Simulation studies of protein folding/unfolding equilibrium under polar and nonpolar confinement

We study the equilibrium folding/unfolding thermodynamics of a small globular miniprotein, the Trp cage, that is confined to the interior of a 2 nm radius fullerene ball. The interactions of the fullerene surface are changed from nonpolar to polar to mimic the interior of the GroEL/ES chaperonin that assists proteins to fold in vivo. We find that nonpolar confinement stabilizes the folded state of the protein due to the effects of volume reduction that destabilize the unfolded state and also due to interactions with the fullerene surface. For the Trp cage, polar confinement has a net destabilizing effect that results from the stabilizing confinement and the competitive exclusion effect that keeps the protein away from the surface hydration shell and stronger interactions between charged side chains in the protein and the polar surface that compete against the formation of an ion pair that stabilizes the protein folded state. We show that confinement effects due to volume reduction can be overcome by sequence-specific interactions of the protein side chains with the encapsulating surface. This study shows that there is a complex balance among many competing effects that determine the mechanism of GroEL chaperonin in enhancing the folding rate of polypeptide inside its cavity.     

Molecular dynamics simulations of polymer transport in nanocomposites

Molecular dynamics simulations on the Kremer-Grest bead-spring model of polymer melts are used to study the effect of spherical nanoparticles on chain diffusion. We find that chain diffusivity is enhanced relative to its bulk value when polymer-particle interactions are repulsive and is reduced when polymer-particle interactions are strongly attractive. In both cases chain diffusivity assumes its bulk value when the chain center of mass is about one radius of gyration R(g) away from the particle surface. This behavior echoes the behavior of polymer melts confined between two flat surfaces, except in the limit of severe confinement where the surface influence on polymer mobility is more pronounced for flat surfaces. A particularly interesting fact is that, even though chain motion is strongly speeded up in the presence of repulsive boundaries, this effect can be reversed by pinning one isolated monomer onto the surface. This result strongly stresses the importance of properly specifying boundary conditions when the near surface dynamics of chains are studied.     

Macrocyclic beta-sheet peptides that mimic protein quaternary structure through intermolecular beta-sheet interactions

This paper reports the design, synthesis, and characterization of a family of cyclic peptides that mimic protein quaternary structure through beta-sheet interactions. These peptides are 54-membered-ring macrocycles comprising an extended heptapeptide beta-strand, two Hao beta-strand mimics [JACS 2000, 122, 7654] joined by one additional alpha-amino acid, and two delta-linked ornithine beta-turn mimics [JACS 2003, 125, 876]. Peptide 3a, as the representative of these cyclic peptides, contains a heptapeptide sequence (TSFTYTS) adapted from the dimerization interface of protein NuG2 [PDB ID: 1mio]. 1H NMR studies of aqueous solutions of peptide 3a show a partially folded monomer in slow exchange with a strongly folded oligomer. NOE studies clearly show that the peptide self-associates through edge-to-edge beta-sheet dimerization. Pulsed-field gradient (PFG) NMR diffusion coefficient measurements and analytical ultracentrifugation (AUC) studies establish that the oligomer is a tetramer. Collectively, these experiments suggest a model in which cyclic peptide 3a oligomerizes to form a dimer of beta-sheet dimers. In this tetrameric beta-sheet sandwich, the macrocyclic peptide 3a is folded to form a beta-sheet, the beta-sheet is dimerized through edge-to-edge interactions, and this dimer is further dimerized through hydrophobic face-to-face interactions involving the Phe and Tyr groups. Further studies of peptides 3b-3n, which are homologues of peptide 3a with 1-6 variations in the heptapeptide sequence, elucidate the importance of the heptapeptide sequence in the folding and oligomerization of this family of cyclic peptides. Studies of peptides 3b-3g show that aromatic residues across from Hao improve folding of the peptide, while studies of peptides 3h-3n indicate that hydrophobic residues at positions R3 and R5 of the heptapeptide sequence are important in oligomerization.     

