Simulation studies of the protein-water interface. II. Properties at the mesoscopic resolution

We report molecular dynamics (MD) simulations of three protein-water systems (ubiquitin, apo-calbindin D(9K), and the C-terminal SH2 domain of phospholipase C-gamma1), from which we compute the dielectric properties of the solutions. Since two of the proteins studied have a net charge, we develop the necessary theory to account for the presence of charged species in a form suitable for computer simulations. In order to ensure convergence of the time correlation functions needed for the analysis, the minimum length of the MD simulations was 20 ns. The system sizes (box length, number of waters) were chosen so that the resulting protein concentrations are comparable to experimental conditions. A dielectric component analysis was carried out to analyze the contributions from protein and water to the frequency-dependent dielectric susceptibility chi(omega) of the solutions. Additionally, an even finer decomposition into protein, two solvation shells, and the remaining water (bulk water) was carried out. The results of these dielectric decompositions were used to study protein solvation at mesoscopic resolution, i.e., in terms of protein, first and second solvation layers, and bulk water. This study, therefore, complements the structural and dynamical analyses at molecular resolution that are presented in the companion paper. The dielectric component contributions from the second shell and bulk water are very similar in all three systems. We find that the proteins influence the dielectric properties of water even beyond the second solvation shell, in agreement with what was observed for the mean residence times of water molecules in protein solutions. By contrast, the protein contributions, as well as the contributions of the first solvation shell, are system specific. Most importantly, the protein and the first water shell around ubiquitin and apo-calbindin are anticorrelated, whereas the first water shell around the SH2 domain is positively correlated.     

Anomalously increased lifetimes of biological complexes at zero force due to the protein-water interface

A number of biological bonds show dramatically increased lifetimes at zero-force conditions, compared to lifetimes when even a small tensile force is applied to the ligand. The discrepancy is so great that it cannot be explained by the traditional receptor-ligand binding models. This generic phenomenon is rationalized here by considering the interaction of water with the receptor-ligand complex. It is argued that the water-protein interaction creates an energy barrier that prevents the ligand unbinding in the absence of the force. The properties of the interaction are such that even application of a relatively low force results in a dramatic drop of the bond lifetime due to the alteration of the water-receptor and water-ligand interaction network. The phenomenon is described by the presence of a second shallow interaction energy minimum for the bound ligand followed by a wide receptor-ligand dissociation barrier. The general analysis is applied quantitatively to the actin-myosin system, which demonstrates the gigantic drop of the bond lifetime at small forces and catch behavior (an increase in the lifetime) at moderate forces. The base hypothesis proposed to explain the small-force abnormal drop in the bond lifetime suggests that the majority of biological bonds may exhibit this phenomenon irrespectively whether they behave as slip or catch-slip bonds.     

Spectroscopic studies of molecular interaction at the liquid–liquid interface

The development of techniques to study the liquid–liquid interface is a major challenge. Spectroscopy in all its forms provides a powerful method of investigation, especially when combined with other optical techniques. Over the last 30 years, there have been significant developments in the methods for studying heterogeneous interfaces. As technology progresses, the sensitivity of existing techniques has been improved but there are major challenges still to be met, such as the measurement of interfacial dielectric constant and viscosity. This paper aims to summarise the use of spectroscopy to study molecular interactions at the liquid–liquid interface.     

Virtual interface substructure synthesis method for normal mode analysis of super-large molecular complexes at atomic resolution

Normal mode analysis of large biomolecular complexes at atomic resolution remains challenging in computational structure biology due to the requirement of large amount of memory space and central processing unit time. In this paper, we present a method called virtual interface substructure synthesis method or VISSM to calculate approximate normal modes of large biomolecular complexes at atomic resolution. VISSM introduces the subunit interfaces as independent substructures that join contacting molecules so as to keep the integrity of the system. Compared with other approximate methods, VISSM delivers atomic modes with no need of a coarse-graining-then-projection procedure. The method was examined for 54 protein-complexes with the conventional all-atom normal mode analysis using CHARMM simulation program and the overlap of the first 100 low-frequency modes is greater than 0.7 for 49 complexes, indicating its accuracy and reliability. We then applied VISSM to the satellite panicum mosaic virus (SPMV, 78,300 atoms) and to F-actin filament structures of up to 39-mer, 228,813 atoms and found that VISSM calculations capture functionally important conformational changes accessible to these structures at atomic resolution. Our results support the idea that the dynamics of a large biomolecular complex might be understood based on the motions of its component subunits and the way in which subunits bind one another.     

