Liquid-structure forces and electrostatic modulation of biomolecular interactions in solution

Molecular interactions in solution are controlled by the bulk medium and by the forces originating in the structured region of the solvent close to the solutes. In this paper, a model of electrostatic and liquid-structure forces for dynamics simulations of biomolecules is presented. The model introduces information on the microscopic nature of the liquid in the vicinity of polar and charged groups and the associated non-pairwise character of the forces, thus improving upon conventional continuum representations. The solvent is treated as a polar and polarizable medium, with dielectric properties described by an inhomogeneous version of the Onsager theory. This treatment leads to an effective position-dependent dielectric permittivity that incorporates saturation effects of the electric field and the spatial variation of the liquid density. The non-pairwise additivity of the liquid-structure forces is represented by centers of force located at specific points in the liquid phase. These out-of-the-solute centers are positioned at the peaks of liquid density and exert local, external forces on the atoms of the solute. The density is calculated from a barometric law, using a Lennard-Jones-type solute-liquid effective interaction potential. The conceptual aspects of the model and its exact numerical solutions are discussed for single alkali and halide ions and for ion-pair interactions. The practical aspects of the model and the simplifications introduced for efficient computation of forces in molecular solutes are discussed in the context of polar and charged amino acid dimers. The model reproduces the contact and solvent-separated minima and the desolvation barriers of intermolecular potentials of mean force of amino acid dimers, as observed in atomistic dynamics simulations. Possible refinements based on an improved treatment of molecular correlations are discussed.     

Measurements of single-molecule electromechanical properties

The electromechanical properties of a single molecule covalently attached to two gold electrodes are studied by simultaneously measuring the conductance and the force during the stretching of the molecule. The conductance, the spring constant of the molecular junction, and the dependence of the conductance on the stretching force are determined. Like the conductance, the spring constant of a molecule depends also on the molecule-electrode contacts. The forces required to break the molecule-gold contacts are 1.5 nN for alkanedithiols and 0.8 nN for 4,4' bipyridine, indicating that the breakdowns take place at the Au-Au bond and at the N-Au bond, respectively.     

Cholesterol packing around lipids with saturated and unsaturated chains: a simulation study

The fundamental role of cholesterol in the regulation of eukaryotic membrane structure is well-established. However the manner in which atomic level interactions between cholesterol and lipids, with varying degrees of chain unsaturation and polar groups, affect the overall structure and organization of the bilayer is only beginning to be understood. In this paper we describe a series of Molecular Dynamics simulations designed to provide new insights into lipid-cholesterol interactions as a function of chain unsaturation. We have run simulations of varying concentrations of cholesterol in dipalmitoyl phosphatidylcholine (DPPC), palmitoyl-oleyol phosphatidylcholine (POPC), and dioleyol phosphatidylcholine (DOPC) bilayers. Structural analysis of the simulations reveals both atomistic and systemic details of the interactions and are presented here. In particular, we find that the minimum partial molecular area of cholesterol occurs in POPC-Chol mixtures implying the most favorable packing. Physically, this appears to be related to the fact that the two faces of the cholesterol molecule are different from each other and that the steric cross section of cholesterol molecules drops sharply near the small chain tails.     

Extending the applicability of the O-ring theory to protein–DNA complexes

Many biological processes depend on protein-based interactions, which are governed by central regions with higher binding affinities, the hot-spots. The O-ring theory or the “Water Exclusion” hypothesis states that the more deeply buried central regions are surrounded by areas, the null-spots, whose role would be to shelter the hot-spots from the bulk solvent. Although this theory is well-established for protein–protein interfaces, its applicability to other protein interfaces remains unclear. Our goal was to verify its applicability to protein–DNA interfaces. We performed Molecular Dynamics simulations in explicit solvent of several protein–DNA complexes and measured a variety of solvent accessible surface area (SASA) features, as well as, radial distribution functions of hot-spots and null-spots. Our aim was to test the influence of water in their coordination sphere. Our results show that hot-spots tend to have fewer water molecules in their neighborhood when compared to null-spots, and higher values of ΔSASA, which confirms their occlusion from solvent. This study provides evidence in support of the O-ring theory with its applicability to a new type of protein-based interface: protein–DNA.     

