Entropic interaction chromatography: separating proteins on the basis of size using end-grafted polymer brushes

Partitioning of a macromolecule into the interfacial volume occupied by a grafted polymer brush decreases the configurational entropy (DeltaSbrush(c)) of the terminally attached linear polymer chains due to a loss of free volume. Self-consistent field theory (SCF) calculations are used to show that DeltaSbrush(c) is a strong function of both the size (MWp) of the partitioning macromolecule and the depth of penetration into the brush volume. We further demonstrate that the strong dependence of DeltaSbrush(c) on MWp provides a novel and powerful platform, which we call entropic interaction chromatography (EIC), for efficiently separating mixtures of proteins on the basis of size. Two EIC columns, differing primarily in polymer grafting density, were prepared by growing a brush of poly(methoxyethyl acrylamide) chains on the surface of a wide-pore (1,000-A pores, 64-microm diameter rigid beads) resin (Toyopearl AF-650M) bearing surface aldehyde groups. Semipreparative 0.1-L columns packed with either EIC resin provide reduced-plate heights of 2 or less for efficient separation of globular protein mixtures over at least three molecular-weight decades. Protein partitioning within these wide-pore EIC columns is shown to be effectively modeled as a thermodynamically controlled process, allowing partition coefficients (K(P)) and elution chromatograms to be accurately predicted using a column model that combines SCF calculation of K(P) values with an equilibrium-dispersion type model of solute transport through the column. This model is used to explore the dependence of column separation efficiency on brush properties, predicting that optimal separation of proteins over a broad MWp range is achieved at low to moderate grafting densities and intermediate chain lengths.     

Lees–Edwards boundary condition for simulation of polymer suspension with dissipative particle dynamics method

The Lees–Edwards boundary condition (LEbc) is widely used in particle-based simulation for producing shear flow. Application of traditional LEbc in dissipative particle dynamics (DPD) method may encounter certain problems, e.g. it will destroy the momentum conservation law at the near boundary region, and the coordinate system gives an incorrect end-to-end vector for polymer beads. Special treatments of the implementation of LEbc in DPD method are introduced in this paper. A single side ghost layer is used to keep the momentum conservation, and the global coordinate system is employed to obtain a correct calculation of the spring force between polymer beads. The simulation results give a good prediction of velocity profile and system temperature, and the elastic dumbbell model for current method can well represent the Oldroyd-B fluid.     

Effect of Temperature and Capsid Tail on the Packing and Ejection of Viral DNA

We use a simulation technique based on molecular dynamics and stochastic rotation model to present the effect of temperature and capsid tail on the packaging and ejection processes of semiflexible polymers. We consider two types of solvents, a good solvent, where the polymer is neutral and repulsion interactions among its various sections are favored, and one where the polymer is charged, giving rise to extra electrostatic reaction. For tailless capsids, we find that packing a neutral polymer is slightly slower at higher temperatures whereas its ejection is slightly slower at lower temperatures. We find the same trend for a charged polymer but the effect is noticeably larger. At a high enough temperature, we notice that packing a charged polymer can be stopped. On the other hand, at fixed temperature and regardless whether the polymer is charged, packing is much easier for a capsid with a tail whereas ejection is much slower. The effect of including the tail on the dynamics of a charged polymer, in particular, is rather significant: more packing fraction is facilitated at higher temperatures due to more ordered polymer configuration inside the capsid. In contrast, during ejection the tail traps the last remaining beads for quite some time before allowing full ejection. We interpret these results in terms of entropic and electrostatic forces.     

Preparation and Friction Force Microscopy Measurements of Immiscible,Opposing Polymer Brushes

Solvated polymer brushes are well known to lubricate high-pressure contacts, because they can sustain a positive normal load while maintaining low friction at the interface. Nevertheless, these systems can be sensitive to wear due to interdigitation of the opposing brushes. In a recent publication, we have shown via molecular dynamics simulations and atomic force microscopy experiments, that using an immiscible polymer brush system terminating the substrate and the slider surfaces, respectively, can eliminate such interdigitation. As a consequence, wear in the contacts is reduced. Moreover, the friction force is two orders of magnitude lower compared to traditional miscible polymer brush systems. This newly proposed system therefore holds great potential for application in industry. Here, the methodology to construct an immiscible polymer brush system of two different brushes each solvated by their own preferred solvent is presented. The procedure how to graft poly(N-isopropylacrylamide) (PNIPAM) from a flat surface and poly(methyl methacrylate) (PMMA) from an atomic force microscopy (AFM) colloidal probe is described. PNIPAM is solvated in water and PMMA in acetophenone. Via friction force AFM measurements, it is shown that the friction for this system is indeed reduced by two orders of magnitude compared to the miscible system of PMMA on PMMA solvated in acetophenone.     

