Hydrophobic effects on partial molar volume

The hydrophobic effects on partial molar volume (PMV) are investigated as a PMV change in the transfer of a benzenelike nonpolar solute from the nonpolar solvent to water, using an integral equation theory of liquids. The volume change is divided into two effects. One is the "packing" effect in the transfer from the nonpolar solvent to hypothetical "nonpolar water" without hydrogen bonding networks. The other is the "iceberg" effect in the transfer from nonpolar water to water. The results indicate that the packing effect is negative and a half compensated by the positive iceberg effect. The packing effect is explained by the difference in the solvent compressibility. Further investigation shows that the sign and magnitude of the volume change depend on the solute size and the solvent compressibility. The finding gives a significant implication that the exposure of a hydrophobic residue caused by protein denaturation can either increase or decrease the PMV of protein depending on the size of the residue and the fluctuation of its surroundings.     

Water properties and potential of mean force for hydrophobic interactions of methane and nanoscopic pockets studied by computer simulations

We consider model systems consisting of a methane molecule and hemispherical pockets of subnanometer radii whose walls are made of hydrophobic material. The potential of mean force for process of translocation of the methane molecule from bulk water into the pockets' interior is obtained, based on an explicit solvent molecular dynamics simulations. Accompanying changes in water density around the interacting objects and spatial distribution of solvent's potential energy are analyzed, allowing for interpretation of details of hydrophobic interactions in relation to hydrophobic hydration properties. Applicability of surface area-based models of hydrophobic effect for systems of interest is also investigated. A total work for the translocation process is not dependent on pocket's size, indicating that pocket desolvation has little contribution to free energy changes, which is consistent with the observation that solvent density is significantly reduced inside "unperturbed" pockets. Substantial solvent effects are shown to have a longer range than in case of a well investigated methane pair. A desolvation barrier is present in a smaller pocket system but disappears in the larger one, suggesting that a form of a "hydrophobic collapse" is observed.     

THE POSSIBLE MECHANISM OF BINDING INTERACTION OF INSULIN MOLECULE WITH ITS RECEPTOR

Detailed structural comparisons and investigation of DPI, 2Zn insulin and some other derivatives of insulin were performed by the least-squares superimposition technique and the graphics technique. It is pointed out in this paper that the binding interaction with the receptor molecule should take place mainly on an amphipathic surface of the insulin molecule. In the middle, there is a hydrophobic surface with an area of about 150 consisting of many hydrophobic residues; while the polar or charged groups distributing around the hydro. phobic surface construct a hydrophilic zone. The hydrophobic surface is usually covered by the extended B-chain C-terminal peptides with great mobility and protected from the solvent molecules. The angle between the amphipathic surface and the surface of dimerization is about 20 degrees. The results from the detailed structural comparison between A1-(L-Trp) insulin and A1-(D-Trp) insulin have provided a very good explanation to their great difference in biological activity,     

A Molecular Torsion Balance Study: A Nearby Anionic Group Exerts Little Influence on Hydrophobic Interactions between Nonpolar Surfaces

Polar groups have a solvent ordering effect on water and therefore may affect hydrophobic binding energies for nearby lipophilic surfaces. This would mean that determinations of excess surface free energy association energies require consideration of nearby polar functional groups. This paper reports results of a study to measure this possible effect. It was concluded from the models used here that an anionic polar group nearby a hydrophobic surface has little or no effect on the magnitude of hydrophobic association.     

The possible mechanism of binding interaction of insulin molecule with its receptor.

Detailed structural comparisons and investigation of DPI, 2 Zn insulin and some other derivatives of insulin were performed by the least-squares superimposition technique and the graphics technique. It is pointed out in this paper that the binding interaction with the receptor molecule should take place mainly on an amphipathic surface of the insulin molecule. In the middle, there is a hydrophobic surface with an area of about 150 A2 consisting of many hydrophobic residues; while the polar or charged groups distributing around the hydrophobic surface construct a hydrophilic zone. The hydrophobic surface is usually covered by the extended B-chain C-terminal peptides with great mobility and protected from the solvent molecules. The angle between the amphipathic surface and the surface of dimerization is about 20 degrees. The results from the detailed structural comparison between Al-(L-Trp) insulin and Al-(D-Trp) insulin have provided a very good explanation to their great difference in biological activity, and confirmed our proposed binding interaction model of the insulin molecule with its receptor as well.     

