In Silico Modeling of the Influence of Environment on Amyloid Folding Using FOD-M Model

The role of the environment in amyloid formation based on the fuzzy oil drop model (FOD) is discussed here. This model assumes that the hydrophobicity distribution within a globular protein is consistent with a 3D Gaussian (3DG) distribution. Such a distribution is interpreted as the idealized effect of the presence of a polar solvent—water. A chain with a sequence of amino acids (which are bipolar molecules) determined by evolution recreates a micelle-like structure with varying accuracy. The membrane, which is a specific environment with opposite characteristics to the polar aquatic environment, directs the hydrophobic residues towards the surface. The modification of the FOD model to the FOD-M form takes into account the specificity of the cell membrane. It consists in “inverting” the 3DG distribution (complementing the Gaussian distribution), which expresses the exposure of hydrophobic residues on the surface. It turns out that the influence of the environment for any protein (soluble or membrane-anchored) is the result of a consensus factor expressing the participation of the polar environment and the “inverted” environment. The ratio between the proportion of the aqueous and the “reversed” environment turns out to be a characteristic property of a given protein, including amyloid protein in particular. The structure of amyloid proteins has been characterized in the context of prion, intrinsically disordered, and other non-complexing proteins to cover a wider spectrum of molecules with the given characteristics based on the FOD-M model.     

Model of Environmental Membrane Field for Transmembrane Proteins

The water environment determines the activity of biological processes. The role of such an environment interpreted in the form of an external field expressed by the 3D Gaussian distribution in the fuzzy oil drop model directs the folding process towards the generation of a centrally located hydrophobic core with the simultaneous exposure of polar residues on the surface. In addition to proteins soluble in the water environment, there is a significant group of membrane proteins that act as receptors or channels, including ion channels in particular. The change of the polar (water) environment into a highly hydrophobic (membrane) environment is quite radical, resulting in a different hydrophobicity distribution within the membrane protein. Modification of the notation of the force field expressing the presence of the hydrophobic environment has been proposed in this work. A modified fuzzy oil drop model with its adaptation to membrane proteins was used to interpret the structure of membrane proteins–mechanosensitive channel. The modified model was also used to describe the so-called negative cases—i.e., for water-soluble proteins with a clear distribution consistent with the fuzzy oil drop model.     

Chaperonin Structure �C The Large Multi-Subunit Protein Complex

The multi sub-unit protein structure representing the chaperonins group is analyzed with respect to its hydrophobicity distribution. The proteins of this group assist protein folding supported by ATP. The specific axial symmetry GroEL structure (two rings of seven units stacked back to back - 524 aa each) and the GroES (single ring of seven units - 97 aa each) polypeptide chains are analyzed using the hydrophobicity distribution expressed as excess/deficiency all over the molecule to search for structure-to-function relationships. The empirically observed distribution of hydrophobic residues is confronted with the theoretical one representing the idealized hydrophobic core with hydrophilic residues exposure on the surface. The observed discrepancy between these two distributions seems to be aim-oriented, determining the structure-to-function relation. The hydrophobic force field structure generated by the chaperonin capsule is presented. Its possible influence on substrate folding is suggested.     

On the Dependence of Prion and Amyloid Structure on the Folding Environment

Currently available analyses of amyloid proteins reveal the necessity of the existence of radical structural changes in amyloid transformation processes. The analysis carried out in this paper based on the model called fuzzy oil drop (FOD) and its modified form (FOD-M) allows quantifying the role of the environment, particularly including the aquatic environment. The starting point and basis for the present presentation is the statement about the presence of two fundamentally different methods of organizing polypeptides into ordered conformations—globular proteins and amyloids. The present study shows the source of the differences between these two paths resulting from the specificity of the external force field coming from the environment, including the aquatic and hydrophobic one. The water environment expressed in the fuzzy oil drop model using the 3D Gauss function directs the folding process towards the construction of a micelle-like system with a hydrophobic core in the central part and the exposure of polarity on the surface. The hydrophobicity distribution of membrane proteins has the opposite characteristic: Exposure of hydrophobicity at the surface of the membrane protein with an often polar center (as in the case of ion channels) is expected. The structure of most proteins is influenced by a more or less modified force field generated by water through the appropriate presence of a non-polar (membrane-like) environment. The determination of the proportion of a factor different from polar water enables the assessment of the protein status by indicating factors favoring the structure it represents.     