Scaling behaviour of different polymer models in dissipative particle dynamics of unentangled melts

We present a dissipative particle dynamics (DPD) study of scaling behaviour for three polymer models. The scaling behaviour is explored for the conformational and dynamic properties of unentangled polymer melts. DPD employs a bead–spring model together with an aggressive coarse-graining to represent polymers at the mesoscale. The first model studied utilises a simple soft repulsion potential for the bead–bead interactions together with a harmonic spring potential to connect beads into a polymer chain. The second model differs from the first model by replacing the harmonic spring with a finitely extensible nonlinear elastic spring. The third model uses realistic coarse-grain potentials for the bead–bead, spring and bending interactions based on the iterative Boltzmann inversion procedure and it corresponds to a mesoscopic model of polyethylene. We systematically vary the chain length and spring constant (in the case of the first and second models), and simulate the conformational properties such as the end-to-end distance or radius of gyration, and dynamic properties such as the centre-of-mass self-diffusion coefficient or viscosity. The scaling of the conformational and dynamic properties with chain length (scaling laws) is compared with the Rouse theory, which is considered as a standard theory for unentangled polymer melts. The comparison shows that simulated scaling laws typically agree with the Rouse scaling laws for the DPD polymer models with more than 10 DPD beads. For the shorter DPD polymers, deviations from the Rouse theory exist and become significant for the dynamic properties, especially for the viscosity of the polymer melts.     

Dissipative particle dynamics simulation of the soft micro actuator using polymer chain displacement in electro-osmotic flow

ABSTRACT

In this research, the numerical simulation of a soft polymer micro actuator performance has been investigated using the dissipative particle dynamics method in electro-osmotic flow. Effective factors including electro-osmotic flow and polymer chain parameters have been studied. First of all, considering a wide range of electro-osmotic parameters, the validation of analytical results is carried out in a simple micro channel. The electric field and zeta potential changes are linearly related to the flow rate, and the kh parameter behaves nonlinearly to around the kh?=?10. In the following, a convergent–divergent channel is used for the soft micro actuator simulation in which a polymer chain as a heart of actuation is embedded in the middle. As the main control parameter, the direction of the electric field is changed every 4?s, and it leads to a reciprocating motion. The numerical results indicate that the displacement of the soft polymer chain will be increased by enhancing the electric field, the number of beads, decreasing the harmonic bond coefficient and also exposing more length of a polymer chain in front of fluid flow. The results of this study may be useful for some future applications such as artificial fibres and muscles.     

Effective separation of peptides using highly dense thermo-responsive polymer brush-grafted porous polystyrene beads

For the development of well-defined highly dense thermo-responsive polymer grafted surface as an improved stationary phase for thermo-responsive chromatography, poly(N-isopropylacrylamide) (PIPAAm) brush-grafted porous polystyrene beads were prepared by surface-initiated atom transfer radical polymerization (ATRP). The PIPAAm grafted region of polystyrene beads was adjusted by the addition of isooctane as a poor solvent for polystyrene upon the reaction of ATRP initiator immobilization. Using a thermo-responsive HPLC column containing the prepared beads with PIPAAm brush grafted on the inside pores nearby the outer surfaces, angiotensin subtypes were effectively separated with aqueous mobile phase, because the densely grafted PIPAAm on nearby the outer surface effectively interacted with the peptides hydrophobically. Retention of basic peptide was achieved by the beads with basic mobile phase. These results indicated that the prepared beads with grafted PIPAAm nearby the outer surface became an effective chromatographic stationary phase for retaining basic peptides using wide pH range of mobile phase.     

Feasibility study of degradation of phenol in a fluidized bed bioreactor with a cyclodextrin polymer as biofilm carrier

This work is focused on the evaluation of a beta-cyclodextrin polymer as a carrier medium in a fluidized bed bioreactor treating aqueous phenol as a model pollutant. The insoluble polymer support was obtained in the shape of spherical beads by crosslinking beta-cyclodextrin with epichlorohydrin. A batch of swollen polymer particles was loaded into the reactor and inoculated with a mixed bacterial culture. Bacterial growth on the polymer beads was initially stimulated by glucose addition to the medium, and then gradually replaced with phenol. The operational variables studied after the acclimation period included phenol load, hydraulic residence time and recirculation flow rate. Low hydraulic residence times and moderate phenol loads were applied. The elimination capacity was usually about 1.0 kg-phenol/m(3)d, although a maximum of 2.8 kg-phenol/m(3)d was achieved with a retention time of only 0.55 h. The depuration efficiency was not affected by the recirculation flow rate in the range studied. Neither operational nor support stability problems were detected during the operation. A high degree of expansion was achieved in the bioreactor due to the hydrogel nature of the cyclodextrin polymer and, consequently, a low energy requirement was necessary to fluidize the bed.     