Localization and quantification of hydrophobicity: The molecular free energy density (MolFESD) concept and its application to sweetness recognition

A method for the localization, the quantification, and the analysis of hydrophobicity of a molecule or a molecular fragment is presented. It is shown that the free energy of solvation for a molecule or the transfer free energy from one solvent to another can be represented by a surface integral of a scalar quantity, the molecular free energy surface density (MolFESD), over the solvent accessible surface of that molecule. This MolFESD concept is based on a model approach where the solvent molecules are considered to be small in comparison to the solute molecule, and the solvent can be represented by a continuous medium with a given dielectric constant. The transfer energy surface density for a 1-octanol/water system is empirically determined employing a set of atomic increment contributions and distance dependent membership functions measuring the contribution of the increments to the surface value of the MolFESD. The MolFESD concept can be well used for the quantification of the purely hydrophobic contribution to the binding constants of molecule-receptor complexes. This is demonstrated with the sweeteners sucrose and sucralose and various halogen derivatives. Therein the relative sweetness, which is assumed to be proportional to the binding constant, nicely correlates to the surface integral over the positive, hydrophobic part of the MolFESD, indicating that the sweetness receptor can be characterized by a highly flexible hydrophobic pocket instead of a localized binding site.     

Adsorption of antimicrobial indolicidin-derived peptides on hydrophobic surfaces

The hydrophobic interaction between antimicrobial peptides and membrane hydrophobic cores is usually related to their cytotoxicity. In this study, the adsorption mechanism of five plasma membrane-associated peptides, indolicidin (IL) and its four derivatives, with hydrophobic ligands was investigated to understand the relationship between peptide hydrophobicity and bioactivity. The hydrophobic adsorption mechanisms of IL and its derivatives were interpreted thermodynamically and kinetically by reversed-phase chromatography (RPC) analysis and surface plasmon resonance (SPR) measurement, respectively. IL and its derivatives possess a similar random coil structure in both aqueous and organic solvents. Thermodynamic analysis showed that the binding enthalpy of peptides with higher electropositivity was lower than those with lower electropositivity and exhibited unfavorable binding entropy. Higher electropositivity peptides adsorbed to the hydrophobic surface arising from the less bound solvent on the peptide surface. A comparison with the kinetic analysis showed that IL and its derivatives adopt a two-state binding model (i.e., adsorption onto and self-association on the hydrophobic acyl chain) to associate with the hydrophobic surface, and the binding affinity of peptide self-association correlates well with peptide hemolysis. Consequently, this study provided a novel concept for understanding the action of plasma membrane-associated peptides.     

Effect of surface hydrophobicity distribution on retention of ribonucleases in hydrophobic interaction chromatography

The effect of surface hydrophobicity distribution of proteins on retention in hydrophobic interaction chromatography (HIC) was investigated. Average surface hydrophobicity as well as hydrophobic contact area between protein and matrix were estimated using a classical thermodynamic model. The applicability of the model to predict protein retention in HIC was investigated on ribonucleases with similar average surface hydrophobicity but different surface hydrophobicity distribution. It was shown experimentally that surface hydrophobicity distribution could have an important effect on protein retention in HIC. The parameter "hydrophobic contact area," which comes from the thermodynamic model, was able to represent well the protein retention in HIC with salt gradient elution. Location and size of the hydrophobic patches can therefore have an important effect on protein retention in HIC, and the hydrophobic contact area adequately describes this.     

Adsorption of pure and mixed solvent solutions of spin probes onto stationary phases

Water, methanol (MeOH), acetonitrile (ACN), and binary MeOH-water and ACN-water solutions of different spin probes (nitroxides), selected to mimic the behavior of different pollutants, were adsorbed onto stationary phases usually used in reversed-phase high-performance liquid chromatography (RP-HPLC). These stationary phases are constituted by porous silica and differ from each other regarding the surface area, the pore size, the particle size, the surface functions (NH2, C8, and C18), and the percentage of functionalization. The electron paramagnetic resonance (EPR) spectra of the probe solutions adsorbed into the pores were analyzed by computer-aided computation of the spectral line shape, which provided structural and dynamical parameters of the probes and their environments. These parameters provided information on the surface properties of the stationary phases, such as alkyl chain density, solvent penetration, stationary-phase ordering, and residual silanol effects, which modify the retention times in HPLC. A different availability of polar surface groups in the pure and mixed solvents was found for the different stationary phases depending on (1) the different functionalization degree, (2) the surface-chain length, (3) the particle size, and (4) the polarity of both the probe and the solvent. The C8 functionalization rendered the surface more hydrophobic with respect to C18. The endcapping process of the residual silanols strongly enhanced the surface hydrophobicity tested by the probes. At the highest water content, the adsorption of the polar or charged probes onto the hydrophobic surface is the lowest and self-aggregation occurs. When the probes bear both hydrophilic and hydrophobic moieties, the adsorption is enhanced by a synergy between hydrophilic and hydrophobic bonds with the surface. A balance between the hydrophilic and hydrophobic forces leads to high adsorption and partial insertion of the surfactant probes in an ordered C18 chain layer at the solid surface which forms in the binary mixtures; this layer is ascertained between 40% and 70% of the less hydrophilic solvent, depending on the type of both the solid and the probe. This insertion and the response on the formation of the ordered layer were favored in ACN-water with respect to MeOH-water.     

