Single particle and collective hydration dynamics for hydrophobic and hydrophilic peptides

We have conducted extensive molecular dynamics simulations to study the single particle and collective dynamics of water in solutions of N-acetyl-glycine-methylamide, a model hydrophilic protein backbone, and N-acetyl-leucine-methylamide, a model (amphiphilic) hydrophobic peptide, as a function of peptide concentration. Various analytical models commonly used in the analysis of incoherent quasielastic neutron scattering (QENS), are tested against the translational and rotational intermediate scattering function, the mean square displacement of the water molecule center of mass, and fits to the second-order rotational correlation function of water evaluated directly from the simulation data. We find that while the agreement between the model-free analysis and analytical QENS models is quantitatively poor, the qualitative feature of dynamical heterogeneity due to caging is captured well by all approaches. The center of mass collective and single particle intermediate scattering functions of water calculated for these peptide solutions show that the crossover from collective to single particle-dominated motions occurs at a higher value of Q for high concentration solutions relative to low concentration because of the greater restriction in movement of water molecules due to confinement. Finally, we have shown that at the same level of confinement of the two peptides, the aqueous amphiphilic amino acid solution shows the strongest deviation between single particle and collective dynamics relative to the hydrophilic amino acid, indicating that chemical heterogeneity induces even greater spatial heterogeneity in the water dynamics.     

Dielectric relaxation of aqueous solutions of hydrophilic versus amphiphilic peptides

We report on molecular dynamics simulations of the frequency-dependent dielectric relaxation spectra at room temperature for aqueous solutions of a hydrophilic peptide and an amphiphilic peptide at two concentrations. We find that only the high-concentration amphiphilic peptide solution exhibits an anomalous dielectric increment over that of pure water, while the hydrophilic peptide exhibits a significant dielectric decrement. The dielectric component analysis carried out by decomposing these peptide solutions into peptide, hydration layer, and outer layer(s) of water clearly shows the presence of a unique dipolar component with a relaxation time scale on the order of approximately 25 ps (compared to the bulk water time scale of approximately 11 ps) that originates from the interaction between the hydration layer water and the outer layer(s) of water. Results obtained from the dielectric component analysis further show the emergence of a distinct and much lower frequency relaxation process for the high-concentration amphiphilic peptide compared to the hydrophilic peptide due to strong peptide dipolar couplings to all constituents, accompanied by a slowing of the structural relaxation in all water layers, giving rise to time scales close to approximately 1 ns. We suggest that the molecular origin of the dielectric relaxation anomalies is due to frustration in the water network arising from the amphiphilic chemistry of the peptide that does not allow it to reorient on the picosecond time scale of bulk water motions. This explanation is consistent with the idea of the "slaving" of residue side chain motions to protein surface water, and furthermore offers the possibility that the anomalous dynamics observed from a number of spectroscopies arises at the interface of hydrophobic and hydrophilic domains on the protein surface.     

Separable cooperative and localized translational motions of water confined by a chemically heterogeneous environment

We report quasi-elastic neutron scattering experiments at two resolutions that probe timescales of picoseconds to nanoseconds for the hydration dynamics of water, confined in a concentrated solution of N-acetyl-leucine-methylamide (NALMA) peptides in water over a temperature range of 248 K to 288 K. The two QENS resolutions used allow for a clean separation of two observable translational components, and ultimately two very different relaxation processes, that become evident when analyzed under a combination of the jump diffusion model and the relaxation cage model. The first translational motion is a localized beta-relaxation process of the bound surface water, and exhibits an Arrhenius temperature dependence and a large activation energy of approximately 8 kcal mol(-1). The second non-Arrhenius translational component is a dynamical signature of the alpha-relaxation of more fluid water, exhibiting a glass transition temperature of approximately 116 K when fit to the Volger Fulcher Tamman functional form. These peptide solutions provide a novel experimental system for examining confinement in order to understand the dynamical transition in bulk supercooled water by removing the unwanted interface of the confining material on water dynamics.     

