Molecular Dynamics Refinement of Open State Serotonin 5-HT3A Receptor Structures.

Pentameric ligand-gated ion channels play an important role in mediating fast neurotransmissions. As a member of this receptor family, cation-selective 5-HT3 receptors are a clinical target for treating nausea and vomiting associated with chemotherapy and radiation therapy (Thompson and Lummis, 2006). Multiple cryo-electron microscopy (cryo-EM) structures of 5-HT3 receptors have been determined in distinct functional states (e.g., open, closed, etc.) (Basak et al., 2018; Basak et al., 2018; Polovinkin et al., 2018; Zhang et al., 2015). However, recent work has shown that the transmembrane pores of the open 5-HT3 receptor structures rapidly collapse and become artificially asymmetric in molecular dynamics (MD) simulations. To avoid this hydrophobic collapse, Dämgen and Biggin developed an equilibration protocol that led to a stable open state structure of the glycine receptor in MD simulations (Dämgen and Biggin, 2020). However, the protocol failed to yield open-like structures of the 5-HT3 receptor in our simulations. Here, we present a refined equilibration protocol that involves the rearrangement of the transmembrane helices to achieve stable open state structures of the 5-HT3 receptor that allow both water and ion permeation through the channel. Notably, channel gating is mediated through collective movement of the transmembrane helices, involving not only pore lining M2 helices but also their cross-talk with the adjacent M1 and M3 helices. Thus, the successful application of our refined equilibration protocol underscores the importance of the conformational coupling between the transmembrane helices in stabilizing open-like structures of the 5-HT3 receptor.

Improved chemical and isotopic labeling of biomembranes in Bacillus subtilis by leveraging CRISPRi inhibition of beta-ketoacyl-ACP synthase (fabF).

Assessing the structure of living microbial cell membranes is a challenging analytical goal. The cell membrane is defined by its transverse structure, an approximately 5 nm-thick selectively permeable bilayer that serves many important cellular functions. Compositionally complex, dynamic, and organized in both the transverse and lateral dimensions, understanding the cell membrane structure-and the role that structure plays in cellular function, communication, and environmental sensing is an active scientific effort. Previously, we have devised a novel isotopic labeling approach for membrane lipids to enable direct in vivo structural studies of the cell membrane in the Gram-positive bacterium, Bacillus subtilis, using small-angle neutron scattering. This was accomplished through a genetic inhibition of fatty acid (FA) degradation (ΔfadN) and a chemical inhibition of FA biosynthesis using cerulenin, an irreversible inhibitor of type II fatty acid synthases. Here, we improve upon the previous system by introducing a dCas9/sgRNA-fabF complex that blocks transcription of the essential fabF gene when under xylose induction. This leads to greater sensitivity to cerulenin in the mutant strain (JEBS102) and more robust cell growth when supplementary FAs are introduced to the culture medium. A subtle change in FA uptake is noted when compared to the prior labeling strategy. This is seen in the gas chromatography/mass spectrometry (GC/MS) data as a higher ratio of n16:0 to a15:0, and manifests in an apparent increase in the membrane thickness determined via neutron scattering. This represents an improved method of isotopic labeling for the cell membrane of Bacillus subtilis; enabling improved investigations of cellular uptake and utilization of FAs, cell membrane structure and organization as a phenotypic response to metabolic and environmental changes.

Refinement of SARS-CoV-2 envelope protein structure in a native-like environment by molecular dynamics simulations.

COVID-19 has become an unprecedented threat to human health. The SARS-CoV-2 envelope (E) protein plays a critical role in the viral maturation process and pathogenesis. Despite intensive investigation, its structure in physiological conditions remains mysterious: no high-resolution full-length structure is available and only an NMR structure of the transmembrane (TM) region has been determined. Here, we present a refined E protein structure, using molecular dynamics (MD) simulations to investigate its structure and dynamics in a 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) bilayer system. Our initial homology model based upon the SARS-CoV E protein structure is shown to be unstable in the lipid bilayer, and the H3 helices tend to move away from the membrane center to the membrane-water interface. A more stable model was developed by replacing all H3 helices with the fully equilibrated H3 structure sampled in the MD simulations. This refined model exhibited more favorable contacts with lipids and water than the original homology model and induced local membrane curvature, decreasing local lipid order. Interestingly, the pore radius profiles showed that the channel in both homology and refined models remained in a closed state throughout the simulations. We also demonstrated the utility of this structure to develop anti-SARS-CoV-2 drugs by docking a library of FDA-approved, investigational, and experimental drugs to the refined E protein structure, identifying 20 potential channel blockers. This highlights the power of MD simulations to refine low-resolution structures of membrane proteins in a native-like membrane environment, shedding light on the structural features of the E protein and providing a platform for the development of novel antiviral treatments.