Absolute free energies of binding of peptide analogs to the HIV-1 protease from molecular dynamics simulations

The constants of binding of five peptide analogs to the active site of the HIV-1 aspartic-protease are calculated based on a novel sampling scheme that is efficient and does not introduce any approximations in addition to the energy function used to describe the system. The results agree with experiments. The squared correlation coefficient of the calculated vs. the measured values is 0.79. The sampling scheme consists of a series of molecular dynamics integrations with biases. The biases are selected based on an estimate of the probability density function of the system in a way to explore the conformational space and to reduce the statistical error in the calculated binding constants. The molecular dynamics integrations are done with a vacuum potential using a short cutoff scheme. To estimate the probability density of the simulated system, the results of the molecular dynamics integrations are combined using an extension of the weighted histogram analysis method (C. Bartels, Chem. Phys. Letters 331 (2000) 446-454). The probability density of the solvated ligand-protein system is obtained by applying a correction for the use of the short cutoffs in the simulations and by taking into account solvation with an electrostatic term and a hydrophobic term. The electrostatic part of the solvation is determined by finite difference Poisson-Boltzmann calculations; the hydrophobic part of the solvation is set proportional to the solvent accessible surface area. Setting the hydrophobic surface tension parameter equal to 8 mol(-1) K(-1) A(-2), absolute binding constants are in the muM to nM range. This is in agreement with experiments. The standard errors determined from eight repeated binding constant determinations are a factor of 14 to 411. A single determination of a binding constant is done with 499700 steps of molecular dynamics integration and 4500 finite difference Poisson-Boltzmann calculations. The simulations can be analyzed with respect to conformational changes of the active site of the HIV-1 protease or the ligands upon binding and provide information that complements experiments and can be used in the drug development process.     

Solvent and substituent effects on aggregation constants of perylene bisimide π-stacks--a linear free energy relationship analysis

A series of six perylene bisimides (PBIs) with hydrophilic and hydrophobic side chains at the imide nitrogens were applied for a comparative study of the solvent and structural effects on the aggregation behaviour of this class of dyes. A comparison of the binding constants in tetrachloromethane at room temperature revealed the highest binding constant of about 10(5) M(-1) for a PBI bearing 3,4,5-tridodecyloxyphenyl substituents at the imide nitrogens, followed by 3,4,5-tridodecylphenyl and alkyl-substituted PBIs, whereas no aggregation could be observed in the accessible concentration range for PBIs equipped with bulky 2,6-diisopropylphenyl substituents at the imide nitrogens. The aggregation behaviour of three properly soluble compounds was investigated in 17 different solvents covering a broad polarity range from nonpolar n-hexane to highly polar DMSO and water. Linear free energy relationships (LFER) revealed a biphasic behaviour between Gibbs free energies of aggregation and common empirical solvent polarity scales indicating particularly strong π-π stacking interactions in nonpolar aliphatic and polar alcoholic solvents whilst the weakest binding is observed in dichloromethane and chloroform. Accordingly, PBI aggregation is dominated by electrostatic interactions in nonpolar solvents and by solvophobic interactions in protic solvents. In water, the aggregation constant is increased far beyond LFER expectations pointing at a pronounced hydrophobic effect.     

Tunable inhibition and denaturation of alpha-chymotrypsin with amino acid-functionalized gold nanoparticles

Water-soluble gold nanoparticles bearing diverse l-amino acid terminals have been fabricated to probe the effect of receptor surface on protein surface binding. The interaction of these nanoparticles with alpha-chymotrypsin (ChT) was investigated by activity assay, gel electrophoresis, zeta-potential, circular dichroism, and fluorescence spectroscopy. The results show that both electrostatic and hydrophobic interactions between the hydrophobic patches of receptors and the protein contribute to the stability of the complex. The microscopic binding constants for these receptor-protein systems are 10(6)-10(7) M(-1), with the capacity of the nanoparticle receptors to bind proteins determined by both their surface area and their surface charge density. Furthermore, it is found that the hydrophilic side chains destabilize the ChT structure through either competitive hydrogen bonding or breakage of salt bridges, whereas denaturation was much slower with hydrophobic amino acid side chains. Significantly, correlation between the hydrophobicity index of amino acid side chains and the binding affinity and denaturation rates was observed.     

