Interactions In Bulk Solution Research Articles

Non-Langmuir Kinetics of DNA Surface Hybridization

Hybridization of complementary single strands of DNA represents a very effective natural molecular recognition process widely exploited for diagnostic, biotechnology, and nanotechnology applications. A common approach relies on the immobilization on a surface of single-stranded DNA probes that bind complementary targets in solution. However, despite the deep knowledge on DNA interactions in bulk solution, the modeling of the same interactions on a surface are still challenging and perceived as strongly system dependent. Here, we show that a two-dimensional analysis of the kinetics of hybridization, performed at different target concentrations and probe surface densities by a label-free optical biosensor, reveals peculiar features inconsistent with an ideal Langmuir-like behavior. We propose a simple non-Langmuir kinetic model accounting for an enhanced electrostatic repulsion originating from the surface immobilization of nucleic acids and for steric hindrance close to full hybridization of the surface probes. The analysis of the kinetic data by the model enables quantifying the repulsive potential at the surface, as well as retrieving the kinetic parameters of isolated probes. We show that the strength and the kinetics of hybridization at large probe density can be improved by a three-dimensional immobilization strategy of probe strands with a double-stranded linker.

Theory of Multicomponent Phenomena in Cation-Exchange Membranes: Part I. Thermodynamic Model and Validation

We present and validate a mathematical model for multicomponent thermodynamic activity in phase-separated cation-exchange membranes (e.g., perfluorinated sulfonic-acid ionomers). The model consists of an expression for the free energy of the membrane and of the surrounding electrolyte solution. A modified Stokes-Robinson ionic solvation framework treats the solution-like non-idealities resulting from hydration, electrostatics, ion association, and physical interactions in bulk solution and in ionomer hydrophilic domains. Inside the membrane, a mechanics-based composite approach accounts for the swelling of the hydrophobic matrix. Treating the membrane microstructure as a disordered system of domains calculates steric exclusion of ions. Electroneutrality guarantees that the charge of mobile ions in the membrane is equal to the charge on polymer groups. Osmotic coefficients for electrolytes from literature parameterize solution-like interactions while mechanical and X-ray scattering characterization gives most membrane-specific parameters. Model predictions compare favorably to measured membrane thermodynamics (i.e., water and ion uptake) in dilute and concentrated binary and ternary salt electrolytes and in water vapor. Interactions between ions in the membrane are similar to those present in bulk electrolytes. Our results reveal that water and ion uptake is dictated by a balance between solution-like energetics and membrane swelling.

Inter-protein interactions govern protein loading into porous vaterite CaCO3 crystals.

The fast development of protein therapeutics has resulted in a high demand for advanced delivery carriers that can effectively host therapeutic proteins, preserve their bioactivity and release them on demand. Accordingly, vaterite CaCO3 crystals have attracted special attention as sacrificial templates for protein encapsulation in micro- and nanoparticles (capsules and beads, respectively) under mild biofriendly conditions. This study aimed to better understand the mechanism of protein loading into crystals as a primary step for protein encapsulation. The loading of three therapeutic proteins (250 kDa catalase, 5.8 kDa insulin, and 6.5 kDa aprotinin) was investigated for crystals with different porosities. However, unexpectedly, the protein loading capacity was not consistent with the protein molecular weight. It solely depends on the inter-protein interactions in the bulk solution in the presence of crystals and that inside the crystals. The smallest protein aprotinin aggregates in the bulk (its aggregate size is about 100 nm), which prohibits its loading into the crystals. Insulin forms hexamers in the bulk, which can diffuse into the crystal pores but tend to aggregate inside the pores, suppressing protein diffusion inward. Catalase, the largest protein tested, does not form any aggregates in the bulk and diffuses freely into the crystals; however, its diffusion into small pores is sterically restricted. These findings are essential for the encapsulation of protein therapeutics by means of templating based on CaCO3 crystals and for the engineering of protein-containing microparticles having desired architectures.

Protein-protein interactions controlling interfacial aggregation of rhIL-1ra are not described by simple colloid models.

We investigated the effects of protein-protein interaction strength on interfacial viscoelastic properties and aggregation of recombinant human interleukin-1 receptor antagonist (rhIL-1ra) at silicone oil-water interfaces. Osmotic second virial coefficients determined by static light scattering were used to quantify protein-protein interactions in bulk solution. Attractive protein-protein interactions dominated at low ionic strengths and their magnitude decreased with increasing ionic strength, in contrast to repulsive interactions that would be expected based on uniformly charged sphere models. Interfacial shear rheometry was used to characterize rhIL-1ra interfacial layers. More attractive protein-protein interactions in bulk solution correlated with stronger interfacial gels. Thioflavin-T fluorescence measurements indicated that the intermolecular β-sheet content of rhIL-1ra incubated in the presence of silicone oil-water interfaces correlated with gel strength. Siliconized syringes were used to probe the effects of mechanical perturbation of the interfacial gel layers. When rhIL-1ra solutions in siliconized glass syringes were subjected to end-over-end rotation, monomeric rhIL-1ra was lost from solution, and particles containing aggregated protein were released into the bulk aqueous phase. The loss of monomeric rhIL-1ra in response to mechanical perturbation was highest under the conditions where the strongest gels were observed. Aggregation of rhIL-1ra was strictly interface-induced and growth of aggregates in the bulk solution was not observed, even in the presence of particles released from silicone oil-water interfaces.

