The meaning of hydrophobicity

Changes in Texture and Collagen Properties of Pork Skin during Salt-Enzyme-Alkali Tenderization Treatment

The effects of salt-enzyme-alkali progressive tenderization treatments on porcine cortical conformation and collagen properties were investigated, and their effectiveness and mechanisms were analyzed. The tenderization treatment comprised three treatment stages: CaCl2 (25 °C/0-30 min), papain (35 °C/30-78 min), and Na2CO3 (25 °C/78-120 min). The textural, microscopic, and collagenous properties (content, solubility, and structure) of pork skin were determined at the 0th, 30th, 60th, 90th, and 120th min of the treatment process. The results showed that the shear force, hardness, and chewability of the skin decreased significantly (p < 0.05), and the elasticity exhibited a gradual increase with the progression of tenderization. The content and solubility of collagen showed no significant change at the CaCl2 treatment stage. However, the soluble collagen content increased, the insoluble collagen content decreased, and the collagen solubility increased by 18.04% during the subsequent treatment with papain and Na2CO3. Meanwhile, the scanning electron microscopy results revealed that the regular, wavy structure of the pig skin collagen fibers gradually disappeared during the CaCl2 treatment stage, the overall structure revealed expansion, and the surface microscopic pores gradually increased during the papain and Na2CO3 treatment stages. The findings of the Fourier transform infrared spectroscopy analysis indicated that the hydrogen bonding interactions between the collagen molecules and the C=O, N-H and C-N bonds in the subunit structure of collagen were substantially altered during treatment and that the breakage of amino acid chains and reduction in structural ordering became more pronounced with prolonged treatment. In the tertiary structure, the maximum emission wavelength was blue-shifted and then red-shifted, and the fluorescence intensity was gradually weakened. The surface hydrophobicity was slowly increased. The salt-enzyme-alkali tenderization treatment considerably improved the physical properties and texture of edible pork skins by dissolving collagen fibers and destroying the structure of collagen and its interaction force.

Protection Mechanism of Metal Ion Pre-Stress on Lactobacillus acidophilus CICC 6074 under Acid Tolerance

The prerequisite for the probiotic effect of lactic acid bacteria is that they could survive the acid stress environment of production and application. In this experiment, the mechanism for the effect of different metal ion pre-stress on the acid-tolerant survival of Lactobacillus was investigated. Scanning electron microscopy, Fourier infrared spectroscopy, and flow cytometry were used to analyze the condition of bacteria after acid treatment, which revealed that different metal ion pre-stress could improve the survival ability of Lactobacillus acidophilus CICC 6074 under low acid conditions by improving cell morphology, mitigating cell membrane damage, and regulating surface protein expression. Furthermore, Tandem Mass Tags (TMT) proteomic analysis revealed that Mn2+ pre-stress showed relatively more superior protective effects on acid tolerance in L. acidophilus CICC 6074 through activation of DNA replication, RNA synthesis, S-layer protein secretion, H+-ATPase enzyme activity, etc. This study will provide new ideas and a theoretical basis for the development and application of lactic acid bacteria.

Water-mediated interactions destabilize proteins

Proteins are folded to avoid exposure of the nonpolar groups to water because water-mediated interactions between nonpolar groups are a promising factor in the thermodynamic stabilities of proteins-which is a well-accepted view as one of the unique effects of hydrophobic interactions. This article poses a critical question for this classical view by conducting an accurate solvation free-energy calculation for a thermodynamic cycle of a protein folding using a liquid-state density functional theory. Here, the solvation-free energy for a leucine zipper formation was examined in the coiled-coil protein GCN4-p1, a typical model for hydrophobic interactions, which demonstrated that water-mediated interactions were unfavorable for the association of nonpolar groups in the native state, while the dispersion forces between them were, instead, responsible for the association. Furthermore, the present analysis well predicted the isolated helical state stabilized by pressure, which was previously observed in an experiment. We reviewed the problems in the classical concept and semiempirical presumption that the energetic cost of the hydration of nonpolar groups is a driving force of folding.

In silico investigation of potential inhibitors to main protease and spike protein of SARS-CoV-2 in propolis

Docking analysis of propolis's natural compound was successfully performed against SARS-CoV-2 main protease (Mpro) and spike protein subunit 2 (S2). Initially, the propolis's protein was screened using chromatography analysis and successfully identified 22 compounds in the propolis. Four compounds were further investigated, i.e., neoblavaisoflavone, methylophiopogonone A, 3'-Methoxydaidzin, and genistin. The binding affinity of 3'-Methoxydaidzin was -7.7 kcal/mol, which is similar to nelfinavir (control), while the others were -7.6 kcal/mol. However, we found the key residue of Glu A:166 in the methylophiopogonone A and genistin, even though the predicted binding energy slightly higher than nelfinavir. In contrast, the predicted binding affinity of neoblavaisoflavone, methylophiopogonone A, 3'-Methoxydaidzin, and genistin against S2 were -8.1, -8.2, -8.3, and -8.3 kcal/mol, respectively, which is far below of the control (pravastatin, -7.3 kcal/mol). Instead of conventional hydrogen bonding, the π bonding influenced the binding affinity against S2. The results reveal that this is the first report about methylophiopogonone A, 3'-Methoxydaidzin, and genistin as candidates for anti-viral agents. Those compounds can then be further explored and used as a parent backbone molecule to develop a new supplementation for preventing SARS-CoV-2 infections during COVID-19 outbreaks.