Mechanochemical Tuning of the Binaphthyl Conformation at the Air–Water Interface

Gradual and reversible tuning of the torsion angle of an amphiphilic chiral binaphthyl, from ?90° to ?80°, was achieved by application of a mechanical force to its molecular monolayer at the air–water interface. This 2D interface was an ideal location for mechanochemistry for molecular tuning and its experimental and theoretical analysis, since this lowered dimension enables high orientation of molecules and large variation in the area. A small mechanical energy (<1 kcal mol^?1) was applied to the monolayer, causing a large variation (>50 %) in the area of the monolayer and modification of binaphthyl conformation. Single‐molecule simulations revealed that mechanical energy was converted proportionally to torsional energy. Molecular dynamics simulations of the monolayer indicated that the global average torsion angle of a monolayer was gradually shifted.     

Force and Stress along Simulated Dissociation Pathways of Cucurbituril-Guest Systems

The field of host-guest chemistry provides computationally tractable yet informative model systems for biomolecular recognition. We applied molecular dynamics simulations to study the forces and mechanical stresses associated with forced dissociation of aqueous cucurbituril-guest complexes with high binding affinities. First, the unbinding transitions were modeled with constant velocity pulling (steered dynamics) and a soft spring constant, to model atomic force microscopy (AFM) experiments. The computed length-force profiles yield rupture forces in good agreement with available measurements. We also used steered dynamics with high spring constants to generate paths characterized by a tight control over the specified pulling distance; these paths were then equilibrated via umbrella sampling simulations and used to compute time-averaged mechanical stresses along the dissociation pathways. The stress calculations proved to be informative regarding the key interactions determining the length-force profiles and rupture forces. In particular, the unbinding transition of one complex is found to be a stepwise process, which is initially dominated by electrostatic interactions between the guest's ammoniums and the host's carbonyl groups, and subsequently limited by the extraction of the guest's bulky bicyclooctane moiety; the latter step requires some bond stretching at the cucurbituril's extraction portal. Conversely, the dissociation of a second complex with a more slender guest is mainly driven by successive electrostatic interactions between the different guest's ammoniums and the host's carbonyl groups. The calculations also provide information on the origins of thermodynamic irreversibilities in these forced dissociation processes.     

Structure, surface excess and effective interactions in polymer nanocomposite melts and concentrated solutions

The Polymer Reference Interaction Site Model (PRISM) theory is employed to investigate structure, effective forces, and thermodynamics in dense polymer-particle mixtures in the one and two particle limit. The influence of particle size, degree of polymerization, and polymer reduced density is established. In the athermal limit, the surface excess is negative implying an entropic dewetting interface. Polymer induced depletion interactions are quantified via the particle-particle pair correlation function and potential of mean force. A transition from (nearly) monotonic decaying, attractive depletion interactions to much stronger repulsive-attractive oscillatory depletion forces occurs at roughly the semidilute-concentrated solution boundary. Under melt conditions, the depletion force is extremely large and attractive at contact, but is proceeded by a high repulsive barrier. For particle diameters larger than roughly five monomer diameters, division of the force by the particle radius results in a nearly universal collapse of the depletion force for all interparticle separations. Molecular dynamics simulations have been employed to determine the depletion force for nanoparticles of a diameter five times the monomer size over a wide range of polymer densities spanning the semidilute, concentrated, and melt regimes. PRISM calculations based on the spatially nonlocal hypernetted chain closure for particle-particle direct correlations capture all the rich features found in the simulations, with quantitative errors for the amplitude of the depletion forces at the level of a factor of 2 or less. The consequences of monomer-particle attractions are briefly explored. Modification of the polymer-particle pair correlations is relatively small, but much larger effects are found for the surface excess including an energetic driven transition to a wetting polymer-particle interface. The particle-particle potential of mean force exhibits multiple qualitatively different behaviors (contact aggregation, steric stabilization, local bridging attraction) depending on the strength and spatial range of the polymer-particle attraction.     

A hydrogen-sensitive analysis of the structure of deuterated liquid formamide

Structural investigations of deuterated liquid formamide were performed by using neutron scattering, ab-initio calculations and classical Molecular Dynamics (MD) simulations. The recorded neutron data are analysed to yield the total structure factor S_M (Q), the molecular form factor F (Q), the distinct pair correlation function g_L(r) and particularly the deuterium-oxygen signature of H-bond interactions. Neutron scattering data, as well as recent x-ray studies, clearly show that the local order of the liquid is largely described by one dimer, two trimers and one tetramer. Molecular Dynamics simulations show that neutron scattering data can be reproduced by three different force fields.     