Layer-by-Layer Self-Assembly of Polymers with Pairing Interactions.

A molecular theory is introduced to model the layer-by-layer self-assembly (LbL-SA) of polymers with pairing interactions. Our theory provides a general framework to describe nonelectrostatic LbL-SA as the pairing interactions generically describe the formation of bonds between two complementary chemical species, for example, hydrogen donor and acceptor in hydrogen-bonding-LbL or host and guest in host-guest-LbL. The theory predicts fundamental observations related to LbL-SA: (i) phase separation of a mixture of polymers with pairing interactions in bulk solution, (ii) linear increase in film thickness with the number of LbL adsorption steps, (iii) stoichiometry overcompensation after each adsorption step, and (iv) interpenetration of polymer layers. Importantly, this study shows that the minimal requirement for nonelectrostatic LbL is the competition of a pairing interaction and an excluded-volume repulsion. A simple analytical model based on this competition predicts the volume fraction of the layers in good agreement with the numerical predictions of the molecular theory.

Colloidal potentials mediated by specific biomolecular interactions.

We present a systematic study of receptor-ligand interactions with increasing complexity from interactions in bulk solution, on planar and colloid surfaces, and as part of mediating colloidal pair interactions. We report analytical models that relate receptor-ligand dissociation constants (KD), interactions potentials (U(r)), and adsorbed amounts (θ) for different ligand sizes, concentrations and immobilized receptor coverages. Analytical results are validated for hard core + harmonic well receptor-ligand interactions in bulk and interfacial systems using Monte Carlo (MC) simulations, although any biomolecular interaction can be incorporated into the reported analysis via a "B2 device". Results from analytical models are used to understand potentials of mean force (W(L)) for ligand mediated interactions between receptor decorated colloids. W(L) are generated using MC-umbrella sampling (MC-US) simulations with cluster moves, which provide self-consistent comparisons of net colloid scale interactions with receptor-ligand scale information. Our findings capture how receptor-ligand interactions mediate colloid scale interactions relevant to self-assembly, drug delivery, and biosensing.

Understanding Ligand Interaction with Different Structures of G-Quadruplex DNA: Evidence of Kinetically Controlled Ligand Binding and Binding-Mode Assisted Quadruplex Structure Alteration

The study of ligand interaction with G-quadruplex DNA is an active research area, because many ligands are shown to bind G-quadruplex structures, showing anticancer effects. Here, we show, for the first time, how fluorescence correlation spectroscopy (FCS) can be used to study binding kinetics of ligands with G-quadruplex DNA at the single molecule level. As an example, we study interaction of a benzo-phenoxazine ligand (Cresyl Violet, CV) with antiparallel and (3 + 1) hybrid G-quadruplex structures formed by human telomeric sequence. By using simple modifications in FCS setup, we describe how one can extract the reaction kinetics from diffusion-coupled correlation curves. It is found that the ligand (CV) binds stronger, by an order of magnitude, to a (3 + 1) hybrid structure, compared to an antiparallel one. Ensemble-averaged time-resolved fluorescence experiments are also carried out to obtain the binding equilibrium constants (K) of ligand-quadruplex interactions in bulk solution for the first time, which are found to match very well with FCS results. Global analysis of FCS data provides association (k(+)) and dissociation (k(-)) rates of the ligand in the two structures. Results indicate that stronger ligand binding to the (3 + 1) hybrid structure is controlled by the dissociation rate, rather than the association rate of ligand in the quadruplexes. Circular dichroism (CD) and induced-CD spectra show that the ligand not only binds at different conformations in the quadruplexes, but also induces antiparallel structure to form a mixed-type hybrid structure in Na(+) solution. However, in K(+) solution, the ligand stabilizes the (3 + 1) hybrid structure. Molecular docking studies predict the possible differences in binding sites of the ligand inside two quadruplexes, which strongly support the experimental observations. Results suggest that different binding modes of the ligand to the quadruplex structures actually assist the alteration of structures differently.

Biomolekulare Interaktionen: Manche mögen’s heiß

The Microscale Thermophoresis (MST) is a biophysical method to characterize biomolecular interactions in bulk solution. Interaction affinities can be quantified in biological liquids, without immobilization and without a size or mass limitation. Its material consumption is very low and today’s resolvable dissoziation constants range from Kd = 100 pM to Kd = 10 mM.

