Mixtures of Associating and Non-associating Chains on Activated Surfaces: A Monte Carlo Approach

Abstract

The behavior of mixtures of associating and non-associating chains confined in pores with activated surfaces is studied by means of molecular simulation. The fluid molecules are modeled as a chain of four tangent Lennard-Jones spheres. Some of the chains have an additional associating square-well site placed in an end sphere. The activated surfaces of the slit pore are modeled via an integrated Lennard-Jones (10-4-3) potential with specific association sites protruding from the surface. We present Gibbs ensemble Monte Carlo simulation results for the partitioning of mixtures of chains in the bulk and confined phases for this particular model. The chain-wall association governs the adsorption behavior of the system. The preferential adsorption of associating chains is seen to strongly depend on temperature and pore width. Selectivities obtained are in the range of those seen in experiments of alkane-alkanol mixtures.     

Combing DNA on CTAB-coated surfaces

A fluorescence microscope (FM) coupled with an intensified charge-coupled device (ICCD) camera was used to investigate the combing of DNA on cetyltrimethyl ammonium bromide (CTAB)-coated glass surfaces. DNA molecules can be combed uniform and straight on CTAB-coated surfaces. Different combing characteristics at different pH values were found. At lower pH (ca. 5.5), DNA molecules were stretched 30% longer than the unextended and DNA extremities bound with CTAB-coated surfaces via hydrophobic interaction. At high pH values (e.g., 6.4 and 6.5), DNA molecules were extended about 10% longer and DNA extremities bound with CTAB-coated surfaces via electrostatic attraction. At pH 6.0, DNA molecules could be extended 30% longer on 0.2-mM CTAB-coated surfaces. CTAB cationic surfactant has both a hydrophobic motif and a positively charged group. So, CTAB-coated surfaces can bind DNA extremities via hydrophobic effect or electrostatic attraction at different pH values. It was also found that combing of DNA on CTAB-coated surfaces is reversible. The number of DNA base pairs binding to CTAB-coated surfaces was calculated.     

Critical polyelectrolyte adsorption under confinement: planar slit, cylindrical pore, and spherical cavity

We explore the properties of adsorption of flexible polyelectrolyte chains in confined spaces between the oppositely charged surfaces in three basic geometries. A method of approximate uniformly valid solutions for the Green function equation for the eigenfunctions of polymer density distributions is developed to rationalize the critical adsorption conditions. The same approach was implemented in our recent study for the "inverse" problem of polyelectrolyte adsorption onto a planar surface, and on the outer surface of rod-like and spherical obstacles. For the three adsorption geometries investigated, the theory yields simple scaling relations for the minimal surface charge density that triggers the chain adsorption, as a function of the Debye screening length and surface curvature. The encapsulation of polyelectrolytes is governed by interplay of the electrostatic attraction energy toward the adsorbing surface and entropic repulsion of the chain squeezed into a thin slit or small cavities. Under the conditions of surface-mediated confinement, substantially larger polymer linear charge densities are required to adsorb a polyelectrolyte inside a charged spherical cavity, relative to a cylindrical pore and to a planar slit (at the same interfacial surface charge density). Possible biological implications are discussed briefly in the end.     

Microexudates from Cells Grown in Tissue Culture

Cellular substrata of known molecular structure and measurable dimensions can be constructed as transferred films from Langmuir troughs or as adsorbed films. In addition, large molecules in culture media form measurable adsorbates. With the techniques of ellipsometry and surface chemistry it is possible to characterize and measure (within ± 3A) as a function of several parameters a microexudate of molecular dimensions deposited when tissue cultured cells contact certain substrata. The selective attraction of substratum and cell for microexudate has been determined, and the time course of deposition in Eagle's medium is characterized by a rapid initial accretion of material. During this period, microexudate can diffuse several cell diameters and cannot be detected in the culture medium. In Eagle's medium the cells cannot be detached from glass surfaces by versene or trypsin unless the surface of cell or substratum is coated with certain molecules. Trypsin becomes adsorbed to cell surfaces, continues to be enzymatically active on the surface, and digests protein components of microexudate and substratum. Microexudate appears to be a complex mosaic of molecules (including protein) synthesized within or on the surfaces of cells and secreted by cells or transferred from their surfaces to specific substrata. It is proposed that this mosaic plays, on the molecular level, a significant role in cell-to-cell interactions, cell locomotion and adhesion, and the selective application and spreading of cells on various surfaces.     

