Water’s contribution in providing strong solvent-induced forces in protein folding

It is commonly accepted that water plays an essential role in determining both the stability of the 3D structure of protein, as well as speed of the protein folding process. How exactly water does that, is still very controversial. Until recently it was believed that various hydrophobic effects, which originate from the solvent, are the dominant factors. In the first part of this article we discuss the paradigm shift from hydrophobic (H?O), to a hydrophilic (H?I) based theory of protein folding. Next, we analyze the types of solvent-induced forces that are exerted on various groups on the protein. We find that the H?I–H?I solvent-induced forces are likely to be the strongest. These forces originate from water molecules forming hydrogen-bonded-bridges between two, or more hydrophilic groups attached to the protein. Therefore, it is argued that these forces are also the forces that force the protein to fold, in a short time, along a narrow range of pathways. This paradigm shift brings us, as close as we can hope for, to a solution to the general problem of protein folding.     

Nanodroplets on rough hydrophilic and hydrophobic surfaces

We present results of Molecular Dynamics (MD) calculations on the behavior of liquid nanodroplets on rough hydrophobic and hydrophilic solid surfaces. On hydrophobic surfaces, the contact angle for nanodroplets depends strongly on the root-mean-square roughness amplitude, but it is nearly independent of the fractal dimension of the surface. Since increasing the fractal dimension increases the short-wavelength roughness, while the long-wavelength roughness is almost unchanged, we conclude that for hydrophobic interactions the short-wavelength (atomistic) roughness is not very important. We show that the nanodroplet is in a Cassie-like state. For rough hydrophobic surfaces, there is no contact angle hysteresis due to strong thermal fluctuations, which occur at the liquid-solid interface on the nanoscale. On hydrophilic surfaces, however, there is strong contact angle hysteresis due to higher energy barrier. These findings may be very important for the development of artificially biomimetic superhydrophobic surfaces.     

理解和应用疏水相互作用的尺度依赖原理

Lum,Chandler 和Week 三人建立起来的尺度依赖的疏水相互作用理论为人们提供了一个 重要的理论框架（LCW 理论）去理解和进一步研究与疏水相互作用相关的现象。按照LCW 理 论,当一个疏水粒子的半径小于1 纳米,它的疏水水合自由能与其半径的三次方成线性关系;而当 一个疏水粒子的半径大于1 纳米,它的疏水水合自由能与其半径的二次方成线性关系。1 纳米是一 个较为普适的转变半径。小于这个尺度,水合的热力学过程是由熵主导的,大于这个尺度,水合的 热力学过程是由焓主导的。在这篇综述里,我们介绍了温度,压强和水里面的添加物对疏水水合自 由能的影响。在实验上,我们对基于原子力显微镜的单分子力谱方法研究疏水高分子水合能作了重 点介绍。同时,对这一理论在蛋白质折叠和膜组装等体系中的应用也做了介绍。     

Fractal protein structure revisited: Topological, kinetic and thermodynamic relationships

The present work explored the definitions and calculations of fractal dimensions in protein structures and the corresponding relationships with the protein class, secondary structure contents, fold type as well as kinetic and thermodynamic parameters like the folding and unfolding rate, the folding–unfolding free energy and others. The results showed a positive correlation of some fractal exponents with the kinetic and thermodynamic variables even considering the effect of the protein length. On the other hand the influences of secondary structures types, especially the turn conformation are significant as well as the fractal exponent profiles according to class and fold types.     

Scale-dependent nature of the surface fractal dimension for bi- and multi-disperse porous solids by mercury porosimetry

The surface fractal dimension was calculated by using a mathematical model and mercury intrusion data for a variety of bi- and multi-disperse porous solids including silica gels, alumina pellets, and building stones. The mathematical model was obtained by modifying the well-established scaling relation published previously [Ind. Eng. Chem. Res., 34 (1995) 1383-1386]. It was also verified by comparing with the theoretical surface fractal dimensions for regular fractal structures (Skerpinski tetrahedron and Menger sponge) and the calculated surface fractal dimensions for silica gel and alumina particles via the linear fitting method established previously. The calculation results for various bi- and multi-disperse porous solids have demonstrated that the scale-dependent nature of the surface fractal dimension is ubiquitous. The difference in the surface fractal dimension between pore size intervals usually exists. The estimation of the surface fractal dimension on an average stand may lead to erroneous results.     