Theoretical and computational models of biological ion channels

The goal of this review is to establish a broad and rigorous theoretical framework to describe ion permeation through biological channels. This framework is developed in the context of atomic models on the basis of the statistical mechanical projection-operator formalism of Mori and Zwanzig. The review is divided into two main parts. The first part introduces the fundamental concepts needed to construct a hierarchy of dynamical models at different level of approximation. In particular, the potential of mean force (PMF) as a configuration-dependent free energy is introduced, and its significance concerning equilibrium and non-equilibrium phenomena is discussed. In addition, fundamental aspects of membrane electrostatics, with a particular emphasis on the influence of the transmembrane potential, as well as important computational techniques for extracting essential information from all-atom molecular dynamics (MD) simulations are described and discussed. The first part of the review provides a theoretical formalism to 'translate' the information from the atomic structure into the familiar language of phenomenological models of ion permeation. The second part is aimed at reviewing and contrasting results obtained in recent computational studies of three very different channels: the gramicidin A (gA) channel, which is a narrow one-ion pore (at moderate concentration), the KcsA channel from Streptomyces lividans, which is a narrow multi-ion pore, and the outer membrane matrix porin F (OmpF) from Escherichia coli, which is a trimer of three beta-barrel subunits each forming wide aqueous multi-ion pores. Comparison with experiments demonstrates that current computational models are approaching semi-quantitative accuracy and are able to provide significant insight into the microscopic mechanisms of ion conduction and selectivity. We conclude that all-atom MD with explicit water molecules can represent important structural features of complex biological channels accurately, including such features as the location of ion-binding sites along the permeation pathway. We finally discuss the broader issue of the validity of ion permeation models and an outlook to the future.

Charge density-dependent strength of hydration and biological structure

Small ions of high charge density (kosmotropes) bind water molecules strongly, whereas large monovalent ions of low charge density (chaotropes) bind water molecules weakly relative to the strength of water-water interactions in bulk solution. The standard heat of solution of a crystalline alkali halide is shown here to be negative (exothermic) only when one ion is a kosmotrope and the ion of opposite charge is a chaotrope; this standard heat of solution is known to become proportionally more positive as the difference between the absolute heats of hydration of the corresponding gaseous anion and cation decreases. This suggests that inner sphere ion pairs are preferentially formed between oppositely charged ions with matching absolute enthalpies of hydration, and that biological organization arises from the noncovalent association of moieties with matching absolute free energies of solution, except where free energy is expended to keep them apart. The major intracellular anions (phosphates and carboxylates) are kosmotropes, whereas the major intracellular monovalent cations (K+; arg, his, and lys side chains) are chaotropes; together they form highly soluble, solvent-separated ion pairs that keep the contents of the cell in solution.

Sticky ions in biological systems.

Aqueous gel sieving chromatography on Sephadex G-10 of the Group IA cations (Li+, Na+, K+, Rb+, Cs+) plus NH4+ as the Cl- salts, in combination with previous results for the halide anions (F-, Cl-, Br-, I-) as the Na+ salts [Washabaugh, M.W. & Collins, K.D. (1986) J. Biol. Chem. 261, 12477-12485], leads to the following conclusions. (i) The small monovalent ions (Li+, Na+, F-) flow through the gel with water molecules attached, whereas the large monovalent ions (K+, Rb+, Cs+, Cl-, Br-, I-) adsorb to the nonpolar surface of the gel, a process requiring partial dehydration of the ion and implying that these ions bind the immediately adjacent water molecules weakly. (ii) The transition from strong to weak hydration occurs at a radius of about 1.78 A for the monovalent anions, compared with a radius of about 1.06 A for the monovalent cations (using ionic radii), indicating that the anions are more strongly hydrated than the cations for a given charge density. (iii) The anions show larger deviations from ideal behavior (an elution position corresponding to the anhydrous molecular weight) than do the cations and dominate the chromatographic behavior of the neutral salts. These results are interpreted to mean that weakly hydrated ions (chaotropes) are "pushed" onto weakly hydrated surfaces by strong water-water interactions and that the transition from strong ionic hydration to weak ionic hydration occurs where the strength of ion-water interactions approximately equals the strength of water-water interactions in bulk solution.

A 59Co NMR chemical shift and relaxation study of preferential solvation toward tris(acetylacetonato)cobalt(III)

AbstractA 59Co NMR chemical shift and relaxation study of the preferential solvation of tris(acetylacetonato)cobalt(III) was undertaken by varying the solute concentration in cyclohexane. As expected, the preferred solvation is most pronounced for hydrogen‐bond donating solutes, such as chloroform and methanol. However, the expected levelling of the 59Co chemical shift curve on increasing the alcohol molar fraction is not observed because of competing solute‐solute interactions in bulk solution. The order of preference is close to that proposed using paramagnetically induced relaxation times or shifts in solutions doped with tris(acetylacetonato)chromium(III). The 59Co line‐width measurements correlate with Co(acac)3 rotational correlation times. Contrary to earlier proposals, the 59Co relaxation is claimed to be controlled by modulation of the static quadrupolar tensor of Co(acac)3.