Nicholas J. Brooks

DNA Double Helices Recognize Mutual Sequence Homology in a Protein Free Environment

The structure and biological function of the DNA double helix are based on interactions recognizing sequence complementarity between two single strands of DNA. A single DNA strand can also recognize the double helix sequence by binding in its groove and forming a triplex. We now find that sequence recognition occurs between intact DNA duplexes without any single-stranded elements as well. We have imaged a mixture of two fluorescently tagged, double helical DNA molecules that have identical nucleotide composition and length (50% GC; 294 base pairs) but different sequences. In electrolytic solution at minor osmotic stress, these DNAs form discrete liquid-crystalline aggregates (spherulites). We have observed spontaneous segregation of the two kinds of DNA within each spherulite, which reveals that nucleotide sequence recognition occurs between double helices separated by water in the absence of proteins, consistent with our earlier theoretical hypothesis. We thus report experimental evidence and discuss possible mechanisms for the recognition of homologous DNAs from a distance.

Pressure effects on lipid membrane structure and dynamics

The effect of hydrostatic pressure on lipid structure and dynamics is highly important as a tool in biophysics and bio-technology, and in the biology of deep sea organisms. Despite its importance, high hydrostatic pressure remains significantly less utilised than other thermodynamic variables such as temperature and chemical composition. Here, we give an overview of some of the theoretical aspects which determine lipid behaviour under pressure and the techniques and technology available to study these effects. We also summarise several recent experiments which highlight the information available from these approaches.

A 3-D Hexagonal Inverse Micellar Lyotropic Phase

Lipids that are found in cell membranes form a variety of self-assembled phases in the presence of water. Many of these structures are liquid-crystalline with structural motifs mirrored in cells and organelles and can be exploited in the delivery of drugs and genes. We report the discovery of a lyotropic liquid crystalline phase based on a 3-D hexagonal close-packed arrangement of inverse micelles, of space group P6(3)/mmc. This is the first new inverse lyotropic liquid-crystalline phase to be reported for two decades and is the only known lyotropic phase whose structure consists of a close packing of identical inverse micelles.

Ordered micellar and inverse micellar lyotropic phases

In this article we review the ordered micellar and inverse micellar lyotropic liquid-crystalline phases that can be formed by amphiphilic molecules such as lipids and surfactants. We focus first on the self-assembly of amphiphiles into aggregates, and then consider the interfacial curvature and the role of curvature elasticity and packing constraints in determining the allowed structures. We then review the range of ordered micellar and inverse micellar phases that have so far been observed in a variety of surfactant and lipid systems. Finally, we describe certain characteristic properties, such as the epitaxy between phases, and the self-diffusion and electrical conductivity within such ordered micellar phases.

Automated high pressure cell for pressure jump x-ray diffraction

A high pressure cell for small and wide-angle x-ray diffraction measurements of soft condensed matter samples has been developed, incorporating a fully automated pressure generating network. The system allows both static and pressure jump measurements in the range of 0.1-500 MPa. Pressure jumps can be performed as quickly as 5 ms, both with increasing and decreasing pressures. Pressure is generated by a motorized high pressure pump, and the system is controlled remotely via a graphical user interface to allow operation by a broad user base, many of whom may have little previous experience of high pressure technology. Samples are loaded through a dedicated port allowing the x-ray windows to remain in place throughout an experiment; this facilitates accurate subtraction of background scattering. The system has been designed specifically for use at beamline I22 at the Diamond Light Source, United Kingdom, and has been fully integrated with the I22 beamline control systems.

Structural basis for recognition of the pore-forming toxin intermedilysin by human complement receptor CD59

Summary Pore-forming proteins containing the structurally conserved membrane attack complex/perforin fold play an important role in immunity and host-pathogen interactions. Intermedilysin (ILY) is an archetypal member of a cholesterol-dependent cytolysin subclass that hijacks the complement receptor CD59 to make cytotoxic pores in human cells. ILY directly competes for the membrane attack complex binding site on CD59, rendering cells susceptible to complement lysis. To understand how these bacterial pores form in lipid bilayers and the role CD59 plays in complement regulation, we determined the crystal structure of human CD59 bound to ILY. Here, we show the ILY-CD59 complex at 3.5 Å resolution and identify two interfaces mediating this host-pathogen interaction. An ILY-derived peptide based on the binding site inhibits pore formation in a CD59-containing liposome model system. These data provide insight into how CD59 coordinates ILY monomers, nucleating an early prepore state, and suggest a potential mechanism of inhibition for the complement terminal pathway.