Helix-Coil Transition at a Glycine Following a Nascent α-Helix: A Synergetic Guidance Mechanism for Helix Growth

A detailed understanding of forces guiding the rapid folding of a polypeptide from an apparently random coil state to an ordered α-helical structure following the rate-limiting preorganization of the initial three residue backbones into helical conformation is imperative to comprehending and regulating protein folding and for the rational design of biological mimetics. However, several details of this process are still unknown. First, although the helix-coil transition was proposed to originate at the residue level (J. Chem. Phys. 1959, 31, 526-535; J. Chem. Phys. 1961, 34, 1963-1974), all helix-folding studies have only established it between time-averaged bulk states of a long-lived helix and several transiently populated random coils, along the whole helix model sequence. Second, the predominant thermodynamic forces driving either this two-state transition or the faster helix growth following helix nucleation are still unclear. Third, the conformational space of the random coil state is not well-defined unlike its corresponding α-helix. Here we investigate the restrictions placed on the conformational space of a Gly residue backbone, as a result of it immediately succeeding a nascent α-helical turn. Analyses of the temperature-dependent 1D-, 2D-NMR, FT-IR, and CD spectra and GROMACS MD simulation trajectory of a Gly residue backbone following a model α-helical turn, which is artificially rigidified by a covalent hydrogen bond surrogate, reveal that: (i) the α-helical turn guides the ϕ torsion of the Gly exclusively into either a predominantly populated entropically favored α-helical (α-ϕ) state or a scarcely populated random coil (RC-ϕ) state; (ii) the α-ϕ state of Gly in turn favors the stability of the preceding α-helical turn, while the RC-ϕ state disrupts it, revealing an entropy-driven synergetic guidance for helix growth in the residue following helix nucleation. The applicability of a current synergetic guidance mechanism to explain rapid helix growth in folded and unfolded states of proteins and helical peptides is discussed.

PEGylation near a Patch of Nonpolar Surface Residues Increases the Conformational Stability of the WW Domain

Many proteins have one or more surface-exposed patches of nonpolar residues; our observations here suggest that PEGylation near such locations might be a useful strategy for increasing protein conformational stability. Specifically, we show that conjugating a PEG-azide to a propargyloxyphenylalanine via the copper(I)-catalyzed azide-alkyne cycloaddition can increase the conformational stability of the WW domain due to a favorable synergistic effect that depends on the hydrophobicity of a nearby patch of nonpolar surface residues.

Investigations into the interaction thermodynamics of TRAP-related peptides with a temperature-responsive polymer-bonded porous silica stationary phase

The interaction thermodynamics of the thrombin receptor agonistic peptide (TRAP-1), H-Ser-Phe-Leu-Leu-Arg-Asn-Pro-OH, and a set of alanine scan substitution peptides, have been investigated with an n-octadecylacrylic polymer-bonded porous silica (Sil-ODA₁₈) and water-acetonitrile mobile phases at temperatures ranging from 5 to 80 °C in 5 °C increments. The retention of these peptides on the Sil-ODA₁₈ stationary phase decreased as the water content in the mobile phase was lowered from 80% (v/v) to ca. 45% (v/v) and reached a minimum value for each peptide at a specific water-acetonitrile composition. Further decreases in the water content of the mobile phase led to increased retention. The magnitude of the changes in enthalpy of interaction, Δ H a s s o c 0 , changes in entropy of interaction, Δ S a s s o c 0 , and changes in heat capacity, Δ C p 0 , were found to be dependent on the molecular properties of the mobile phase, the temperature, the structure/mobility of the stationary phase, and the conformation and solvation state of the peptides. With water-rich mobile phases, the retention behaviour of the TRAP analogues was dominated by enthalpic processes, consistent with the participation of strong hydrogen bonding effects, but became dominated by entropic effects with acetonitrile-rich mobile phases as the temperature was increased. These changes in the retention behaviour of these TRAP peptides are consistent with the generation of water or acetonitrile clusters in the mobile phase depending on the volume fractions of the organic solvent as the Sil-ODA₁₈ stationary phase transitions from its crystalline to its isotropic state.

