Investigating the specific interactions between carbonic anhydrase and a sulfonamide inhibitor by single-molecule force spectroscopy

In this communication, we report on the interaction landscape of an active site-specific enzyme-inhibitor complex by single-molecule force spectroscopy. Electrostatic immobilization was employed to orient a carbonic anhydrase enzyme on a positively charged surface so its active site is pointing upward. This approach to immobilization effectively increases the number of specific interactions measured between the zinc ion of the active site on carbonic anhydrase and a sulfonamide inhibitor tethered to an atomic force microscope (AFM) probe. Further, it reduces the time required for data collection and thereby minimizes the possible mechanical damage to the probe and contamination of the enzyme surface. The rupture force measured at various loading rates is interpreted in terms of a single energy barrier for the carbonic anhydrase enzyme-sulfonamide inhibitor complex from which the kinetic and thermodynamic parameters were estimated on the basis of microscopic models and were compared to the Bell-Evans model. The dissociation rate for the enzyme-inhibitor complex was found to be significantly faster (~35 times) than the natural spontaneous dissociation rate.     

Supramolecular interactions between beta-cyclodextrin and hydrophobically end-capped poly(ethylene glycol)s: a quartz crystal microbalance study

In this study, the supramolecular interactions occurring between beta-cyclodextrin-based surfaces and macromolecular chains modified at one end with naphthyl, adamantyl, or phenyladamantyl hydrophobic groups were investigated by means of a quartz crystal microbalance. beta-Cyclodextrin-functionalized gold electrodes were obtained through the amide-coupling reaction between mono-6-deoxy-6-amino-beta-cyclodextrin and 11-mercaptoundecanoic acid self-assembled monolayer allowing the reproducible preparation of densely grafted surfaces with host properties. The interaction data obtained for the three different modified poly(ethylene glycol)s are in good agreement with our previous studies performed by high performance liquid chromatography and surface plasmon resonance. This evidences that the driving force for the supramolecular interaction is based on the inclusion of the hydrophobic terminal group of the chains within the cyclodextrin cavities. The reversibility of the inclusion process was proven through the regeneration of the original host properties of the sensing surfaces using sodium dodecylsulfate as a competitor for the desorption of the poly(ethylene glycol) chains.     

Molecular interactions between phospholipids and mangostin in a lipid bilayer

Molecular interactions between phospholipids and mangostin in a lipid bilayer have been investigated in terms of the maximum additive concentration (MAC) of mangostin in liposomes, the surface potential, particle size, microscopic-viscosity and microscopic-polarity of liposomes, and the permeability of glucose. The mangostin used is a natural product extract: 1,3,6-trihydroxy-7-methoxy-2,8-bis(3-methyl-2-butenyl)-9-xanthenenone.

The MAC of mangostin was fairly dependent upon the nature of the liposomes (uncharged, negatively charged or positively charged). Solubilization of mangostin in the liposomal bilayer resulted in both an increase in the negative charge on the liposomal surface, strenghthening the state of the bilayer membrane, and a depression in the release of the glucose involved. Mangostin was found to temporarily stabilize the liposomal bilayer, although the bilayer membrane is still unstable in the long run.     

Probing interactions between aggrecan and mica surface by the atomic force microscopy

Aggrecan is a bottlebrush shaped macromolecule found in the extracellular matrix of cartilage. The negatively charged glycosaminoglycan (GAG) chains attached to its protein backbone give aggrecan molecules a high charge density, which is essential for exerting high osmotic swelling pressure and resisting compression under external load. In solution, aggrecan assemblies are insensitive to the presence of calcium ions, and show distinct osmotic pressure versus concentration regimes. The aim of this study is to investigate the effect of ionic environment on the structure of aggrecan molecules adsorbed onto well‐controlled mica surfaces. The conformation of the aggrecan was visualized using Atomic Force Microscopy. On positively charged APS mica the GAG chains of the aggrecan molecules are distinguishable, and their average dimensions are practically unaffected by the presence of salt ions. With increasing aggrecan concentration they form clusters, and at higher concentrations they form a continuous monolayer of conforming molecules. On negatively charged mica, the extent of aggrecan adsorption varies with salt composition. Understanding aggrecan adsorption onto a charged surface provides insight into its interactions with bone and implant surfaces in the biological milieu. © 2010 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys, 2010     

