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.     

Water activity, pH and density of aqueous amino acids solutions

The water activity, pH and density of some aqueous amino acid solutions were determined at 25 degrees C in three different types of solvents. Previous published experimental data on water activity and solubility of amino acids in aqueous solutions were used together with data from this work to test the applicability of a group contribution model. The activity coefficients were estimated by the UNIFAC-Larsen model combined with the Debye-Hückel equation, taking also into account the partial dissociation phenomena of species in solution. Interaction energies between the charged species Na(+) and Cl(-) and the specific groups of amino acids (COOH and NH(2)) were adjusted using experimental solubility data.     

Effect of natural amino acids on ethanol oxidation in isolated rat hepatocytes]

The effects of the various naturally occurring amino acids on ethanol oxidation in hepatocytes from starved rats was systematically studied. In order to minimize the non ADH pathways, the ethanol concentration used was 4 mmol/litre, the amino acids being added at the same concentration. In hepatocytes from fasted rats, alanine, arginine, asparagine, aspartate, citrulline, cysteine, glutamate, glutamine, glycine, histidine, hydroxyproline, ornithine and serine increase significantly ethanol consumption. The stimulatory effect of glutamine being much less pronounced than the asparagine one and proline being devoid of action, the influence of ammonium chloride addition on ethanol consumption in the presence of these amino acids was studied. Ammonium chloride determines an enhancement of ethanol oxidation in these conditions, the results showing no apparent correlation between intracellular glutamate concentration and ethanol oxidation rate, contrarily to previous data. In hepatocytes from fed rats, only alanine, asparagine, cysteine, glycine, hydroxyproline, ornithine and serine increase ethanol oxidation, although to a lesser extent than in cells from starved rats.     

Polyethylene glycol behaves like weak organic solvent

Effect of polyethylene glycol (PEG) on protein solubility has been primarily ascribed to its large hydrodynamic size and thereby molecular crowding effect. However, PEG also shows characteristics of organic solvents. Here, we have examined the solubility of glycine and aliphatic and aromatic amino acids in PEG solutions. PEG400, PEG4000, and PEG20000 decreased the solubility of glycine, though to a much smaller magnitude than the level achieved by typical organic solvents, including ethanol and dimethyl sulfoxide. PEG4000 showed varying degree of interactions with amino acid side chains. The free energy of aliphatic side chains marginally increased by the addition of PEG4000, indicating their weak unfavorable interactions. However, it significantly decreased the free energy of the aromatic side chains and hence stabilized them. Thus, it was concluded that PEG behaves like weak organic solvents; namely PEG destabilized (interacted unfavorably with) polar and charged groups and stabilized (interacted favorably with) aromatic groups. Interestingly, the interaction of PEG20000, but neither PEG400 nor PEG4000, with glycine resulted in phase separation under the saturated concentration of glycine.     

Effect of temperature on viscosity properties of some alpha-amino acids in aqueous urea solutions

Viscosities for solutions of glycine, DL-alpha-alanine, DL-alpha-amino-n-butyric acid, DL-valine, DL-leucine and L-serine in 5 mol kg(-1) aqueous urea have been determined at 278.15, 288.15, 298.15 and 308.15 K. The viscosity B-coefficients for the amino acids in the aqueous urea solution have been calculated at different temperatures. The effect of temperature on the B-coefficients is discussed on the basis of the Feakins equation. The contribution of solute to the activation parameters (delta mu0*2, deltaH0*2, deltaS0*2) for viscous flow of the solution have been calculated, together with the Gibbs energy, enthalpy and entropy of transfer for the amino acids from the ground-state solvent to the hypothetical viscous transition state solvent. The contributions of the charged end group (NH3+, COO-) and CH2 groups of the amino acids to B-coefficient and delta mu0*2 have been also estimated using the linear correlations between B-coefficient or delta mu0*2 and the number of carbon atoms in the alkyl chains of the amino acids. All the activation parameters are discussed in terms of the solute-solvent interactions in the ground and transition states.     

Formation of ethanol and higher alcohols by immobilized zymomonas mobilis in continuous culture

Cells of Zymomonas mobilis ATCC 10988 were immobilized in 1.5% calcium alginate and packed in a column bioreactor for a series of fermentations utilizing 10.0% glucose media with the addition of one of the following amino acids or keto acids: L-leucine, L-isoleucine, L-valine, α-ketoisocaproic acid, α-ketobutyric acid, or α-ketoisovaleric acid. This was done in order to study the rates of production of higher alcohols during ethanolic fermentations at varying dilution rates while under the influence of amino acids or keto acids. Results indicate that the EHRLICH mechanism is operative in Zymomonas sp. α-Ketobutyrate enhanced the production of n-propanol and act-amyl alcohol. α-Ketoisocaproic acid stimulated the production of isoamyl alcohol. α-Ketoisovaleric acid increased the levels of isobutanol. The amino acids also gave rise to their corresponding alcohols but to a far lesser degree than did the keto acids. During high glucose utilization, ethanol yields ranged from 87% to 94% of theoretical with productivity ranging from 60.08 g/l/h in one fermentation (at a dilution rate of 1.35 h^?1) to 70.42 g/l/h in another (at a dilution rate of 1.58 h^?1). At dilution rates of 1.58 h^?1, higher alcohol productivity rose to as high as 4,313 mg/l/h in the presence of α-ketoisocaproic acid, 1,734.49 mg/l/h using α-ketoisovaleric acid, and 1,618.05 mg/l/h in α-ketobutyric acid. The concomitant production of ethanol and higher alcohols in all of the fermentations indicates that glucose is required for the production of the higher alcohols from their corresponding amino acids or keto acids.     