Modulatory role of rutin on 2,5-hexanedione-induced chromosomal and DNA damage in rats: validation of computational predictions

The aim of this study was to evaluate the potentials of rutin on 2,5-hexanedione-induced toxicities. Two successive phases were involved using in silico and in vivo approaches. The in silico was adopted for potential oral toxicity and docking. The in vivo was carried-out in two stages for two weeks; the ameliorative (stage 1, first week), preventive, and curative studies (stage 2, extended to second week). In stage 1, rats were divided into four groups of seven each (distilled water, 3% (v/v) 2,5-hexanedione, 10 mg/kg rutin, and co-administration). In stage 2, the experimental groups were given either rutin or 2,5-hexanedione and treated in reverse order. Lipid peroxidation, protein carbonyl, and DNA fragmentation in tissues and bone marrow cells micronucleus were determined. The predicted Median lethal dose (LD₅₀) of >5000 mg/kg and toxicity class of five (5) indicates the safety of rutin when orally administered. 2,5-Hexanedione comfortably docked in to the active sites of SOD (-22.857Kcal/mol; KI = 0.9621 µM), GPx (-11.2032Kcal/mol; KI = 0.9813 µM), and CAT (-16.446Kcal/mol; KI = 0.9726 µM) with strong hydrogen bond and hydrophobic interactions. However, only strong hydrophobic interaction was observed in the case of DNA (-3.3296Kcal/mol; KI = 0.9944). In vivo findings revealed deleterious effects of 2,5-hexanedione through induction of oxidative and chromosomal/DNA damage characterized by higher level of malondialdehyde, micronuclei formations, and DNA fragmentation. These have invariably, validates the findings from in silico experiments. Furthermore, rutin was able to ameliorate, protect, and reverse these effects, and was relatively non-toxic corroborating toxicity predictions. Rutin exhibited counteractive effects on 2,5-hexanedione-induced oxidative, chromosomal, and DNA damage.

Repeatability of n-octanol/water partition coefficient values between liquid chromatography measurement methods

The n-octanol/water partition coefficient (K_OW) is a physical/chemical property that is extensively used for regulatory and environmental risk and exposure assessments. The K_OW value can estimate various chemical properties such as water solubility, bioavailability, and toxicity using quantitative structure-activity relationships which demands an accurate knowledge of this property. The present investigation aims to compare outcomes of three commonly cited methods of K_OW measurement in the literature for six hydrophobic chemicals with insecticidal functions as well as highly volatile petroleum constituents. This measurement has been difficult to obtain for the selected pyrethroid insecticides, cypermethrin, and bifenthrin and is a novel measurement for the latter: polycyclic aromatic sulfur heterocycles, dibenzothiophene (DBT), and three of its alkyl derivatives except for DBT. The K_OW values were obtained using two liquid chromatographic methods with isocratic and gradient programming, and the slow-stirring method following OECD 117 and 123 guidelines, respectively. The mean log K_OW values of bifenthrin, cypermethrin, DBT, methyl-DBT, dimethyl-DBT, and diethyl-DBT were 8.4 ± 0.1, 6.0 ± 0.3, 4.8 ± 0.0, 5.4 ± 0.1, 6.0 ± 0.1, and 6.8 ± 0.0 using the HPLC method with gradient programing. The K_OW values were significantly reproducible within a method, however, not between the methods. Results suggest assessing a chemical's property and environmental risk and exposure solely based on the K_OW value should be practiced with caution.

Volumetric and calorimetric properties of aqueous ionene solutions

The volumetric (partial and apparent molar volumes) and calorimetric properties (apparent heat capacities) of aqueous cationic polyelectrolyte solutions - ionenes - were studied using the oscillating tube densitometer and differential scanning calorimeter. The polyion's charge density and the counterion properties were considered as variables. The special attention was put to evaluate the contribution of electrostatic and hydrophobic effects to the properties studied. The contribution of the CH₂ group of the polyion's backbone to molar volumes and heat capacities was estimated. Synergistic effect between polyion and counterions was found.

Characterizing hydrophobicity of amino acid side chains in a protein environment via measuring contact angle of a water nanodroplet on planar peptide network

Hydrophobicity of macroscopic planar surface is conventionally characterized by the contact angle of water droplets. However, this engineering measurement cannot be directly extended to surfaces of proteins, due to the nanometer scale of amino acids and inherent nonplanar structures. To measure the hydrophobicity of side chains of proteins quantitatively, numerous parameters were developed to characterize behavior of hydrophobic solvation. However, consistency among these parameters is not always apparent. Herein, we demonstrate an alternative way of characterizing hydrophobicity of amino acid side chains in a protein environment by constructing a monolayer of amino acids (i.e., artificial planar peptide network) according to the primary and the β-sheet secondary structures of protein so that the conventional engineering measurement of the contact angle of a water droplet can be brought to bear. Using molecular dynamics simulations, contact angles θ of a water nanodroplet on the planar peptide network, together with excess chemical potentials of purely repulsive methane-sized Weeks-Chandler-Andersen solute, are computed. All of the 20 types of amino acids and the corresponding planar peptide networks are studied. Expectedly, all of the planar peptide networks with nonpolar amino acids are hydrophobic due to θ [Formula: see text] 90°, whereas all of the planar peptide networks of the polar and charged amino acids are hydrophilic due to θ [Formula: see text] 90°. Planar peptide networks of the charged amino acids exhibit complete-wetting behavior due to θ [Formula: see text] 0°. This computational approach for characterization of hydrophobicity can be extended to artificial planar networks of other soft matter.

