Elastic properties of poly(ethylene-glycol) studied by molecular dynamics stretching simulations

Iodination of PEGylated Polymers Counteracts the Inhibition of Fibrinogen Adsorption by PEG

Poly(ethylene glycol), PEG, known to inhibit protein adsorption, is widely used on the surfaces of biomedical devices when biofilm formation is undesirable. Poly(desaminotyrosyl-tyrosine ethyl ester carbonate), PDTEC, PC for short, has been a promising coating polymer for insertion devices, and it has been anticipated that PEG plays a similar role if it is copolymerized with PC. Earlier studies show that no fibrinogen (Fg) is adsorbed onto PC polymers with PEG beyond the threshold weight percentage. This is attributed to the phase separation of PEG. Further, iodination of the PC units in the PC polymer, (I₂PC), has been found to counteract this Fg-repulsive effect by PEG. In this study, we employ surface-sensitive X-ray techniques to demonstrate the surface affinity of Fg toward the air-water interface, particularly in the presence of self-assembled PC-based film, in which its constituent polymer units are assumed to be much more mobile as a free-standing film. Fg is found to form a Gibbs monolayer with its long axis parallel to the aqueous surface, thus maximizing its interactions with hydrophobic interfaces. It influences the amount of insoluble, surface-bound I₂PC likely due to the desorption of the formed Fg-I₂PC complex and/or the penetration of Fg onto the I₂PC film. The results show that the phase behavior at the liquid-polymer interface shall be taken into account for the surface behavior of bulk polymers surrounded by tissue. The ability of PEG units rearranging into a protein-blocking layer, rather than its mere presence in the polymer, is the key to antifouling characteristics desired for polymeric coating on insertion devices.

Angle-dependent strength of a single chemical bond by stereographic force spectroscopy

A wealth of chemical bonds and polymers have been studied with single-molecule force spectroscopy, usually by applying a force perpendicular to the anchoring surface. However, the direction-dependence of the bond strength lacks fundamental understanding. Here we establish stereographic force spectroscopy to study the single-bond strength for various pulling angles. Surprisingly, we find that the apparent bond strength increases with increasing pulling angle relative to the anchoring surface normal, indicating a sturdy mechanical anisotropy of a chemical bond. This finding can be rationalized by a fixed pathway for the rupture of the bond, resulting in an effective projection of the applied pulling force onto a nearly fixed rupture direction. Our study is fundamental for the molecular understanding of the role of the direction of force application in molecular adhesion and friction. It is also a prerequisite for the nanoscale tailoring of the anisotropic strength of bottom-up designed materials.

Stereographic force spectroscopy reveals that a chemical bond ruptures along a fixed pathway such that the apparent bond strength strongly depends on the angle of force application.

A PEGylated N-heterocyclic carbene-gold(i) complex: an efficient catalyst for cyclization reaction in water

A recyclable, PEGylated N-heterocyclic carbene(NHC)–gold(i) catalyst was synthesized, which exhibited high reactivity and regio-selectivity in the cyclization of alkynoic acids and cascade reaction of tryptamine and alkynoic acids in water.

Insight into structural properties of polyethylene glycol monolaurate in water and alcohols from molecular dynamics studies

By means of molecular dynamics (MD) simulations, we explored the structural properties of polyethylene glycol monolaurate (PEGML) in water and in various aliphatic alcohols (methanol, ethanol, 2-propanol, 2-butanol, tert-butanol, and 1-pentanol). The PEGML and the alcohols were simulated using the optimized potentials for liquid simulations, all-atom (OPLS-AA) force field and water using the extended simple point charge (SPC/E) model. From the isothermal-isobaric (NPT, constant number of particles, constant pressure, and constant temperature) ensemble, we extracted the densities from the simulations and compared them with those from experimental results in order to confirm the validity of the selected force fields. The densities from MD simulations are in good agreement with the experimental values. To gain more insight into the nature of interactions between the PEGML and the solvent molecules, we analyzed the hydrogen-bonds, the electrostatic (Coulomb) interactions, and the van der Waals (Lennard-Jones) interaction energies extracted from MD simulations. The results were further strengthened by computing the solvation free energy by employing the free energy perturbation (FEP) approach. In this method, the free energy difference was computed by using the Bennet Acceptance Ratio (BAR) method. Moreover, the radial distribution functions were analyzed in order to gain more understanding of the solution behavior at the molecular level.