Specific ion binding to macromolecules: effects of hydrophobicity and ion pairing

Using molecular dynamics simulations in an explicit aqueous solvent, we examine the binding of fluoride versus iodide to a spherical macromolecule with both hydrophobic and positively charged patches. Rationalizing our observations, we divide the ion association interaction into two mechanisms: (1) poorly solvated iodide ions are attracted to hydrophobic surface patches, while (2) the strongly solvated fluoride and to a minor extent also iodide bind via cation-anion interactions. Quantitatively, the binding affinities vary significantly with the accessibility of the charged groups as well as the surface potential; therefore, we expect the ion-macromolecule association to be modulated by the local surface characteristics of the (bio-)macromolecule. The observed cation-anion pairing preference is in excellent agreement with experimental data.     

Disruption of supported lipid bilayers by semihydrophobic nanoparticles

Understanding the interaction between functional nanoparticles and cell membranes is critical to use nanomaterials for broad biomedical applications with minimal cytotoxicity. In this work, we have investigated the effect of adsorbed semihydrophobic nanoparticles (NPs) on the dynamics and morphology of model cell membranes. We have systematically varied the degree of surface hydrophobicity of carboxyl end-functionalized polystyrene NPs of varied size in buffer solutions with varied ionic strength. It is observed that semihydrophobic NPs can readily adsorb on neutral SLBs and drag lipids from SLBs to NP surfaces. Above a critical NP concentration, the disruption of SLBs is observed, accompanied with the formation and rapid growth of lipid-poor regions on NP-adsorbed SLBs. In the study of the effect of solution ionic strength on NP surface hydrophobic degree and the growth of lipid-poor regions, we have concluded that the hydrophobic interaction enhanced by screened electrostatic interaction underlies the envelopment of NPs by lipids that are attracted from SLBs to the surface of NPs or their aggregates. Hence, the formation and growth of lipid-poor regions, or vaguely referred as "pores" or "holes" in the literature, can be controlled by NP concentration, size, and surface hydrophobicity, which is critical to design functional nanomaterials for effective nanomedicine while minimizing possible cytotoxicity.     

Development of PEG-PLA/PLGA microparticles for pulmonary drug delivery prepared by a novel emulsification technique assisted with amphiphilic block copolymers

We developed a novel "spray dry-based" method for preparing surface-modified particle via "block copolymer-assisted" emulsification/evaporation for pulmonary drug delivery. The method included three steps: (1) o/w emulsion containing both hydrophobic polymers and amphiphilic block copolymers was obtained by emulsification of water and a polymer-containing organic solvent, (2) the o/w emulsion was misted with a nebulizer, and (3) the emulsion mists were dried by a heater. In this way, the hydrophobic polymers and the hydrophobic part of the amphiphilic block copolymers gradually tangled during the evaporation of organic solvents from the o/w emulsion. Consequently, the hydrophilic polymer chain was introduced on the particle surface. The particle surface can be easily modified although there are no reactive groups in the hydrophobic polymer molecules. We successfully obtained dry PEG-PLA/PLGA microparticles by controlling the weight ratio of the block copolymer and the hydrophobic polymer. The introduction of PEG to the particle surface involves an increase in the Zeta potential of the particles. Interestingly, the "dimpled" microparticles having a diameter of approximately 2 μm were obtained. The "dimpled" microparticles can serve as drug carriers for pulmonary drug delivery, because the particles have a large surface area. We expect that this novel surface-modification technique will enable efficient fabrication of particles in drug delivery systems.     

Thermal signature of hydrophobic hydration dynamics

Hydrophobic hydration, the perturbation of the aqueous solvent near an apolar solute or interface, is a fundamental ingredient in many chemical and biological processes. Both bulk water and aqueous solutions of apolar solutes behave anomalously at low temperatures for reasons that are not fully understood. Here, we use (2)H NMR relaxation to characterize the rotational dynamics in hydrophobic hydration shells over a wide temperature range, extending down to 243 K. We examine four partly hydrophobic solutes: the peptides N-acetyl-glycine-N'-methylamide and N-acetyl-leucine-N'-methylamide, and the osmolytes trimethylamine N-oxide and tetramethylurea. For all four solutes, we find that water rotates with lower activation energy in the hydration shell than in bulk water below 255 +/- 2 K. At still lower temperatures, water rotation is predicted to be faster in the shell than in bulk. We rationalize this behavior in terms of the geometric constraints imposed by the solute. These findings reverse the classical "iceberg" view of hydrophobic hydration by indicating that hydrophobic hydration water is less ice-like than bulk water. Our results also challenge the "structural temperature" concept. The two investigated osmolytes have opposite effects on protein stability but have virtually the same effect on water dynamics, suggesting that they do not act indirectly via solvent perturbations. The NMR-derived picture of hydrophobic hydration dynamics differs substantially from views emerging from recent quasielastic neutron scattering and pump-probe infrared spectroscopy studies of the same solutes. We discuss the possible reasons for these discrepancies.     