Photoinduced electron transfer at the polymer-solution interface. I. Surface property-reactivity relation

Photooxidation of leuco crystal violet(LCV) to the dye(CV⁺) by interfacial sensitization with polymer-bonded pyrenyl groups was studied. Poly(ethylene-g-acrylic acid) was esterified by 1-hydroxymethylpyrene in tetrahydrofuran (THF) (Film 1) or in acetonitrile (Film 2). Film 2 had a more condensed but thinner pyrene-containing surface layer than Film 1. Differences in surface structure were investigated by fluorescence and absorption spectra, as well as by measuring contant angle to water as a function of the total amount of bonded pyrene. Films 1 and 2 behaved differently in the photoreaction, which was interpreted as due to the difference in the affinity of LCV solution to the film surface, hence the diffusion of LCV into the film. The quantum efficiency of CV⁺ formation (?cv⁺) is therefore the function of the thickness of the photoabsorbing layer and the effective reaction volume determined by the depth of LCV diffusion. The role of excimer formation and energy migration among pyrenyl groups was concluded to be of minor importance.     

High-field NMR studies of molecular recognition and structure-function relationships in antimicrobial piscidins at the water-lipid bilayer interface

High magnetic field solid-state NMR was performed on amphipathic cationic antimicrobial peptides from fish to characterize their secondary structure and orientation in hydrated phospholipid bilayers. High-resolution distance and orientational restraints on 13C- and 15N-labeled amidated piscidins 1 and 3 provided site-specific information establishing alpha-helicity and an orientation parallel to the membrane surface. Few membrane-bound natural peptides with this topology have been structurally studied at high resolution in the presence of hydrated lipid bilayers. This orientation was foreseen since the partitioning of amphipathic cationic antimicrobial peptides at the water-bilayer interface allows for favorable peptide-lipid interactions, and it may be related to the mechanism of action. The enhanced resolution obtained at 900 MHz evidences a determinant advantage of ultra-high-field NMR for the structural determination of multiple-labeled peptides and proteins.     

Ellipsometric studies of behenic acid at the air-water interface

The rich phase behaviour of monolayers of behenic acid (=docosanoic acid) has been analyzed by null ellipsometry in isothermic and isobaric measurements. By using structural data known from x-ray measurements the anisotropy and refractive indices in the vicinity of the S-CS phase transition have been calculated with a minimum of model assumptions. The calculated values are: n^s_x=1.47. n^cs_x=1.48. n^sz=1.54. n^cs_z=1.55. and anisotropy γ=n_x/n_z ≈︁0.95. It is also shown that ellipsometry is a very sensitive and convenient method of detecting phase transitions. Its value for quantifying the roughness of the monolayer in the close vicinity of phase transitions due to thickness and density fluctuations is shown by the measurement of the parabolic intensity variations of the ellipsometric angle δΔ. The intensity minimum at the phase transition is much wider than in the adjacent homogeneous phases.     

Catalase monolayers at the air/water interface I. Reversibilities and irreversibilities

/A-isotherms of catalase monolayers established at the air/water-interface are discussed quantitatively on the basis of molecular data: A relationship between a critical value of the surface pressure, the corresponding molecular area, and the molecular dimension of the molecules at the interface is proposed. It is shown that the unfolding of molecules at the water surface is pH-dependent. For each pH-value there is a distinct degree of unfolding; the molecules keep their globular state at neutral pH. Establishment at the surface of bulk solutions corresponding to globular and partly unfolded states, respectively, catalase molecules keep their original configuration on changing the pH-value of bulk-phase. The monolayers are confirmed to show reversibility with regard to lateral changes of state as well as irreversibility with respect to desorption of molecules.A model is proposed to explain the nature of the critical/A-value occurring in the/A-isotherms: on compression beyond _c, molecular segments are transferred from the surface into the bulkphase via a subsurface layer. From the experiments it is concluded that the surface pressure is determined, not only by the surface itself, but also by this subsurface layer.     