高温壁面润湿性对气层稳定性及其壁面滑移性能的分子动力学研究

针对流体在纳米通道的小尺度效应,采用分子动力学方法模拟了传热效应以及流体流动行为,研究在壁面温度影响下,不同润湿性壁面上方气层生成状态以及流体流动时气层的稳定特性和相应的减阻性能.结果表明:当壁面为纯疏水壁面时,不能形成气层;疏水基底+亲水组合壁面形成不规则气层;纯亲水壁面和亲水基底+疏水组合壁面能形成规则气层.当流体流动时,疏水基底+亲水组合壁面气层消失,而纯亲水壁面和亲水基底+疏水组合壁面气层较为稳定.纯疏水壁面主流区域速度较大,而纯亲水壁面主流区域最低.对于壁面滑移速度,存在气层的壁面滑移速度与纯疏水表面相对接近,甚至稍优于纯属疏水表面,而疏水基底+亲水组合壁面滑移速度最小.     

Magnetic hydrophobic nanocomposites: Silica aerogel/maghemite

Magnetic hydrophobic aerogels (MHA) in the form of nanocomposites of silica and maghemite (γ-Fe₂O₃) were prepared by one step sol–gel procedure followed by supercritical solvent extraction. Silica alcogels were obtained from TEOS, MTMS, methanol and H₂O, and Fe(III) nitrate as magnetic precursor. The hydrophobic property was achieved using the methytrimethoxysilane (MTMS) as co-precursor for surface modification. The so produced nanocomposite aerogels are monolithic, hydrophobic and magnetic. The interconnected porous structure hosts ∼6 nm size γ-Fe₂O₃ particles, has a mean pore diameter of 5 nm, and a specific surface area (SSA) of 698 m²/g. Medium range structure of MHA is determined by SAXS, which displays the typical fractal power law behavior with primary particle radius of ∼1 nm. Magnetic properties of the nanoparticle ensembles hosted in them are studied by means of dc-magnetometry.     

A Monte Carlo method for simulating fractal surfaces

A Monte Carlo method is presented for simulating rough surfaces with the fractal behavior. The simulation is based on power-law size distribution of asperity diameter and self-affine property of roughness on surfaces. A probability model based on random number for asperity sizes is developed to generate the surfaces. By iteration, this method can be used to simulate surfaces that exhibit the aforementioned properties. The results indicate that the variation of the surface topography is related to the effects of scaling constant G and the fractal dimension D of the profile of rough surface. The larger value of D or smaller value of G signifies the smoother surface topography. This method may have the potential in prediction of the transport properties (such as friction, wear, lubrication, permeability and thermal or electrical conductivity, etc.) on rough surfaces.     

Moisture diffusivity in structure of random fractal fiber bed

A theoretical expression related to effective moisture diffusivity to random fiber bed is derived by using fractal theory and considering both parallel and perpendicular channels to diffusion flow direction. In this Letter, macroporous structure of hydrophobic nonwoven material is investigated, and Knudsen diffusion and surface diffusion are neglected. The effective moisture diffusivity predicted by the present fractal model are compared with water vapor transfer rate (WVTR) experiment data and calculated values obtained from other theoretical models. This verifies the validity of the present fractal diffusivity of fibrous structural beds.     

A study of Barstar folding events using boundary value simulations

From extensive biophysical studies of protein folding, two competing mechanisms emerged: hydrophobic collapse and the framework model. Our protein of choice is Barstar—a barnase inhibitor. The approximation algorithm we used to study Barstar folding trajectories is called SDEL—stochastic difference equation in length. Using the native structure as the final boundary value and a collection of unfolded structures as the varying initial boundary value, SDEL calculates an ensemble of least action pathways between these boundaries. The results are atomically detailed folding pathways, with as many intermediate structures as you request in the input. We generated 12 pathways, starting from a structurally wide selection of unfolded conformations. Using the protein's radius of gyration as our primary reaction coordinate, we tracked H-bonds, dihedral angles, native and non-native contacts, and energy along the folding pathways. This paper will follow our findings, with special emphasis on pinpointing hydrophobic collapse as a more appropriate mechanism for Barstar. Comparison with pathway predictions for Barstar using experimental techniques will also be discussed.     

