Exploring the role of hydrophilic amino acids in unfolding of protein in aqueous ethanol solution

Hydrophobic association is the key contributor behind the formation of well packed core of a protein which is often believed to be an important step for folding from an unfolded chain to its compact functional form. While most of the protein folding/unfolding studies have evaluated the changes in the hydrophobic interactions during chemical denaturation, the role of hydrophilic amino acids in such processes are not discussed in detail. Here we report the role of the hydrophilic amino acids behind ethanol induced unfolding of protein. Using free energy simulations, we show that chicken villin head piece (HP‐36) protein unfolds gradually in presence of water‐ethanol binary mixture with increasing composition of ethanol. However, upon mutation of hydrophilic amino acids by glycine while keeping the hydrophobic amino acids intact, the compact state of the protein is found to be stable at all compositions with gradual flattening of the free energy landscape upon increasing compositions. The local environment around the protein in terms of ethanol/water number significantly differs in wild type protein compared to the mutated protein. The calculated Wyman‐Tanford preferential binding coefficient of ethanol for wild type protein reveals that a greater number of cosolutes (here ethanol) bind to the unfolded state compared to its folded state. However, no significant increase in binding coefficient of ethanol at the unfolded state is found for mutated protein. Local‐bulk partition coefficient calculation also suggests similar scenarios. Our results reveal that the weakening of hydrophobic interactions in aqueous ethanol solution along with larger preferential binding of ethanol to the unfolded state mediated by hydrophilic amino acids combinedly helps unfolding of protein in aqueous ethanol solution.     

Regioselective phosphorylation of branched cyclodextrins with cyclo-mono-mu-imidotriphosphate

The phosphorylation of the branched cyclodextrins, mono-6-O-(alpha-D-glucopyranosyl)cyclomaltohexaose, mono-6-O-(alpha-D-maltosyl)cyclomaltohexaose, mono-6-O-(alpha-D-glucopyranosyl)cyclomaltoheptaose, and mono-6-O-(alpha-D-maltosyl)cyclomaltoheptaose, in aqueous solution by sodium cyclo-mono-mu-imidotriphosphate (cMITP) was examined. In these reactions, only the 2-OH group of a single alpha-D-glucopyranosyl residue of the cyclodextrin ring was phosphorylated, in a maximum yield of 67%. A possible mechanism for the phosphorylation is discussed.     

C.P.-D.D.-M.A.S. 13C-N.M.R. investigations of anhydrous and hydrated cyclomalto-oligosaccharides: The role of water of hydration

Hydrated and anhydrous cyclomaltohexaose, cyclomaltoheptaose, and cyclomalto-octaose (cyclodextrins) have been investigated by the c.p.-d.d.-m.a.s. ¹³C-n.m.r. technique. The chemical shifts of the signals of C-1 and C-6 provide information about conformation and the results agree fairly well with the earlier scattering data on hydrated systems, but some discrepancies have been found for cyclomaltohexaose. Th conformation of the macro-rings seems to be determined by the hydration water. The unique role of water in forming crystals of cyclomalto-oligosaccharides is demonstrated.     

Alkaline pre-treatment of oilseed rape straw for bioethanol production: evaluation of glucose yield and pre-treatment energy consumption

The objective of the research was to investigate the effect of biomass loading, alkali (NaOH) concentration and pre-treatment time on the yield of glucose obtained following alkaline pre-treatment and enzymatic hydrolysis of oilseed rape (OSR) straw. A maximum glucose yield of (440.6 ± 14.9) g glucose kg⁻¹ biomass was obtained when OSR straw was pre-treated at a biomass loading of 50 g kg⁻¹ and an alkali concentration of 0.63 mol dm⁻³ NaOH for 30 min. The energy efficiency of glucose extraction (0.39 kg glucose MJ⁻¹ consumed) was highest when OSR straw was pre-treated at a biomass loading of 50 g kg⁻¹ and an alkali concentration of 0.63 or 0.75 mol dm⁻³ for 30 min. The study demonstrated alkaline pre-treatment of OSR straw is superior to acid pre-treatment in terms of glucose yield and energy efficiency.     