Forces between hydrophilic surfaces adsorbed with apolipoprotein AII alpha helices

To provide better understanding of how a protein secondary structure affects protein-protein and protein-surface interactions, forces between amphiphilic alpha-helical proteins (human apolipoprotein AII) adsorbed on a hydrophilic surface (mica) were measured using an interferometric surface force apparatus (SFA). Forces between surfaces with adsorbed layers of this protein are mainly composed of electrostatic double layer forces at large surface distances and of steric repulsive forces at small distances. We suggest that the amphiphilicity of the alpha-helix structure facilitates the formation of protein multilayers next to the mica surfaces. We found that protein-surface interaction is stronger than protein-protein interaction, probably due to the high negative charge density of the mica surface and the high positive charge of the protein at our experimental conditions. Ellipsometry was used to follow the adsorption kinetics of this protein on hydrophilic silica, and we observed that the adsorption rate is not only controlled by diffusion, but rather by the protein-surface interaction. Our results for dimeric apolipoprotein AII are similar to those we have reported for the monomeric apolipoprotein CI, which has a similar secondary structure but a different peptide sequence and net charge. Therefore, the observed force curves seem to be a consequence of the particular features of the amphiphilic alpha-helices.     

Communication: On the origin of the non-Arrhenius behavior in water reorientation dynamics

We combine molecular dynamics simulations and analytic modeling to determine the origin of the non-Arrhenius temperature dependence of liquid water's reorientation and hydrogen-bond dynamics between 235 K and 350 K. We present a quantitative model connecting hydrogen-bond exchange dynamics to local structural fluctuations, measured by the asphericity of Voronoi cells associated with each water molecule. For a fixed local structure the regular Arrhenius behavior is recovered, and the global anomalous temperature dependence is demonstrated to essentially result from a continuous shift in the unimodal structure distribution upon cooling. The non-Arrhenius behavior can thus be explained without invoking an equilibrium between distinct structures. In addition, the large width of the homogeneous structural distribution is shown to cause a growing dynamical heterogeneity and a non-exponential relaxation at low temperature.     

Why are water-hydrophobic interfaces charged?

We report ab initio molecular dynamics simulations of hydroxide and hydronium ions near a hydrophobic interface, indicating that both ions behave like amphiphilic surfactants that stick to a hydrophobic hydrocarbon surface with their hydrophobic side. We show that this behavior originates from the asymmetry of the molecular charge distribution which makes one end of the ions strongly hydrophobic while the other end is even more hydrophilic than the regular water (H2O) molecules. The effect is more pronounced for the hydroxide than for the hydronium. Our results are consistent with several experimental observations and explain why hydrophobic surfaces in contact with water acquire a net negative charge, a phenomenon that has important implications for biology and polymer science.     

Dynamics of water confined in the interdomain region of a multidomain protein

Molecular dynamics simulations are performed to study the dynamics of interfacial water confined in the interdomain region of a two-domain protein, BphC enzyme. The results show that near the protein surface the water diffusion constant is much smaller and the water-water hydrogen bond lifetime is much longer than that in bulk. The diffusion constant and hydrogen bond lifetime can vary by a factor of as much as 2 in going from the region near the hydrophobic domain surface to the bulk. Water molecules in the first solvation shell persist for a much longer time near local concave sites than near convex sites. Also, the water layer survival correlation time shows that on average water molecules near the extended hydrophilic surfaces have longer residence times than those near hydrophobic surfaces. These results indicate that local surface curvature and hydrophobicity have a significant influence on water dynamics.     