Intricate packing in the hydrophobic core of barstar through a CH–π interaction

Identification of specific packing interactions within in the hydrophobic core of proteins is important for understanding the integrity of protein structure. Finding such interactions is challenging because few tools allow monitoring of a specific interaction in the presence of several non‐specific forces that hold proteins together. It is important to understand how and when such interactions develop during protein folding. In this study, we have used the intrinsic tryptophan residue, Trp53, as an ultraviolet resonance Raman probe to elucidate the packing interactions in the hydrophobic core of the protein barstar. Barstar is extensively studied for its folding, unfolding and aggregation properties. The Trp53 residue is known to be completely buried in the hydrophobic core of the protein and is used extensively as an intrinsic probe to monitor the folding and unfolding reactions of barstar. A comparison of the resonance Raman cross sections of some bands of Trp53 with those observed for N‐acetyl‐tryptophanoamide in water suggests that Trp53 in barstar is indeed isolated from water. Intensity ratio of the Fermi doublet suggests that Trp53 is surrounded by several aliphatic amino acid residues in corroboration with the crystal structure of barstar. Importantly, we show that the side chain of Trp53 is involved in a unique CH–π interaction with CH groups of Phe56 as well as a steric interaction with the methyl group of Ile5. Copyright © 2014 John Wiley & Sons, Ltd.     

Small-angle neutron scattering at fractal objects

The calculation of the correlation function of an isotropic fractal particle with the finite size ξ and the dimension D is presented. It is shown that the correlation function γ(r) of volume and surface fractals is described by a generalized expression and is proportional to the Macdonald function (D–3)/2 of the second order multiplied by the power function r ^(D–3)/2. For volume and surface fractals, the asymptotics of the correlation function at the limit r/ξ < 1 coincides with the corresponding correlation functions of unlimited fractals. The one-dimensional correlation function G(z), which, for an isotropic fractal particle, is described by an analogous expression with a shift of the index of the Macdonald function and the exponent of the power function by 1/2, is measured using spin-echo small-angle neutron scattering. The boundary case of the transition from a volume to a surface fractal corresponding to the cubic dependence of the neutron scattering cross section Q ^?3 leads to an exact analytical expression for the one-dimensional correlation function G(z) = exp(?z/ξ), and the asymptotics of the correlation function in the range of fractal behavior for r/ξ < 1 is proportional to ln(ξ/r). This corresponds to a special type of self-similarity with the additive law of scaling rather than the multiplicative one, as in the case of a volume fractal.     

Survival of Virus Particles in Water Droplets: Hydrophobic Forces and Landauer’s Principle

Many small biological objects, such as viruses, survive in a water environment and cannot remain active in dry air without condensation of water vapor. From a physical point of view, these objects belong to the mesoscale, where small thermal fluctuations with the characteristic kinetic energy of k_BT (where k_B is the Boltzmann’s constant and T is the absolute temperature) play a significant role. The self-assembly of viruses, including protein folding and the formation of a protein capsid and lipid bilayer membrane, is controlled by hydrophobic forces (i.e., the repulsing forces between hydrophobic particles and regions of molecules) in a water environment. Hydrophobic forces are entropic, and they are driven by a system’s tendency to attain the maximum disordered state. On the other hand, in information systems, entropic forces are responsible for erasing information, if the energy barrier between two states of a switch is on the order of k_BT, which is referred to as Landauer’s principle. We treated hydrophobic interactions responsible for the self-assembly of viruses as an information-processing mechanism. We further showed a similarity of these submicron-scale processes with the self-assembly in colloidal crystals, droplet clusters, and liquid marbles.     

Monte Carlo simulation to study surface diffusion and reaction processes on a fractal catalyst

The surface of a catalyst is a fractal, and its fractal dimension can strongly influence the performance of a catalytic reaction. By means of the Monte Carlo method, the decompositions of N₂O on a square lattice and a fractal surface are investigated in this paper. From the simulation it is found that the fractal surface can change both the reaction rate constant K and the reaction order α in the N₂O decomposition, and all of these changes are caused by the abnormal diffusion of the surface species on the fractal surface.     