Molecular Dynamics Simulations of Strain-Induced Phase Transition of Poly(ethylene oxide) in Water

We study the dilute aqueous solutions of poly(ethylene oxide) (PEO) oligomers that are subject to an elongating force dipole acting on both chain ends using atomistic molecular dynamics. By increasing the force, liquid-liquid demixing can be observed at room temperature far below the lower critical solution temperature. For forces above 35 pN, fibrillar nanostructures are spontaneously formed related to a decrease in hydrogen bonding between PEO and water. Most notable is a rapid decrease in the bifurcated hydrogen bonds during stretching, which can also be observed for isolated single chains. The phase-segregated structures display signs of chain ordering, but a clear signature of the crystalline order is not obtained during the simulation time, indicating a liquid-liquid phase transition induced by chain stretching. Our results indicate that the solvent quality of the aqueous solution of PEO depends on the conformational state of the chains, which is most likely related to the specific hydrogen-bond-induced solvation of PEO in water. The strain-induced demixing of PEO opens the possibility to obtain polymer fibers with low energy costs because crystallization starts via the strain-induced demixing in the extended state only.

Designing a main-chain visible-light-labile picolinium-caged polymer and its biological applications

A picolinium-caged main-chain photolabile polymer (MCPP) is reported with a high degradation efficiency (∼95%) upon visible light irradiation (452 nm).

Characterizing the structure and properties of dry and wet polyethylene glycol using multi-scale simulations

Multi-scale simulations to study the structure and material properties of PEG in dry and wet conditions.

Synthesis of Ferrofluids Made of Iron Oxide Nanoflowers: Interplay between Carrier Fluid and Magnetic Properties

Ferrofluids are nanomaterials consisting of magnetic nanoparticles that are dispersed in a carrier fluid. Their physical properties, and hence their field of application are determined by intertwined compositional, structural, and magnetic characteristics, including interparticle magnetic interactions. Magnetic nanoparticles were prepared by thermal decomposition of iron(III) chloride hexahydrate (FeCl₃·6H₂O) in 2-pyrrolidone, and were then dispersed in two different fluids, water and polyethylene glycol 400 (PEG). A number of experimental techniques (especially, transmission electron microscopy, Mössbauer spectroscopy and superconducting quantum interference device (SQUID) magnetometry) were employed to study both the as-prepared nanoparticles and the ferrofluids. We show that, with the adopted synthesis parameters of temperature and FeCl₃ relative concentration, nanoparticles are obtained that mainly consist of maghemite and present a high degree of structural disorder and strong spin canting, resulting in a low saturation magnetization (~45 emu/g). A remarkable feature is that the nanoparticles, ultimately due to the presence of 2-pyrrolidone at their surface, are arranged in nanoflower-shape structures, which are substantially stable in water and tend to disaggregate in PEG. The different arrangement of the nanoparticles in the two fluids implies a different strength of dipolar magnetic interactions, as revealed by the analysis of their magnetothermal behavior. The comparison between the magnetic heating capacities of the two ferrofluids demonstrates the possibility of tailoring the performances of the produced nanoparticles by exploiting the interplay with the carrier fluid.