Characterization of functional intermediates of endoglucanase from Aspergillus aculeatus during urea and guanidine hydrochloride unfolding

Low concentrations of urea and GuHCl (2 M) enhanced the activity of endoglucanase (EC 3.1.2.4) from Aspergillus aculeatus by 2.3- and 1.9-fold, respectively. The K_m values for controls, in the presence of 2 M urea and GuHCl, were found to be 2.4 ± 0.2 × 10⁻⁸ mol L⁻¹, 1.4 ± 0.2 × 10⁻⁸ mol L⁻¹, and 1.6 ± 0.2 × 10⁻⁸ mol L⁻¹, respectively. The dissociation constant (K_d) showed changes in the affinity of the enzyme for the substrate with increases in the K_cat suggesting an increased turnover number in the presence of urea and GuHCl. Fluorescence studies showed changes in the microenvironment of the protein. The increase in the activity of this intermediate state was due to conformational changes accompanied by increased flexibility at the active site.     

Synthesis and spectroscopic characterization of 4-butoxyethoxy-N-octadecyl-1,8-naphthalimide as a new fluorescent probe for the determination of proteins

A novel 4-butoxyethoxy-N-octadecyl-1,8-naphthalimide (BON) was synthesized as a fluorescent probe for the determination of proteins. The interactions between BON and bovine serum albumin (BSA) were studied by fluorescence spectroscopy and UV-vis absorption spectroscopy. Fluorescence data revealed that the fluorescence quenching of BSA by BON was likely the result of the formation of the BON-BSA complex. According to the modified Stern-Volmer equation, the binding constants of BON with BSA at four different temperatures were obtained. The thermodynamic parameters, enthalpy change (ΔH) and entropy change (ΔS) for the reaction were calculated to be −23.27 kJ mol⁻¹ and 10.40 J mol⁻¹ K⁻¹ according to van’t Hoff equation, indicating that the hydrogen bonds and hydrophobic interactions played a dominant role in the binding of BON to BSA. Furthermore, displacement experiments using warfarin indicated that BON could bind to site I of BSA. The effect of BON on the conformation of BSA was also analyzed by synchronous fluorescence and three-dimensional fluorescence spectra. A new fluorescence quenching assay of the proteins BSA using BON in the HCl-Tris (pH 7.4) buffer solution was developed with maximum excitation and emission wavelengths of 373 and 489 nm, respectively. The linear range was 0.1-10.0 × 10⁻⁵ mol L⁻¹ with detection limits were determined to be 1.76 × 10⁻⁸ mol L⁻¹. The effect of metal cations on the fluorescence spectra of BON in ethanol was also investigated. Determination of protein in human serum by this method gave results which were very close to those obtained by using Coomassie Brilliant Blue G-250 colorimetry.     

Aggregation of some water-soluble derivatives of chitin in aqueous solutions: Role of the degree of acetylation and effect of hydrogen bond breaker

By dynamic light scattering in combination with fluorescence spectroscopy and TEM it was shown that aggregation in aqueous solutions is inherent not only to chitosan, but also to two other water-soluble derivatives of chitin: O-carboxymethylchitin and di-N,N-carboxymethylchitosan. Aggregation is observed even for the samples without N-acetyl-d-glucosamine units, which remain upon incomplete chemical modification of chitin, indicating that specific interactions between residual chitin repeat units cannot be the main reason for the aggregation. At the same time, 7 M urea weakens the aggregation, thus testifying that hydrogen bonding and/or hydrophobic interactions are partially responsible for this phenomenon. The incomplete disruption of aggregates in 7 M urea may arise from crystallization of junction zones between different macromolecules, which makes some hydrogen bonds inaccessible for urea or too stable for breaking by this agent.     

