery. High concentration mAbs can provide higher efficacy therapeutics (e.g.

Electrical Impedance Spectroscopy with Bacterial Biofilms: Neuronal-like Behavior.

Negative capacitance at low frequencies for spiking neurons was first demonstrated in 1941 (K. S. Cole) by using extracellular electrodes.

Heterogeneous anomalous transport in cellular and molecular biology.

It is well established that a wide variety of phenomena in cellular and molecular biology involve anomalous transport e.g. the statistics for the motility of cells and molecules are fractional and do not conform to the archetypes of simple diffusion or ballistic transport.

Ensemble heterogeneity mimics ageing for endosomal dynamics within eukaryotic cells.

Transport processes of many structures inside living cells display anomalous diffusion, such as endosomes in eukaryotic cells. They are also heterogeneous in space and time. Large ensembles of single particle trajectories allow the heterogeneities to be quantified in detail and provide insights for mathematical modelling.

Intramembrane Nanoaggregates of Antimicrobial Peptides Play a Vital Role in Bacterial Killing.

Recent developments in antimicrobial peptides (AMPs) have focused on the rational design of short sequences with less than 20 amino acids due to their relatively low synthesis costs and ease of correlation of the structure-function relationship. However, gaps remain in the understanding of how short cationic AMPs interact with the bacterial outer and inner membranes to affect their antimicrobial efficacy and dynamic killing. The membrane-lytic actions of two designed AMPs, G(IIKK) I-NH (G ) and G(IIKK) I-NH (G ), and previously-studied controls GLLDLLKLLLKAAG-NH (LDKA, biomimetic) and GIGAVLKVLTTGLPALISWIKRKR-NH (Melittin, natural) are examined.

Assessing the risk of resistance to cationic biocides incorporating realism-based and biophysical approaches.

The control of microorganisms is a key objective in disease prevention and in medical, industrial, domestic, and food-production environments. Whilst the effectiveness of biocides in these contexts is well-evidenced, debate continues about the resistance risks associated with their use. This has driven an increased regulatory burden, which in turn could result in a reduction of both the deployment of current biocides and the development of new compounds and formulas.

Local Analysis of Heterogeneous Intracellular Transport: Slow and Fast Moving Endosomes.

Trajectories of endosomes inside living eukaryotic cells are highly heterogeneous in space and time and diffuse anomalously due to a combination of viscoelasticity, caging, aggregation and active transport. Some of the trajectories display switching between persistent and anti-persistent motion, while others jiggle around in one position for the whole measurement time. By splitting the ensemble of endosome trajectories into slow moving subdiffusive and fast moving superdiffusive endosomes, we analyzed them separately.

Network organisation and the dynamics of tubules in the endoplasmic reticulum.

The endoplasmic reticulum (ER) is a eukaryotic subcellular organelle composed of tubules and sheet-like areas of membrane connected at junctions. The tubule network is highly dynamic and undergoes rapid and continual rearrangement. There are currently few tools to evaluate network organisation and dynamics.

Structural Disruptions of the Outer Membranes of Gram-Negative Bacteria by Rationally Designed Amphiphilic Antimicrobial Peptides.

Gram-negative bacteria are covered by both an inner cytoplasmic membrane (IM) and an outer membrane (OM). Antimicrobial peptides (AMPs) must first permeate through the OM and cell wall before attacking the IM to cause cytoplasmic leakage and kill the bacteria. The bacterial OM is an asymmetric bilayer with the outer leaflet primarily composed of lipopolysaccharides (LPSs) and the inner leaflet composed of phospholipids (PLs).

How do Self-Assembling Antimicrobial Lipopeptides Kill Bacteria?

Antimicrobial peptides are promising alternatives to traditional antibiotics. A group of self-assembling lipopeptides was formed by attaching an acyl chain to the N-terminus of α-helix-forming peptides with the sequence C-G(IIKK)I-NH (CG, = 4-12 and = 2). CG self-assemble into nanofibers above their critical aggregation concentrations (CACs).

Aggregated Amphiphilic Antimicrobial Peptides Embedded in Bacterial Membranes.

Molecular dynamics (MD) simulations, stochastic optical reconstruction microscopy (STORM), and neutron reflection (NR) were combined to explore how antimicrobial peptides (AMPs) can be designed to promote the formation of nanoaggregates in bacterial membranes and impose effective bactericidal actions. Changes in the hydrophobicity of the designed AMPs were found to have a strong influence on their bactericidal potency and cytotoxicity. G(IIKK)I-NH (G) achieved low minimum inhibition concentrations (MICs) and effective dynamic kills against both antibiotic-resistant and -susceptible bacteria.

A versatile route to edge-specific modifications to pristine graphene by electrophilic aromatic substitution.

Electrophilic aromatic substitution produces edge-specific modifications to CVD graphene and graphene nanoplatelets that are suitable for specific attachment of biomolecules.

Deciphering anomalous heterogeneous intracellular transport with neural networks.

Intracellular transport is predominantly heterogeneous in both time and space, exhibiting varying non-Brownian behavior. Characterization of this movement through averaging methods over an ensemble of trajectories or over the course of a single trajectory often fails to capture this heterogeneity. Here, we developed a deep learning feedforward neural network trained on fractional Brownian motion, providing a novel, accurate and efficient method for resolving heterogeneous behavior of intracellular transport in space and time.