Electrokinetic stretching of tethered DNA

During electrophoretic separations of DNA in a sieving medium, DNA molecules stretch from a compact coil into elongated conformations when encountering an obstacle and relax back to a coil upon release from the obstacle. These stretching dynamics are thought to play an important role in the separation mechanism. In this article we describe a silicon microfabricated device to measure the stretching of tethered DNA in electric fields. Upon application of an electric field, electro-osmosis generates bulk fluid flow in the device, and a protocol for eliminating this flow by attaching a polymer brush to all silicon oxide surfaces is shown to be effective. Data on the steady stretching of DNA in constant electric fields is presented. The data corroborate the approximate theory of hydrodynamic equivalence, indicating that DNA is not free-draining in the presence of both electric and nonelectric forces. Finally, these data provide the first quantitative test of a Stigter and Bustamante's detailed theory of electrophoretic stretching of DNA without adjustable parameters. The agreement between theory and experiment is good.     

NIST/ISAC standardization study: Variability in assignment of intensity values to fluorescence standard beads and in cross calibration of standard beads to hard dyed beads

Results from a standardization study cosponsored by the International Society for Advancement of Cytometry (ISAC) and the US National Institute of Standards and Technology (NIST) are reported. The study evaluated the variability of assigning intensity values to fluorophore standard beads by bead manufacturers and the variability of cross calibrating the standard beads to stained polymer beads (hard-dyed beads) using different flow cytometers. Hard dyed beads are generally not spectrally matched to the fluorophores used to stain cells, and spectral response varies among flow cytometers. Thus if hard dyed beads are used as fluorescence calibrators, one expects calibration for specific fluorophores (e.g., FITC or PE) to vary among different instruments. Using standard beads surface-stained with specific fluorophores (FITC, PE, APC, and Pacific Blue?), the study compared the measured intensity of fluorophore standard beads to that of hard dyed beads through cross calibration on 133 different flow cytometers. Using robust CV as a measure of variability, the variation of cross calibrated values was typically 20% or more for a particular hard dyed bead in a specific detection channel. The variation across different instrument models was often greater than the variation within a particular instrument model. As a separate part of the study, NIST and four bead manufacturers used a NIST supplied protocol and calibrated fluorophore solution standards to assign intensity values to the fluorophore beads. Values assigned to the reference beads by different groups varied by orders of magnitude in most cases, reflecting differences in instrumentation used to perform the calibration. The study concluded that the use of any spectrally unmatched hard dyed bead as a general fluorescence calibrator must be verified and characterized for every particular instrument model. Close interaction between bead manufacturers and NIST is recommended to have reliable and uniformly assigned fluorescence standard beads. ? 2012 International Society for Advancement of Cytometry.     

Polymer dynamics as a mechanistic model for the flow-independent viscoelasticity of cartilage

The initial, rapid, flow independent, apparent stress relaxation of articular cartilage disks deformed by unconfined compressive displacement is shown to be consistent with the theory of polymer dynamics. A relaxation function for polymers based upon a mechanistic model of molecular interaction (reptation) appropriately approximated early, flow independent relaxation of stress. It is argued that the theory of polymer dynamics, with its reliance on mechanistic models of molecular interaction, is an appropriate technique for application to and the understanding of rapid, flow independent, stress relaxation in cartilage.     

The 110-kD protein-calmodulin complex of the intestinal microvillus (brush border myosin I) is a mechanoenzyme

The 110-kD protein-calmodulin complex (110K-CM) of the intestinal brush border serves to laterally tether microvillar actin filaments to the plasma membrane. Results from several laboratories have demonstrated that this complex shares many enzymatic and structural properties with myosin. The mechanochemical potential of purified avian 110K-CM was assessed using the Nitella bead motility assay (Sheetz, M. P., and J. A. Spudich. 1983. Nature (Lond.). 303:31-35). Under low Ca2+ conditions, 110K-CM-coated beads bound to actin cables, but no movement was observed. Using EGTA/calcium buffers (approximately 5-10 microM free Ca2+) movement of 110K-CM-coated beads along actin cables (average rate of approximately 8 nm/s) was observed. The movement was in the same direction as that for beads coated with skeletal muscle myosin. The motile preparations of 110K-CM were shown to be free of detectable contamination by conventional brush border myosin. Based on these and other observations demonstrating the myosin-like properties of 110K-CM, we propose that this complex be named "brush border myosin I."     