Ellipsometry studies of nonionic surfactant adsorption at the oil--water interface

In the presented study we have developed and implemented a methodology for ellipsometry measurements at liquid interfaces that makes it possible to determine the amount adsorbed without assumptions of refractive index or thickness of the adsorbed layer. It was demonstrated that this is possible by combined measurements from different aqueous phases, H(2)O and D(2)O, which were shown to have sufficiently different refractive indices. The methodology was tested by studying adsorption of two types of nonionic poly(ethylene glycol) alkyl ether surfactants, C(n)H(2)(n)(+1)(OC(2)H(4))(m)OH or C(n)E(m) at the decane--aqueous interface, where C(12)E(5) was adsorbed from the oil phase and C(18)E(50) from the aqueous phase. The observed plateau values of the adsorbed amounts were 1.38 and 0.93 mg/m(2) for C(12)E(5) and C(18)E(50), respectively, which is in agreement with the corresponding values of 1.49 and 1.15 mg/m(2) obtained from applying the Gibbs equation to interfacial tension data for the same systems. We will briefly discuss the adsorption behavior in relation to the molecular structure of the surfactant and the phase behavior of the oil--surfactant--aqueous systems in relation to our experimental results.     

Electrochemical activation of molecular nitrogen at the Ir/YSZ interface

Nitrogen is often used as an inert background atmosphere in solid state studies of electrode and reaction kinetics, of solid state studies of transport phenomena, and in applications e.g. solid oxide fuel cells (SOFC), sensors and membranes. Thus, chemical and electrochemical reactions of oxides related to or with dinitrogen are not supposed and in general not considered. We demonstrate by a steady state electrochemical polarisation experiments complemented with in situ photoelectron spectroscopy (XPS) that at a temperature of 450 °C dinitrogen can be electrochemically activated at the three phase boundary between N(2), a metal microelectrode and one of the most widely used solid oxide electrolytes--yttria stabilized zirconia (YSZ)--at potentials more negative than E = -1.25 V. The process is neither related to a reduction of the electrolyte nor to an adsorption process or a purely chemical reaction but is electrochemical in nature. Only at potentials more negative than E = -2 V did new components of Zr 3d and Y 3d signals with a lower formal charge appear, thus indicating electrochemical reduction of the electrolyte matrix. Theoretical model calculations suggest the presence of anionic intermediates with delocalized electrons at the electrode/electrolyte reaction interface. The ex situ SIMS analysis confirmed that nitrogen is incorporated and migrates into the electrolyte beneath the electrode.     

Comparative Raman studies of molecular interactions at a dye/polymer and a dye/glass interface

Integrated optical techniques and resonance Raman spectroscopy have been combined to investigate the intermolecular interactions at dye/polymer and dye/glass interfaces. Frequency shifts and intensity changes of bands assigned to the stretching vibrations of the bridged quinoline rings of the cyanine dye chromophore have been utilized to gain insight into the relative strength of adhesive forces at the surface. Polarized Raman measurements were made to determine the orientation of the chromophores on a poly(vinyl alcohol) surface. This was done to assess the possibility of hydrogen bond formation between the ring nitrogen atoms and the polar hydroxyl groups at the surface.     

Probing the organic-mineral interface at the molecular level in model biominerals

It is widely known that macromolecules, such as proteins, can control the nucleation and growth of inorganic solids in biomineralizing organisms. However, what is not known are the complementary molecular interactions, organization, and rearrangements that occur when proteins interact with inorganic solids during the formation of biominerals. The organic-mineral interface (OMI) is expected to be the site for these phenomena, and is therefore extraordinarily interesting to investigate. In this report, we employ X-ray absorption near edge (XANES) spectromicroscopy to investigate the electronic structure of both calcium carbonate mineral crystals and polypeptides, and detect changing bonds at the OMI during crystal growth in the presence of polypeptides. We acquired XANES spectra from calcium carbonate crystals grown in the presence of three mollusk nacre-associated polypeptides (AP7N, AP24N, n16N) and in the presence of a sea urchin spicule matrix protein, LSM34. All these model biominerals gave similar results, including the disruption of CO bonds in calcite and enhancement of the peaks associated with C-H bonds and C-O bonds in peptides, indicating ordering of the amino acid side chains in the mineral-associated polypeptides and carboxylate binding. This is the first evidence of the mutual effect of calcite on peptide chain and peptide chain on calcite during biomineralization. We also show that these changes do not occur when Asp and Glu are replaced in the n16N sequence with Asn and Gln, respectively, demonstrating that carboxyl groups in Asp and Glu do participate in polypeptide-mineral molecular associations.     