Electrostatic Contributions to the Binding Free Energy of Nicotine to the Acetylcholine Binding Protein.

Biomolecular binding relies on specific attractive interactions between two partner molecules, including electrostatics, dispersion, hydrophobicity, and solvation. Assessing the contributions of electrostatic interactions to binding is key to the understanding of ligand binding mechanisms and the design of improved biomolecular binders. For example, nicotine is a well-known agonist of nicotinic acetylcholine receptors (nAChRs), but the molecular mechanisms for the differential action of nicotine on brain and muscle nAChRs remain elusive. In this work, we have chosen the acetylcholine binding protein (AChBP) in complex with nicotine as a model system to interrogate the electrostatic contributions to nicotine binding. Our absolute binding free energy simulations confirm that nicotine binds AChBP predominantly in its protonated (charged) form. By comparing energetic contributions from decomposed interactions for either neutral or charged nicotine, our calculations shed light on the nature of the binding of nicotine to the AChBP. The preferred binding of charged nicotine over neutral nicotine originates from its stronger electrostatic interactions with AChBP, a cation-π interaction to a tryptophan residue and a hydrogen bond between nicotine and the backbone carbonyl of the tryptophan, whereas the major force driving the binding process appears to be van der Waals interactions. The various nonelectrostatic terms can also indirectly modulate the electrostatic interactions through fine-tuning the binding pose of the ligand in the binding site, providing an explanation of why the binding specificity of nicotine to the brain versus muscle nAChRs is driven by electrostatic interaction, given that the immediate binding site residues, including the key tryptophan residue, are identical in the two receptors.

Influence of vanillic acid immobilization in Nafion membranes on intramembrane diffusion and structural properties.

Pulsed field gradient (PFG) NMR in combination with quasielastic neutron scattering (QENS) was used to investigate self-diffusion of water and acetone in Nafion membranes with and without immobilized vanillic acid (VA). Complementary characterization of these membranes was performed by small angle X-ray scattering (SAXS) and NMR relaxometry. This study was motivated by the recent data showing that an organic acid, such as VA, in Nafion can preserve its catalytic activity in the presence of water even at high intra-polymer water concentrations corresponding up to 100% ambient relative humidity. However, there is currently no clear understanding of how immobilized organic acid molecules influence the microscopic transport properties and related structural properties of Nafion. Microscopic diffusion data measured by PFG NMR and QENS are compared for Nafion with and without VA. For displacements smaller than the micrometer-sized domains previously reported for Nafion, the VA addition was not observed to lead to any significant changes in the water and/or acetone self-diffusivity measured by each technique inside Nafion. However, the reported PFG NMR data present evidence of a different influence of acetone concentration in the membranes with and without VA on the water permeance of the interfaces between neighboring micrometer-sized domains. The reported diffusion data are correlated with the results of SAXS structural characterization and NMR relaxation data for water and acetone.

Multiscale Microstructure, Composition, and Stability of Surfactant/Polymer Foams.

Inclusion of polymer additives is a known strategy to improve foam stability, but questions persist about the amount of polymer incorporated in the foam and the resulting structural changes that impact material performance. Here, we study these questions in sodium dodecyl sulfate (SDS)/hydroxypropyl methylcellulose (HPMC) foams using a combination of flow injection QTOF mass spectrometry and small-angle neutron scattering (SANS) measurements leveraging contrast matching. Mass spectrometry results demonstrate polymer incorporation and retention in the foam during drainage by measuring the HPMC-to-SDS ratio. The results confirm a ratio matching the parent solution and stability over the time of our measurements. The SANS measurements leverage precise contrast matching to reveal detailed descriptions of the micellar structure (size, shape, and aggregation number) along with the foam film thickness. The presence of HPMC leads to thicker films, correlating with increased foam stability over the first 15-20 min after foam production. Taken together, mass spectrometry and SANS present a structural and compositional picture of SDS/HPMC foams and an approach amenable to systematic study for foams, gathering mechanistic insights and providing formulation guidance for rational foam design.