Solubility of cyclomaltooligosaccharides (cyclodextrins) in H2O and D2O: a comparative study

Cyclomaltooligosaccharides (cyclodextrins, CDs) are cyclic oligomers having six, seven, or eight units of alpha-D-glucose, named as cyclomaltohexaose (alpha-CD), cyclomaltoheptaose (beta-CD) and cyclomaltooctaose (gamma-CD), respectively. The molecule of CD has a cavity in which the interior is hydrophobic relative to its outer surface. The solubility of cyclodextrins in water is unusual, as an irregular trend is observed in the series of the cyclic oligomers of glucose. beta-CD is at least nine times less soluble than the others CDs. This intriguing behavior has been investigated, and some interesting explanations in terms of the effect caused by CD on the water lattice structure have been proposed. In this work a comparative study on the solubility of alpha, beta, and gamma-cyclodextrins was carried out in H2O and D2O and reveals a much lower solubility of the three CDs in D2O. The solid-phase structure of the CDs in equilibrium with the solution is quite similar with both solvents. The results are discussed in terms of the CD molecular structure and the differences in the hydrogen bonds formed between H2O and D2O.     

Task-specific ionic liquid-assisted extraction and separation of astaxanthin from shrimp waste

Astaxanthin, as an outstanding antioxidant reagent, was successfully extracted from shrimp waste by the ionic liquids based ultrasonic-assisted extraction. Seven kinds of imidazolium ionic liquids with different cations and anions were investigated in this work and one task-specific ionic liquid in ethanol with 0.50 mol L⁻¹ was selected as the solvent. At the optimized ultrasonic extraction conditions, the extraction amount of astaxanthin increased 98% (92.7 μg g⁻¹) compared to the conventional method (46.7 μg g⁻¹). Furthermore, the extracted solution was isolated through the solid-phase extraction with a molecularly imprinted polymer sorbent. After loading the samples on molecularly imprinted polymer cartridge, the different washing and elution solvents, such as water, methanol, n-hexane, acetone and dichloromethane, were evaluated, and finally, astaxanthin was separated from the shrimp waste extract.     

C.P.-M.A.S. 13C-N.M.R. study of some solid-state inclusion complexes of cyclomalto-oligosaccharides with para-substituted benzenes

Cross polarisation—magic-angle sample spinning ¹³C-n.m.r. spectral have been measured in the solid state for p-nitrophenol, p-iodophenol, and their inclusion complexes with cyclomaltohexaose, cyclomaltoheptaose, and methylated cyclomaltohexaose. Analysis of the line-shapes of the resonances and the dipolar-dephasing experiments indicate that the guest molecules undergo motion in the host cavities, whereas the host molecules are almost static. The mode and rate of guest motion depend on the size of the cavity.     

Elucidating the mode of action of urea on mammalian serum albumins and protective effect of sodium dodecyl sulfate

The effect of sodium dodecyl sulfate (SDS) on human, bovine, porcine, rabbit and sheep serum albumins were investigated at pH 3.5 by using various spectroscopic techniques like circular dichroism (CD), intrinsic fluorescence and dynamic light scattering (DLS). In the presence of 4.0 mM SDS the secondary structure of all the albumins were not affected as measured by CD but fluorescence spectra revealed 8.0 nm blue shift in emission maxima. We further checked the stability of albumins in the absence and presence of 4.0 mM SDS by urea and temperature at pH 3.5. In the absence of SDS, urea starts unfolding both secondary as well as tertiary structural elements of the all the albumins at ∼2.0 M urea but in the presence of 4.0 mM SDS, urea was unable to unfold even up to 9.0 M. The albumins were thermally less stable at pH 3.5 with decrease in T_m but in the presence of 4.0 mM SDS, the T_m was increased. From this study, it was concluded that SDS is showing a protective effect against urea as well as thermal denaturation of albumins. This behavior may be due to electrostatic as well as the hydrophobic interaction of SDS with albumins. Further, we have proposed the mechanism of action of urea. It was found that urea interacted with proteins directly when proteins are in charged form. Indirect interaction may be taking place when the environment is more hydrophobic.     