Water in channel-like cavities: structure and dynamics.

Ion channels contain narrow columns of water molecules. It is of interest to compare the structure and dynamics of such intrapore water with those of the bulk solvent. Molecular dynamics simulations of modified TIP3P water molecules confined within channel-like cavities have been performed and the orientation and dynamics of the water molecules analyzed. Channels were modeled as cylindrical cavities with lengths ranging from 15 to 60 A and radii from 3 to 12 A. At the end of the molecular dynamics simulations water molecules were observed to be ordered into approximately concentric cylindrical shells. The waters of the outermost shell were oriented such that their dipoles were on average perpendicular to the normal of the wall of the cavity. Water dynamics were analyzed in terms of self-diffusion coefficients and rotational reorientation rates. For cavities of radii 3 and 6 A, water mobility was reduced relative to that of simulated bulk water. For 9- and 12-A radii confined water molecules exhibited mobilities comparable with that of the bulk solvent. If water molecules were confined within an hourglass-shaped cavity (with a central radius of 3 A increasing to 12 A at either end) a gradient of water mobility was observed along the cavity axis. Thus, water within simple models of transbilayer channels exhibits perturbations of structure and dynamics relative to bulk water. In particular the reduction of rotational reorientation rate is expected to alter the local dielectric constant within a transbilayer pore.     

DNA Strands Attached Inside Single Conical Nanopores: Ionic Pore Characteristics and Insight into DNA Biophysics

Single nanopores attract a great deal of scientific interest as a basis for biosensors and as a system to study the interactions and behavior of molecules in a confined volume. Tuning the geometry and surface chemistry of nanopores helps create devices that control transport of ions and molecules in solution. Here, we present single conically shaped nanopores whose narrow opening of 8 or 12 nm is modified with single-stranded DNA molecules. We find that the DNA occludes the narrow opening of nanopores and that the blockade extent decreases with the ionic strength of the background electrolyte. The results are explained by the ionic strength dependence of the persistence length of DNA. At low KCl concentrations (10 mM) the molecules assume an extended and rigid conformation, thereby blocking the pore lumen and reducing the flow of ionic current to a greater extent than compacted DNA at high salt concentrations. Attaching flexible polymers to the pore walls hence creates a system with tunable opening diameters in order to regulate transport of both neutral and charged species.     

Effects of inter-organism interactions in biofouling on microtopographic surfaces

An extended model of the surface energetic attachment (SEA) model is introduced to study the fouling of marine organisms on microtopographic surfaces, taking into account the excluded volume interaction and the attraction between the organisms. It is shown that the excluded volume interaction leads to changes in the site-typed attachment probabilities which increase with the average spore density on the surface. As a result of these changes, the spore density map is flattened under very high density fouling. The attractive interaction on the other hand leads to aggregation of spores and the average aggregate size increased with the strength of attraction. The model can be mapped to a specific experiment to determine the attachment energy parameters. In contrast to various prior empirical approaches, the extended SEA model is rigorous from the statistical mechanics viewpoint, thus it provides a reliable tool for studying complex attachment behaviors of microorganisms on topographic surfaces.     

A model for enhanced nucleation of protein crystals on a fractal porous substrate

The phenomenon of enhanced nucleation and crystallization of proteins on porous silicon (PS) is theoretically studied and explained. The PS layer is treated as a fractal structure, and a new mechanism of local supersaturation associated with the fractality is proposed. It is shown that the number of adsorbed molecules on a fragment with a fractal surface significantly exceeds that on one with flat surfaces. For a fractal PS surface, a local concentration of molecules that is sufficient for nucleation is possible inside and in the close vicinity of the pores, even when the average conditions in the bulk of the solution correspond to metastability. The wide distribution of fractal pore size is favorable for the crystallization of a wide range of macromolecules using the same sample. In addition, the PS technology is very flexible, allowing tailoring the pore size and concentration as well as the fractal properties to specific proteins by changing the fabrication conditions.     