Terminal Acetylated/Acrylated Poly(ethylene glycol) Fabricated Drug Carriers: Design, Synthesis, and Biological Evaluation

The simple acetylation or acrylation of poly(ethylene glycol) (PEG) terminus leads to the aggregation of PEG chains into spherical nanoparticles in water at room temperature and very low concentrations. The experiment results suggest that this aggregation happens by the variation of the local conformation of the O-CH₂-CH₂-O segments of PEG chains caused by the introduced acyl group, which disturbs the originally strict hydrogen bond mode between the O-CH₂-CH₂-O groups and the water molecules. The simple modified PEG nanoparticles are excellent carriers for drug delivery. As examples, the cross-linkable 1d-based drug delivery systems, cPEG@SN-38 and targeted cPEG@SN-38, are successfully established by their high drug loading content (18 wt %/wt) and enhanced anticancer efficacy both in vitro and in vivo while obviating the inherent toxicity of the employed chemotherapeutics. This strategy that revolves around the simple modification of the generally regarded as safe (GRAS) modules to fabricate drug carriers represents a new direction for the drug delivery systems with clinical potential.

Hydration Effects Turn a Highly Stretched Polymer from an Entropic into an Energetic Spring

Polyethylene glycol (PEG) is a structurally simple and nontoxic water-soluble polymer that is widely used in medical and pharmaceutical applications as molecular linker and spacer. In such applications, PEG's elastic response against conformational deformations is key to its function. According to text-book knowledge, a polymer reacts to the stretching of its end-to-end separation by a decrease in entropy that is due to the reduction of available conformations, which is why polymers are commonly called entropic springs. By a combination of single-molecule force spectroscopy experiments with molecular dynamics simulations in explicit water, we show that entropic hydration effects almost exactly compensate the chain conformational entropy loss at high stretching. Our simulations reveal that this entropic compensation is due to the stretching-induced release of water molecules that in the relaxed state form double hydrogen bonds with PEG. As a consequence, the stretching response of PEG is predominantly of energetic, not of entropic, origin at high forces and caused by hydration effects, while PEG backbone deformations only play a minor role. These findings demonstrate the importance of hydration for the mechanics of macromolecules and constitute a case example that sheds light on the antagonistic interplay of conformational and hydration degrees of freedom.

Oriented Membrane Protein Reconstitution into Tethered Lipid Membranes for AFM Force Spectroscopy

Membrane proteins act as a central interface between the extracellular environment and the intracellular response and as such represent one of the most important classes of drug targets. The characterization of the molecular properties of integral membrane proteins, such as topology and interdomain interaction, is key to a fundamental understanding of their function. Atomic force microscopy (AFM) and force spectroscopy have the intrinsic capabilities of investigating these properties in a near-native setting. However, atomic force spectroscopy of membrane proteins is traditionally carried out in a crystalline setup. Alternatively, model membrane systems, such as tethered bilayer membranes, have been developed for surface-dependent techniques. While these setups can provide a more native environment, data analysis may be complicated by the normally found statistical orientation of the reconstituted protein in the model membrane. We have developed a model membrane system that enables the study of membrane proteins in a defined orientation by single-molecule force spectroscopy. Our approach is demonstrated using cell-free expressed bacteriorhodopsin coupled to a quartz glass surface in a defined orientation through a protein anchor and reconstituted inside an artificial membrane system. This approach offers an effective way to study membrane proteins in a planar lipid bilayer. It can be easily transferred to all membrane proteins that possess a suitable tag and can be reconstituted into a lipid bilayer. In this respect, we anticipate that this technique may contribute important information on structure, topology, and intra- and intermolecular interactions of other seven-transmembrane helical receptors.

Effect of the size of solvent molecules on the single-chain mechanics of poly(ethylene glycol): implications on a novel design of a molecular motor

Excluded-volume (EV) interaction, also known as the EV effect, can drive the collapse of polymer chains in a polymer solution and promote the crystallization of polymer chains. Herein we report, for the first time, the effect of EV interaction on the single-chain mechanics of a polymer, poly(ethylene glycol) (PEG). By using AFM-based single-molecule force spectroscopy, the single-chain mechanics of a PEG chain has been detected in various nonpolar organic solvents with different molecule sizes. It is observed that the nonpolar solvents can be classified into two categories. In the small-sized organic solvents (e.g., tetrachloroethane and n-nonane), PEG presents its inherent elasticity, which is consistent with the theoretical single-chain elasticity from quantum mechanical calculations. However, in the middle-sized solvents (e.g., n-dodecane and n-hexadecane), the single-chain entropic elasticity of PEG is influenced by EV interactions noticeably, which indicates that the PEG chain tends to adopt a compact conformation under these conditions. To stretch a PEG chain from a free state to a fully extended state, more energy (1.54 k_BT per repeating unit) is needed in small-sized organic solvents than in middle-sized organic solvents. It is expected that a partially stretched PEG chain would shrink to some extent when the solvent is changed from a middle-sized organic solvent to a small-sized one. Accordingly, a novel design of a PEG-based single-molecule motor that works with solvent stimuli is proposed.