Simultaneous enhancement of cell proliferation and thermally induced harvest efficiency based on temperature-responsive cationic copolymer-grafted microcarriers

The development of large-scale suspension cell cultures using microcarriers has long been a focus of attention in the fields of pharmacy and biotechnology. Previously, we developed cell-detachable microcarriers based on temperature-responsive poly(N-isopropylacrylamide) (PIPAAm)-grafted beads, on which adhering cells can be noninvasively harvested by only reducing the temperature without the need for proteolytic enzyme treatment. In this study, to improve the cell harvest efficiency from bead surfaces while maintaining cell adhesion and proliferation properties, we prepared temperature-responsive cationic copolymer-grafted beads bearing a copolymer brush consisting of IPAAm, positively charged quaternary amine monomer (3-acrylamidopropyl trimethylammonium chloride; APTAC), and hydrophobic monomer (N-tert-butylacrylamide; tBAAm). The incorporation of positively charged APTAC into the grafted copolymer brush facilitated bead dispersibility in a cell culture system containing Chinese hamster ovary (CHO-K1) cells and consequently allowed for enhanced cell proliferation in the system compared to that of unmodified CMPS and conventional PIPAAm homopolymer-grafted beads. Additionally, P(IPAAm-co-APTAC-co-tBAAm) terpolymer-grafted beads exhibited the most rapid and efficient cell detachment behavior after the temperature was reduced to 20 °C, presumably because the highly hydrated APTAC promoted the overall hydration of the P(IPAAm-co-APTAC-co-tBAAm) chains. Therefore, P(IPAAm-co-APTAC-co-tBAAm) terpolymer-grafted microcarriers are effective in facilitating both cell proliferation and thermally induced cell detachment in a suspension culture system.     

Deformation of dynamin helices damped by membrane friction

Dynamin and other proteins of the dynamin superfamily are widely used by cells to sever lipid bilayers. During this process, a short helical dynamin polymer (one to three helical turns) assembles around a membrane tubule and reduces its radius and pitch upon guanosine triphosphate hydrolysis. This deformation is thought to be crucial for dynamin's severing action and results in an observable twisting of the helix. Here, we quantitatively characterize the dynamics of this deformation by studying long dynamin helices (many helical turns). We perform in vitro experiments where we attach small beads to the dynamin helix and track their rotation in real time, thus collecting information about the space and time dependence of the deformation. We develop a theoretical formalism to predict the dynamics of a mechanically continuous helix deforming on long timescales. Longer helices deform more slowly, as predicted by theory. This could account for the previously reported observation that they are less fission-competent. Comparison between experiments and our model indicates that the deformation dynamics is dominated by the draining of the membrane out of the helix, allowing quantification of helix-membrane interactions.     

Kinetic Analysis of Analyte Binding by Optical Biosensors: Hydrodynamic Penetration of the Analyte Flow into the Polymer Matrix Reduces the Influence of Mass Transport

I examined the penetration of the hydrodynamic flow into a polymer matrix immobilized by grafting to a surface, such as used in optical biosensors designed to measure binding reactions in real time. I show that the flow penetrates with an appreciable velocity into a region located at the tip of such a polymer brush, corresponding to about 10 to 15% of the total mass of the grafted polymer. Furthermore, under the conditions recommended for kinetic measurements, the concentrations of both polymer and immobilized ligands are low in these regions of the matrix, where crowding effects are negligible. Under such conditions, the hydrodynamic flow penetrating into the dextran matrix flow will bring the analytes close to their targets, thus considerably reducing transport problems.     

Predicting properties of intrinsically unstructured proteins

There is increasing evidence that intrinsically unstructured proteins or protein domains have important biological functions. These types of proteins may be productively analyzed using polymer theory developed to predict global physical properties of polymers. In these theories molecular detail is “coarse grained” out of the models, and replaced with a small number of parameters that characterize the polymer. This reduction in complexity allows extremely large systems to be studied. In the case of simulations, the time scales accessible also increase significantly. Here we discuss the application of polymer theory to unstructured proteins, and consider how to classify proteins within a polymer framework. We then review polymer theory that is relevant to predicting functionally important properties, such as radius of gyration, height of a polymer brush and force required to compress a polymer brush.     