Thermodynamics of aggregate formation between a non-ionic polymer and ionic surfactants: An isothermal titration calorimetric study

This report examines the energetics of aggregate formation between hydroxypropyl methylcellulose (HPMC) and model ionic surfactants including sodium dodecyl sulfate (SDS) at pharmaceutically relevant concentrations using the isothermal titration calorimetry (ITC) technique and a novel treatment of calorimetric data that accounts for the various species formed. The influence of molecular weight of HPMC, temperature and ionic strength of solution on the aggregate formation process was explored. The interaction between SDS and HPMC was determined to be an endothermic process and initiated at a critical aggregation concentration (CAC). The SDS-HPMC interactions were observed to be cooperative in nature and dependent on temperature and ionic strength of the solution. Molecular weight of HPMC significantly shifted the interaction parameters between HPMC and SDS such that at the highest molecular weight (HPMC K-100M;>240kDa), although the general shape of the titration curve (enthalpogram) was observed to remain similar, the critical concentration parameters (CAC, polymer saturation concentration (C_sat) and critical micelle concentration (CMC)) were significantly altered and shifted to lower concentrations of SDS. Ionic strength was also observed to influence the critical concentration parameters for the SDS-HPMC aggregation and decreased to lower SDS concentrations with increasing ionic strength for both anionic and cationic surfactant-HPMC systems. From these data, other thermodynamic parameters of aggregation such as ΔH_agg^°, ΔG_agg^°, H_agg^°, ΔS_agg^°, and ΔC_p were calculated and utilized to postulate the hydrophobic nature of SDS-HPMC aggregate formation. The type of ionic surfactant head group (anionic vs. cationic i.e., dodecyltrimethylammonium bromide (DTAB)) was found to influence the strength of HPMC-surfactant interactions wherein a distinct CAC signifying the strength of HPMC-DTAB interactions was not observed. The interpretation of the microcalorimetric data at different temperatures and ionic strengths while varying properties of polymer and surfactant was a very effective tool in investigating the nature and energetics of HPMC and ionic surfactant interactions.

Critical examination of the colloidal particle model of globular proteins

Recent studies of globular protein solutions have uniformly adopted a colloidal view of proteins as particles, a perspective that neglects the polymeric primary structure of these biological macromolecules, their intrinsic flexibility, and their ability to sample a large configurational space. While the colloidal perspective often serves as a useful idealization in many cases, the macromolecular identity of proteins must reveal itself under thermodynamic conditions in which the native state is no longer stable, such as denaturing solvents and high protein concentrations where macromolecules tend to have screened excluded volume, charge, and hydrodynamic interactions. Under extreme pH conditions, charge repulsion interactions within the protein chain can overcome the attractive hydrogen-bonding interactions, holding it in its native globular state. Conformational changes can therefore be expected to have great significance on the shear viscosity and other rheological properties of protein solutions. These changes are not envisioned in conventional colloidal protein models and we have initiated an investigation of the scattering and rheological properties of model proteins. We initiate this effort by considering bovine serum albumin because it is a globular protein whose solution properties have also been extensively investigated as a function of pH, temperature, ionic strength, and concentration. As we anticipated, near-ultraviolet circular dichroism measurements and intrinsic viscosity measurements clearly indicate that the bovine serum albumin tertiary structure changes as protein concentration and pH are varied. Our findings point to limited validity of the colloidal protein model and to the need for further consideration and quantification of the effects of conformational changes on protein solution viscosity, protein association, and the phase behavior. Small-angle Neutron Scattering measurements have allowed us to assess how these conformational changes influence protein size, shape, and interprotein interaction strength.

Effect of single-site mutations on hydrophobic-polar lattice proteins

We developed a heuristic method for determining the ground-state degeneracy of hydrophobic-polar (HP) lattice proteins, based on Wang-Landau and multicanonical sampling. It is applied during comprehensive studies of single-site mutations in specific HP proteins with different sequences. The effects in which we are interested include structural changes in ground states, changes of ground-state energy, degeneracy, and thermodynamic properties of the system. With respect to mutations, both extremely sensitive and insensitive positions in the HP sequence have been found. That is, ground-state energies and degeneracies, as well as other thermodynamic and structural quantities, may be either largely unaffected or may change significantly due to mutation.

Blocking monocyte transmigration in in vitro system by a human antibody scFv anti-CD99. Efficient large scale purification from periplasmic inclusion bodies in E. coli expression system

Migration of leukocytes into site of inflammation involves several steps mediated by various families of adhesion molecules. CD99 play a significant role in transendothelial migration (TEM) of leukocytes. Inhibition of TEM by specific monoclonal antibody (mAb) can provide a potent therapeutic approach to treating inflammatory conditions. However, the therapeutic utilization of whole IgG can lead to an inappropriate activation of Fc receptor-expressing cells, inducing serious adverse side effects due to cytokine release. In this regard, specific recombinant antibody in single chain variable fragments (scFvs) originated by phage library may offer a solution by affecting TEM function in a safe clinical context. However, this consideration requires large scale production of functional scFv antibodies and the absence of toxic reagents utilized for solubilization and refolding step of inclusion bodies that may discourage industrial application of these antibody fragments. In order to apply the scFv anti-CD99 named C7A in a clinical setting, we herein describe an efficient and large scale production of the antibody fragments expressed in E. coli as periplasmic insoluble protein avoiding gel filtration chromatography approach, and laborious refolding step pre- and post-purification. Using differential salt elution which is a simple, reproducible and effective procedure we are able to separate scFv in monomer format from aggregates. The purified scFv antibody C7A exhibits inhibitory activity comparable to an antagonistic conventional mAb, thus providing an excellent agent for blocking CD99 signaling. This protocol can be useful for the successful purification of other monomeric scFvs which are expressed as periplasmic inclusion bodies in bacterial systems.