High-resolution neutron-scattering study of slow dynamics of surface water molecules in zirconium oxide

We have performed a quasielastic neutron-scattering experiment on backscattering spectrometer with sub-mueV resolution to investigate the slow dynamics of surface water in zirconium oxide using the sample studied previously with a time-of-flight neutron spectrometer [E. Mamontov, J. Chem. Phys. 121, 9087 (2004)]. The backscattering measurements in the temperature range of 240-300 K have revealed a translational dynamics slower by another order of magnitude compared to the translational dynamics of the outer hydration layer observed in the time-of-flight experiment. The relaxation function of this slow motion is described by a stretched exponential with the stretch factors between 0.8 and 0.9, indicating a distribution of the relaxation times. The temperature dependence of the average residence time is non-Arrhenius, suggesting that the translational motion studied in this work is more complex than surface jump diffusion previously observed for the molecules of the outer hydration layer. The observed slow dynamics is ascribed to the molecules of the inner hydration layer that form more hydrogen bonds compared to the molecules of the outer hydration layer. Despite being slower by two orders of magnitude, the translational motion of the molecules of the inner hydration layer may have more in common with bulk water compared to the outer hydration layer, the dynamics of which is slower than that of bulk water by just one order of magnitude.     

The ultrafast dynamics of hydrogen-bonded liquids: molecular structure-dependent occurrence of normal arrhenius or fractional Stokes-Einstein-Debye rotational diffusive relaxation

The ultrafast rotational-diffusive dynamics of the peptide linkage model compounds N-methylacetamide (NMA), acetamide (Ac), and N,N-dimethylacetamide (DMA) have been studied as a function of temperature using optically heterodyne-detected optical Kerr effect (OHD-OKE) spectroscopy. Both NMA and Ac exhibit a non-Arrhenius temperature dependence of the rotational diffusive relaxation time. By contrast, the non-hydrogen-bonding DMA exhibits normal hydrodynamic behavior. The unusual dynamics of NMA and Ac are attributed to the decoupling of single-molecule rotational diffusive relaxation from the shear viscosity via a transition between stick and slip boundary conditions, which arises from local heterogeneity in the liquid due to the formation of hydrogen-bonded chains or clusters. This provides new insight into the structure and dynamics of an important peptide model compound and the first instance of such a phenomenon in a room-temperature liquid. The OHD-OKE responses of carboxylic acids acetic acid (AcOH) and dichloroacetic acid (DCA) are also reported. These, along with the terahertz Raman spectra, show no evidence of the effects observed in amide systems, but display trends consistent with the presence of an equilibrium between the linear and cyclic dimer structures at all temperatures and moderate-to-high mole fractions in aqueous solution. This equilibrium manifests itself as hydrodynamic behavior in the liquid phase.     

Orientational dynamics and energy landscape features of thermotropic liquid crystals: An analogy with supercooled liquids

Recent optical kerr effect (OKE) studies have revealed that orientational relaxation of rodlike nematogens near the isotropic-nematic (I-N) phase boundary and also in the nematic phase exhibit temporal power law decay at intermediate times. Such behaviour has drawn an intriguing analogy with supercooled liquids. Here, we have investigated the single-particle and collective orientational dynamics of a family of model system of thermotropic liquid crystals using extensive computer simulations. Several remarkable features of glassy dynamics are on display including non-exponential relaxation, dynamical heterogeneity, and non-Arrhenius temperature dependence of the orientational relaxation time. Over a temperature range near the I-N phase boundary, the system behaves like a fragile glass-forming liquid. Using proper scaling, we construct the usual relaxation time versus inverse temperature plot and explicitly demonstrate that one can successfully define a density dependent fragility of liquid crystals. The fragility of liquid crystals shows a temperature and density dependence which is remarkably similar to the fragility of glass forming supercooled liquids. Energy landscape analysis of inherent structures shows that the breakdown of the Arrhenius temperature dependence of relaxation rate occurs at a temperature that marks the onset of the growth of the depth of the potential energy minima explored by the system.     