Forces between surfaces across nanoparticle solutions: role of size, shape, and concentration

Using a surface force apparatus, we have measured the normal forces between mica surfaces across various types of nanoparticles consisting of ZnS cores coated with a monolayer of physisorbed surfactant, dispersed in organic solvents. We focused on the effects of nanoparticle size, shape, and concentration on the force-distance profiles. Forces were exponentially repulsive when the surfactant layers were strongly bound to the nanoparticles and were roughly linear when there was adhesion between the nanoparticle cores, i.e., when the surfactant layers detached from the nanoparticles. In both cases, the range and magnitude of the forces were dependent upon the particle size, shape, and solution concentration. Fine details in the otherwise smooth force-distance profiles indicate specific effects due to particle chemistry and geometry and the existence of first-order disorder-order phase transitions upon confinement. Small amounts of water in the (hydrophobic) organic solvents had dramatic effects on the measured forces. Understanding and controlling the effects of particle shape, size, and concentration and the presence of water (or other surface-active solutes) on particle-particle and particle-surface interactions are important for the processing of nanoparticles into ordered superstructured materials.     

Monte Carlo Calculations of Polymer Adsorption at the Entrance of Cylindrical Pores in Flat Adsorbing Surfaces

The influence of surface interactions on the conformation of flexible polymers partially confined inside narrow cylindrical pores in a flat surface is studied above the critical adsorption energy in a good solvent. We use a static configurational bias computational sampling method to calculate the adsorption free energy and the radius of gyration components parallel and perpendicular to the pore axis as a function of the polymer center of mass position at different degrees of confinement. We find strong free‐energy minima just in front of the pore entry for all degrees of confinement studied. At the location of the free‐energy minimum, polymers are partially adsorbed inside the pore and on the outer solid surface and adopt “drawing pin”‐like conformations. A distinct maximum in the average loop length at the pore entry indicates that the polymer bridges the pore entry of small pores.     

Protein-protein interactions in complex cosolvent solutions.

The effects of various kosmotropic and chaotropic cosolvents and salts on the intermolecular interaction potential of positively charged lysozyme is evaluated at varying protein concentrations by using synchrotron small-angle X-ray scattering in combination with liquid-state theoretical approaches. The experimentally derived static structure factors S(Q) obtained without and with added cosolvents and salts are analysed with a statistical mechanical model based on the Derjaguin-Landau-Verwey-Overbeek (DLVO) potential, which accounts for repulsive and attractive interactions between the protein molecules. Different cosolvents and salts influence the interactions between protein molecules differently as a result of changes in the hydration level or solvation, in charge screening, specific adsorption of the additives at the protein surface, or increased hydrophobic interactions. Intermolecular interaction effects are significant above protein concentrations of 1 wt %, and with increasing protein concentration, the repulsive nature of the intermolecular pair potential V(r) increases markedly. Kosmotropic cosolvents like glycerol and sucrose exhibit strong concentration-dependent effects on the interaction potential, leading to an increase of repulsive forces between the protein molecules at low to medium high osmolyte concentrations. Addition of trifluoroethanol exhibits a multiphasic effect on V(r) when changing its concentration. Salts like sodium chloride and potassium sulfate exhibit strong concentration-dependent changes of the interaction potential due to charge screening of the positively charged protein molecules. Guanidinium chloride (GdmCl) at low concentrations exhibits a similar charge-screening effect, resulting in increased attractive interactions between the protein molecules. At higher GdmCl concentrations, V(r) becomes more repulsive in nature due to the presence of high concentrations of Gdm(+) ions binding to the protein molecules. Our findings also imply that in calculations of thermodynamic properties of proteins in solution and cosolvent mixtures, activity coefficients may not generally be neglected in the concentration range above 1 wt % protein.     