Transition between Different Diffusion Regimes and Its Relationship with Structural Properties in Nafion by High Field Diffusion NMR in Combination with Small-Angle X-ray and Neutron Scattering.

Pulsed field gradient (PFG) NMR at high field was utilized to directly observe a transition between two different diffusion regimes in a Nafion 117 membrane loaded with water and acetone. Although water self-diffusivity at small water loadings was observed to be diffusion time-independent in the limit of small and large diffusion times, it showed a significant decrease with increasing diffusion time at intermediate times corresponding to root mean square displacements on the order of several microns. Under our experimental conditions, no self-diffusivity dependence on diffusion time was found for water at large water loadings and for acetone at all studied acetone loadings. The diffusion time-dependent self-diffusivity at small water concentration is explained by the existence of finite domains of interconnected water channels with sizes in the range of several microns that form in Nafion in the presence of acetone. The domain sizes and permeance of transport barriers separating adjacent domains are estimated based on the measured PFG NMR data. At large water concentrations, the water channels form a fully interconnected network, resulting in time-independent self-diffusivity. The absence of such a percolation-like transition with increasing molecular concentration for acetone is attributed to a difference in the regions available for water and acetone diffusion in Nafion. The diffusion data are correlated with and supported by structural data obtained using small-angle X-ray and neutron scattering techniques. These techniques reveal distinct water channels with radial dimensions in the nanometer range increasing upon water addition, while acetone appears to be in an interfacial perfluoroether region, reducing the size of the radial channel dimension.

Structure, Hydration, and Interactions of Native and Hydrophobically Modified Phytoglycogen Nanoparticles.

Phytoglycogen is a highly branched polymer of glucose produced as soft, compact nanoparticles by sweet corn. Properties such as softness, porosity, and mechanical integrity, combined with nontoxicity and biodegradability, make phytoglycogen nanoparticles ideal for applications involving the human body, ranging from skin moisturizing and rejuvenation agents in personal care formulations to functional therapeutics in biomedicine. To further broaden the range of applications, phytoglycogen nanoparticles can be chemically modified with hydrophobic species such as octenyl succinic anhydride (OSA). Here, we present a self-consistent model of the particle structure, water content, and degree of chemical modification of the particles, as well as the emergence of well-defined interparticle spacings in concentrated dispersions, based on small-angle neutron scattering (SANS) measurements of aqueous dispersions of native phytoglycogen nanoparticles and particles that were hydrophobically modified using octenyl succinic anhydride (OSA) in both its protiated (pOSA) and deuterated (dOSA) forms. Measurements on native particles with reduced polydispersity have allowed us to refine the particle morphology, which is well described by a hairy particle (core-chain) geometry with short chains decorating the surface of the particles. The isotopic variants of OSA-modified particles enhanced the scattering contrast for neutrons, revealing lightly modified hairy chains for small degrees of substitution (DS) of OSA, and a raspberry particle geometry for the largest DS value, where the OSA-modified hairy chains collapse to form small seeds on the surface of the particles. This refined model of native and OSA-modified phytoglycogen nanoparticles establishes a quantitative basis for the development of new applications of this promising sustainable nanotechnology.

Impact of Fatty-Acid Labeling of Bacillus subtilis Membranes on the Cellular Lipidome and Proteome.

Developing cultivation methods that yield chemically and isotopically defined fatty acid (FA) compositions within bacterial cytoplasmic membranes establishes an in vivo experimental platform to study membrane biophysics and cell membrane regulation using novel approaches. Yet before fully realizing the potential of this method, it is prudent to understand the systemic changes in cells induced by the labeling procedure itself. In this work, analysis of cellular membrane compositions was paired with proteomics to assess how the proteome changes in response to the directed incorporation of exogenous FAs into the membrane of Bacillus subtilis. Key findings from this analysis include an alteration in lipid headgroup distribution, with an increase in phosphatidylglycerol lipids and decrease in phosphatidylethanolamine lipids, possibly providing a fluidizing effect on the cell membrane in response to the induced change in membrane composition. Changes in the abundance of enzymes involved in FA biosynthesis and degradation are observed; along with changes in abundance of cell wall enzymes and isoprenoid lipid production. The observed changes may influence membrane organization, and indeed the well-known lipid raft-associated protein flotillin was found to be substantially down-regulated in the labeled cells - as was the actin-like protein MreB. Taken as a whole, this study provides a greater depth of understanding for this important cell membrane experimental platform and presents a number of new connections to be explored in regard to modulating cell membrane FA composition and its effects on lipid headgroup and raft/cytoskeletal associated proteins.

