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.

Modeling the partitioning of amphiphilic molecules and co-solvents in biomembranes

Amphiphilic co-solvents can have a significant impact on the structure, organization and physical properties of lipid bilayers. Describing the mutual impact of partitioning and induced structure changes is therefore a crucial consideration for a range of topics such as anesthesia and other pharmacokinetic effects, as well as microbial solvent tolerance in the production of biofuels and other fermentation products, where molecules such as ethanol, butanol or acetic acid might be generated. Small-angle neutron scattering (SANS) is a key method for studying lipid and polymer bilayer structures, with many models for extracting bilayer structure (thickness, area per lipid etc.) from scattering data in use today. However, the molecular details of co-solvent partitioning are conflated with induced changes to bilayer structure, making interpretation and modeling of the scattering curves a challenge with the existing set of models. To address this, a model of a bilayer structure is presented which invokes a two-term partition constant accounting for the localization of the co-solvent within the bilayer. This model was validated using a series of SANS measurements of lipid vesicles in the presence of the co-solvent tetrahydrofuran (THF), showing several strategies of how to deploy the two-parameter partition constant model to describe scattering data and extract both structure and partitioning information from the data. Molecular dynamics simulations are then used to evaluate assumptions of the model, provide additional molecular scale details and illustrate its complementary nature to the data fitting procedure. This approach results in estimates of the partition coefficient for THF in 1,2-dimyristoyl-sn-glycero-3-phosphocholine at 35°C, along with an estimate of the fraction of THF residing in the hydrophobic core of the membrane. The authors envision that this model will be applicable to a wide range of other bilayer/amphiphile interactions and provide the associated code needed to implement this model as a fitting algorithm for scattering data in the SasView suite.

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.

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.

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.

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 shear viscous response of water is closely associated with changes in network connectivity on the sub ps timescale. The bulk viscous response is shown here to be associated with local density fluctuations and rotational motion around 1–3 ps.

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.

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.

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

The structure and dynamics of the model H-bonding liquid,n-methylacetamide (NMA) have been studied, revealing the connection between the timescale of H-bond network reorganization and viscosity.

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.

On scattered waves and lipid domains: detecting membrane rafts with X-rays and neutrons

In order to understand the biological role of lipids in cell membranes, it is necessary to determine the mesoscopic structure of well-defined model membrane systems. Neutron and X-ray scattering are non-invasive, probe-free techniques that have been used extensively in such systems to probe length scales ranging from angstroms to microns, and dynamics occurring over picosecond to millisecond time scales. Recent developments in the area of phase separated lipid systems mimicking membrane rafts will be presented, and the underlying concepts of the different scattering techniques used to study them will be discussed in detail.

Elasticity and Inverse Temperature Transition in Elastin

Elastin is a structural protein and biomaterial that provides elasticity and resilience to a range of tissues. This work provides insights into the elastic properties of elastin and its peculiar inverse temperature transition (ITT). These features are dependent on hydration of elastin and are driven by a similar mechanism of hydrophobic collapse to an entropically favorable state. Using neutron scattering, we quantify the changes in the geometry of molecular motions above and below the transition temperature, showing a reduction in the displacement of water-induced motions upon hydrophobic collapse at the ITT. We also measured the collective vibrations of elastin gels as a function of elongation, revealing no changes in the spectral features associated with local rigidity and secondary structure, in agreement with the entropic origin of elasticity.

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.

Dynamics and rigidity in an intrinsically disordered protein, β-casein

The emergence of intrinsically disordered proteins (IDPs) as a recognized structural class has forced the community to confront a new paradigm of structure, dynamics, and mechanical properties for proteins. We present novel data on the similarities and differences in the dynamics and nanomechanical properties of IDPs and other biomacromolecules on the picosecond time scale. An IDP, β-casein (CAS), has been studied in a calcium bound and unbound state using neutron and light scattering techniques. We show that CAS partially folds and stiffens upon calcium binding, but in the unfolded state, it is softer than folded proteins such as green fluorescence protein (GFP). We also see that some localized diffusive motions in CAS have a larger amplitude than in GFP at this time scale but are still smaller than those observed in tRNA. In spite of these differences, CAS dynamics are consistent with the classes of motions seen in folded protein on this time scale.

Secondary structure and rigidity in model proteins

There is tremendous interest in understanding the role that secondary structure plays in the rigidity and dynamics of proteins. In this work we analyze nanomechanical properties of proteins chosen to represent different secondary structures: α-helices (myoglobin and bovine serum albumin), β-barrels (green fluorescent protein), and α + β + loop structures (lysozyme). Our experimental results show that in these model proteins, the β motif is a stiffer structural unit than the α-helix in both dry and hydrated states. This difference appears not only in the rigidity of the protein, but also in the amplitude of fast picosecond fluctuations. Moreover, we show that for these examples the secondary structure correlates with the temperature- and hydration-induced changes in the protein dynamics and rigidity. Analysis also suggests a connection between the length of the secondary structure (α-helices) and the low-frequency vibrational mode, the so-called boson peak. The presented results suggest an intimate connection of dynamics and rigidity with the protein secondary structure.