限进介质烷基-二醇基硅胶(ADS)的制备

 烷基 二醇基硅胶 (ADS)系限进介质的一种 ,可用于含生物大分子的复杂生物样品的直接进样与分析。一种新的、非常经济的方法可用于烷基 二醇基硅胶的制备。首先 ,将γ 环氧丙基氧丙基三甲氧基硅烷基键合至微孔硅胶上 (粒度 5 μm ,孔径 6nm)以制备环氧基硅胶 ,再令环氧基硅胶与硬脂酸在有机溶液中进行反应以制备酯型十八烷基反相填料。将制得的反相填料填充至色谱柱中 ,并令含有酯酶的溶液通过色谱柱。通过酶解作用可将硅胶表面的酯基除去 ,而硅胶的内孔表面仍保持疏水特性不变 ,这是由于硅胶上的小孔对酶分子具有体积排除作用。     

Dual binding modes of Congo red to amyloid protofibril surface observed in molecular dynamics simulations

Congo red has been used to identify amyloid fibrils in tissues for more than 80 years and is also a weak inhibitor to both amyloid-beta fibril formation and toxicity. However, the specificity of the binding and its inhibition mechanism remain unclear. Using all-atom molecular dynamics simulations with the explicit solvent model, we have identified and characterized two specific binding modes of Congo red molecules to a protofibril formed by an amyloidogenic fragment (GNNQQNY) of the yeast prion protein Sup35. The observation of dual-mode was consistent with the experimentally observed dual-mode binding to Abeta fibrils by a series of compounds similar to Congo red. In the primary mode, Congo red bound to a regular groove formed by the first three residues (GNN) of the beta-strands along the beta-sheet extension direction. Comparative simulations demonstrated that Thioflavin T also bound to the grooves on KLVFFAE protofibril surface. Because of the ubiquitous long grooves on the amyloid fibril surface, we propose that this binding interaction could be a general recognition mode of amyloid fibrils by Congo red, Thioflavin T, and other long flat molecules. In the secondary mode, Congo red bound parallel to the beta-strands on the edge or in the middle of a beta-sheet. The primary binding mode of Congo red and GNNQQNY protofibril was more stable than the secondary mode by -5.7 kcal/mol as estimated by the MM-GBSA method. Detailed analysis suggests that the hydrophobic interactions play important roles for burial of the hydrophobic part of the Congo red molecules. Two potential inhibition mechanisms of disrupting beta-sheet stacking were inferred from the primary mode, which could be exploited for the development of non-peptidic amyloid-specific inhibitors.     

Increasing sensitivity and decreasing spot size using an inexpensive, removable hydrophobic coating for matrix-assisted laser desorption/ionisation plates

Spot size reduction and increased detection sensitivity in matrix-assisted laser desorption/ionisation (MALDI) of small molecules are accomplished by using an inexpensive and removable hydrophobic coating for MALDI targets, based on 3M Scotch Gard surface treatment. Several variations in sample preparation were explored, such as surface coating technique, identity of the matrix, solvent composition, and the type of metal support plate used. These were investigated on both uncoated and coated surfaces and their impact on spot size, crystal coverage, and sensitivity is presented here. Additionally, crystallisation behaviour obtained on coated plates is compared with that on uncoated plates using scanning electron microscope analysis. To demonstrate the potential of the new coating technique, erythromycin A and valinomycin are studied to determine the increase in detection sensitivity of coated plates in comparison to uncoated plates, and to reveal the suitability of the plates for application in combined high-performance liquid chromatography/MALDI (HPLC/MALDI), where widely varying solvent compositions and droplet volumes are observed. It is shown that enhancements in detection sensitivities correlate very well with the achieved spot size reduction. The versatility of the coated plates is also exhibited by the ease of removing the surface layer, after which the plates can be rigorously cleaned without worry about damaging the hydrophobic surface, followed by a quick reapplication of new hydrophobic coating material. This makes the non-polar coating superior to more expensive commercial hydrophobic-coated targets, which are much more delicate to clean. Furthermore, cleaning and reapplication eliminate potential carry-over effects and the easy application procedure also makes the fabrication of inexpensive, disposable MALDI targets readily possible.