Molecular origins of bulk viscosity in liquid water.

The rapid equilibrium fluctuations of water molecules are intimately connected to the rheological response; molecular motions resetting the local structure and stresses seen as flow and volume changes. In the case of water or hydrogen bonding liquids generally, the relationship is a non-trivial consideration due to strong directional interactions complicating theoretical models and necessitating clear observation of the timescale and nautre of the associated equilibrium motions. Recent work has illustrated a coincidence of timescales for short range sub-picosecond motions and the implied timescale for the shear viscosity response in liquid water. Here, neutron and light scattering methods are used to experimentally illustrate the timescale of bulk viscosity and provide a description of the associated molecular relaxation. Brillouin scattering has been used to establish the timescale of bulk viscosity; and borrowing the Maxwell approach, the ratio of the bulk viscosity, ζ, to the bulk modulus, K, yields a relaxation time, τB, which emerges on the order of 1-2 ps in the 280 K to 303 K temperature range. Inelastic neutron scattering is subsequently used to describe the motions of water and heavy water at the molecular scale, providing both coherent and incoherent scattering data. A rotational (alternatively described as localized) motion of water protons on the 1-2 ps timescale is apparent in the incoherent scattering spectra of water, while the coherent spectra from D2O on the length scale of the first sharp diffraction peak, describing the microscopic density fluctuations of water, confirms the relaxation of water structure at a comparable timescale of 1-2 ps. The coincidence of these three timescales provides a mechanistic description of the bulk viscous response, with the local structure resetting due to rotational/localized motions on the order of 1-2 ps, approximately three times slower than the relaxations associated with shear viscosity. In this way we show that the shear viscous response is most closely associated with changes in water network connectivity, while the bulk viscous response is associated with local density fluctuations.

Branched-Chain Fatty Acid Content Modulates Structure, Fluidity, and Phase in Model Microbial Cell Membranes.

Recent progress in understanding the importance and origins of lipid rafts in microbial cell membranes has focused attention on membranes containing branched-chain fatty acids. The working hypothesis is that branched fatty acids increase the fluidity of the bilayer, analogous to unsaturated fatty acids in membranes of higher organisms. Here, we perform a series of 7 µs long atomistic simulations on biomimetic, branched-chain lipid containing bilayer patches, systematically varying the amount of the straight-chain fatty acid component, n16:0, from 7.0 to 47.3 mol %. The simulations reveal thickening and ordering of the bilayer as well as higher bilayer viscosity and bending modulus with increasing n16:0 content, thus providing quantitative support that branched fatty acids increase the bilayer fluidity. A sharp transition in these properties is observed at ∼20% n16:0 content, resembling a phase change. The simulations provide the first access to ordered and disordered phases in a bacterial cell membrane mimic containing branched-chain lipids. Granted several assumptions, a comparison of these phases provides estimates of physical properties such as hydrophobic mismatch (∼1.2 Å), difference in bending moduli (∼15.7 kBT), and the line tension (∼0.6 pN) for a putative lipid raft in the cell membrane of an organism such as Bacillus subtilis or Staphylococcus aureus.

Lipid Rafts: Buffers of Cell Membrane Physical Properties.

Lateral organization of lipids in the cell membrane appears to be an ancient feature of the cell, given the existence of lipid rafts in both eukaryotic and prokaryotic cells. Currently seen as platforms for protein partitioning, we posit that lipid rafts are capable of playing another role: stabilizing membrane physical properties over varying temperatures and other environmental conditions. Membrane composition defines the mechanical and viscous properties of the bilayer. The composition also varies strongly with temperature, with systematic changes in the partitioning of high and low melting temperature membrane components. In this way, rafts function as buffers of membrane physical properties, progressively counteracting environmental changes via compositional changes; i.e., more high melting lipids partition to the fluid phase with increasing temperature, increasing the bending modulus and viscosity, as thermal effects decrease these same properties. To provide an example of this phenomenon, we have performed neutron scattering experiments and atomistic molecular dynamics simulations on a phase separated model membrane. The results demonstrate a buffering effect in both the lateral diffusion coefficient and the bending modulus of the fluid phase upon changing temperature. This demonstration highlights the potentially advantageous stabilizing effect of complex lipid compositions in response to temperature and potentially other membrane destabilizing environmental conditions.