High-resolution X-ray analysis reveals binding of arginine to aromatic residues of lysozyme surface: implication of suppression of protein aggregation by arginine

While biotechnological applications of arginine (Arg) as a solution additive that prevents protein aggregation are increasing, the molecular mechanism of its effects remains unclear. In this study, we investigated the Arg-lysozyme complex by high-resolution crystallographic analysis. Three Arg molecules were observed to be in close proximity to aromatic amino acid residues of the protein surface, and their occupancies gradually increased with increasing Arg concentration. These interactions were mediated by electrostatic, hydrophobic and cation-π interactions with the surface residues. The binding of Arg decreased the accessible surface area of aromatic residues by 40%, but increased that of charged residues by 10%. These changes might prevent intermolecular hydrophobic interactions by shielding hydrophobic regions of the lysozyme surface, resulting in an increase in protein solubility.     

环境对改性塑料表面亲/疏水转变的作用机制

塑料制品因其质量轻、性质稳定等优点而得到广泛使用,但大部分废旧塑料未被合理回收而成为污染物,对环境造成了危害。因此,废旧塑料回收、再加工成为保护环境和资源利用的有效途径。而分离是废旧塑料能进行再加工的重要环节,目前已经发展了丰富的分离方法,其中塑料浮选法因具有工艺简单、污染少的特点而受到人们的青睐。但在塑料浮选中,其表面亲疏水性受环境的影响,该过程进一步恶化分离效果。为了避免分离过程的波动性,急需探究环境因素对亲疏水性的作用。基于此,本文选取了ABS、PC、PS三种废旧塑料,探究环境对浮选分离及表面亲疏水性基团重构的影响。结果表明：氧化改性后的ABS、PC、PS处于极性环境时,塑料可浮性基本未发生改变,接触角发生轻微浮动,表面仍保持亲水性。处于乙醇环境中,塑料可浮性上升,其接触角上升至75°左右,表面疏水性恢复速度大于极性环境。而在非极性环境中,塑料可浮性上升速度较快,表面完全恢复为未改性前的疏水性。在极性环境中,亲水基团更容易停留在表面,随着极性的减小,亲水基团逐渐迁移至本体,塑料表面恢复为疏水。因此,极性环境更有利于塑料表面保持亲水性。     

全原子分子动力学模拟反相色谱分离细胞色素C的过程

采用全原子分子动力学方法模拟了反相色谱分离蛋白质的吸附和洗脱过程。采用表面键合C4烷基链的硅胶基质作为反相色谱介质和细胞色素C作为蛋白质模型,模拟蛋白质在反相色谱分离过程中的构象变化。结果显示:在吸附过程中,蛋白质在释放出表面结合水分子的同时置换出色谱介质表面的水分子。与其在溶液中的天然构象相比,吸附态蛋白质的构象发生改变。在洗脱过程中,随着溶剂从水切换到甲醇,甲醇取代水分子包覆在介质和蛋白质表面,将蛋白质从介质表面置换下来。分子模拟的结果再现了有关反相色谱"优先水化"的吸附机制,并从分子水平上展现了吸附和洗脱过程中蛋白质、色谱介质和溶剂之间相互作用,对反相色谱介质设计和过程优化提供了参考。     

Hydrophobic regions on protein surfaces: definition based on hydration shell structure and a quick method for their computation

The hydrophobic part of the solvent-accessible surface of atypical monomeric globular protein consists of a single, largeinterconnected region formed from faces of apolar atoms andconstituting –60% of the solvent-accessible surface area.Therefore, the direct delineation of the hydrophobic surfacepatches on an atom-wise basis is impossible. Experimental dataindicate that, in a two-state hydration model, a protein canbe considered to be unified with its first hydration shell inits interaction with bulk water. We show that, if the surfacearea occupied by water molecules bound at polar protein atomsas generated by AUTOSOL is removed, only about two-thirds ofthe hydrophobic part of the protein surface remains accessibleto bulk solvent. Moreover, the organization of the hydrophobicpart of the solvent-accessible surface experiences a drasticchange, such that the single interconnected hydrophobic regiondisintegrates into many smaller patches, i.e. the physical definitionof a hydrophobic surface region as unoccupied by first hydrationshell water molecules can distinguish between hydrophobic surfaceclusters and small interconnecting channels. It is these remaininghydrophobic surface pieces that probably play an important rolein intraand intermolecular recognition processes such as ligandbinding, protein folding and protein–protein associationin solution conditions. These observations have led to the developmentof an accurate and quick analytical technique for the automaticdetermination of hydrophobic surface patches of proteins. Thistechnique is not aggravated by the limiting assumptions of themethods for generating explicit water hydration positions. Formationof the hydrophobic surface regions owing to the structure ofthe first hydration shell can be computationally simulated bya small radial increment in solvent-accessible polar atoms,followed by calculation of the remaining exposed hydrophobicpatches. We demonstrate that a radial increase of 0.35–0.50Å resembles the effect of tightly bound water on the organizationof the hydrophobic part of the solvent-accessible surface.     