Concentration enrichment of urea at cellulose surfaces: results from molecular dynamics simulations and NMR spectroscopy

A combined solid-state NMR and Molecular Dynamics simulation study of cellulose in urea aqueous solution and in pure water was conducted. It was found that the local concentration of urea is significantly enhanced at the cellulose/solution interface. There, urea molecules interact directly with the cellulose through both hydrogen bonds and favorable dispersion interactions, which seem to be the driving force behind the aggregation. The CP/MAS ¹³C spectra was affected by the presence of urea at high concentrations, most notably the signal at 83.4 ppm, which has previously been assigned to C4 atoms in cellulose chains located at surfaces parallel to the (110) crystallographic plane of the cellulose Iβ crystal. Also dynamic properties of the cellulose surfaces, probed by spin-lattice relaxation time ¹³CT ₁ measurements of C4 atoms, are affected by the addition of urea. Molecular Dynamics simulations reproduce the trends of the T ₁ measurements and lends new support to the assignment of signals from individual surfaces. That urea in solution is interacting directly with cellulose may have implications on our understanding of the mechanisms behind cellulose dissolution in alkali/urea aqueous solutions.     

Potential of mean force of water–proton bath and molecular dynamic simulation of proteins at constant pH

An advanced implicit solvent model of water–proton bath for protein simulations at constant pH is presented. The implicit water–proton bath model approximates the potential of mean force of a protein in water solvent in a presence of hydrogen ions. Accurate and fast computational implementation of the implicit water–proton bath model is developed using the continuum electrostatic Poisson equation model for calculation of ionization equilibrium and the corrected MSR6 generalized Born model for calculation of the electrostatic atom–atom interactions and forces. Molecular dynamics (MD) method for protein simulation in the potential of mean force of water–proton bath is developed and tested on three proteins. The model allows to run MD simulations of proteins at constant pH, to calculate pH‐dependent properties and free energies of protein conformations. The obtained results indicate that the developed implicit model of water–proton bath provides an efficient way to study thermodynamics of biomolecular systems as a function of pH, pH‐dependent ionization‐conformation coupling, and proton transfer events. © 2012 Wiley Periodicals, Inc.     

Molecular dynamics simulations of cyclosporin A: The crystal structure and dynamic modelling of a structure in apolar solution based on NMR data

Summary The conformation of the immunosuppressive drug cyclosporin A (CPA), both in apolar solution and in crystalline state, has been studied by computer simulation techniques. Three molecular dynamics (MD) simulations have been performed: one modelling the crystal structure and two modelling the structure in apolar solution, using a restrained MD approach in which data from nuclear magnetic resonance (NMR) and infrared (IR) spectroscopy are taken into account. The simulation of the crystalline state (MDC) concerns a system of 4 unit cells containing 16 cyclosporin A molecules and 22 water molecules, which is simulated using crystalline periodic boundary conditions. The simulations modelling the apolar solvent conformation (MDS) concern one isolated cyclosporin A molecule. In these simulations an extra term in the interatomic potential function is used, which forces the molecule to satisfy a set of 57 atom-atom distance constraints originating from nuclear Overhauser effects (NOEs) obtained from NMR spectroscopy and one distance constraint deduced from IR spectroscopy.From a comparison of the results of the crystal simulation to those of the X-ray experiment in terms of structure, atomic fluctuations, hydrogen bond pattern, etc., it is concluded that the force field that is used yields an adequate representation of crystalline cyclosporin A. Secondly, it is shown that the dynamic modelling technique that is used to obtain a structure in a polar solution from NMR distance information works well. Starting from initial conformations which have a root mean square difference of 0.14 nm both distance restrained MD simulations converge to the same final solution structure. A comparison of the crystal structure of cyclosporin A and the one in apolar solution shows that there are significant differences. The overall difference in atomic positions is 0.09 nm for the C_x atoms and 0.17 nm for all atoms. In apolar solution, the molecule is slightly more bent and the side chains of 1 MeBmt and 10 MeLeu adopt a different conformation.Abbreviations MeBmt (4R)-4[(E)-2-butenyl]-4-methyl-l-Threonine - MD Molecular dynamics - EM Energy minimization - MDC Molecular dynamics simulation of the crystal - MDS1 Restrained molecular dynamics simulation to obtain the structure in solution starting from the crystal structure - MDS2 Like MDS1, but starting from the SMS structure - SMS Proposed structure in solution, obtained by model building - XRAY An X-ray structure - CPA Cyclosporin A - NMR Nuclear magnetic resonance spectroscopy - NOE Nuclear Overhauser enhancement - MDS1 Mean simulated structure obtained by averaging over the time period 20–40 ps of the MDS1 simulation - MDS2 Mean simulated structure obtained by averaging over the time period 10–30 ps of the MDS2 simulation - Mean simulated structure obtained by averaging over the time period 7–15 ps and over the 16 asymmetric units in the computational box of the MDC simulation.     