Origin of repulsive force and structure/dynamics of interfacial water in OEG-protein interactions: a molecular simulation study

Molecular simulations were performed to investigate the origin of the strong repulsive force acting on a protein as the protein approaches an oligo (ethylene glycol) self-assembled monolayer (OEG-SAM) surface. Since the repulsive force is mainly generated from water molecules, the force from the water molecules near the surface was calculated layer by layer to further identify the molecular origin of the repulsive force. Results show that the strong repulsive force acting on the protein near the OEG-SAM surface is dominantly generated by the interfacial water molecules located between the OEG-SAM surface and lysozyme. A hydroxyl-terminated SAM (OH-SAM) surface was used for comparison. No significant repulsive force was observed from the water molecules between the protein and OH-SAM surface. Further studies show that the dipole distribution of the interfacial water molecules is significantly affected by the OEG-SAM surface, as opposed to the negligible impact from the OH-SAM surface. The interfacial water molecules above the OEG-SAM surface stay longer and reorient more slowly than those above the OH-SAM surface. These results from this work support the hypothesis that the OEG-SAM surface interacts strongly with interfacial water molecules and creates a stable hydration layer that prevents proteins from adsorbing to the surface.     

Tunable nanopatterning by diblock copolymers in small confinements*

Here we study the effects of confinement on the self‐assembly of diblock copolymers. Specifically, we study the hexagonal cylindrical phase as it self‐assembles within a narrow confinement. We quantify the structural deformation of the cylindrical morphology that arises from the frustration that the narrow confinements exert on the system when the confinement width is incompatible with the lattice structure of the bulk mesophase. © 2004 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 42: 3695–3700, 2004     

Adsorption behavior of repulsive molecules

Recently, it has been shown that adsorption of gases on solid surfaces often leads to repulsive forces between adsorbate molecules. In this paper, adsorption of molecules on a one-dimensional lattice is considered for repulsive interactions between adsorbate molecules. Exact adsorption isotherms are calculated and analyzed for finite and infinite chains of active sites (i.e., a one-dimensional lattice). Although the mathematical solution for the one-dimensional lattice is known for attractive and repulsive systems, the effects of intermolecular repulsions on adsorption behavior have not been studied in detail previously. Similarly, though the mathematics for the one-dimensional lattice has been solved for any arbitrary lattice length, the effect of finite size on adsorption isotherms for repulsive adsorbate interactions has never been examined. This paper shows that spatial confinement and strong attraction to active sites can cause compression of an adsorbed phase and that repulsive interactions between adsorbed molecules result in steps in the adsorption isotherms. For higher chemical potentials, the density increases until saturating at the lattice capacity. These steps in the adsorption isotherm have not been observed in previous studies of lattice systems. For small lattices, the adsorption behavior was found to be fundamentally different for even and odd values of lattice length. Lattices with an even number of lattice sites can have two steps in the adsorption isotherm, whereas systems with an odd number of sites only have a single step occurring at a coverage slightly greater than half the lattice capacity.     

Conformational mechanics, adsorption, and normal force interactions of lubricin and hyaluronic acid on model surfaces