Elastic constants of polymer-grafted lipid membranes

The surface expansion that is induced by the lateral pressure in the brush region of lipid membranes containing grafted polymers is deduced from the scaling and mean-field theories for the polymer brush, together with the equation of state for a lipid monolayer at the equivalence pressure with fluid lipid bilayers. Depending on the length and mole fraction of the polymer lipid, the membrane expansion can be appreciable. Direct experimental evidence for this lateral expansion comes from recent spin-label measurements with lipid membranes containing poly(ethylene glycol)-grafted lipids. The expansion in lipid area modifies the elastic constants of the polymer-grafted membranes in a way that opposes the direct elastic response of the polymer itself. Calculations as a function of polymer lipid content indicate that the net change in isothermal area expansion modulus of the membrane is negative but small, in contrast to previous predictions. A similar situation applies to the curvature elastic moduli of membranes containing short polymer lipids. For longer polymer lipids, however, the direct contribution of the polymer brush to the bending elastic constants dominates, and the increase in bending moduli with increasing polymer lipid content rapidly exceeds the basal values of the bare lipid membrane. The spontaneous (or intrinsic) curvature of the component monolayer of polymer lipid-containing membranes is calculated for the first time. The polymer brush contribution to spontaneous curvature scales quadratically with the polymer length, and at least quadratically with the mole fraction of polymer lipid.     

Dynamical Properties of Condensed Charged Polymer Melts

Abstract

Dynamical properties of condensed charged polymer melts are studied with a two-dimensional model and molecular dynamics simulation. Screened Coulombic interactions are assumed for the interactions between the monomer charges as well as the counterions which were introduced to neutralize the total monomer charges of polymer chains. Through molecular dynamics calculations, we have obtained the radial distribution function and velocity auto-correlation function, and their density dependences. As a structural characteristics in condensed charged polymer melts, we find that the monomers tend to form triangular structures locally. The radial distribution function for the center monomers implies that the polymer chains on our two-dimensional model are not entangled. The diffusion properties for both the counter-ions and innermost monomers are studied in detail. In this paper, we have also computed neutral polymer melts to study the effects of the presence of the long-range Coulombic interactions on the dynamical properties of polymer melts. We find that the Coulombic interactions significantly reduce the self diffusion. Snapshots analyses obtained from the molecular dynamics simulation suggest that the reptation model is not a proper model for two-dimensional polymer-chain melts, in which there are little entanglement effects in agreement with the result of the analyses for the radial distribution function.     

Molecular dynamics simulations of the interaction of phospholipid bilayers with polycaprolactone

The molecular interaction between common polymer chains and the cell membrane is unknown. Molecular dynamics simulations offer an emerging tool to characterise the nature of the interaction between common degradable polymer chains used in biomedical applications, such as polycaprolactone, and model cell membranes. Herein we characterise with all-atomistic and coarse-grained molecular dynamics simulations the interaction between single polycaprolactone chains of varying chain lengths with a phospholipid membrane. We find that the length of the polymer chain greatly affects the nature of interaction with the membrane, as well as the membrane properties. Furthermore, we next utilise advanced sampling techniques in molecular dynamics to characterise the two-dimensional free energy surface for the interaction of varying polymer chain lengths (short, intermediate, and long) with model cell membranes. We find that the free energy minimum shifts from the membrane-water interface to the hydrophobic core of the phospholipid membrane as a function of chain length. Finally, we perform coarse-grained molecular dynamics simulations of slightly larger membranes with polymers of the same length and characterise the results as compared with all-atomistic molecular dynamics simulations. These results can be used to design polymer chain lengths and chemistries to optimise their interaction with cell membranes at the molecular level.     

Effect of polymer brush architecture on antibiofouling properties

Polymer brushes show great promise in next-generation antibiofouling surfaces. Here, we have studied the influence of polymer brush architecture on protein resistance. By carefully optimizing reaction conditions, we were able to polymerize oligoglycerol-based brushes with sterically demanding linear or dendronized side chains on gold surfaces. Protein adsorption from serum and plasma was analyzed by surface plasmon resonance. Our findings reveal a pronounced dependence of biofouling on brush architecture. Bulky yet flexible side chains as in dendronized brushes provide an ideal environment to repel protein-possibly through formation of a hydration layer, which can be further enhanced by presenting free hydroxyl groups on the polymer brushes. A deeper understanding of how brush architecture influences protein resistance will ultimately enable fabrication of surface coatings tailored to specific requirements in biomedical applications.