In situ adsorption studies of a 14-amino acid leucine-lysine peptide onto hydrophobic polystyrene and hydrophilic silica surfaces using quartz crystal microbalance, atomic force microscopy, and sum frequency generation vibrational spectroscopy

The adsorption of a 14-amino acid amphiphilic peptide, LK14, which is composed of leucine (L, nonpolar) and lysine (K, charged), on hydrophobic polystyrene (PS) and hydrophilic silica (SiO2) was investigated in situ by quartz crystal microbalance (QCM), atomic force microscopy (AFM), and sum frequency generation (SFG) vibrational spectroscopy. The LK14 peptide, adsorbed from a pH 7.4 phosphate-buffered saline (PBS) solution, displayed very different coverage, surface roughness and friction, topography, and surface-induced orientation when adsorbed onto PS versus SiO2 surfaces. Real-time QCM adsorption data revealed that the peptide adsorbed onto hydrophobic PS through a fast (t < 2 min) process, while a much slower (t > 30 min) multistep adsorption and rearrangement occurred on the hydrophilic SiO2. AFM measurements showed different surface morphologies and friction coefficients for LK14 adsorbed on the two surfaces. Surface-specific SFG spectra indicate very different ordering of the adsorbed peptide on hydrophobic PS as compared to hydrophilic SiO2. At the LK14 solution/PS interface, CH resonances corresponding to the hydrophobic leucine side chains are evident. Conversely, only NH modes are observed at the peptide solution/SiO2 interface, indicating a different average molecular orientation on this hydrophilic surface. The surface-dependent difference in the molecular-scale peptide interaction at the solution/hydrophobic solid versus solution/hydrophilic solid interfaces (measured by SFG) is manifested as significantly different macromolecular-level adsorption properties on the two surfaces (determined via AFM and QCM experiments).     

Adsorption of the fusogenic peptide B18 onto solid surfaces: insights into the mechanism of peptide assembly

The adsorption and assembly of B18 peptide on various solid surfaces were studied by reflectometry techniques and atomic force microscopy. B18 is the minimal membrane binding and fusogenic motif of the sea urchin protein bindin, which mediates the fertilization process. Silicon substrates were modified to obtain hydrophilic charged surfaces (oxide layer and polyelectrolyte multilayers) and hydrophobic surfaces (octadecyltrichlorosilane). B18 does not adsorb on hydrophilic positively charged surfaces, which was attributed to electrostatic repulsion since the peptide is positively charged. In contrast, the peptide irreversibly adsorbs on negatively charged hydrophilic as well as on hydrophobic surfaces. B18 showed higher affinity for hydrophobic surfaces than for hydrophilic negatively charged surfaces, which must be due to the presence of hydrophobic side chains at both ends of the molecule. Atomic force microscopy provided the indication that lateral diffusion on the surface affects the adsorption process of B18 on hydrophobic surfaces. The adsorption of the peptide on negatively charged surfaces was characterized by the formation of globular clusters.     

A Phytic Acid Induced Super‐Amphiphilic Multifunctional 3D Graphene‐Based Foam

Surfaces with super‐amphiphilicity have attracted tremendous interest for fundamental and applied research owing to their special affinity to both oil and water. It is generally believed that 3D graphenes are monoliths with strongly hydrophobic surfaces. Herein, we demonstrate the preparation of a 3D super‐amphiphilic (that is, highly hydrophilic and oleophilic) graphene‐based assembly in a single‐step using phytic acid acting as both a gelator and as a dopant. The product shows both hydrophilic and oleophilic intelligence, and this overcomes the drawbacks of presently known hydrophobic 3D graphene assemblies. It can absorb water and oils alike. The utility of the new material was demonstrated by designing a heterogeneous catalytic system through incorporation of a zeolite into its amphiphilic 3D scaffold. The resulting bulk network was shown to enable efficient epoxidation of alkenes without prior addition of a co‐solvent or stirring. This catalyst also can be recovered and re‐used, thereby providing a clean catalytic process with simplified work‐up.     