Mechanical stability of bivalent transition metal complexes analyzed by single-molecule force spectroscopy

Multivalent biomolecular interactions allow for a balanced interplay of mechanical stability and malleability, and nature makes widely use of it. For instance, systems of similar thermal stability may have very different rupture forces. Thus it is of paramount interest to study and understand the mechanical properties of multivalent systems through well-characterized model systems. We analyzed the rupture behavior of three different bivalent pyridine coordination complexes with Cu²⁺ in aqueous environment by single-molecule force spectroscopy. Those complexes share the same supramolecular interaction leading to similar thermal off-rates in the range of 0.09 and 0.36 s⁻¹, compared to 1.7 s⁻¹ for the monovalent complex. On the other hand, the backbones exhibit different flexibility, and we determined a broad range of rupture lengths between 0.3 and 1.1 nm, with higher most-probable rupture forces for the stiffer backbones. Interestingly, the medium-flexible connection has the highest rupture forces, whereas the ligands with highest and lowest rigidity seem to be prone to consecutive bond rupture. The presented approach allows separating bond and backbone effects in multivalent model systems.

Kosmotrope-like hydration behavior of polyethylene glycol from microcalorimetry and binding isotherm measurements

Polyethylene glycol (PEG) at various molecular weights (MWs) has been regarded as a wonder molecule in biomedical applications. For instance, PEG serves as a unique moiety for pegylation of "biobetter" drug development, PEG provides controlled-release and preserved activity of biologics, and PEG modified surface works as an antibiofouling surface. The primary characteristics of PEG molecules used in relevant applications have been attributed mainly to the hydration behavior in aqueous solutions. However, the effects on the solvation of solutes in solution caused by presenting PEG molecules as a cosolvent, as well as the thermodynamics aspect of the hydration behavior of PEG in solution, have not been well documented. The solvation behavior of solutes, such as protein, with PEG as a cosolvent, indicates the success of PEG applications, such as biofouling and controlled release. In this investigation, we examined the effects of a buffer solution containing PEG molecules on the solution behavior of solute and the interactions between solid surfaces with solutes. We adapted the study by selecting a lysozyme as a solute in a buffer solution with either ammonium sulfate (kosmotrope) or sodium chloride (chaotrope) and anionic resin (SP-Sepharose) as solid surfaces. The experiments primarily involved binding equilibrium measurements and thermodynamics analysis. The results revealed that, in both saline buffers, adding PEG increases the binding affinity between the lysozyme and the resin, similar to kosmotropic salt in the examined salt concentrations. The thermodynamics analyses involving microcalorimetric measurements show that the bindings are mainly driven by enthalpy, indicating that electrostatic interaction was the primary binding force under these experimental conditions. The variations of the enthalpy and entropy of the binding thermodynamics when adding PEG to different salt types in the buffer solution showed opposite behavior, and the results support the concept of kosmotrope-like behavior of PEG. The equilibrium and thermodynamics data demonstrate that PEG has a kosmotrope-like hydration behavior, and the extent of kosmotrope-like behavior depends on the molecular weight of PEG with the outcomes of various molecular weights of PEG being added to the binding solution. The results of this study provide essential knowledge for PEG as an additive (or cosolvent) in various research applications.