Reorganization of lipid nanocapsules at air-water interface. I. Kinetics of surface film formation

The size, the electrical properties and the behaviour at air-water interface of lipid nanocapsules (LNC) with various compositions were investigated. Two populations of LNC are presented in the suspension after the preparation: with (LNC II) and without (LNC I) phospholipid molecules. After the spreading at air-water interface, a rapid disaggregation of LNC I, located in the vicinity of interface, occurs leading to formation of surface film. The phospholipid molecules stabilize the structure of nanocapsules and LNC II are more stable at the interface in comparison with LNC I. The formation of a surface film was followed after by measuring the evolution of the surface pressure, relative surface area change and surface potential. A kinetic approach describing the various processes during the surface film formation was proposed. The corresponding kinetic constants were estimated.     

Tuning molecular orientation with STM at the solid/liquid interface

Triptycene molecular orientation has been tuned with a STM tip at a Cu(111) surface in solution from flat, to tilt, to vertical. The tuning is completely bias dependent and reversible. The study is important in the fields of nanoscience and technology.     

Two-dimensional self-assembly of linear molecular rods at the liquid/solid interface

We report on the synthesis and scanning tunneling microscopy (STM) studies of a series of linear molecular rods (1-5) comprising different numbers and/or spatial arrangements of perfluorinated benzene and benzene subunits interlinked with diacetylenes in the para position and decorated with or without terminal dodecyl chains. The molecules organize themselves into well-ordered 2D crystal structures at the liquid/solid interface through intermolecular and molecule-substrate interactions. Whereas the molecules substituted by dodecyl chains form the lamellar structures with alternating rigid core rows and alkyl chain rows, the unsubstituted ones change the orientation of the rigid backbones with respect to the lamellar axis. The molecular arrangement is not influenced by fluoro substituents on any phenyl ring of the backbone, which suggests that the interactions between the π-conjugated backbones are dominated by close packing rather than by the dipole moments of the rods or fluorine-based intermolecular interactions.     

Shear-induced long-range uniaxial assembly of polyaromatic monolayers at molecular resolution

The control of spatial arrangements of molecular building blocks on surfaces opens the foundational step of the bottom-up approach toward future nanotechnologies. Contemporarily, the domain size of monolayers exhibiting crystallinity falls in the submicrometer scale. Developed herein is a method that allows the alignment of polyaromatics with one-single domain for as long as 7 mm. Even more exciting is the fact that the method is applicable to every laboratory and costs practically nothing. The monolayers are prepared simply by placing a piece of folded lens paper against the substrate and the deposition solution containing the compound of interest. The preparation scheme is similar to the Couette flow where the laminar flow takes place between two concentric walls, one of which rotates and creates viscous drag proven useful to align macromolecules. The method can induce an edge-on orientation for 3,6,11,14-tetradodecyloxydibenzo[g,p]chrysene (DBC-OC12), 3,6,12,15-tetrakis(dodecyloxy)tetrabenz[a,c,h,j]anthracene (TBA-OC12), and hexakis(4-dodecyl)-peri-hexabenzocoronene (HBC-C12) and unsubstituted coronene which would otherwise adopt the face-on arrangement on graphite. This finding will be useful to the research and industry that demands high quality alignment of polyaromatics such as OTFTs, optical polarizers, and nanodevices associated with molecular self-assembly.     

Condensed thymine films at the mercury/water interface: Part I. General features

The general features of the condensed films formed by thymine at the mercury/water interface are described. The kinetics of their formation are those of nucleation and growth, i.e., of phase formation. The slow nucleation is responsible for the observed capacitance hysteresis. The interfacial capacitance in the presence of a condensed thymine film is remarkably insensitive to thymine or electrolyte concentration, to the nature of the electrolyte or to temperature, but the region of potentials over which the condensed film is stable depends strongly on these variables. At low temperatures, additional condensed films are observed.