Elastic and conformational softness of a globular protein

Flexibility, or softness, is crucial for protein function and consists of a conformational component, involving jumps between potential wells, and an elastic component, involving fluctuations within the wells. Combining molecular dynamics simulation with incoherent neutron scattering and light scattering measurements on green fluorescent protein, we reveal a relationship between the intrawell fluctuations and elastic moduli of the protein. This finding leads to a simple means of experimentally separating the conformational from the elastic atomic displacements.

Surface modification of the conducting polymer, polypyrrole, via affinity peptide

A novel strategy for affinity-based surface modification of the conducting polymer, polypyrrole, (PPy), has been developed. A 12-amino acid peptide (THRTSTLDYFVI, hereafter denoted T59) was previously identified via the phage display technique. This peptide noncovalently binds to the chlorine-doped conducting polymer polypyrrole (PPyCl). Studies have previously shown that conductive polymers have promising application in neural electrodes, sensors, and for improving regeneration and healing of peripheral nerves and other tissues. Thus, the strong and specific attachment of bioactive molecules to the surface of PPy using the T59 affinity peptide is an exciting new approach to enhance the bioactivity of electrically active materials for various biomedical applications. We demonstrate this by using T59 as a tether to modify PPyCl with the laminin fragment IKVAV to enhance cell interactions, as well as with the so-called stealth molecule poly(ethylene glycol; PEG) to decrease cell interactions. Using these two modification strategies, we were able to control cell attachment and neurite extension on the PPy surface, which is critical for different applications (i.e., the goal for tissue regeneration is to enhance cell interactions, whereas the goal for electrode and sensor applications is to reduce glial cell interactions and thus decrease scarring). Significantly, the conductivity of the PPyCl surface was unaffected by this surface modification technique, which is not the case with other methods that have been explored to surface modify conducting polymers. Finally, using subcutaneous implants, we confirmed that the PPyCl treated with the T59 peptide did not react in vivo differently than untreated PPyCl.

Dynamics of protein and its hydration water: neutron scattering studies on fully deuterated GFP

We present a detailed analysis of the picosecond-to-nanosecond motions of green fluorescent protein (GFP) and its hydration water using neutron scattering spectroscopy and hydrogen/deuterium contrast. The analysis reveals that hydration water suppresses protein motions at lower temperatures (<~ 200 K), and facilitates protein dynamics at high temperatures. Experimental data demonstrate that the hydration water is harmonic at temperatures <~ 180-190 K and is not affected by the proteins' methyl group rotations. The dynamics of the hydration water exhibits changes at ~ 180-190 K that we ascribe to the glass transition in the hydrated protein. Our results confirm significant differences in the dynamics of protein and its hydration water at high temperatures: on the picosecond-to-nanosecond timescale, the hydration water exhibits diffusive dynamics, while the protein motions are localized to <~3 Å. The diffusion of the GFP hydration water is similar to the behavior of hydration water previously observed for other proteins. Comparison with other globular proteins (e.g., lysozyme) reveals that on the timescale of 1 ns and at equivalent hydration level, GFP dynamics (mean-square displacements and quasielastic intensity) are of much smaller amplitude. Moreover, the suppression of the protein dynamics by the hydration water at low temperatures appears to be stronger in GFP than in other globular proteins. We ascribe this observation to the barrellike structure of GFP.

An assessment of comparative methods for approaching electrode polarization in dielectric permittivity measurements

We examine the validity of three common methods for analysis and correction of the electrode polarization (EP) effect in dielectric spectroscopy measurements of conductive liquid samples. The methods considered are (i) algorithmic treatment by modeling the EP behavior at constant phase angle, (ii) varying the size of the electrode gap, and (iii) polypyrrole (PPyPss) layered electrodes. The latter is a relatively recent innovation suggested to be an efficient solution. We demonstrate that PPyPss coated electrodes do not diminish the effect of EP, and even add relaxation processes of its own. Our conclusion is that these polymer coated electrodes are not suitable for the correction of electrode polarization.

The effects of hyaluronic acid hydrogels with tunable mechanical properties on neural progenitor cell differentiation

We report the ability to direct the differentiation pathway of neural progenitor cells (NPCs) within hydrogels having tunable mechanical properties. By modifying the polymeric sugar hyaluronic acid (HA), a major extracellular matrix component in the fetal mammalian brain, with varying numbers of photocrosslinkable methacrylate groups, hydrogels could be prepared with bulk compressive moduli spanning the threefold range measured for neonatal brain and adult spinal cord. Ventral midbrain-derived NPCs were photoencapsulated into HA hydrogels and remained viable after encapsulation. After three weeks, the majority of NPCs cultured in hydrogels with mechanical properties comparable to those of neonatal brain had differentiated into neurons (ss-III tubulin-positive), many of which had extended long, branched processes, indicative of a relatively mature phenotype. In contrast, NPCs within stiffer hydrogels, with mechanical properties comparable to those of adult brain, had differentiated into mostly astrocytes (glial fibrillary acidic protein (GFAP)-positive). Primary spinal astrocytes cultured in the hydrogel variants for two weeks acquired a spread and elongated morphology only in the stiffest hydrogels evaluated, with mechanical properties similar to adult tissue. Results demonstrate that the mechanical properties of these scaffolds can assert a defining influence on the differentiation of ventral midbrain-derived NPCs, which have strong clinical relevance because of their ability to mature into dopaminergic neurons of the substantia nigra, cells that idiopathically degenerate in individuals suffering from Parkinson's disease.