Effect of magnesium chloride (2:1 electrolyte) on the aqueous solution behavior of some saccharides over the temperature range of 288.15-318.15 K: a volumetric approach

Infinite-dilution standard partial molar volumes, , for various mono-, di-, and trisaccharides, and their derivatives (methyl glycosides) at molalities ranging from 0.04 to 0.12 mol kg⁻¹ in aqueous solutions of magnesium chloride of 0.5, 1.0, 2.0, and 3.0 mol kg⁻¹, have been evaluated over a range of temperatures from 288.15 to 318.15 K by density measurements employing a vibrating-tube densimeter. These data have been utilized to determine the corresponding standard partial molar volumes of transfer, , of saccharides and methyl glycosides from water to aqueous magnesium chloride solutions. The values have been found to be positive, and their magnitudes increase with an increasing concentration of magnesium chloride in all cases. Partial molar expansion coefficients, and second derivatives thereof, have been estimated. The magnitude of values increases with an increase in temperature, indicating that hydration effects in solutions are strongly sensitive to temperature. Pair and higher order volumetric interaction coefficients (V_AB, V_ABB) have also been obtained from values by using the McMillan-Mayer theory. The various parameters have been discussed in terms of the solute (saccharide or methyl glycoside)-co-solute (magnesium chloride) interactions and are thus used to understand the mixing effects due to these interactions. These results have been compared with those earlier reported in the presence of electrolytes. An attempt is made to interpret the volumetric properties data in terms of the stereochemistry of the solutes.     

Interactions of hydrophobin proteins in solution studied by small-angle X-ray scattering

Hydrophobins are a group of very surface-active, fungal proteins known to self-assemble on various hydrophobic/hydrophilic interfaces. The self-assembled films coat fungal structures and mediate their attachment to surfaces. Hydrophobins are also soluble in water. Here, the association of hydrophobins HFBI and HFBII from Trichoderma reesei in aqueous solution was studied using small-angle x-ray scattering. Both HFBI and HFBII exist mainly as tetramers in solution in the concentration range 0.5-10 mg/ml. The assemblies of HFBII dissociate more easily than those of HFBI, which can tolerate changes of pH from 3 to 9 and temperatures in the range 5°C-60°C. The self-association of HFBI and HFBII is mainly driven by the hydrophobic effect, and addition of salts along the Hofmeister series promotes the formation of larger assemblies, whereas ethanol breaks the tetramers into monomers. The possibility that the oligomers in solution form the building blocks of the self-assembled film at the air/water interface is discussed.     

Estimate of the number of urea transport sites in erythrocyte ghosts using a hydrophobic mercurial

Summary In this paper a variety of mercurials, including a pCMB-nitroxide analogue, were used to study urea transport in human red cell ghosts. It was determined that the rate of inhibition for pCMBS, pCMB, pCMB-nitroxide, and chlormerodrin extended over four orders of magnitude consistent with their measured oil/water partition coefficients. From these results, we concluded that a significant hydrophobic barrier limits access to the urea inhibition site, suggesting that the urea site is buried in the bilayer or in a hydrophobic region of the transporter. In contrast, the rate of water inhibition by the mercurials ranged by only a factor of four and did not correlate with their hydrophobicities. Thus, the water inhibition site may be more directly accessible via the aqueous phase. Under conditions that leave water transport unaffected, we determined that 32,000 labeled sites per cell corresponded to complete inhibition of urea transport. This rules out major transmembrane proteins such as band 3, the glucose carrier, and CHIP28 as candidates for the urea transporter. In contrast, this result is consistent with the Kidd (Jk) antigen being the urea transporter with an estimated 14,000 copies per cell. From the experimental number of urea sites, a turnover number between 2–6×10⁶ sec^–1 at 22°C is calculated suggesting a channel mechanism.We would like to thank Kate Van Fossen for her faithful technical support. This work was supported by NIH grants No. HL-20985 and HL-37593.     

Purification and characterization of a soluble,cytoplasmic decycling maltodextrinase from aLactobacillus species,strain 26X,isolated from kitchen waste water

A soluble, cytoplasmic decycling maltodextrinase with a relative molecular mass (M _r) of around 62 000, and an isoelectric point (pI) of about 4 was purified to 93% homogeneity from aLactobacillus species, strain 26X, that was isolated from the waste water of a kitchen and resembledLactobacillus plantarum in its physiological and biochemical characteristics, but differed from this species in producing exclusively L( + )-lactic acid. The enzyme exhibited higher activities with maltotetraose to maltoheptaose than with cyclodextrins, in which cyclomaltohexaose was hydrolysed fastest, and the amounts of the linearized cyclic substrates were in the order cyclomaltohexaose < cyclomaltoheptaose < cyclomaltooctaose. The substituents of cyclomaltoheptaose derivatives considerably blocked the enzymic activity, and the accessibility to enzymic attack depended on the degree of substitution. The main product of hydrolysis proved to be maltose. The maltodextrinase exhibited, above all with maltotetraose, some transglycosylation activity. Except for maltopentaose, maltosyl transfer predominated. Starch and pullulan were degraded at low rates, the main products from starch being glucose and maltose, and from pullulan a branched trisaccharide, presumably panose.     