Structure-function analysis of a conserved aromatic cluster in the N- terminal domain of human epidermal growth factor

The importance of a cluster of conserved aromatic residues of human epidermal growth factor (hEGF) to the receptor binding epitope is suggested by the interaction of His10 and Tyr13 of the A-loop with Tyr22 and Tyr29 of the N-terminal beta-sheet to form a hydrophobic surface on the hEGF protein. Indeed, Tyr13 has previously been shown to contribute a hydrophobic determinant to receptor binding. The roles of His10, Tyr22 and Tyr29 were investigated by structure-function analysis of hEGF mutant analogues containing individual replacements of each residue. Substitutions with aromatic residues or a leucine at position 10 retained receptor affinities and agonist activities similar to wild- type indicating that an aromatic residue is not essential. Variants with polar, charged or aliphatic substitutions altered in size and/or hydrophobicity exhibited reduced binding and agonist activities. 1- Dimensional 1H NMR spectra of high, moderate and low-affinity analogues at position 10 suggested only minor alterations in hEGF native structure. In contrast, a variety of replacements were tolerated at position 22 or 29 indicating that neither aromaticity nor hydrophobicity of Tyr22 and Tyr29 is required for receptor binding. CD spectra of mutant analogues at position 22 or 29 indicated a correlation between loss of receptor affinity and alterations in hEGF structure. The results indicate that similar to Tyr13, His10 of hEGF contributes hydrophobicity to the receptor binding epitope, whereas Tyr22 and Tyr29 do not appear to be directly involved in receptor interactions. The latter conclusion, together with previous studies, suggests that hydrophobic residues on only one face of the N-terminal beta-sheet of hEGF are important in receptor recognition.      

Overlimiting mass transfer through cation-exchange membranes modified by Nafion film and carbon nanotubes

Eight cation-exchange membranes different in the surface morphology and the degree of hydrophobicity were studied by contact angle, voltammetry and mass transfer rate measurements. One series of membranes was prepared starting from heterogeneous MK-40 membranes, and another, from homogeneous Nafion? 117 membranes. Coating a membrane with a thin film of Nafion resulted in increasing surface hydrophobicity, while the doping of the Nafion surface film with carbon nanotubes (CNT) led to an unexpected decrease in hydrophobicity. It was found however that after 100 h operation of a Nafion? 117 membrane coated with a Nafion film doped with CNT, the contact angle increased from 51 to 81°. This increase in the surface hydrophobicity was accompanied by a significant rise in overlimiting transfer rate, more than 1.5 times, under the same voltage. High correlation between the overlimiting mass transfer rate and the degree of hydrophobicity was observed also in all studied cases: more hydrophobic surface leads to a higher mass transfer rate. The effect is explained by increasing electroconvection occurring as electroosmosis of the second kind: the slip of water over a hydrophobic surface enhances the tangential velocity of electroconvective vortex having its maximum at a distance of several hundreds of nm from the surface.     