Glycoproteins, such as lubricin, and hyaluronic acid (HA) play a prominent role in the boundary lubrication mechanism in diarthrodial joints. Although many studies have tried to elucidate the lubrication mechanisms of articular cartilage, the molecular details of how lubricin and HA interact with cartilage surfaces and mediate their interaction still remain poorly understood. Here we used model substrates, functionalized with self-assembled monolayers terminating in hydroxyl or methyl groups, (1) to determine the effect of surface chemistry on lubricin and HA adsorption using surface plasmon resonance (SPR) and (2) to study normal force interactions between these surfaces as a function of lubricin and HA concentration using colloidal probe microscopy. We found that lubricin is amphiphilic and adsorbed strongly onto both methyl- and hydroxyl-terminated surfaces. On hydrophobic surfaces, lubricin likely adopts a compact, looplike conformation in which its hydrophobic domains at the N and C termini serve as surface anchors. On hydrophilic surfaces, lubricin likely adsorbs anywhere along its hydrophilic central domain and adopts, with increasing solution concentration, an extended tail-like conformation. Overall, lubricin develops strong repulsive interactions when compressing two surfaces into contact. Furthermore, upon surface separation, adhesion occurs between the surfaces as a result of molecular bridging and chain disentanglement. This behavior is in contrast to that of HA, which does not adsorb appreciably on either of the model surfaces and does not develop significant repulsive interactions. Adhesive forces, particularly between the hydrophobic surfaces, are large and not appreciably affected by HA. For a mixture of lubricin and HA, we observed slightly larger adsorptions and repulsions than those found for lubricin alone. Our experiments suggest that this interaction depends on unspecific physical rather than chemical interactions between lubricin and HA. We speculate that in mediating interactions at the cartilage surface, an important role of lubricin, possibly in conjunction with HA, is one of providing a protective coating on cartilage surfaces that maintains the contacting surfaces in a sterically repulsive state.     

On the behavior of electrokinetic streaming potential during protein filtration with fully and partially retentive nanopores

An experimental investigation of the electrokinetic streaming potentials of both fully and partially retentive nanopores as compared with the filtration progress of dilute globular protein solution under different surface charge conditions was performed using hollow fibers. The streaming potential is generated by the electrokinetic flow effect within the electric double layer of the charged surface. Depending on the solution pH, both the protein and the pore wall can be either repulsive or attractive due to the long-range electrostatic interaction. The repulsive electrostatic interaction allows the protein particles to stay in a suspended state above the outer surface of hollow fibers instead of being deposited. The apparent streaming potential value at partially retentive pores is larger than that at fully retentive pores for the oppositely charged case; however, the opposite behavior is shown for the same-charged case. The axial-position-dependent streaming potential was also observed in order to explore the development of a concentration polarization layer during the cross-flow filtration. The time evolution of the streaming potential during the filtration of protein particles is related to the filtrate flux, from which it can be found to provide useful real-time information on particle deposition onto the outer surfaces of hollow fibers.     

Brownian dynamics simulations of polyelectrolyte adsorption onto topographically patterned surfaces

The effect of patterned surface topography on the adsorption of single polyelectrolyte molecules is explored using Brownian dynamics simulations. The polyelectrolyte is modeled as a free-draining, freely jointed bead-rod chain, and electrostatic interactions are incorporated using a screened Coulombic potential with excluded volume interactions accounted for by the repulsive part of a Lennard-Jones potential. Topography consisting of periodically spaced valleys of square cross section separated by flat hills is considered. Chain conformations are characterized for a wide range of valley widths, depths, and spacings as well as for several different types of surface charge distributions. Depending on the parameter values describing the topography, the chains are found to adopt conformations ranging from flat and extended to those associated with bridge-, brush-, or semi-bridge-like structures. The formation of these structures is rationalized on the basis of a free-energy model that takes into account the increase in free energy due to entropic confinement, excluded volume interactions, and chain stretching as well as the decrease in free energy due to bead-surface electrostatic attraction. The results of this work are expected to be useful in designing patterned surface topography to control the conformations of adsorbed polyelectrolyte molecules.     