Relative Domain Folding and Stability of a Membrane Transport Protein

There is a limited understanding of the folding of multidomain membrane proteins. Lactose permease (LacY) of Escherichia coli is an archetypal member of the major facilitator superfamily of membrane transport proteins, which contain two domains of six transmembrane helices each. We exploit chemical denaturation to determine the unfolding free energy of LacY and employ Trp residues as site-specific thermodynamic probes. Single Trp LacY mutants are created with the individual Trps situated at mirror image positions on the two LacY domains. The changes in Trp fluorescence induced by urea denaturation are used to construct denaturation curves from which unfolding free energies can be determined. The majority of the single Trp tracers report the same stability and an unfolding free energy of approximately + 2 kcal mol^− 1. There is one exception; the fluorescence of W33 at the cytoplasmic end of helix I on the N domain is unaffected by urea. In contrast, the equivalent position on the first helix, VII, of the C-terminal domain exhibits wild-type stability, with the single Trp tracer at position 243 on helix VII reporting an unfolding free energy of + 2 kcal mol^− 1. This indicates that the region of the N domain of LacY at position 33 on helix I has enhanced stability to urea, when compared the corresponding location at the start of the C domain. We also find evidence for a potential network of stabilising interactions across the domain interface, which reduces accessibility to the hydrophilic substrate binding pocket between the two domains.     

Ovalbumin labeling with p-hydroxymercurybenzoate: The effect of different denaturing agents and the kinetics of reaction

The aim of our study was to investigate how denaturing agents commonly used in protein analysis influence the labeling between a reactive molecule and proteins. For this reason, we investigated the labeling of ovalbumin (OVA) as a globular model protein with p-hydroxymercurybenzoate (pHMB) in its native state (phosphate buffer solution) and in different denaturing conditions (8 mol L⁻¹ urea, 3 mol L⁻¹ guanidinium thiocyanate, 6 mol L⁻¹ guanidinium chloride, 0.2% sodium dodecyl sulfate, and 20% methanol). In addition to chemical denaturation, thermal denaturation was also tested. The protein was pre-column simultaneously denatured and derivatized, and the pHMB-labeled denatured OVA complexes were analyzed by size exclusion chromatography (SEC) coupled online with chemical vapor generation–atomic fluorescence spectrometry (CVG–AFS). The number of –SH groups titrated greatly depends on the protein structure in solution. Indeed, we found that, depending on the adopted denaturing conditions, OVA gave different aggregate species that influence the complexation process. The results were compared with those obtained by a common alternative procedure for the titration of –SH groups that employs monobromobimane (mBBr) as tagging molecule and molecular fluorescence spectroscopy as detection technique.     

Cyclomaltoheptaose mixed esters of anti-inflammatory drugs and short-chain fatty acids and study of their enzymatic hydrolysis in vitro

In an effort to enhance the drug-loading capacity of cyclomaltoheptaose (β-cyclodextrin, βCD) and to combine the function of anti-inflammatory drugs with short-chain fatty acids (SCFA), ternary esters incorporating seven copies of an anti-inflammatory drug and 14 copies of a SCFA onto a β-cyclodextrin core were designed and prepared. Acetic, propionic, or butyric esters were introduced at secondary OH groups, and ibuprofen, flurbiprofen, or felbinac was attached to primary OH groups through ester bonds. Heptakis[2,3-di-O-butanoyl-6-O-2-(biphenyl-4-yl)-ethanoyl]-cyclomaltoheptaose was very stable in aqueous and esterase solution. It was hydrolyzed by α-amylase (4 units/mL) with t_1/2 value of 18 h. The total released amount of biphenyl acetic acid was 38% after 24 h when the esterase was added after the α-amylase hydrolysis. The present results suggest that these nine βCD conjugates may release the anti-inflammatory drug in the colonic contents.     