Peptide conformations for a microarray surface-tethered epitope of the tumor suppressor p53

Peptides or proteins near surfaces exhibit different structural properties from those present in a homogeneous solution, and these differences give rise to varied biological activity. Therefore, understanding the detailed molecular structure of these molecules tethered to a surface is important for interpreting the performance of the various microarrays based on the activities of the immobilized peptides or proteins. We performed molecular dynamics simulations of a pentapeptide, RHSVV, an epitope of the tumor suppressor protein p53, tethered via a spacer on a functionalized silica surface and free in solution, to study their structural and conformational differences. These calculations allowed analyses of the peptide-surface interactions, the sequence orientations, and the translational motions of the peptide on the surface to be performed. Conformational similarities are found among dominant structures of the tethered and free peptide. In the peptide microarray simulations, the peptide fluctuates between a parallel and tilted orientation driven in part by the hydrophobic interactions between the nonpolar peptide residues and the methyl-terminated silica surface. The perpendicular movement of the peptide relative to the surface is also restricted due to the hydrophobic nature of the microarray surface. With regard to structures available for recognition and binding, we find that similar conformations to those found in solution are available to the peptide tethered to the surface, but with a shifted equilibrium constant. Comparisons with experimental results show important implications of this for peptide microarray design and assays.     

Molecular dynamics study of translational and rotational diffusion in liquid ortho-terphenyl

NVT molecular dynamics simulations were performed on liquid o-terphenyl as a function of temperature in the range 320-480 K. Computed translational diffusion coefficients displayed the non-Arrhenius behavior expected of a fragile glass-forming liquid and were in good, semiquantitative agreement with experimental results. Rotational correlation functions calculated for various vectors within the molecule exhibited a very short time (0-1 ps) initial decay, followed by a reversal, which corresponds to free reorientation within the "solvent" cage prior to collision with a wall. Rotational correlation times of three orthogonal vectors fixed on the central benzene were close to equal at all temperatures, indicating nearly isotropic overall molecular reorientation. The average correlation times exhibited a non-Arrhenius temperature dependence and were in very good agreement with experimental values derived from 2D and 1H NMR relaxation times. Correlation times of vectors located on the lateral phenyl rings were used to calculate the "spinning" internal rotation diffusion coefficients, which were approximately twice as great as the overall rotational diffusion constants, indicating rapid internal rotation of the phenyl side groups over wide ranges of angle in the liquid.     

Surface immobilization of fibronectin-derived PHSRN peptide on functionalized polymer films – Effects on fibroblast spreading

The Pro-His-Ser-Arg-Asn (PHSRN) sequence in fibronectin is a second cell-binding site that synergistically affects Arg-Gly-Asp (RGD). The PHSRN peptide also induces cell invasion and accelerates wound healing. We report on the surface immobilization of PHSRN by spontaneous adsorption on polysiloxane thin films which have different surface free energy characteristics. Low-surface energy (hydrophobic) polysiloxane and the corresponding high-surface energy (hydrophilic) surfaces obtained by UV–ozone treatments were used as adsorbing substrates. The peptide adsorption process was investigated by quartz crystal microbalance with dissipation monitoring and atomic force microscopy. Both adsorption kinetics and peptide rearrangement dynamics at the solid interface were significantly different on the surface-modified films compared to the untreated ones. Fibroblast cells cultures at short times and in a simplified environment, i.e., a medium-free solution, were prepared to distinguish interaction events at the interface between cell membrane and surface-immobilized peptide for the two cases. It turned out that the cell-adhesive effect of immobilized PHSRN was different for hydrophobic compared to hydrophilic ones. Early signatures of cell spreading were only observed on the hydrophilic substrates. These effects are explained in terms of different spatial arrangements of PHSRN molecules immobilized on the two types of surfaces.     