Measurement of dimensions of pentagonal doughnut-shaped C-reactive protein using an atomic force microscope and a dual polarisation interferometric biosensor

In order to develop the C-reactive protein (CRP) sensor chips for clinical detection of atherosclerosis and coronary heart disease, we used an atomic force microscope (AFM) and a dual polarization interferometric (DPI) biosensor to probe the surface ultrastructure and to measure the dimensions of CRP. A single pentagonal structure was directly visualized by AFM, and quantitative measurements of the dimensions of the protein were provided. The average height calculated for each pentagonal CRP particle was approximately 3.03+/-0.37 nm, which basically corresponds to that (36 A in protomer diameter) previously obtained from the structure of CRP determined by X-ray crystallography. Moreover, a experiment using dual polarization interferometric (DPI) as a biosensor was then performed, and the average monolayer thickness value (3.18+/-0.43 nm) that was calculated basically corresponds to that obtained from the experimental value (3.03+/-0.37 nm) of the height measured by an AFM method for CRP. Further investigations will be performed to study the surface ultrastructure of a single pentagonal CRP molecule, and for this purpose a CRP sample (at low concentration) was scanned in vacuum by AFM. The higher-resolution images clearly revealed the presence of doughnut-shaped CRP molecules. In addition, phase images of CRP molecules were captured simultaneously with their height images, and the lateral dimensions of the doughnut-shaped CRP molecules were then measured. It was found that the average values calculated for the outer diameter (11.13+/-1.47 nm) and pore diameter (3.52+/-0.42 nm) are respectively close to those (102 A in outer diameter and 30 A in pore diameter) previously obtained from the structure of CRP determined by X-ray crystallography. This study represents the first direct characterization of the surface ultrastructure and dimensional measurement of the CRP molecule on the sensor chip.     

Modeling the electrophoresis of rigid polyions: application to lysozyme.

An algorithm is developed to determine the electrophoretic mobility of a rigid polyion modeled as a low dielectric volume element of arbitrary shape containing an arbitrary charge distribution. The solvent is modeled as a high dielectric continuum with salt distributed according to the linearized Poisson Boltzmann equation. Account is also taken of a Stern layer that separates the molecular surface and the surface of hydrodynamic shear, or Stern surface. Relaxation of the ion atmosphere because of the presence of the external field is ignored. The electrostatic and hydrodynamic problems are both solved by boundary element methods. The procedure is first applied to spherical polyions containing monopolar, dipolar, and quadrupolar charge distributions, and calculated mobilities are found to be in excellent agreement with the theory of Yoon and Kim. It is then applied to lysozyme by using models that account for the detailed shape and charge distribution of the enzyme. For reasonable choices of the molecular and Stern surfaces, calculated and experimental mobilities are found to be in fair agreement with each other. However, if a pH independent Stern layer (or, equivalently, translational diffusion constant, Dt) is assumed, the calculated mobilities exhibit a stronger pH dependence than is observed experimentally. A small increase in Dt with increasing pH could correct this discrepancy.     

The Glassy Wall Boundary for Simulations of Inhomogeneous Systems

Abstract

For simulations on systems that invlove a physical inhomogeneity at infinite dilution, the usual periodic boundary conditions are inappropriate. In previous studies on such systems, surfaces have been re-introduced in order to contain the particles of the sample. When smooth surfaces are used to contain liquids, undesirable structural artifacts in the liquid are promoted by these surfaces. In this study a rigid but structurally liquid-like containing surface, that we call a glassy wall boundary, is introduced, in an attempt to solve this problem. It serves as a containing surface, but “looks” nearly liquid-like to molecules in the mobile liquid near it. We illustrate the properties of this boundary for a system that consists of an isolated polyion surrounded by SPC water at 300K and ～ 1 gcm^?3. We show that this boundary reduces or eliminates some of the problems caused by a smooth surface.     

Electrostatic modeling of ion pores. Energy barriers and electric field profiles

This paper presents calculations of the image potential for an ion in an aqueous pore through lipid membrane and the electric field produced in such a pore when a transmembrane potential is applied. The method used is one introduced by Levitt (1978, Biophys. J. 22:209), who solved an equivalent problem, in which a surface charge density is placed at the dielectric boundary. It is shown that there are singularities in this surface charge density if the model system has sharp corners. Numerically accurate calculations require exact treatment of these singularities. The major result of this paper is the development of a projection method that explicitly accounts for this behavior. It is shown how this technique can be used to compute, both reliably and efficiently, the electrical potential within a model pore in response to any electrical source. As the length of a channel with fixed radius is increased, the peak in the image potential approaches that of an infinitely long channel more rapidly than previously believed. When a transmembrane potential is applied the electric field within a pore is constant over most of its length. Unless the channel is much longer than its radius, the field extends well into the aqueous domain. For sufficiently dissimilar dielectrics the calculated values for the peak in the image potential and for the field well within the pore can be summarized by simple empirical expressions that are accurate to within 5%.     