Real-space visualization of intercalated water phases at the hydrophobic graphene interface with atomic force microscopy

The phase behavior of water is a topic of perpetual interest due to its reinai kable anomalous properties and importance to biology,material science,geoscience,nanoscience,etc.It is predicted confined water at interface can exist in large amounts of crystalline or amorphous states.However,the experimental evidence of coexistence of liquid water phases at interface is still insufficient.Here,a special folding few-layers graphene film was elaborate prepared to form a hydrophobic/hydrophobic interface,which can provide a suited platform to study the structure and properties of confined liquid water.The real-space visualization of intercalated water layers phases at the folding interface is obtained using advanced atomic force microscopy(AFM).The folding graphene interface displays complicated internal interfacial characteristics.The intercalated water molecules present themselves as two phases,low-density liquid(LDL,solid-like)and high-density liquid(HDL,liquid-like),according to their specific mechanical properties taken in two multifrequency-AFM(MF-AFM)modes.Furthermore,the water molecules structural evolution is demonstrated in a series of continuous MF-AFM measurements.The work preliminary confirms the existence of two liquid phases of water in real space and will inspire further experimental work to deeply understanding their liquid dynamics behavior.     

Adhesion between an elastic body and a randomly rough hard surface

I have developed a theory of adhesion between an elastic solid and a hard randomly rough substrate. The theory takes into account that partial contact may occur between the solids on all length scales. I present numerical results for the case where the substrate surface is self-affine fractal. When the fractal dimension is close to 2, complete contact typically occurs in the macro-asperity contact areas, while when the fractal dimension is larger than 2.5, the area of (apparent) contact decreases continuously when the magnification is increased. An important result is that even when the surface roughness is so high that no adhesion can be detected in a pull-off experiment, the area of real contact (when adhesion is included) may still be several times larger than when the adhesion is neglected. Since it is the area of real contact which determines the sliding friction force, the adhesion interaction may strongly affect the friction force even when no adhesion can be detected in a pull-off experiment. Received 3 April 2002     

Nanoscale aggregation phenomena at the contact line of air-drying pure water droplets on silicon revealed by atomic force microscopy

In the present work, silicon wafer surfaces were studied during a pure water dewetting process in ambient conditions by intermittent-contact atomic force microscopy (AFM). With an acid-free surface cleaning, large network structures of tens of microns in extension but only a few nanometers in height were observed, being stable for days. Fractal-like assemblies have been previously reported in a variety of different scenarios, for example, when an aqueous solution of carbon-based species, especially carbon nanotubes, is left to evaporate on a solid substrate, provided that no complete wetting was produced. Chemical mapping of silicon wafer surfaces, while unable to provide a spatial resolution comparable to that of the AFM, clearly showed the initially formed contact line to be enriched in carbon. Therefore, hydrophobic and/or non-soluble (or slightly soluble) substances which are present on every surface exposed to air are expected to be responsible for the observed fractal structures. Reactions of the network structures toward changing environmental conditions were analyzed. When increasing the ambient humidity, the structures grew only slightly, which is indicative of their highly (but not totally) hydrophobic nature. Heating the sample above 100 °C for about 10 h led to an almost complete disappearance of these nanostructures. Due to the lateral extension of these stable network heterogeneities, they are expected to affect contact angle measurements in wetting studies, especially at the micro- and nanoscale. When acid-cleaned wafers are used as substrate, deposited water extends as a film over the silicon surface without droplet formation. No fractal structures are then observed.     

Adhesion between elastic bodies with randomly rough surfaces

I have developed a theory of adhesion between an elastic solid and a hard randomly rough substrate. The theory takes into account the fact that partial contact may occur between the solids on all length scales. I present numerical results for the case where the substrate surface is self-affine fractal. When the fractal dimension is close to 2, complete contact typically occurs in the macroasperity contact areas. For a fractal dimension larger than 2.5, the area of (apparent) contact decreases continuously when the magnification is increased.