Neutron scattering in the biological sciences: progress and prospects.

The scattering of neutrons can be used to provide information on the structure and dynamics of biological systems on multiple length and time scales. Pursuant to a National Science Foundation-funded workshop in February 2018, recent developments in this field are reviewed here, as well as future prospects that can be expected given recent advances in sources, instrumentation and computational power and methods. Crystallography, solution scattering, dynamics, membranes, labeling and imaging are examined. For the extraction of maximum information, the incorporation of judicious specific deuterium labeling, the integration of several types of experiment, and interpretation using high-performance computer simulation models are often found to be particularly powerful.

Bacillus subtilis Lipid Extract, A Branched-Chain Fatty Acid Model Membrane.

Lipid extracts are an excellent choice of model biomembrane; however at present, there are no commercially available lipid extracts or computational models that mimic microbial membranes containing the branched-chain fatty acids found in many pathogenic and industrially relevant bacteria. We advance the extract of Bacillus subtilis as a standard model for these diverse systems, providing a detailed experimental description and equilibrated atomistic bilayer model included as Supporting Information to this Letter and at ( http://cmb.ornl.gov/members/cheng ). The development and validation of this model represents an advance that enables more realistic simulations and experiments on bacterial membranes and reconstituted bacterial membrane proteins.

Structural relaxation, viscosity, and network connectivity in a hydrogen bonding liquid.

In liquids, the ability of neighboring molecules to rearrange and jostle past each other is directly related to viscosity, the property which describes the propensity to flow. The presence of hydrogen bonds (H-bonds) complicates the molecular scale picture of viscosity. H-Bonds are attractive, directional interactions between molecules which, in some cases, result in transient network structures. In this work, we use experimental and computational methods to demonstrate that the timescale of H-bond network reorganization is the dominant dynamical timescale associated with viscosity for the case of the model H-bonding liquid n-methylacetamide (NMA). This molecule is a peptide analog which forms a transient linear H-bond network. Individual H-bond lifetimes and dynamical fluctuations were observed on the timescale of 1.5 ps, while collective motions and the longest lived population of H-bond partner lifetimes were observed on the order of 20 ps, in agreement with the Maxwell relaxation time. This identifies a mechanism which may aid in understanding the emergence of various complex phenomena arising from transient molecular structures, with implications ranging from the internal dynamics of proteins, to the glass transition, to better understanding the origins of the unique properties of H-bonding liquids.

The in vivo structure of biological membranes and evidence for lipid domains.

Examining the fundamental structure and processes of living cells at the nanoscale poses a unique analytical challenge, as cells are dynamic, chemically diverse, and fragile. A case in point is the cell membrane, which is too small to be seen directly with optical microscopy and provides little observational contrast for other methods. As a consequence, nanoscale characterization of the membrane has been performed ex vivo or in the presence of exogenous labels used to enhance contrast and impart specificity. Here, we introduce an isotopic labeling strategy in the gram-positive bacterium Bacillus subtilis to investigate the nanoscale structure and organization of its plasma membrane in vivo. Through genetic and chemical manipulation of the organism, we labeled the cell and its membrane independently with specific amounts of hydrogen (H) and deuterium (D). These isotopes have different neutron scattering properties without altering the chemical composition of the cells. From neutron scattering spectra, we confirmed that the B. subtilis cell membrane is lamellar and determined that its average hydrophobic thickness is 24.3 ± 0.9 Ångstroms (Å). Furthermore, by creating neutron contrast within the plane of the membrane using a mixture of H- and D-fatty acids, we detected lateral features smaller than 40 nm that are consistent with the notion of lipid rafts. These experiments-performed under biologically relevant conditions-answer long-standing questions in membrane biology and illustrate a fundamentally new approach for systematic in vivo investigations of cell membrane structure.

Description of Hydration Water in Protein (Green Fluorescent Protein) Solution.