Phase transition of a DPPC bilayer induced by an external surface pressure: from bilayer to monolayer behavior. a molecular dynamics simulation study

Understanding the lipid phase transition of lipid bilayers is of great interest from biophysical, physicochemical, and technological points of view. With the aim of elucidating the structural changes that take place in a DPPC phospholipid bilayer induced by an external isotropic surface pressure, five computer simulations were carried out in a range from 0.1 to 40 mN/m. Molecular dynamics simulations provided insight into the structural changes that took place in the lipid structure. It was seen that low pressures ranging from 0.1 to 1 mN/m had hardly any effect on the structure, electrical properties, or hydration of the lipid bilayer. However, for pressures above 40 mN/m, there was a sharp change in the lipid-lipid interactions, hydrocarbon lipid fluidity, and electrostatic potential, corresponding to the mesomorphic transition from a liquid crystalline state (L(alpha)) to its gel state (P'(beta)). The head lipid orientation remained almost unaltered, parallel to the lipid layer, as the surface pressure was increased, although a noticeable change in its angular distribution function was evident with the phase transition.     

Complex formation between a tetramesityl sulfonated resorcarene and alkylammonium ions: a mass spectrometric study of noncovalent interactions

Noncovalent complex formation between a tetramesityl sulfonated tetramethyl resorcarene and primary, secondary, and tertiary alkylammonium ions was investigated by electrospray ionization (ESI) Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometry. Competition measurements, collision-induced dissociation, and gas-phase hydrogen/deuterium (H/D)-exchange reactions were employed to elucidate the interactions involved in complexation, the stability of the complexes, and the position of the guest with relation to the resorcarene. The complex formation ability of tetramesityl sulfonated resorcarene and the stability of the compexes were compared with the corresponding properties of tetratosylium tetraethyl resorcarene, which has been studied previously. Complex formation and the properties of the complexes were most strongly determined by the steric properties of the guests and their ability to form hydrogen bonds. Comparison of the two host molecules revealed the impact of steric hindrance in tetramesityl sulfonated tetramethyl resorcarene.     

Vesicle adsorption and lipid bilayer formation on glass studied by atomic force microscopy

The adsorption of phosphatidylcholine (PC) vesicles (30, 50, and 100 nm nominal diameters) and of dye-labeled PC vesicles (labeled with 6% Texas Red fluorophore (TR) and encapsulated carboxy fluorescein (CF)) to glass surfaces was studied by contact mode atomic force microscopy in aqueous buffer. These studies were performed in part to unravel details of the previously observed isolated rupture of dye-labeled PC vesicles on glass (Johnson, J. M.; Ha, T.; Chu, S.; Boxer, S. G. Biophys. J. 2002, 83, 3371-3379), specifically to differentiate partial rupture, that is, pore formation and leakage of entrapped dye, from full rupture to form bilayer disks. In addition, the adhesion potential of PC vesicles on glass was calculated based upon the adhesion-driven flattening of adsorbed vesicles and a newly developed theoretical model. The vesicles were found to flatten considerably upon adsorption to glass (width-to-height ratio of approximately 5), which leads to an estimate for the adhesion potential and for the critical rupture radius of 1.5 x 10(-4) J/m2 and 250 nm, respectively. Independent of vesicle size and loading with dye molecules, the adsorption of intact vesicles was observed at all concentrations below a threshold concentration, above which the formation of smooth lipid bilayers occurred. In conjunction with previous work (Johnson, J. M.; Ha, T.; Chu, S.; Boxer, S. G. Biophys. J. 2002, 83, 3371-3379), these data show that 6% TR 20 mM CF vesicles adsorb to the surface intact but undergo partial rupture in which they exchange content with the external buffer.     

Ternary complex formation in aqueous solution between a beta-cyclodextrin polymer, a cationic surfactant and DNA

Polyelectrolyte complexes have been elaborated by mixing in water neutral poly(beta-CD), a cationic surfactant (DTAC) and herring sperm DNA fragments. The driving forces for the poly(beta-CD)/DTAC/DNA association in aqueous solution are, on the one hand, reversible inclusion interactions between the CD cavities of poly(beta-CD) and the alkyl group of DTAC, leading to the formation of a polycation and, on the other hand, electrostatic interactions between the opposite charges of the cationic surfactant and anionic DNA. Viscometry and SANS have been used to prove the occurrence of such ternary complexes in dilute aqueous solutions.     