Entropy-Enthalpy Compensations Fold Proteins in Precise Ways

Exploring the protein-folding problem has been a longstanding challenge in molecular biology and biophysics. Intramolecular hydrogen (H)-bonds play an extremely important role in stabilizing protein structures. To form these intramolecular H-bonds, nascent unfolded polypeptide chains need to escape from hydrogen bonding with surrounding polar water molecules under the solution conditions that require entropy-enthalpy compensations, according to the Gibbs free energy equation and the change in enthalpy. Here, by analyzing the spatial layout of the side-chains of amino acid residues in experimentally determined protein structures, we reveal a protein-folding mechanism based on the entropy-enthalpy compensations that initially driven by laterally hydrophobic collapse among the side-chains of adjacent residues in the sequences of unfolded protein chains. This hydrophobic collapse promotes the formation of the H-bonds within the polypeptide backbone structures through the entropy-enthalpy compensation mechanism, enabling secondary structures and tertiary structures to fold reproducibly following explicit physical folding codes and forces. The temperature dependence of protein folding is thus attributed to the environment dependence of the conformational Gibbs free energy equation. The folding codes and forces in the amino acid sequence that dictate the formation of β-strands and α-helices can be deciphered with great accuracy through evaluation of the hydrophobic interactions among neighboring side-chains of an unfolded polypeptide from a β-strand-like thermodynamic metastable state. The folding of protein quaternary structures is found to be guided by the entropy-enthalpy compensations in between the docking sites of protein subunits according to the Gibbs free energy equation that is verified by bioinformatics analyses of a dozen structures of dimers. Protein folding is therefore guided by multistage entropy-enthalpy compensations of the system of polypeptide chains and water molecules under the solution conditions.     

Controlled preparation of nanocolorants via a modified miniemulsion polymerization process

Nanocolorants were successfully prepared via a modified miniemulsion polymerization process into which styrene, a polar monomer, crosslinkers, a highly hydrophobic solvent, dyes, and so forth were introduced. The obtained nanocolorants were nanocomposite entities in which a fraction of dye molecules attached to the crosslinked macromolecular chains and more dye molecules formed clustering because of the phase separation between the dye and polymer during the polymerization process and were further embedded in the interior of the crosslinked polymer because of the high hydrophobicity of the dyes. The effects of the polar monomers, the amounts of the dyes dissolved in styrene, and the polymer crosslinking, as well as the effects of the water‐soluble and oil‐soluble initiator, the amount of the surfactant, and the ultrasonic homogenization time, on the preserving fastness of the dyes in the polymeric matrix and the morphology and particle size distribution of the nanocolorants were studied. © 2007 Wiley Periodicals, Inc. J Appl Polym Sci 2007     

Effect of crosslinking density on the physical properties of interpenetrating polymer networks of polyurethane and 2-hydroxyethyl methacrylate-teminated polyurethane

Interpenetrating polymer networks (IPNs) of 2-hydroxyethyl methacrylate-terminated polyurethane (HPU) and polyurethane (PU) with different crosslinking densities of the PU network were prepared by simultaneous solution polymerization. Dynamic mechanical analysis (DMA) and differential scanning calorimetry (DSC) show that compatibility of component polymers in IPN formation depends on the crosslinking density of the PU network. Physical properties such as density and water absorption rely on the subtle balance between the degree of phase separation and the crosslinking density of the PU network. In spite of the occurrence of phase separation, the tensile moduli and tensile strength of the IPNs increase with the crosslinking density of the PU network. Morphological observation by scanning electron microscopy revealed different fracture surfaces between the compatible and incompatible IPNs. Surface characteristics of the IPNs, indicated as hydrogen bonding index and hard-to-soft segment ratio, are altered considerably by varying surface morphologies. Improved blood compatibility of IPN membranes is due to the variation of the hydrophilic and hydrophobic domain distribution.     

Biocidal activity of cellulose materials for medical implants

Surface wettability trends, and blood component adhesion of some cellulose acetate phthalate/hydroxypropyl cellulose blend films are analyzed in view of adapting the system to biomedical applications. The results show that intermediate blend compositions of the corresponding films influence the surface tension parameters—controlled by the interactions occurring in the system. Increasing hydrophobicity and, implicitly, decreasing the polar surface tension components, are correlated with the adhesion/cohesion of blood components and plasma proteins. Thus, the work of spreading proteins on the hydrophobic blend surfaces indicated that albumin is not absorbed preferentially, while fibrinogen is characterized by a higher degree of adhesion on the surfaces, and also that selective adsorption of plasma proteins modifies blood compatibility. In addition, the obtained results and the ascertained antimicrobial activity of the studied blends contribute to the development of new applications in the biomedical field. © 2015 Wiley Periodicals, Inc. J. Appl. Polym. Sci. 2015 , 132, 41932     

Effect of corona discharge on the stability of the adhesion of thin silicone-organic coating to polyamide fiber surface made by the sol–gel method