Biocompatibility studies of poly(ethylene glycol)–modified titanium for cardiovascular devices

The rapid protein adsorption on a material surface causes blood coagulation, platelet activation, and complement system activation, which poses a risk for failure of cardiovascular devices. In this study, a chemically hydroxylated titanium surface was aminosilanized and covalently grafted with poly(ethylene glycol). The reaction conditions on the grafted quantity were studied by the respective amine and carboxyl densities. The blood compatibility of the PEGylated surfaces with different poly(ethylene glycol) densities and chain lengths was evaluated; the PEGylated surfaces with higher grafted density and longer chain length had less fibrinogen adsorption, less fibrinogen γ-chain exposed, less adherent platelets, and lower activation of the adherent platelets. In addition to the influence on blood, the longer chain PEGylated surfaces resisted, not only smooth muscle cell attachment and proliferation, but also macrophage attachment and death. This method is a good candidate for improving cardiovascular implant surfaces.

Hydrogels with well-defined peptide-hydrogel spacing and concentration: impact on epithelial cell behavior()

The spacing of peptides away from a hydrogel matrix dramatically impacts their availability and subsequent interactions with cells. Peptides were synthesized with monodisperse poly(ethylene glycol) spacers of different lengths that separate the peptide from the monomeric functionality which reacts during hydrogel polymerization. Specifically, bioactive RGD ligands were conjugated to PEG(5), PEG(11) or PEG(27) spacers via solid phase techniques and then functionalized with an acryloyl end group. These acryloyl-PEGx-RGD conjugates were then copolymerized with PEGDA to form an inert hydrogel network decorated with RGD ligands for cell interactions. As the PEG spacer length increases, the RGD concentration required to support cell attachment and spreading decreases. The competitive detachment of hTCEpi cells in the presence of soluble linear RGD also shows non-linear dependence on the PEG spacer length, as more cells remained attached and spread on gels functionalized with longer PEG-RGD conjugates in comparison to the shorter PEG-RGD conjugates. The strategy and synthetic techniques developed here allow for reproducible control over peptide-hydrogel spacing and peptide concentration, and may be extended for incorporation of multiple peptides and to other hydrogel platforms.

Equilibrium sampling for biomolecules under mechanical tension

In the studies of force-induced conformational transitions of biomolecules, the large timescale difference from experiments presents the challenge of obtaining convergent sampling for molecular dynamics simulations. To circumvent this fundamental problem, an approach combining the replica-exchange method and umbrella sampling (REM-US) was developed to simulate mechanical stretching of biomolecules under equilibrium conditions. Equilibrium properties of conformational transitions can be obtained directly from simulations without further assumptions. To test the performance, we carried out REM-US simulations of atomic force microscope (AFM) stretching and relaxing measurements on the polysaccharide pustulan, a (1-->6)-beta-D-glucan, which undergoes well-characterized rotameric transitions in the backbone bonds. With significantly enhanced sampling convergence and efficiency, the REM-US approach closely reproduced the equilibrium force-extension curves measured in AFM experiments. Consistent with the reversibility in the AFM measurements, the new approach generated identical force-extension curves in both stretching and relaxing simulations-an outcome not reported in previous studies, proving that equilibrium conditions were achieved in the simulations. REM-US may provide a robust approach to modeling of mechanical stretching on polysaccharides and even nucleic acids.

Biosensing by densely packed and optically coupled plasmonic particle arrays

Densely packed plasmonic particle arrays are investigated for biosensing applications. Such particle arrays exhibit interparticle optical coupling creating a strong field between the particles, which is useful for sensing purposes. The sensor properties, such as bulk sensitivity, layer sensitivity, and the depth of sensitivity are investigated with the aid of a multiple multipole program. Sensitivity to the analyte with low concentration is also examined by a dynamic adsorption processes. The detectable concentration limit of streptavidin within 3000 s in the detection system is expected from the signal-to-noise to be less than 150 pM.