The Effect of Solute Concentration on Equilibrium Partitioning in Polymeric Gels

The effect of solute concentration on the equilibrium partitioning of sphere-like, colloidal solutes in stiff polymer hydrogels is examined theoretically and experimentally. The theoretical development is a statistical mechanics approach, and allows quantitative calculations to be performed to determine the concentration-dependent partition coefficient correct to first order in solute concentration at specific surface charge densities. The theory predicts that repulsive steric and/or electrostatic solute-fiber interactions exclude solute from the gel phase, but that repulsive solute-solute interactions cause partitioning into the gel to increase with increasing solute concentration. These trends are enhanced for larger solutes, increased fiber volume fractions, or stronger electrostatic repulsion. Partition coefficients have also been measured for two proteins, bovine serum albumin (BSA) and alpha-lactalbumin (ALA), in a system consisting of a salt solution and cubes of agarose hydrogel. To investigate the effect of electrostatic interactions, the experiments were performed at 0.15 M KCl and 0.01 M KCl. The theory underpredicts the strong electrostatic repulsion between BSA macromolecules at the lower ionic strength. The experimental results for ALA show the influence of an attractive interaction between the protein macromolecules, in addition to hard-sphere repulsive and electrostatic interactions. Copyright 2001 Academic Press.     

Influence of DNA adsorption and DNA/cationic surfactant coadsorption on the interaction forces between hydrophobic surfaces

The forces between hydrophobic surfaces with physisorbed DNA are markedly and irreversibly altered by exposure to DNA/cetyltrimethylammonium bromide (CTAB) mixtures. In this colloidal probe atomic force microscopy study of the interactions between a hydrophobic polystyrene particle and an octadecyltrimethylethoxysilane-modified mica surface in sodium bromide solutions, we measure distinct changes in colloidal forces depending on the existence and state of an adsorbed layer of DNA or CTAB-DNA complexes. For bare hydrophobic surfaces, a monotonically attractive approach curve and very large adhesion are observed. When DNA is adsorbed at low bulk concentrations, a long-range repulsive force dominates the approach, but on retraction some adhesion persists and DNA bridging is clearly observed. When the DNA solution is replaced with a CTAB-DNA mixture at relative low CTAB concentration, the length scale of the repulsive force decreases, the adhesion due to hydrophobic interactions greatly decreases, and bridging events disappear. Finally, when the surface is rinsed with NaBr solution, the length scale of the repulsive interaction increases modestly, and only a very tiny adhesion remains. These pronounced changes in the force behavior are consistent with CTAB-induced DNA compaction accompanied by increased DNA adsorption, both of which are partially irreversible.     

Effect of charge distribution on the translocation of an inhomogeneously charged polymer through a nanopore

We investigate the voltage-driven translocation of an inhomogeneously charged polymer through a nanopore by utilizing discrete and continuous stochastic models. As a simplified illustration of the effect of charge distribution on translocation, we consider the translocation of a polymer with a single charged site in the presence and absence of interactions between the charge and the pore. We find that the position of the charge that minimizes the translocation time in the absence of pore-polymer interactions is determined by the entropic cost of translocation, with the optimum charge position being at the midpoint of the chain for a rodlike polymer and close to the leading chain end for an ideal chain. The presence of attractive and repulsive pore-charge interactions yields a shift in the optimum charge position toward the trailing end and the leading end of the chain, respectively. Moreover, our results show that strong attractive or repulsive interactions between the charge and the pore lengthen the translocation time relative to translocation through an inert pore. We generalize our results to accommodate the presence of multiple charged sites on the polymer. Our results provide insight into the effect of charge inhomogeneity on protein translocation through biological membranes.     

采用优化的DFTB参数对铜(111)表面碳二聚化的分子动力学研究

针对铜表面化学反应,我们发展了一套铜-碳体系的密度泛函紧束缚(DFTB)参数。测试结果表明这套参数可以很好的描述吸附铜或碳原子前后铜表面的几何结构和能量。基于这套参数,我们对Cu(111)表面的碳二聚化过程进行了分子模拟研究。即使在高温下,直接的分子动力学模拟也很难观察到碳二聚体的形成。这是因为高温下铜表面显著的结构弛豫一定程度上阻止了二聚化。为了研究高温下铜表面碳二聚化的机理,我们进行了赝动力学模拟。发现在二聚化的过程中,碳原子形成C-Cu-C桥状结构以后,会绕中间Cu原子转动,最后形成碳二聚体。1300 K下碳二聚化的自由能垒约0.9 eV。     