UV-Vis and fluorimetric Al, Zn, Cd and Pb complexation studies of two 3-hydroxyflavones and a 3-hydroxythioflavone

The complexation of Al³⁺, Zn²⁺, Cd²⁺ and Pb²⁺ by the 3-hydroxyflavones: 3-hydroxy-2-(2-methoxyphenyl)-4H-1-benzopyran-4-one (H1) and 3-hydroxy-2-(4-methoxyphenyl)-4H-1-benzopyran-4-one (H2), and by the 3-methoxythioflavone: 3-hydroxy-2-(2-methoxyphenyl)-4H-1-benzopyran-4-thione (H3) have been studied spectrophotometrically and fluorimetrically to determine the corresponding complexation constants, K_sp and K_fl, in 5:95 water:ethanol (v/v) solution for which [HClO₄] was either 10⁻² or 10⁻⁵ mol dm⁻³ and I = 0.10 mol dm⁻³ (NaClO₄) at 298.2 K. Complexation occurs dominantly through the deprotonated ligand for [Al(1)]²⁺ and [Al(2)]²⁺ for which log K_sp = 4.51 and 4.73, respectively, in 10⁻² mol dm⁻³ HClO₄ and 4.21 and 4.61 in 10⁻⁵ mol dm⁻³ HClO₄. For Pb²⁺ complexation by H1, H2 and H3 is characterized by log K_sp = 2.20, 2.57 and 3.22, respectively, in 10⁻² mol dm⁻³ HClO₄ and 4.70, 5.38 and 5.74 in 10⁻⁵ mol dm⁻³ HClO₄. Equilibrium mixtures of [Pb(H1)]²⁺ and [Pb1]⁺, [Pb(H2)]²⁺ and [Pb2]⁺, and [Pb(H3)]²⁺ and [Pb3]⁺ appear to be formed. Complexation of Zn²⁺ and Cd²⁺ by all three ligands was only detected in 10⁻⁵ mol dm⁻³ HClO₄. For Zn²⁺ complexation by H1, H2 and H3 log K_sp = 3.22, 3.74 and 4.46 and for Cd²⁺ the corresponding values are 2.39, 2.40 and 3.72 for Cd²⁺. Only [Al1]²⁺ and [Al2]²⁺ show significant fluorescence and are characterized by log K_fl = 6.30 and 7.49 in 10⁻² mol dm⁻³ HClO₄.     

Application of ANS fluorescent probes to identify hydrophobic sites on the surface of DREAM

DREAM (calsenilin or KChIP-3) is a calcium sensor involved in regulation of diverse physiological processes by interactions with multiple intracellular partners including DNA, K_v4 channels, and presenilin, however the detailed mechanism of the recognition of the intracellular partners remains unclear. To identify the surface hydrophobic surfaces on apo and Ca^2 +DREAM as a possible interaction sites for target proteins and/or specific regulators of DREAM function the binding interactions of 1,8-ANS and 2,6-ANS with DREAM were characterized by fluorescence and docking studies. Emission intensity of ANS–DREAM complexes increases upon Ca^2 + association which is consistent with an overall decrease in surface polarity. The dissociation constants for ANS binding to apoDREAM and Ca^2 +DREAM were determined to be 195 ± 20 μM and 62 ± 4 μM, respectively. Fluorescence lifetime measurements indicate that two ANS molecules bind in two independent binding sites on DREAM monomer. One site is near the exiting helix of EF-4 and the second site is located in the hydrophobic crevice between EF-3 and EF-4. 1,8-ANS displacement studies using arachidonic acid demonstrate that the hydrophobic crevice between EF-3 and EF-4 serves as a binding site for fatty acids that modulate functional properties of K_v4 channel:KChIP complexes. Thus, the C-terminal hydrophobic crevice may be involved in DREAM interactions with small hydrophobic ligands as well as other intracellular proteins.