Discovery of highly potent and selective D4 ligands by interactive SAR study

A series of thienylmethylphenylpiperazins was synthesized and tested for affinity towards the five subtypes of dopaminergic receptors. Compound 5f showed more than 1000 folds selectivity to D4 receptors; analogue 5e showed the highest affinity to D4 receptors with Ki 3.9 nM. An interactive SAR approach was adopted and lead to compound 14a with Ki (D4) as low as 0.03 nM. Molecular docking studies showed a potential, first to report arene cation interaction between the D4 unique residue Arg-186 and the ligands' arene moiety, explaining the importance of having a strong negative electrostatic potential at this area of the compound structure.

Natural biomolecules and protein aggregation: emerging strategies against amyloidogenesis

Biomolecular self-assembly is a fundamental process in all organisms. As primary components of the life molecular machinery, proteins have a vast array of resources available to them for self-assembly in a functional structure. Protein self-assembly, however, can also occur in an aberrant way, giving rise to non-native aggregated structures responsible for severe, progressive human diseases that have a serious social impact. Different neurodegenerative disorders, like Huntington's, Alzheimer's, and spongiform encephalopathy diseases, have in common the presence of insoluble protein aggregates, generally termed "amyloid," that share several physicochemical features: a fibrillar morphology, a predominantly beta-sheet secondary structure, birefringence upon staining with the dye Congo red, insolubility in common solvents and detergents, and protease resistance. Conformational constrains, hydrophobic and stacking interactions can play a key role in the fibrillogenesis process and protein-protein and peptide-peptide interactions-resulting in self-assembly phenomena of peptides yielding fibrils-that can be modulated and influenced by natural biomolecules. Small organic molecules, which possess both hydrophilic and hydrophobic moieties able to bind to peptide/protein molecules through hydrogen bonds and hydrophobic and aromatic interactions, are potential candidates against amyloidogenesis. In this review some significant case examples will be critically discussed.

Effect of hydrophobic interactions on volume and thermal expansivity as derived from micelle formation

Volumetric parameters have long been used to elucidate the phenomena governing the stability of protein structures, ligand binding, or transitions in macromolecular or colloidal systems. In spite of much success, many problems remain controversial. For example, hydrophobic groups have been discussed to condense adjacent water to a volume lower than that of bulk water, causing a negative contribution to the volume change of unfolding. However, expansivity data were interpreted in terms of a structure-making effect that expands the water interacting with the solute. We have studied volume and expansivity effects of transfer of alkyl chains into micelles by pressure perturbation calorimetry and isothermal titration calorimetry. For a series of alkyl maltosides and glucosides, the methylene group contribution to expansivity was obtained as 5 uL/(mol K) in a micelle (mimicking bulk hydrocarbon) but 27 uL/(mol K) in water (20 °C). The latter value is virtually independent of temperature and similar to that obtained from hydrophobic amino acids. Methylene contributions of micellization are about -60 J/(mol K) to heat capacity and 2.7 mL/mol to volume. Our data oppose the widely accepted assumption that water-exposed hydrophobic groups yield a negative contribution to expansivity at low temperature that would imply a structure-making, water-expanding effect.

Molecular hydrogels from bolaform amino acid derivatives: a structure-properties study based on the thermodynamics of gel solubilization

Insight is provided into the aggregation thermodynamics associated to hydrogel formation by molecular gelators derived from L-valine and L-isoleucine. Solubility data from NMR measurements are used to extract thermodynamic parameters for the aggregation in water. It is concluded that at room temperature and up to 55 °C, these systems form self-assembled fibrillar networks in water with quite low or zero enthalpic component, whereas the entropy of the aggregation is favorable. These results are explained by considering that the hydrophobic effect is dominant in the self-assembly. However, studies by NMR and IR spectroscopy reveal that intermolecular hydrogen bonding is also a key issue in the aggregation process of these molecules in water. The low enthalpy values measured for the self-assembly process are ascribed to the result of a compensation of the favorable intermolecular hydrogen-bond formation and the unfavorable enthalpy component of the hydrophobic effect. Additionally, it is shown that by using the hydrophobic character as a design parameter, enthalpy-controlled hydrogel formation, as opposed to entropy-controlled hydrogel formation, can be achieved in water if the gelator is polar enough. It is noteworthy that these two types of hydrogels, enthalpy-versus entropy-driven hydrogels, present quite different response to temperature changes in properties such as the minimum gelator concentration (mgc) or the rheological moduli. Finally, the presence of a polymorphic transition in a hydrogel upon heating above 70 °C is reported and ascribed to the weakening of the hydrophobic effect upon heating. The new soft polymorphic materials present dramatically different solubility and rheological properties. Altogether these results are aimed to contribute to the rational design of molecular hydrogelators, which could be used for the tailored preparation of this type of soft materials. The reported results could also provide ground for the rationale of different self-assembly processes in aqueous media.