The structurally and dynamically perturbed hydration shells that surround proteins and biomolecules have a substantial influence upon their function and stability. This makes the extent and degree of water perturbation of practical interest for general biological study and industrial formulation. We present an experimental description of the dynamical perturbation of hydration water around green fluorescent protein in solution. Less than two shells (∼5.5 Å) were perturbed, with dynamics a factor of 2-10 times slower than bulk water, depending on their distance from the protein surface and the probe length of the measurement. This dependence on probe length demonstrates that hydration water undergoes subdiffusive motions (τ ∝ q-2.5 for the first hydration shell, τ ∝ q-2.3 for perturbed water in the second shell), an important difference with neat water, which demonstrates diffusive behavior (τ ∝ q-2). These results help clarify the seemingly conflicting range of values reported for hydration water retardation as a logical consequence of the different length scales probed by the analytical techniques used.

Subnanometer Structure of an Asymmetric Model Membrane: Interleaflet Coupling Influences Domain Properties.

Cell membranes possess a complex three-dimensional architecture, including nonrandom lipid lateral organization within the plane of a bilayer leaflet, and compositional asymmetry between the two leaflets. As a result, delineating the membrane structure-function relationship has been a highly challenging task. Even in simplified model systems, the interactions between bilayer leaflets are poorly understood, due in part to the difficulty of preparing asymmetric model membranes that are free from the effects of residual organic solvent or osmotic stress. To address these problems, we have modified a technique for preparing asymmetric large unilamellar vesicles (aLUVs) via cyclodextrin-mediated lipid exchange in order to produce tensionless, solvent-free aLUVs suitable for a range of biophysical studies. Leaflet composition and structure were characterized using isotopic labeling strategies, which allowed us to avoid the use of bulky labels. NMR and gas chromatography provided precise quantification of the extent of lipid exchange and bilayer asymmetry, while small-angle neutron scattering (SANS) was used to resolve bilayer structural features with subnanometer resolution. Isotopically asymmetric POPC vesicles were found to have the same bilayer thickness and area per lipid as symmetric POPC vesicles, demonstrating that the modified exchange protocol preserves native bilayer structure. Partial exchange of DPPC into the outer leaflet of POPC vesicles produced chemically asymmetric vesicles with a gel/fluid phase-separated outer leaflet and a uniform, POPC-rich inner leaflet. SANS was able to separately resolve the thicknesses and areas per lipid of coexisting domains, revealing reduced lipid packing density of the outer leaflet DPPC-rich phase compared to typical gel phases. Our finding that a disordered inner leaflet can partially fluidize ordered outer leaflet domains indicates some degree of interleaflet coupling, and invites speculation on a role for bilayer asymmetry in modulating membrane lateral organization.

Structure and Hydration of Highly-Branched, Monodisperse Phytoglycogen Nanoparticles.

Phytoglycogen is a naturally occurring polysaccharide nanoparticle made up of extensively branched glucose monomers. It has a number of unusual and advantageous properties, such as high water retention, low viscosity, and high stability in water, which make this biomaterial a promising candidate for a wide variety of applications. In this study, we have characterized the structure and hydration of aqueous dispersions of phytoglycogen nanoparticles using neutron scattering. Small angle neutron scattering results suggest that the phytoglycogen nanoparticles behave similar to hard sphere colloids and are hydrated by a large number of water molecules (each nanoparticle contains between 250% and 285% of its mass in water). This suggests that phytoglycogen is an ideal sample in which to study the dynamics of hydration water. To this end, we used quasielastic neutron scattering (QENS) to provide an independent and consistent measure of the hydration number, and to estimate the retardation factor (or degree of water slow-down) for hydration water translational motions. These data demonstrate a length-scale dependence in the measured retardation factors that clarifies the origin of discrepancies between retardation factor values reported for hydration water using different experimental techniques. The present approach can be generalized to other systems containing nanoconfined water.

Water and Lipid Bilayers.

Water is crucial to the structure and function of biological membranes. In fact, the membrane's basic structural unit, i.e. the lipid bilayer, is self-assembled and stabilized by the so-called hydrophobic effect, whereby lipid molecules unable to hydrogen bond with water aggregate in order to prevent their hydrophobic portions from being exposed to water. However, this is just the beginning of the lipid-bilayer-water relationship. This mutual interaction defines vesicle stability in solution, controls small molecule permeation, and defines the spacing between lamella in multi-lamellar systems, to name a few examples. This chapter will describe the structural and dynamical properties central to these, and other water- lipid bilayer interactions.