Inclusion complexes between beta-cyclodextrin and a Gemini surfactant in aqueous solution: an NMR study

(1)H NMR spectra, diffusion-ordered NMR (DOSY), and 2D rotating-frame Overhauser enhancement spectroscopy (ROESY) experiments for aqueous solutions at 298 K containing the gemini surfactant, bis (dodecyl dimethylammonium)diethyl ether dibromide (12-EO(1)-12), in the absence and presence of beta-cyclodextrin (beta-CD) were used to characterize the surfactant and to determine the effects of the complexation in the micellization. For the binary system, the critical micelle concentration (cmc), the aggregation number, the stepwise micellization constant, and the size of the monomer have been obtained by studying the dependence of the chemical shifts and the self-diffusion coefficients with the concentration of surfactant. For the ternary system, the analysis of the (1)H NMR spectra and the self-diffusion coefficients reveal the formation of complexes of 1:1 and 2:1 stoichiometry (beta-CD:gemini), with a calculated stability constant for the second binding step higher than that of the first. The values of the hydrodynamic radii of the complexes were obtained from the calculated diffusion coefficients. The presence of beta-CD modifies the cmc in an extension that indicates mainly the formation of a 2:1 complex. The analysis of the chemical shifts of the surfactant indicates the nonparticipation of the complexes into the micelles. ROE enhancements depend substantially on the amount of the macrocycle added and therefore on the stoichiometry; at low concentrations of beta-CD, one of the hydrocarbon chains binds favorably with the cavity whereas the other interacts with the outer face. By contrast, at higher concentrations of beta-CD, the two hydrocarbon tails are included in two different macrocycles.     

Complex formation between cationically modified gold nanoparticles and DNA: an atomic force microscopic study

Atomic force microscopy has been used for direct visualization of the wrapping of DNA around 30-nm-sized functionalized gold nanoparticles for the first time. The morphology of the complexes seems to be dictated by the relative concentration of the nanoparticles and DNA. A higher concentration of the former leads to the formation of a network of nanoparticles assembled on DNA. This assembly pattern seems to be significantly different from the manner in which cationically modified gold nanoparticles of smaller size (< 5 nm) arrange linearly on DNA, as shown in the literature. A DNA-gold nanoparticle can be developed as a model system for in vitro studies on the mechanism of DNA condensation and also for developing novel methods of nanoparticle self-assembly on the DNA template.     

Pressure-induced ordering in adamantane: a Monte Carlo simulation study

Isothermal-isobaric ensemble Monte Carlo simulation of adamantane has been carried out with a variable shape simulation cell. The low-temperature crystalline phase and the room-temperature plastic crystalline phases have been studied employing the modified Williams potential. We show that at room temperature, the plastic crystalline phase transforms to the crystalline phase on increase in pressure. Further, we show that this is the same phase as the low-temperature ordered tetragonal phase of adamantane. The high-pressure ordered phase appears to be characterized by a slightly larger shift of the first peak toward a lower value of r in C-C, C-H, and H-H radial distribution functions as compared to the low-temperature tetragonal phase. The coexistence curve between the crystalline and plastic crystalline phase has been obtained approximately up to a pressure of 4 GPa.     

Combinatorial approach to study enzyme/surface interactions

A fast combinatorial approach to access information about the immobilization behavior and kinetics of enzymes on a variation of surfaces is presented. As a test system, Candida Antarctica Lipase B was immobilized on a self-assembled monolayer bearing a gradient of surface energy. The respective immobilization behavior was monitored by Fourier transform infrared micro-spectroscopy. In addition, the activity of the immobilized enzyme was monitored over the entire film in real time with a specially developed fluorescence activity assay embedded into a siloxane gel. It was found that the highest amount of active protein was immobilized on the hydrophilic end of the gradient surface. This effect is associated with a higher surface roughness of this area resulting in hydrophobic micro-environments in which the enzyme gets immobilized.     

Template-directed excimer formation via specific non-covalent interactions between pyrene guanidinium derivatives and nucleic acids

Structurally distinct guanidinium derivatives were evaluated for their ability to interact non-covalently with various nucleic acid sequences. Among the evaluated derivatives, 4-[(pyrene-1-ylmethyl)amino]butyl] guanidinium (pbg) was found to demonstrate strong excimer emission upon nucleic acid addition and high levels of discrimination between ds- and ss-DNA. The intensity of excimer emission proved to be dependent on the length of the linker probe as well as the oligonucleotide length and sequence. In particular, G-quadruplex prone structures were found to induce the highest excimer emissions among all nucleic acids tested.     