High hydrophobic amino acid exposure is responsible of the neurotoxic effects induced by E200K or D202N disease-related mutations of the human prion protein

Mutations in prion protein are thought to be causative of inherited prion diseases favoring the spontaneous conversion of the normal prion protein into the scrapie-like pathological prion protein. We previously reported that, by controlled thermal denaturation, human prion protein fragment 90-231 acquires neurotoxic properties when transformed in a β-rich conformation, resembling the scrapie-like conformation. In this study we generated prion protein fragment 90-231 bearing mutations identified in familial prion diseases (D202N and E200K), to analyze their role in the induction of a neurotoxic conformation. Prion protein fragment 90-231(wild type) and the D202N mutant were not toxic in native conformation but induced cell death only after thermal denaturation. Conversely, prion protein fragment 90-231(E200K) was highly toxic in its native structure, suggesting that E200K mutation per se favors the acquisition of a peptide neurotoxic conformation. To identify the structural determinants of prion protein fragment 90-231 toxicity, we show that while the wild type peptide is structured in α-helix, hPrP90-231 E200K is spontaneously refolded in a β-structured conformer characterized by increased proteinase K resistance and propensity to generate fibrils. However, the most significant difference induced by E200K mutation in prion protein fragment 90-231 structure in native conformation we observed, was an increase in the exposure of hydrophobic amino-acids on protein surface that was detected in wild type and D202N proteins only after thermal denaturation. In conclusion, we propose that increased hydrophobicity is one of the main determinants of toxicity induced by different mutations in prion protein-derived peptides.

Membrane partitioning: "classical" and "nonclassical" hydrophobic effects

The free energy of transfer of nonpolar solutes from water to lipid bilayers is often dominated by a large negative enthalpy rather than the large positive entropy expected from the hydrophobic effect. This common observation has led to the idea that membrane partitioning is driven by the “nonclassical” hydrophobic effect. We examined this phenomenon by characterizing the partitioning of the well-studied peptide melittin using isothermal titration calorimetry (ITC) and circular dichroism (CD). We studied the temperature dependence of the entropic (−TΔS) and enthalpic (ΔH) components of free energy (ΔG) of partitioning of melittin into lipid membranes made of various mixtures of zwitterionic and anionic lipids. We found significant variations of the entropic and enthalpic components with temperature, lipid composition and vesicle size but only small changes in ΔG (entropy–enthalpy compensation). The heat capacity associated with partitioning had a large negative value of about −0.5 kcal mol⁻¹ K⁻¹. This hallmark of the hydrophobic effect was found to be independent of lipid composition. The measured heat capacity values were used to calculate the hydrophobic-effect free energy ΔG_hΦ, which we found to dominate melittin partitioning regardless of lipid composition. In the case of anionic membranes, additional free energy comes from coulombic attraction, which is characterized by a small effective peptide charge due to the lack of additivity of hydrophobic and electrostatic interactions in membrane interfaces [Ladokhin and White J Mol Biol 309:543–552, 2001]. Our results suggest that there is no need for a special effect—the nonclassical hydrophobic effect—to describe partitioning into lipid bilayers.

Investigation of the dynamical properties of water in elastin by deuterium Double Quantum Filtered NMR

The anisotropic motion of tightly bound waters of hydration in bovine nuchal ligament elastin has been studied by deuterium Double Quantum Filtered (DQF) NMR. The experiments have allowed for a direct measurement of the degree of anisotropy within pores of elastin over a time scale ranging from 100 micros to 30 ms, corresponding to a tortuous spatial displacement ranging from 0.2 to 7 microm. We studied the anisotropic motion of deuterium nuclei in D2O hydrated elastin over a temperature of -15 degrees C to 37 degrees C and in solvents with varying dielectric constants. Our experimental measurements of the residual quadrupolar interaction as a function of temperature are correlated to the existing notion of hydrophobic collapse near 20 degrees C.

Synthesis, biophysical, and biological studies of wild-type and mutant psalmopeotoxins--anti-malarial cysteine knot peptides from Psalmopoeus cambridgei

Psalmopeotoxin I and II (PcFK1 and PcFK2), an anti-malarial peptide first extracted from Psalmopoeus cambridgei was synthesized and characterized. Both peptides belong to the Inhibitor Cystine Knot (ICK) superfamily, containing three disulfide bridges. The six cysteine residues are conserved similar to other members of the ICK superfamily, suggesting their critical role for either folding or function. In this study, the peptides were synthesized using Fmoc solid-phase peptide synthesis (SPPS). The three disulfide bonds of were constructed by regioselective and random oxidative approaches. The resulting disulfide bond patterns were verified by the HPLC-MS analysis of intact peptides and by the disulfide bond mapping using tryptic digestion. Implications of the disulfide bonds on the biophysical and biological properties of PcFKs were studied using three disulfide mutants in which a particular pair of cysteines was replaced with two isosteric serine residues. Structures and biophysical characteristics of all variants were studied using far-UV CD and fluorescence spectroscopy. Biological activities of all variants were evaluated using antiplasmodial assay against the K1 multi-drug-resistant strain of P. falciparum. The experimental results showed that the three disulfide bridges could not be correctly synthesized by the random oxidative strategy. Structural and biophysical analyses revealed that all variants had similar structures to the twisted beta-sheet. However, the studies of disulfide bond removal indicated that each disulfide bond had different effects on both biophysical and biological activities of PcFKs. Correlation of biophysical parameters and biological activities showed that both PcFKs may have different mechanisms of actions for antiplasmodial activity.