Dual self-assembly of supramolecular peptide nanotubes to provide stabilisation in water.

Self-assembling peptides have the ability to spontaneously aggregate into large ordered structures. The reversibility of the peptide hydrogen bonded supramolecular assembly make them tunable to a host of different applications, although it leaves them highly dynamic and prone to disassembly at the low concentration needed for biological applications. Here we demonstrate that a secondary hydrophobic interaction, near the peptide core, can stabilise the highly dynamic peptide bonds, without losing the vital solubility of the systems in aqueous conditions.

Hydrophobic Control of the Bioactivity and Cytotoxicity of de Novo-Designed Antimicrobial Peptides.

Antimicrobial peptides (AMPs) can target bacterial membranes and kill bacteria through membrane structural damage and cytoplasmic leakage. A group of surfactant-like cationic AMPs was developed from substitutions to selective amino acids in the general formula of G(IIKK)I-NH, (called G, a de novo AMP), to explore the correlation between AMP hydrophobicity and bioactivity. A threshold surface pressure over 12 mN/m was required to cause measurable antimicrobial activity and this corresponded to a critical AMP concentration.

Reversible Thermoresponsive Peptide-PNIPAM Hydrogels for Controlled Drug Delivery.

Mixed thermoreversible gels were successfully fabricated by the addition of a thermosensitive polymer, poly(-isopropylacrylamide) (PNIPAM), to fibrillar nanostructures self-assembled from a short peptide IK. When the temperature was increased above the lower critical solution temperature of the PNIPAM, the molecules collapsed to form condensed globular particles, which acted as cross-links to connect different peptide nanofibrils and freeze their movements, resulting in the formation of a hydrogel. Since these processes were physically driven, such hydrogels could be reversibly switched between the sol and gel states as a function of temperature.

Super-Resolution Fluorescence Microscopy Study of the Production of K1 Capsules by Escherichia coli: Evidence for the Differential Distribution of the Capsule at the Poles and the Equator of the Cell.

The production of Escherichia coli K1 serotype capsule was investigated using direct stochastic optical reconstruction microscopy with live bacteria and graphene oxide-coated coverslips, overcoming many morphological artifacts found in other high-resolution imaging techniques. Super-resolution fluorescence images showed that the K1 capsular polysaccharide is not uniformly distributed on the cell surface, as previously thought. These studies demonstrated that on the cell surfaces the K1 capsule at the poles had bimodal thicknesses of 238 ± 41 and 323 ± 62 nm, whereas at the equator, there was a monomodal thickness of 217 ± 29 nm.

Active Modulation of States of Prestress in Self-Assembled Short Peptide Gels.

Peptide hydrogels are excellent candidates for medical therapeutics due to their tuneable viscoelastic properties, however, in vivo they will be subject to various osmotic pressures, temperature changes, and biological co-solutes, which could alter their performance. Peptide hydrogels formed from the synthetic peptide IK have a temperature-induced hardening of their shear modulus by a factor of 2. We show that the addition of uncross-linked poly( N-isopropylacrylamide) chains to the peptide gels increases the gels' temperature sensitivity by 3 orders of magnitude through the control of osmotic swelling and cross-linking.

Nanoribbons self-assembled from short peptides demonstrate the formation of polar zippers between β-sheets.

Peptide self-assembly is a hierarchical process, often starting with the formation of α-helices, β-sheets or β-hairpins. However, how the secondary structures undergo further assembly to form higher-order architectures remains largely unexplored. The polar zipper originally proposed by Perutz is formed between neighboring β-strands of poly-glutamine via their side-chain hydrogen bonding and helps to stabilize the sheet.

Non-Markovian intracellular transport with sub-diffusion and run-length dependent detachment rate.

Intracellular transport of organelles is fundamental to cell function and health. The mounting evidence suggests that this transport is in fact anomalous. However, the reasons for the anomaly is still under debate.

Quenched Stochastic Optical Reconstruction Microscopy (qSTORM) with Graphene Oxide.

Quenched Stochastic Optical Reconstruction Microscopy (qSTORM) was demonstrated with graphene oxide sheets, peptides and bacteria; a method of contrast enhancement with super-resolution fluorescence microscopy. Individual sheets of graphene oxide (GO) were imaged with a resolution of 16 nm using the quenching of fluorescence emission by GO via its large Resonant Energy Transfer (RET) efficiency. The method was then extended to image self-assembled peptide aggregates (resolution 19 nm) and live bacterial cells (resolution 55 nm, the capsular structure of E.

Single-Molecule Study of Peptide Gel Dynamics Reveals States of Prestress.

De novo peptide surfactant (IK) gels provide an ideal system to study the complex dynamics of lightly cross-linked semiflexible fibers because of their large contour lengths, simple chemistry, and slow dynamics. We used single-molecule fluorescence microscopy to record individual fibers and Fourier decomposition of the fiber dynamics to separate thermal contributions to the persistence length from compressive states of prestress (SPS). Our results show that SPS in the network depend strongly on peptide concentration, buffer, and pH and that the fibril energies in SPS follow a Lévy distribution.