RNA LEGO: magnesium-dependent formation of specific RNA assemblies through kissing interactions

The high affinity and specificity of nucleic acid base complementarity has been proven to be a powerful method for constructing specific molecular assemblies. On the other hand, recent structural studies of RNA have revealed the wide range of tertiary interactions utilized in RNA folding, which may potentially be used as tools for the design of specific macromolecular assemblies. Here, RNA building blocks containing two hairpin loops, based on the dimerization initiation site (DIS) of HIV RNA, connected by a short linker were used to construct large RNA assemblies through hairpin loop-loop ("kissing") interactions. We show that specific linear and circular assemblies can be constructed in a magnesium-dependent manner using several non-self-complementary loop-loop interactions designed in this study. These results show that the use of RNA tertiary interactions may broaden the repertoire of nucleic acid-based nanostructures.     

Correlation between desorption force measured by atomic force microscopy and adsorption free energy measured by surface plasmon resonance spectroscopy for peptide-surface interactions

Surface plasmon resonance (SPR) spectroscopy is a useful technique for thermodynamically characterizing peptide-surface interactions; however, its usefulness is limited to the types of surfaces that can readily be formed as thin layers on the nanometer scale on metallic biosensor substrates. Atomic force microscopy (AFM), on the other hand, can be used with any microscopically flat surface, thus making it more versatile for studying peptide-surface interactions. AFM, however, has the drawback of data interpretation due to questions regarding peptide-to-probe-tip density. This problem could be overcome if results from a standardized AFM method could be correlated with SPR results for a similar set of peptide-surface interactions so that AFM studies using the standardized method could be extended to characterize peptide-surface interactions for surfaces that are not amenable for characterization by SPR. In this article, we present the development and application of an AFM method to measure adsorption forces for host-guest peptides sequence on surfaces consisting of alkanethiol self-assembled monolayers (SAMs) with different functionality. The results from these studies show that a linear correlation exists between these data and the adsorption free energy (ΔG(o)(ads)) values associated with a similar set of peptide-surface systems available from SPR measurements. These methods will be extremely useful to characterize thermodynamically the adsorption behavior for peptides on a much broader range of surfaces than can be used with SPR to provide information related to understanding protein adsorption behavior to these surfaces and to provide an experimental database that can be used for the evaluation, modification, and validation of force field parameters that are needed to represent protein adsorption behavior accurately for molecular simulations.     

Use of a laminar flow chamber to study the rate of bond formation and dissociation between surface-bound adhesion molecules: effect of applied force and distance between surfaces

It has recently been shown that much information on the behaviour of surface-bound adhesion molecules could be obtained by monitoring the motion of receptor-coated particles along ligand-derivatized surfaces in the presence of a hydrodynamic force of a few pN. This procedure is expected to allow direct monitoring of the formation and dissociation of individual bonds. We present experimental results on the interaction between streptavidin-coated spheres (1.4 microns diameter) and control or biotinylated mica surfaces in a laminar flow chamber. Moving spheres are found to display numerous arrests whose frequency is markedly increased (5-13-fold) in the presence of biotin groups. For a given shear rate, the binding frequency is strongly dependent on the sphere-surface separation. Indeed, this frequency displayed a 14-fold decrease when the velocity increased from 7 to 15 microns s-1 for a wall shear rate of 20 s-1. Furthermore, the lifetime of observed arrests was of the order of several seconds, i.e. 5-50-fold higher than previously determined on models such as selectin-ligand, CD2-CD48 or cadherin-cadherin. Finally, this lifetime did not decrease when the wall shear rate was increased from ca. 10 to 40 s-1.     

Simulation of the specific interactions between polyamide-6 and a thermoplastic polyurethane

Polyamides have many desirable properties such as high melting temperatures, chemical resistance and superior mechanical properties. However, its crystalline morphology can limit its applications. It is the specific interaction, hydrogen bonding that gives rise to the crystalline structure of polyamides. This interaction is strong and important when blending on the final morphology and mechanical properties. Polyurethane contains polar functionality that can also interact with the polar component of polyamide. Hence, it is important to study the interaction between such a blend as polyurethane can enhance the toughness of polyamide due to its elastic properties. This study is an insight into the specific interaction between two polar polymers in a simulation whereby the interaction is maximised. Hydrogen bonding has been observed between molecules of either polyamide–polyurethane and polyamide–polyamide, and it is sufficiently strong to cause the polymer chains to distort rather than disrupt the hydrogen bonds. When groups of like polarity, such as carbonyl groups, come into proximity, the polymer chains again distort from their regular conformation because of mutual repulsion.     