This paper presents the effect of pretreatment of polyamide (PA6) nonwoven with corona discharge on the stability of the adhesion of thin hydrophobic silicone-organic coating based on vinyltriethoxysilane, made by the sol–gel method. This pretreatment with corona discharge causes a change in the physicochemical properties of the PA6 fiber surface. These changes include, among others, an increase in the fiber surface roughness, wettability, and surface free energy. At the same time, XPS and EDS investigations have shown an increase in the degree of oxidation and the formation of functional polar groups on the fiber surface (C–O–, C–OH, and O=C–O–). As a result of the changes in the surface properties of pretreated PA6 fibers, a higher degree of the sol deposition was obtained compared with that for untreated nonwoven surface. The assessment of the stability of the adhesion of thin hydrophobic coating to the fiber surface was carried out on the basis of changes in the content of silica deposited on fibers and the kinetics of water contact angle after washing and abrasion processes. In the end, the PA6 nonwoven, pretreated with corona discharge, shows a higher stability of the adherence of the thin silicone-organic coating and a higher degree of hydrophobicity than the untreated nonwoven.     

Local polarity analysis: a sensitive method that discriminates between native proteins and incorrectly folded models

The evaluation of calculated protein structures is an importantstep in the protein design cycle. Known criteria for this assessmentof proteins are the polar and apolar, accessible and buriedsurface area, electrostatic interactions and other interactionsbetween the protein atoms (e.g. HO, S-S),atomic packing, analysisof amino acid environment and surface charge distribution. Weshow that a powerful test of accuracy of protein structure canbe derived by analysing the water contact of atoms and additionallytaking into account their polarity. On the basis of estimatedreference values of the polar fraction of typical globular proteinswith known structure (mean, SD and distribution), the evaluationof misfolded structures can be improved significantly. The referencevalues are derived by moving windows of different length (3–99amino acid residues) over the amino acid sequence. Model proteins,which are included in the Brookhaven protein structure databank,deliberately misfolded proteins, hypothetical proteins and predictedprotein structures are diagnosed as at least partially incorrectlyfolded. The local fault, mostly observed, is that polar groupsare buried too frequently in the interior of the protein. Thedatabase-derived quantities are useful in screening the designedproteins prior to experimentation and may also be useful inthe assessment of errors in the experimentally determined proteinstructures.     

天然矿石粉表面的氟烷烃处理对其表面疏水性的影响

表征了几种天然矿石粉粉末压实样品的疏水性,探索了氟碳表面处理剂对碳酸钙表面浸润性和表面能的影响。粉末表面的氟烷烃使材料与水的接触角增大,表面能各分量下降。     

Metabolically stable cellular adhesion to inert surfaces

The structure of D-amino acid hexapeptides that promote cellular adhesion was determined by screening D-amino acid hexapeptide libraries synthesized on otherwise inert beaded PEGA resin. These new adhesion molecules provide a completely stable cellular environment and facilitate the maintenance of a monolayer of cells on beads for extended periods. The presence of the peptides promotes spreading of the cells on the bead surface. Not surprisingly, the molecules contained a significant number of arginines and/or lysines. However, the exact structure of each peptide is quite important for the degree of adhesion observed, and a motif with three or four basic amino acids spaced within amino acids of intermediate polarity clearly prevailed, for example, k-l/r-h-r-i/v-r-a; this maintains a polar/hydrophobic balance.     

Hydrophobically Functionalized Chitosan Particles

Particles of chitosan have a very polar surface, and thus they are easily wetted by water and also dissolve in acidic media. The hydroxyl and amino groups offer a high potential for grafting reactions. Aldehydes and carbonic acid derivatives were covalently grafted, preferably onto the amino groups. The reactions were carried out in solution as homogeneous phase reactions as well as on the particle surfaces as heterogeneous phase reactions. Covalently bonded alkyl chains impart the chitosan molecules with hydrophobic properties. We employed different methods such as NMR, XPS, elemental analysis and FT-IR spectroscopy to study the reactions and to estimate the degree of functionalization. The wetting behavior of the particles was investigated by a modified Wilhelmy technique, where an adhesive tape completely coated with the particles was dipped in water. Some of the samples having a high degree of functionalization showed super-hydrophobic surface properties. The observed super-hydrophobic effect results from a combination of the hydrophobic properties of the modified particles and the roughness of the particle coating.