Functionalized self-assembled monolayers for measuring single molecule lectin carbohydrate interactions

The specific interactions between sugar-binding proteins (lectins) and their complementary carbohydrates mediate several complex biological functions. There is a great deal of interest in uncovering the molecular basis of these interactions. In this study, we demonstrate the use of an efficient one-step amination reaction strategy to fabricate carbohydrate arrays based on mixed self-assembled monolayers. These allow specific lectin carbohydrate interactions to be interrogated at the single molecule level via AFM. The force required to directly rupture the multivalent bonds between Concanavalin A (Con A) and mannose were subsequently determined by chemical force microscopy. The mixed self-assembled monolayer provides a versatile platform with active groups to attach a 1-amino-1-deoxy sugar or a protein (Con A) while minimizing non-specific adhesion enabling quick and reliable detection of rupture forces. By altering the pH of the environment, the aggregation state of Con A was regulated, resulting in different dominant rupture forces, corresponding to di-, tri- and multiple unbinding events. We estimate the value of the rupture force for a single Con A-mannose bond to be 95 ± 10 pN. The rupture force is consistent even when the positions of the binding molecules are switched. We show that this synthesis strategy in conjunction with a mixed SAM allows determination of single molecules bond with high specificity, and may be used to investigate lectin carbohydrate interactions in the form of carbohydrate arrays as well as lectin arrays.     

Unbinding of the streptavidin-biotin complex by atomic force microscopy: a hybrid simulation study

A hybrid molecular simulation technique, which combines molecular dynamics and continuum mechanics, was used to study the single-molecule unbinding force of a streptavidin-biotin complex. The hybrid method enables atomistic simulations of unbinding events at the millisecond time scale of atomic force microscopy (AFM) experiments. The logarithmic relationship between the unbinding force of the streptavidin-biotin complex and the loading rate (the product of cantilever spring constant and pulling velocity) in AFM experiments was confirmed by hybrid simulations. The unbinding forces, cantilever and tip positions, locations of energy barriers, and unbinding pathway were analyzed. Hybrid simulation results from this work not only interpret unbinding AFM experiments but also provide detailed molecular information not available in AFM experiments.     

Peptide backbone folding induced by the C(alpha)-tetrasubstituted cyclic alpha-amino acids 4-amino-1,2-dithiolane-4-carboxylic acid (Adt) and 1-aminocyclopentane-1-carboxylic acid (Ac5c). A joint computational and experimental study

The conformational study of a new group of synthetic peptides containing 4-amino-1,2-dithiolane-4-carboxylic acid (Adt), a cysteine-related achiral residue, has been carried out through a joint application of computational and experimental methodologies. Molecular Dynamics simulations clearly suggest the tendency of this molecule to adopt a gamma-turn conformation in vacuum and help in analyzing the complex and crucial conformational behaviour of the dithiolane ring which appears to preferentially adopt a C(S)-like structure. Electronic structure calculations carried out in solution using the Density Functional Theory also indicate the preservation of the gamma-like folding in apolar solvents and the helix-like one in more polar solvents. A comparison with the achiral 1-aminocycloalkane-1-carboxylic acid (Ac5c) has been carried out using the same computational tools. NMR and IR data on dipeptide derivatives containing the Adt or Ac5c residue show that in chloroform solution all the models prefer a gamma-turn structure, centered at the cyclic residue, stabilized by an intramolecular H-bond, whereas in a more polar solvent, i.e. dimethyl sulfoxide, this folding is not maintained. The experimental conformational studies, extended to N-Boc protected tripeptides, clearly indicate the remarkable tendency of both the five-membered C(alpha)-tetrasubstituted cyclic amino acids Adt and Ac5c to induce the gamma-turn structure also in models able to adopt the beta-bend conformation.     