The origin of long-range attraction between hydrophobes in water

When water-coated hydrophobic surfaces meet, direct contacts form between the surfaces, driving water out. However, long-range attractive forces first bring those surfaces close. This analysis reveals the source and strength of the long-range attraction between water-coated hydrophobic surfaces. The origin is in the polarization field produced by the strong correlation and coupling of the dipoles of the water molecules at the surfaces. We show that this polarization field gives rise to dipoles on the surface of the hydrophobic solutes that generate long-range hydrophobic attractions. Thus, hydrophobic aggregation begins with a step in which water-coated nonpolar solutes approach one another due to long-range electrostatic forces. This precursor regime occurs before the entropy increase of releasing the water layers and the short-range van der Waals attraction provide the driving force to "dry out" the contact surface. The effective force of attraction is derived from basic molecular principles, without assumptions of the structure of the hydrophobe-water interaction. The strength of this force can be measured directly from atomic force microscopy images of a hydrophobic molecule tethered to a surface but extending into water, and another hydrophobe attached to an atomic force probe. The phenomenon can be observed in the transverse relaxation rates in water proton magnetic resonance as well. The results shed light on the way water mediates chemical and biological self-assembly, a long outstanding problem.     

Investigation of DNA orientation on gold by EC-STM.

The immobilization of thiol-derivatized DNA on a Au (111) single crystal surface by self-assembly has been investigated by electrochemical scanning tunneling microscopy (EC-STM). Continuous potential-dependent orientation changes of double-stranded oligodeoxynucleotides (ODN) have been observed in a certain potential range from 200 to 600 mV (versus SCE). It is suggested that the DNA duplexes stand straight on the gold surface at potentials negative of the potential of zero charge (pzc) and then lay down on the surface when the potential shifts positively. These results are in agreement with the expectation based on the Coulombic interaction consideration between negatively charged DNA helices and gold surface. As the applied potential shifts positively, the surface charge changes from negative to positive, that is, the Coulombic force between negatively charged DNA helices and gold surfaces changes from repulsion to attraction. However, for the single-stranded oligodeoxynucleotides, no distinct changes in the surface structure were observed with the applied potential.     

Enhanced ionic interaction in narrow pores and ion pair formation

The same physical phenomenon that gives rise to the increase in the electrostatic self-energy of an ion within a narrow water-filled pore is shown to result in interionic electrical interactions within the pore that are much stronger and of longer range than those between the same ions in the same solution in bulk. Because of the much enhanced attraction between ions of opposite charge within the pore the formation of ion pairs becomes likely, even for strong electrolytes that are fully dissociated in the same solution when not spatially confined. Some predicted consequences of ion pair formation in narrow pores that may be experimentally detected are discussed. It is shown that, in a simple passive pore, due to ion pair formation, an Ussing unidirectional flux ratio exponent of less than 1 is predicted. This is usually thought to characterize a carrier rather than a pore.     

Solvent Dielectric Effect and Side Chain Mutation on the Structural Stability of Burkholderia cepacia Lipase Active Site: A Quantum Mechanical/Molecular Mechanics Study

Quantum mechanical and molecular dynamics methods were used to analyze the structure and stability of neutral and zwitterionic configurations of the extracted active site sequence from a Burkholderia cepacia lipase, histidyl-seryl-glutamin (His86-Ser87-Gln88) and its mutated form, histidyl-cysteyl-glutamin (His86-Cys87-Gln88) in vacuum and different solvents. The effects of solvent dielectric constant, explicit and implicit water molecules and side chain mutation on the structure and stability of this sequence in both neutral and zwitterionic forms are represented. The quantum mechanics computations represent that the relative stability of zwitterionic and neutral configurations depends on the solvent structure and its dielectric constant. Therefore, in vacuum and the considered non-polar solvents, the neutral form of the interested sequences is more stable than the zwitterionic form, while their zwitterionic form is more stable than the neutral form in the aqueous solution and the investigated polar solvents in most cases. However, on the potential energy surfaces calculated, there is a barrier to proton transfer from the positively charged ammonium group to the negatively charged carboxylat group or from the ammonium group to the adjacent carbonyl oxygen and or from side chain oxygen and sulfur to negatively charged carboxylat group. Molecular dynamics simulations (MD) were also performed by using periodic boundary conditions for the zwitterionic configuration of the hydrated molecules in a box of water molecules. The obtained results demonstrated that the presence of explicit water molecules provides the more compact structures of the studied molecules. These simulations also indicated that side chain mutation and replacement of sulfur with oxygen leads to reduction of molecular flexibility and packing.     