Thermotropic and lyotropic liquid crystalline phases of Guerbet branched-chain -D-glucosides

The effect of chain branching on glycolipid thermotropic and lyotropic phases was investigated for a series of synthetic β-D-glucosides derived from Guerbet alcohols, whose total hydrocarbon chain length ranged from C8 to C24. The compounds, which can be viewed as isosteric mimics for glycoglycerolipids, were synthesised in high purity and their liquid crystalline phases were studied using optical polarising microscopy (OPM), and small-angle X-ray diffraction. When dry, the shortest compound (total C8) exhibits a monotropic Lα phase while longer ones (C16 and C20) adopt inverse hexagonal HII phases. The C24 compound forms an ordered lamellar phase at room temperature, but exhibits a metastable HII phase upon cooling. Curiously the intermediate chain length homologue (C12) adopts an isotropic inverse micellar (L2) phase in the dry state over the range of temperatures studied. Upon hydration, the C8 compound dissolves, and the C12 compound forms a fluid lamellar Lα phase. The C16 Guerbet glucoside (i.e. β-Glc-C10C6) exhibits an inverse bicontinuous cubic phase of space group Ia3d in excess water, never previously observed in branched-chain lipids, and very seldom observed in excess water. The C20 compound remains in the HII phase upon hydrating, with the lattice parameter swelling substantially.

Imaging phase separation in model lipid membranes through the use of BODIPY based molecular rotors

In order to fully understand the dynamics of processes within biological lipid membranes, it is necessary to possess an intimate knowledge of the physical state and ordering of lipids within the membrane. Here we report the use of three molecular rotors based on meso-substituted boron-dipyrrin (BODIPY) in combination with fluorescence lifetime spectroscopy to investigate the viscosity and phase behaviour of model lipid bilayers. In phase-separated giant unilamellar vesicles, we visualise both liquid-ordered (Lo) and liquid-disordered (Ld) phases using fluorescence lifetime imaging microscopy (FLIM), determining their associated viscosity values, and investigate the effect of composition on the viscosity of these phases. Additionally, we use molecular dynamics simulations to investigate the orientation of the BODIPY probes within the bilayer, as well as using molecular dynamics simulations and fluorescence correlation spectroscopy (FCS) to compare diffusion coefficients with those predicted from the fluorescence lifetimes of the probes.

Hydrostatic pressure effects on the lamellar to gyroid cubic phase transition of monolinolein at limited hydration.

Monoacylglycerol based lipids are highly important model membrane components and attractive candidates for drug encapsulation and as delivery agents. However, optimizing the properties of these lipids for applications requires a detailed understanding of the thermodynamic factors governing the self-assembled structures that they form. Here, we report on the effects of hydrostatic pressure, temperature, and water composition on the structural behavior and stability of inverse lyotropic liquid crystalline phases adopted by monolinolein (an unsaturated monoacylglycerol having cis-double bonds at carbon positions 9 and 12) under limited hydration conditions. Six pressure-temperature phase diagrams have been determined using small-angle X-ray diffraction at water contents between 15 wt % and 27 wt % water, in the range 10-40 °C and 1-3000 bar. The gyroid bicontinuous cubic (Q(II)(G)) phase is formed at low pressure and high temperatures, transforming to a fluid lamellar (L(α)) phase at high pressures and low temperature via a region of Q(II)(G)/L(α) coexistence. Pressure stabilizes the lamellar phase over the Q(II)(G) phase; at fixed pressure, increasing the water content causes the coexistence region to move to lower temperature. These trends are consistent throughout the hydration range studied. Moreover, at fixed temperature, increasing the water composition increases the pressure at which the Q(II)(G) to L(α) transition takes place. We discuss the qualitative effect of pressure, temperature, and water content on the stability of the Q(II)(G) phase.

Engineering Compartmentalized Biomimetic Micro- and Nanocontainers

Compartmentalization of biological content and function is a key architectural feature in biology, where membrane bound micro- and nanocompartments are used for performing a host of highly specialized and tightly regulated biological functions. The benefit of compartmentalization as a design principle is behind its ubiquity in cells and has led to it being a central engineering theme in construction of artificial cell-like systems. In this review, we discuss the attractions of designing compartmentalized membrane-bound constructs and review a range of biomimetic membrane architectures that span length scales, focusing on lipid-based structures but also addressing polymer-based and hybrid approaches. These include nested vesicles, multicompartment vesicles, large-scale vesicle networks, as well as droplet interface bilayers, and double-emulsion multiphase systems (multisomes). We outline key examples of how such structures have been functionalized with biological and synthetic machinery, for example, to manufacture and deliver drugs and metabolic compounds, to replicate intracellular signaling cascades, and to demonstrate collective behaviors as minimal tissue constructs. Particular emphasis is placed on the applications of these architectures and the state-of-the-art microfluidic engineering required to fabricate, functionalize, and precisely assemble them. Finally, we outline the future directions of these technologies and highlight how they could be applied to engineer the next generation of cell models, therapeutic agents, and microreactors, together with the diverse applications in the emerging field of bottom-up synthetic biology.