Non-specific and specific interactions on functionalized polymer surface studied by FT-SPR

Fourier transform surface plasmon resonance (FT-SPR) was utilized to study specific and non-specific interactions between proteins and a biotinylated polymer film by monitoring adsorptions of streptavidin (SAv) and bovine serum albumin (BSA) on the polymer films. The biotinylated polymer, poly(lactide-co-2,2-dihydroxymethyl-propylene carbonate-graft-biotin) [P(LA-co-DHC/biotin)], was prepared by ring-opening copolymerization of lactide and a OH-bearing cyclic carbonate monomer, followed by biotinylation of the OH groups. The copolymer was coated onto the FT-SPR chip and vacuum-dried, hydrated at 70°C, and treated with a blocking agent respectively to achieve different surface status. The FT-SPR results showed that the vacuum-dried film had the most BSA adsorption; hydration treatment led to migration of the biotin moieties from inner film to surface and thus resulted in less BSA adsorption; blocking layer on the polymer surface saturated the active sites for physical and chemical adsorptions on the surface and thus weakened the BSA adsorption. Adsorption of SAv displayed similar polymer-surface-status dependence, i.e., more adsorption on vacuum-dried surface, less adsorption on hydrated surface and the least adsorption on blocked surface. Compared with BSA, SAv showed more enhanced adsorptions on P(LA-co-DHC/biotin) surface because of the specific interaction of biotin moieties in the polymer with SAv molecules, especially on the blocked surface. The above semi-quantified results further indicate that the FT-SPR system is suitable for investigating interactions between polymer surface and bio-molecules.     

Investigating ligand-receptor interactions at bilayer surface using electronic absorption spectroscopy and fluorescence resonance energy transfer

We investigate interactions between receptors and ligands at bilayer surface of polydiacetylene (PDA) liposomal nanoparticles using changes in electronic absorption spectroscopy and fluorescence resonance energy transfer (FRET). We study the effect of mode of linkage (covalent versus noncovalent) between the receptor and liposome bilayer. We also examine the effect of size-dependent interactions between liposome and analyte through electronic absorption and FRET responses. Glucose (receptor) molecules were either covalently or noncovalently attached at the bilayer of nanoparticles, and they provided selectivity for molecular interactions between glucose and glycoprotein ligands of E. coli. These interactions induced stress on conjugated PDA chain which resulted in changes (blue to red) in the absorption spectrum of PDA. The changes in electronic absorbance also led to changes in FRET efficiency between conjugated PDA chains (acceptor) and fluorophores (Sulphorhodamine-101) (donor) attached to the bilayer surface. Interestingly, we did not find significant differences in UV-vis and FRET responses for covalently and noncovalently bound glucose to liposomes following their interactions with E. coli. We attributed these results to close proximity of glucose receptor molecules to the liposome bilayer surface such that induced stress were similar in both the cases. We also found that PDA emission from direct excitation mechanism was ～2-10 times larger than that of the FRET-based response. These differences in emission signals were attributed to three major reasons: nonspecific interactions between E. coli and liposomes, size differences between analyte and liposomes, and a much higher PDA concentration with respect to sulforhodamine (SR-101). We have proposed a model to explain our experimental observations. Our fundamental studies reported here will help in enhancing our knowledge regarding interactions involved between soft particles at molecular levels.     

Hydrophobic scale: a second parameter to elucidating various specific ligand-protein interactions

In the sequence Fourier analysis (SFA) of specific interactions such as those between fibroblast growth factors (FGFs)/FGF receptors (FGFRs), bone morphogenetic proteins (BMPs)/BMP receptors (BMPRs), or tumor repressor protein p53/mouse double minute 2 homolog (MDM2), the characteristic frequency peak(s) could be observed with the hydrophobic scale for 20 amino acids as well as 4 nucleotides as the physicochemical parameter, but not successfully with the absolute electronegativity scale. This result implies that these two independent scales should be appropriately selected in various specific ligand-protein interactions, though the critical difference has to be determined.