Synthesis and Characterization of Elastin-Mimetic Hybrid Polymers with Multiblock, Alternating Molecular Architecture and Elastomeric Properties

We are interested in developing elastin-mimetic hybrid polymers (EMHPs) that capture the multiblock molecular architecture of tropoelastin as well as the remarkable elasticity of mature elastin. In this study, multiblock EMHPs containing flexible synthetic segments based on poly(ethylene glycol) (PEG) alternating with alanine-rich, lysine-containing peptides were synthesized by step-growth polymerization using α,ω-azido-PEG and alkyne-terminated AKA(3)KA (K = lysine, A = alanine) peptide, employing orthogonal click chemistry. The resulting EMHPs contain an estimated three to five repeats of PEG and AKA(3)KA and have an average molecular weight of 34 kDa. While the peptide alone exhibited α-helical structures at high pH, the fractional helicity for EMHPs was reduced. Covalent cross-linking of EMHPs with hexamethylene diisocyanate (HMDI) through the lysine residue in the peptide domain afforded an elastomeric hydrogel (xEMHP) with a compressive modulus of 0.12 MPa when hydrated. The mechanical properties of xEMHP are comparable to a commercial polyurethane elastomer (Tecoflex SG80A) under the same conditions. In vitro toxicity studies showed that while the soluble EMHPs inhibited the growth of primary porcine vocal fold fibroblasts (PVFFs) at concentrations ≥0.2 mg/mL, the cross-linked hybrid elastomers did not leach out any toxic reagents and allowed PVFFs to grow and proliferate normally. The hybrid and modular approach provides a new strategy for developing elastomeric scaffolds for tissue engineering.

Effect of PEGylation on the Solution Conformation of Antibody Fragments

Covalent attachment of poly(ethylene glycol) (PEG) to therapeutic antibody fragments has been found effective in prolonging the half-life of the protein molecule in vivo. In this study analytical ultracentrifugation (AUC) in combination with small angle X-ray scattering (SAXS) has been applied to a number of antibody fragments and to their respective PEGylated conjugates. Despite the large increase in molecular weight due to the attachment of a 20-40 kDa PEG moiety, the PEGylated conjugates have smaller sedimentation coefficients, s, than their parent antibody fragments, due to a significant increase in frictional ratio f/f(o) (from approximately 1.3 to 2.3-2.8): the solution hydrodynamic properties of the conjugates are clearly dominated by the PEG moiety (f/f(o) approximately 3.0). This observation is reinforced by SAXS data at high values of r (separation of scattering centres within a particle) that appear dominated by the PEG part of the complex. By contrast, SAXS data at low values of r suggest that there are no significant conformational changes of the protein moiety itself after PEGylation The location of the PEGylation site within the conjugate was identified, and found to be consistent with expectation from the conjugation chemistry.

Dynamic force spectroscopy on soft molecular systems: Improved analysis of unbinding spectra with varying linker compliance

Dynamic force spectroscopy makes it possible to measure the breaking of single molecular bonds or the unfolding of single proteins subjected to a time-dependent pulling force. The force needed to break a single bond or to unfold a domain in a protein depends critically on the time dependence of the applied force. In this way the elastic response couples to the unbinding force. We have performed an experimental and theoretical examination of this coupling by studying the well-known biotin-streptavidin bond in systems incorporating two common types of linkers. In the first case biotin is linked by bovine serum albumin (BSA) and it is observed that this linker has a linear elastic response. More surprisingly we find that its force constant varies significantly between repeated force curves. It is demonstrated that by sorting the force curves according to the force constant of the linker we can improve the data analysis and obtain a better agreement between experimental data and theory. In the second case biotin is linked by poly(ethylene glycol) (PEG), which has a soft nonlinear elastic response. A numerical calculation of the unbinding statistics for the polymer system agrees quantitatively with experiments. It demonstrates a clear decrease in unbinding forces resulting from the polymer linker.