Binding mechanisms in supramolecular complexes

Supramolecular chemistry has expanded dramatically in recent years both in terms of potential applications and in its relevance to analogous biological systems. The formation and function of supramolecular complexes occur through a multiplicity of often difficult to differentiate noncovalent forces. The aim of this Review is to describe the crucial interaction mechanisms in context, and thus classify the entire subject. In most cases, organic host-guest complexes have been selected as examples, but biologically relevant problems are also considered. An understanding and quantification of intermolecular interactions is of importance both for the rational planning of new supramolecular systems, including intelligent materials, as well as for developing new biologically active agents.

Effects of glycosylation on the stability of protein pharmaceuticals

In recent decades, protein-based therapeutics have substantially expanded the field of molecular pharmacology due to their outstanding potential for the treatment of disease. Unfortunately, protein pharmaceuticals display a series of intrinsic physical and chemical instability problems during their production, purification, storage, and delivery that can adversely impact their final therapeutic efficacies. This has prompted an intense search for generalized strategies to engineer the long-term stability of proteins during their pharmaceutical employment. Due to the well known effect that glycans have in increasing the overall stability of glycoproteins, rational manipulation of the glycosylation parameters through glycoengineering could become a promising approach to improve both the in vitro and in vivo stability of protein pharmaceuticals. The intent of this review is therefore to further the field of protein glycoengineering by increasing the general understanding of the mechanisms by which glycosylation improves the molecular stability of protein pharmaceuticals. This is achieved by presenting a survey of the different instabilities displayed by protein pharmaceuticals, by addressing which of these instabilities can be improved by glycosylation, and by discussing the possible mechanisms by which glycans induce these stabilization effects.

How general is the nucleation-condensation mechanism?

We investigate the structures of the major folding transition states of nine proteins by correlation of published Phi-values with inter-residue contact maps. Combined with previous studies on six proteins, the analysis suggests that at least 10 of the 15 small globular proteins fold via a nucleation-condensation mechanism with a concurrent build-up of secondary and tertiary structure contacts, but a structural consolidation that is clearly nonuniformly distributed over the molecule and most intense in a single structural region suggesting the occurrence of a single folding nucleus. However, on average helix- and sheet-forming residues show somewhat larger Phi-values in the major transition state, suggesting that secondary structure formation is one important driving force in the nucleation-condensation in many proteins and that secondary-structure forming residues tend to be more prominent in folding nuclei. We synthesize the combined information on these 10 of 15 proteins into a unified nucleation-condensation mechanism which also accounts for effects described by the framework, hydrophobic collapse, zipper, and funnel models.

Crystal structure of a family 16 endoglucanase from the hyperthermophile Pyrococcus furiosus--structural basis of substrate recognition

Bacterial and archaeal endo-beta-1,3-glucanases that belong to glycoside hydrolase family 16 share a beta-jelly-roll fold, but differ significantly in sequence and in substrate specificity. The crystal structure of the laminarinase (EC 3.2.1.39) from the hyperthermophilic archaeon Pyrococcus furiosus (pfLamA) has been determined at 2.1 A resolution by molecular replacement. The pfLamA structure reveals a kink of six residues (72-77) at the entrance of the catalytic cleft. This peptide is absent in the endoglucanases from alkaliphilic Nocardiopsis sp. strain F96 and Bacillus macerans, two proteins displaying an overall fold similar to that of pfLamA, but with different substrate specificity. A deletion mutant of pfLamA, lacking residues 72-75, hydrolyses the mixed-linkage beta-1,3-1,4-glucan lichenan 10 times more efficiently than the wild-type protein, indicating the importance of the kink in substrate preference.

Biomolecular self-assembly and its relevance in silica biomineralization

Biomineralization, which means the formation of inorganic materials by biological processes, currently finds increasing research interest. It involves the synthesis of calcium-based minerals such as bones and teeth in vertebrates, and of shells. Silica biomineralization occurs, for example, in diatoms and silica sponges. Usually, biominerals are made up of amorphous compounds or small microcrystalline domains embedded into an amorphous matrix. Nevertheless, they exhibit very regular shapes and, as in the case of diatoms, intricate nanopatterns of amazing beauty. It is, therefore, commonly assumed that biominerals are formed under the structure-directing influence of templates. However, single molecules are by far too small to direct the formation of the observed shapes and patterns. Instead, supramolecular aggregates are shown to be involved in the formation of templating superstructures relevant in biomineralization. Specific biomolecules were identified in both diatoms and silica sponges, which elegantly combine two indispensable functions: on the one hand, the molecules are capable of inducing silica precipitation from precursor compounds. On the other hand, these molecules are capable of self-assembling into larger, structure-directing template aggregates. Such molecules are the silaffins in the case of diatoms and the silicateins in sponges. Long-chain polyamines of similar composition have meanwhile been discovered in both organisms. The present review is especially devoted to the discussion of the self-assembly behavior of these molecules. Physico-chemical studies on a model compound, poly(allylamine), are discussed in detail in order to elucidate the nature of the interactions responsible for self-assembly of long-chain polyamines and the parameters controlling this process. Numerous biomimetic silica synthesis experiments are discussed and evaluated with respect to the observations made on the aforementioned "natural" biomolecules.