Mixed monte carlo/molecular dynamics simulations in explicit solvent

A mixed Monte Carlo/Molecular Dynamics method using the trial moves for peptide backbone sampling known as Concerted Rotations with Angles was implemented. The algorithm was used to study polyalanine systems. Equivalent results to conventional Molecular Dynamics were obtained for simulations of Ala₆ in implicit solvent. To test the efficiency of the implemented method, several 150 ns simulations of Ala₁₂ in explicit water were performed. The results show that the present method yields significantly faster formation of secondary structure than the conventional Molecular Dynamics simulations. This opens the possibility to selectively sample alanine‐rich regions of larger peptides or proteins. It remains to be established whether hydrophilic amino acid residues can be successfully treated with the present methodology. © 2012 Wiley Periodicals, Inc.     

The role of surface forces in mineral flotation

Flotation is an interfacial separation technique, which plays a major role in mineral processing industry. It separates particles according to their wetting properties. In flotation pulp, particles and bubbles are highly dispersed in aqueous medium and in the presence of various flotation reagents. Almost all interfacial interactions including inter-particle, inter-bubble, and bubble-particle interactions in the complex pulp medium are driven by surface forces. Therefore, a fundamental understanding of the role of surface forces in flotation is a prerequisite to enhance practical flotation performance and adapt it for treatment of complex and refractory ores. In this paper, recent advances in the field of surface forces encountered in mineral flotation are reviewed. In particular, we highlight the latest progress in the attachment mechanism between bubble and particle with the aid of atomic force microscope and interference microscope. The current knowledge gap and future directions are also discussed.     

Modeling β-lactam interactions in aqueous solution through combined quantum mechanics–molecular mechanics methods

In this article, we have carried out a series of theoretical computations intended to analyze the interactions of β-lactam compounds in aqueous solution. The final aim is to rationalize the influence of the medium on β-lactam antibiotics reactivity. In particular, the hydrolysis reaction has been studied because of the considerable interest due to its relationship with resistance mechanisms developed by bacteria. The study is extended to the simplest β-lactam molecule, propiolactam or 2-azetidinone, and to the corresponding hydroxylated complex (resulting from the addition of a hydroxyl anion to the carbonyl group) that plays a crucial role in hydrolysis processes. Molecular Dynamics simulations have been carried out using a hybrid quantum mechanics–molecular mechanics potential: the solute is described using the density functional theory, whereas water solvent molecules are treated classically. This represents a sophisticated computational level which, compared to usual force-field simulations, has the advantage of allowing a detailed analysis of solute's electronic properties. The discussion of results is focused on the role played by solute–solvent hydrogen bonds and solvent fluctuations on solute's structure. ©1999 John Wiley & Sons, Inc. J Comput Chem 20: 1401–1411, 1999     

Role of water in atomic resolution AFM in solutions

We use computer modelling to investigate the mechanism of atomic-scale corrugation in frequency modulation atomic force microscopy imaging of inorganic surfaces in solution. Molecular dynamics simulations demonstrate that the forces acting on a model microscope tip result from the direct interaction between a tip and a surface, and forces entirely due to the water structure around both tip and surface. The observed force is a balance between largely repulsive potential energy changes as the tip approaches and the entropic gain when water is sterically prevented from occupying sites near the tip and surface. Only extremely sharp tips are likely to measure direct tip-surface interactions. An investigation into the dynamics of water confined between tip and surface shows that water diffusion can be slowed by at least two orders of magnitude compared to its rate in bulk solution.     

Molecular mechanism of transporting a polarizable iodide anion across the water-CCl4 liquid/liquid interface

The result of transferring a polarizable iodide anion across the H2O-CCl4 liquid/liquid interface was investigated in this study. The computed transfer-free energy profile or potential of mean force exhibits a minimum near the Gibbs dividing surface. These system characteristics are similar to those found in a corresponding study of iodide transfer across the H2O-vapor interface; however, the free energy minimum was lower at the H2O-vapor interface. Molecular dynamics simulations were also carried out to compare the concentrations of NaCl, NaBr, and NaI at the H2O-vapor and H2O-CCl4 interfaces. While the concentration of bromide and iodide ions were lower at the H2O-CCl4 interface when compared to the H2O-vapor interface, the chloride ion concentrations were similar at both interfaces. Analysis of the solvation structures of iodide and chloride ions revealed that the more polarizable iodide ion was less solvated than the chloride ion at the interface. This characteristic brought the iodide ion into greater contact with CCl4, resulting in repulsive interactions with CCl4 and reducing its tendency to move to the interface.