Structure and Dynamics of Hydrogen Bonds in the Interface of a C12E6 Spherical Micelle in Water Solution: A MD Study at Various Temperatures

The temperature dehydration of a C(12)E(6) spherical micelle is characterized through the study of the structure and dynamics of the hydrogen bonds formed by water within the micellar interface. Water molecules in proximity of the hydrophilic fragment of the C(12)E(6) surfactants form strong H-bonds with the oxyethilene units E and with the polar alcoholic heads. The activation energies of such H-bonds fall in the range 2-3 Kcal mol(-1). On the exposed oil core, the number of water-water H-bonds decreases as an effect of dehydration. The dynamics of such bonds exhibits a slow relaxation with respect to the bulk, and two time scales can be discerned: the first one, tau approximately 3-6 ps, is typical of water-water H-bonds around small hydrophobic molecules, whereas the second one, tau approximately 40-80 ps, is probably due to the confining effect of the long hydrophilic fragments which reduces the probability of a water molecule to leave the hydration layer of the exposed oil core. Water molecules around the core form H-bond clusters whose size and distribution change with temperature. From a cluster analysis, the system appears to be below the percolation threshold, suggesting that the exposed oily surface is formed by disconnected patches of size around 1 nm(2), close to the estimate of the solvated hydrophobic patches on protein surfaces. The network connectivity is also considered for concentric hydration shells along the interface: it turns out that near the oil core, the cluster size is larger than elsewhere in the interface demonstrating a strong structural effect induced by the exposed hydrocarbon tails. Temperature affects the cluster size only in the innermost shell.

Modified Chemistry of Siloxanes under Tensile Stress: Interaction with Environment

We present first principles molecular dynamics simulations of stretched siloxane oligomers in an environment representative of that present in single molecule atomic force microscopy experiments. We determine that the solvent used (hexamethyldisiloxane) does not influence the stretching of the siloxane in the high force regime or the rupture process, but trace amounts of water can induce rupture before the maximum siloxane extension has been attained. This would result in a significantly lower rupture force. The simulations show that the rupture of a covalent bond through a reaction with a molecule from the environment, which would not normally occur between the species when the polymer is not stressed, is possible, opening a route to mechanically induced chemical reactions. The attack of the normally hydrophobic siloxane by water when it is stretched has wider implications for the material failure under tensile stress, where trace amounts of water could induce tearing of the material.

Force spectroscopy with a small dithering of AFM tip: a method of direct and continuous measurement of the spring constant of single molecules and molecular complexes

A new method of direct and continuous measurement of the spring constant of single molecule or molecular complex is elaborated. To that end the standard force spectroscopy technique with functionalized tips and samples is combined with a small dithering of the tip. The change of the dithering amplitude as a function of the pulling force is measured to extract the spring constant of the complex. The potentialities of this method are illustrated for the experiments with single bovine serum albumin-its polyclonal antibody (Ab-BSA) and fibrinogen-fibrinogen complexes.

How Does Huperzine A Enter and Leave the Binding Gorge of Acetylcholinesterase? Steered Molecular Dynamics Simulations

The entering and leaving processes of Huperzine A (HupA) binding with the long active-site gorge of Torpedo californica acetylcholinesterase (TcAChE) have been investigated by using steered molecular dynamics simulations. The analysis of the force required along the pathway shows that it is easier for HupA to bind to the active site of AChE than to disassociate from it, which for the first time interprets at the atomic level the previous experimental result that unbinding process of HupA is much slower than its binding process to AChE. The direct hydrogen bonds, water bridges, and hydrophobic interactions were analyzed during two steered molecular dynamics (SMD) simulations. Break of the direct hydrogen bond needs a great pulling force. The steric hindrance of bottleneck might be the most important factor to produce the maximal rupture force for HupA to leave the binding site but it has a little effect on the binding process of HupA with AChE. Residue Asp72 forms a lot of water bridges with HupA leaving and entering the AChE binding gorge, acting as a clamp to take out HupA from or put HupA into the active site. The flip of the peptide bond between Gly117 and Gly118 has been detected during both the conventional MD and SMD simulations. The simulation results indicate that this flip phenomenon could be an intrinsic property of AChE and the Gly117-Gly118 peptide bond in both HupA bound and unbound AChE structures tends to adopt the native enzyme structure. At last, in a vacuum the rupture force is increased up to 1500 pN while in water solution the greatest rupture force is about 800 pN, which means water molecules in the binding gorge act as lubricant to facilitate HupA entering or leaving the binding gorge.