Self-assembly of model amphiphilic Janus particles

We apply molecular dynamics simulations to investigate the structure formation of amphiphilic Janus particles in the bulk phase. The Janus particles are modeled as (soft) spheres composed of a hydrophilic and hydrophobic part. Their orientation is described by a vector representing an internal degree of freedom. Investigating energy fluctuations and cluster size distributions, we determine the aggregation line in a temperature-density-diagram, where the reduced temperature is an inverse measure for the anisotropic coupling. Below this aggregation line clusters of various sizes depending on density and reduced temperature are found. For low densities in the range ρ? ≤ 0.3, the cluster size distribution has a broad maximum, indicating simultaneous existence of various cluster sizes between 5 and 10. We find no hint of a condensation transition of these clustered systems. In the case of higher densities (ρ? = 0.5 and 0.6), the cluster size distribution shows an extremely narrow peak at clusters of size 13. In these icosahedrons, the particles are arranged in a closed-packed manner, thereby maximizing the number of bonds. Analyzing the translational mean-square displacement we also observe indications of hindered diffusion due to aggregation.     

The fragile-to-strong dynamic crossover transition in confined water: nuclear magnetic resonance results

By means of a nuclear magnetic resonance experiment, we give evidence of the existence of a fragile-to-strong dynamic crossover transition (FST) in confined water at a temperature T(L)=223+/-2 K. We have studied the dynamics of water contained in 1D cylindrical nanoporous matrices (MCM-41-S) in the temperature range 190-280 K, where experiments on bulk water were so far hampered by crystallization. The FST is clearly inferred from the T dependence of the inverse of the self-diffusion coefficient of water (1D) as a crossover point from a non-Arrhenius to an Arrhenius behavior. The combination of the measured self-diffusion coefficient D and the average translational relaxation time tau(T), as measured by neutron scattering, shows the predicted breakdown of Stokes-Einstein relation in deeply supercooled water.     

Interaction of micrometer-scale particles with nanotextured surfaces in shear flow

Dynamic particle adhesion from flow over collecting surfaces with nanoscale heterogeneity occurs in important natural systems and current technologies. Accurate modeling and prediction of the dynamics of particles interacting with such surfaces will facilitate their use in applications for sensing, separating, and sorting colloidal-scale objects. In this paper, the interaction of micrometer-scale particles with electrostatically heterogeneous surfaces is analyzed. The deposited polymeric patches that provide the charge heterogeneity in experiments are modeled as 11-nm disks randomly distributed on a planar surface. A novel technique based on surface discretization is introduced to facilitate computation of the colloidal interactions between a particle and the heterogeneous surface based on expressions for parallel plates. Combining these interactions with hydrodynamic forces and torques on a particle in a low Reynolds number shear flow allows particle dynamics to be computed for varying net surface coverage. Spatial fluctuations in the local surface density of the deposited patches are shown responsible for the dynamic adhesion phenomena observed experimentally, including particle capture on a net-repulsive surface.     

Self-diffusion of supercooled o-terphenyl near the glass transition temperature

Self-diffusion coefficients for the low molecular weight glass former o-terphenyl have been measured near Tg by isothermally desorbing thin film bilayers of deuterio and protio o-terphenyl in a vacuum chamber. We observe translational diffusion that is about 100 times faster at Tg + 3 K than the Stokes-Einstein prediction. Predictions from random first order transition theory and a dynamic facilitation approach are in reasonable agreement with our results; in these approaches, enhanced translational diffusion is associated with spatially heterogeneous dynamics. Self-diffusion controls crystallization in o-terphenyl for most of the supercooled liquid regime, but at temperatures below Tg + 10 K, the reported crystallization rate increases suddenly while the self-diffusion coefficient does not. This work and previous work on trisnaphthylbenzene both find a self-diffusion-controlled crystal growth regime and an enhancement in self-diffusion near Tg, suggesting that these phenomena are general characteristics of fragile low molecular weight glass formers. We discuss the width of the relaxation time distributions of o-terphenyl and trisnaphthylbenzene as they relate to the observation of enhanced translational diffusion.