Simulation of adsorption of DNA on carbon nanotubes

We report molecular dynamics simulations of DNA adsorption on a single-walled carbon nanotube (SWNT) in an aqueous environment. We have modeled a DNA segment with 12 base pairs (Dickerson dodecamer) and a (8,8) SWNT in water, with counterions to maintain total charge neutrality. Simulations show that DNA binds to the external surface of an uncharged or positively charged SWNT on a time scale of a few hundred picoseconds. The hydrophobic end groups of DNA are attracted to the hydrophobic SWNT surface of uncharged SWNTs, while the hydrophilic backbone of DNA does not bind to the uncharged SWNT. The binding mode of DNA to charged SWNTs is qualitatively different from uncharged SWNTs. The phosphodiester groups of the DNA backbone are attracted to a positively charged SWNT surface while DNA does not adsorb on negatively charged SWNTs. There is no evidence for canonical double-stranded DNA wrapping around either charged or uncharged SWNTs on the very short time scales of the simulations. The adsorption process appears to have negligible effect on the internal stacking structure of the DNA molecule but significantly affects the A to B form conversion of A-DNA. The adsorption of A-DNA onto an uncharged SWNT inhibits the complete relaxation of A-DNA to B-DNA within the time scale of the simulations. In contrast, binding of the A-DNA onto a positively charged SWNT may promote slightly the A to B conversion.

Low-temperature-induced swelling of a hydrophobic polymer: A lattice approach

The authors investigate equilibrium properties of a simple model of hydrophobic polymer in aqueous solution by means of dynamic Monte Carlo simulations. The solvent is described by a simplified two-dimensional model, defined on a triangular lattice, which has been previously shown to account for most thermodynamic anomalies of pure water and of hydrophobic solvation for monomeric solutes. The polymer is modeled as a self-avoiding walk on the same lattice. In this framework, the degrees of freedom of water are taken into account explicitly, and in principle there is no need to introduce effective self-contact interactions for the polymer in order to mimic the hydrophobic effect. In certain conditions, the authors observe low-temperature-induced swelling, i.e., expansion of the polymer globule upon decreasing temperature. The authors discuss the relationship between this phenomenon and the anomalous properties of the solvent.

Energetics in correlation with structural features: the case of micellization

Understanding micellization processes at the molecular level has direct relevance for biological self-assembly, folding, and association processes. As such, it requires complete characterization of the micellization thermodynamics, including its correlation with the corresponding structural features. In this context, micellization of a series of model non-ionic surfactants (poly(ethylene glycol) monooctyl ethers, C(8)E(gamma)) was studied by isothermal titration calorimetry (ITC) and differential scanning calorimetry (DSC). The corresponding structural properties of C(8)E(gamma) micelles were investigated by small-angle X-ray scattering (SAXS). The C(8)E(gamma) micellization, characterized independently from ITC, DSC, and structural data, reveals that deltaH(M)(o) > 0, deltaS(M)(o) > 0, and deltaC(P)(M)(o) < 0, while the dissection of its energetics shows that it is primarily governed by the transfer of 20-30 C(8) alkyl chains from aqueous solution into the nonpolar core (r approximately 1.3 nm) of the spherical micelle. Moreover, thermodynamic parameters of micellization, estimated from the structural features related to the changes in solvent-accessible surface areas upon micellization, are in a good agreement with the corresponding parameters obtained from the analysis of ITC and DSC data. We have shown that the contributions to deltaS(M)(o) other than from hydration (deltaS(M)(other)(o)), estimated from experimental data, appear to be small (deltaS(M)(other)(o) < 0.1 deltaS(M)(other)(o)) and agree well with the theoretical estimates expressed as a sum of the corresponding translational, conformational, and size contributions. These deltaS(M)(other)(o) contributions are much less unfavorable than those estimated for a rigid-body association, which indicates the dynamic nature of the C(8)E(gamma) micellar aggregates. the dynamic nature of the C8EY micellar aggregates.

Fundamental measure theory of hydrated hydrocarbons

To calculate the solvation of hydrophobic solutes, we have developed a method based on the fundamental measure treatment of density functional theory. This method allows us to carry out calculations of density profiles and the solvation energy for various hydrophobic molecules with high accuracy. We have applied the method to the hydration of various hydrocarbons (linear, branched and cyclic). The calculations of the entropic and enthalpic parts are also carried out. We have examined the question of the temperature dependence of the entropy convergence. Finally, we have calculated the mean force potential between two large hydrophobic nanoparticles immersed in water.