Vapour–liquid phase equilibria of simple fluids confined in patterned slit pores

We present the influence of surface heterogeneity on the vapour–liquid phase behaviour of square-well fluids in slit pores using grand-canonical transition-matrix Monte Carlo simulations along with the histogram-reweighting method. Properties such as phase coexistence envelopes, critical properties and local density profiles of the confined SW fluid are reported for chemically and physically patterned slit surfaces. It is observed that in the chemically patterned pores, fluid–fluid and surface attraction parameters along with the width of attractive and inert stripes play fundamentally different roles in the phase coexistence and critical properties. On the other hand, pillar gap and height significantly affect the vapour–liquid equilibria in the physically patterned slit pores. We also present the effect of chemically and physically patterned slit surfaces on the spreading pressure.     

Molecular dynamics simulation of solvated azurin: correlation between surface solvent accessibility and water residence times

A system containing the globular protein azurin and 3,658 water molecules has been simulated to investigate the influence on water dynamics exerted by a protein surface. Evaluation of water mean residence time for elements having different secondary structure did not show any correlation. Identically, comparison of solvent residence time for atoms having different charge and polarity did not show any clear trend. The main factor influencing water residence time in proximity to a specific site was found to be its solvent accessibility. In detail for atoms belonging to lateral chains and having solvent-accessible surface lower than approximately 16 A(2)a relation is found for which charged and polar atoms are surrounded by water molecules characterized by residence times longer than the non polar ones. The involvement of the low accessible protein atom in an intraprotein hydrogen bond further modulates the length of the water residence time. On the other hand for surfaces having high solvent accessibility, all atoms, independently of their character, are surrounded by water molecules which rapidly exchange with the bulk solvent. Proteins 2000;39:56-67.     

Effect of boundary conditions on yield properties of human femoral trabecular bone

Trabecular bone plays an important mechanical role in bone fractures and implant stability. Homogenized nonlinear finite element (FE) analysis of whole bones can deliver improved fracture risk and implant loosening assessment. Such simulations require the knowledge of mechanical properties such as an appropriate yield behavior and criterion for trabecular bone. Identification of a complete yield surface is extremely difficult experimentally but can be achieved in silico by using micro-FE analysis on cubical trabecular volume elements. Nevertheless, the influence of the boundary conditions (BCs), which are applied to such volume elements, on the obtained yield properties remains unknown. Therefore, this study compared homogenized yield properties along 17 load cases of 126 human femoral trabecular cubic specimens computed with classical kinematic uniform BCs (KUBCs) and a new set of mixed uniform BCs, namely periodicity-compatible mixed uniform BCs (PMUBCs). In stress space, PMUBCs lead to 7–72 % lower yield stresses compared to KUBCs. The yield surfaces obtained with both KUBCs and PMUBCs demonstrate a pressure-sensitive ellipsoidal shape. A volume fraction and fabric-based quadric yield function successfully fitted the yield surfaces of both BCs with a correlation coefficient \(R^{2} \ge 0.93\). As expected, yield strains show only a weak dependency on bone volume fraction and fabric. The role of the two BCs in homogenized FE analysis of whole bones will need to be investigated and validated with experimental results at the whole bone level in future studies.     

How thick is the layer of thermal volume surrounding the protein?

Investigation on the volume properties of protein hydration layers is reported. Presented results are based on combination of Monte Carlo modeling and available experimental data. Six globular proteins with known data are chosen for analysis. Analyzing the model and the experimental results we found that water molecules bound to proteins by hydrogen bond are preferentially located at the places with local depressions on the protein surface. Consequently, the hydration level is not strictly proportional to the area of charged and polar surfaces, but also depends on the shape of the molecular surface. The thickness of the thermal volume layer as calculated in the framework of the scaled particle theory is 0.6-0.65 A for chosen proteins. The obtained value is significantly lower than that presented for proteins in earlier papers (where proportionality between the hydration level and the area of charged and polar surfaces was assumed), but is close to the value published for small solute molecules. Discussion including the influence of protein size and the thermal motion of the surface is presented.