Mild and selective palladium-catalyzed dimerization of terminal alkynes to form symmetrical (Z,Z)-1,4-dihalo-1,3-dienes

A regioselective and stereoselective palladium-catalyzed dimerization of terminal alkynes method for the synthesis of symmetrical (Z,Z)-1,4-dihalo-1,3-dienes is presented. In the presence of a catalytic amount of PdX(2) and 3 equiv of CuX(2) (X = Cl and Br), terminal alkynes were dimerized to afford (Z,Z)-1,4-dihalo-1,3-dienes in good yields. The results showed that the effect of solvent had a fundamental influence on the chemoselectivity of the dimerization reaction. The mechanism of the palladium-catalyzed dimerization reaction is also discussed.     

Simulations of the confinement of ubiquitin in self-assembled reverse micelles

We describe the effects of confinement on the structure, hydration, and the internal dynamics of ubiquitin encapsulated in reverse micelles (RM). We performed molecular dynamics simulations of the encapsulation of ubiquitin into self-assembled protein/surfactant reverse micelles to study the positioning and interactions of the protein with the RM and found that ubiquitin binds to the RM interface at low salt concentrations. The same hydrophobic patch that is recognized by ubiquitin binding domains in vivo is found to make direct contact with the surfactant head groups, hydrophobic tails, and the iso-octane solvent. The fast backbone N-H relaxation dynamics show that the fluctuations of the protein encapsulated in the RM are reduced when compared to the protein in bulk. This reduction in fluctuations can be explained by the direct interactions of ubiquitin with the surfactant and by the reduced hydration environment within the RM. At high concentrations of excess salt, the protein does not bind strongly to the RM interface and the fast backbone dynamics are similar to that of the protein in bulk. Our simulations demonstrate that the confinement of protein can result in altered protein dynamics due to the interactions between the protein and the surfactant.     

Eluotropic strength in non-aqueous liquid chromatography with porous graphitic carbon

Protein adsorption can be either endothermic or exothermic depending upon the protein, the sorbent and process conditions. In the case of protein adsorption onto ion-exchange surfaces exothermic adsorption heats are usually characterized as representing the electrostatic interaction between two oppositely charged surfaces. Endothermic adsorption heats are typically characterized as representing protein reconfiguration and/or repulsive interactions between adsorbed molecules. In certain segments of the literature surface dehydration and solution non-idealities have been suggested as possible sources of endothermic heats of adsorption. Each of these phenomena was investigated during studies concerning the adsorption of bovine serum albumin and ovalbumin onto an anion-exchange sorbent. The results demonstrated that electrostatic repulsive interactions between adsorbed molecules appears to be a larger contributor to endothermic heats of adsorption than surface dehydration or solution non-idealities. The presence of mobile phase cations can reduce the magnitude of endothermic adsorption heats by screening repulsive interactions between adsorbed molecules. Although water release was not found to be a major contributor to endothermic adsorption heats, it is likely to be a contributor to the entropic driving force associated with the adsorption of bovine serum albumin.     

Transformations of griseofulvin in strong acidic conditions--crystal structures of 2'-demethylgriseofulvin and dimerized griseofulvin

The structure of griseofulvic acid, C16H15ClO6, at 100 K has orthorhombic (P2(1)2(1)2) symmetry. It is of interest with respect to biological activity. The structure displays intermolecular O-H...O, C-H...O hydrogen bonding as well as week C-H...pi and pi...pi interactions. In strong acidic conditions the griseofulvin undergoes dimerization. The structure of dimerized griseofulvin, C34H32C12O12 x C2H6O x H2O, at 100 K has monoclinic (P2(1)) symmetry. The molecule crystallized as a solvate with one ethanol and one water molecule. The dimeric molecules form intermolecular O-H...O hydrogen bonds to solvents molecules only but they interact via week C-H...O, C-H...pi, C-Cl...pi and pi...pi interactions with other dimerized molecules.