Effect of the composition of branched chain amino acids, taurine, and tryptophan on the amino acid metabolism in experimental models of alcoholism

Ethanol withdrawal after forced alcoholization of rats according to Majchrowicz led to the development of amino acid imbalance in the pool of free amino acids in the liver (increasing levels of alanine, aspartate, glutamate, glutamine and histidine, decreasing levels of glycine, lysine, threonine and taurine) and blood plasma (increasing levels of tyrosine and alanine, decreasing levels of most glycogen aminoacids, branched-chain aminoacids and Lys). Less profound changes were observed after prolonged alcohol intoxication (decreasing levels of alanine, ornitine, citrulline and increasing level of Glu in liver, increasing levels of sulfur-containing compounds, Asp and Lys in blood plasma). Amino acid mixture which contained branched-chain amino acids, taurine and tryptophan administered intragastrically was found to correct levels of sulfur-containing amino acids, threonine, lysine and isoleucine after ethanol withdrawal and to eliminate disorders in urea cycle, exchange of threonine, glycine and phenylalanine after prolonged alcohol intoxication.     

The complexation of aqueous metal ions relevant to biological applications. 2. Reactions of copper(II) citrate and copper(II) succinate with selected amino acids

Abstract

Addition of amino acids, glycine, alanine, and serine, to poorly soluble copper(II) salts [copper(II) citrate and copper(II) succinate] all increase solubility of the copper(II) salts. Relative increases in solubility follow the polarity trend in the selected amino acids, with serine creating the greatest increase in solubility. Simultaneous equilibria calculations indicate the formation of mixed-ligand complexes in the copper(II) succinate–amino acid systems, the first time such mixed-ligand complexes have been observed. In contrast, mixed-ligand complexes are not predicted in the copper(II) citrate–amino acid systems. Potential bioavailability of copper(II) appears to be increased by the inclusion of amino acids in solution, roughly in parallel with the increase in solubility of the copper(II) salt. Therefore, measurement of the change in solubility caused by addition of amino acids to aqueous solution gives qualitative insight to the potential increase in bioavailability of the metal ion.     

Ethanol inhibition of N-methyl-D-aspartate receptors is reduced by site-directed mutagenesis of a transmembrane domain phenylalanine residue

N-Methyl-D-aspartate (NMDA) receptors (NRs) are ionotropic receptors activated by glutamate and the co-agonist glycine. Ethanol inhibits NMDA receptor function, although its site of action is undefined. We hypothesized that ethanol acts at specific amino acids contained within the transmembrane (TM) domains of the receptor. In this study, NR1 and NR2A subunits were altered by mutagenesis and tested for sensitivity to ethanol. Three NR1 mutants (W636A, F817A, and L819A) and one NR2A mutant (F637A) failed to generate functional receptors. Pre-TM1 (I546A, L551A, F554A, and F558A), TM1 (W563A), and TM2 (W611A) NR1 mutations did not affect ethanol sensitivity of heteromeric receptors. In contrast, altering a TM3 phenylalanine to alanine (F639A) reduced the ethanol inhibition of NMDA receptors expressed in oocytes and human embryonic kidney 293 cells. Mutation of the nearby methionine (M641) to alanine did not affect ethanol sensitivity, whereas changing Phe(639) to tryptophan slightly enhanced ethanol inhibition. NR1(F639A) did not alter the agonist potency of glutamate but did produce a leftward shift in the glycine concentration response for receptors containing NR2A and NR2B subunits. NR1(F639A) also reduced the potency of the competitive glycine antagonist 5,7-dichlorokynurenic acid and increased the efficacy of the glycine partial agonist 3-amino-1-hydroxy-2-pyrrolidinone ((+)-HA-966). These results suggest that ethanol may interact with amino acids contained in the TM3 domain of NMDA subunits that are involved in transducing agonist binding to channel opening.     

Mechanisms of interaction of amino acids with phospholipid bilayers during freezing

In this study we compare the ability of various amino acids to protect small unilamellar vesicles against damage during freeze/thaw. Liposomes were composed of 75% palmitoyloleoyl phosphatidylcholine and 25% phosphatidylserine. Damage to liposomes frozen in liquid nitrogen and thawed at 20 degrees C was assessed by resonance energy transfer. Cryoprotection by numerous amino acids was compared in the presence and absence of 350 mM NaCl. The majority of amino acids with hydrocarbon side chains increased membrane damage during freeze/thaw regardless of the presence of salt. However, amino acids with hydrocarbon side chains of less than three carbons long, e.g. glycine, alanine, and 2-aminobutyric acid, were cryoprotective only in the presence of salt. We suggest that NaCl selectively increases the solubility of such amino acids, allowing them to act as cryoprotectants. In contrast, amino acids with side chains containing charged amine groups were cryoprotective regardless of the presence of salt. The degree of charge on the second amine group is shown to be important for cryoprotection by these molecules. We present evidence that suggests an interaction between the positively charged, second amine group of the amino acid, and the negatively charged phospholipid headgroup.     

Effect of aliphatic alcohols on the conformation of poly (l-ornithine hydrobromide) as studied by square-pulse and reversing-pulse electric birefringence

The electric birefringence and circular dichroism spectra of poly(l-ornithine hydrobromide) have been measured in ethanol/water, 2-propanol/water and tertiary butyl alcohol/water mixtures of various compositions. This charged polypeptide underwent a transition from the coil conformation to the helical conformation at high alcohol content in every case tested. Anomalous birefringence signals, indicative of a field-induced helix-to-coil transition. were observed at high electric fields only in the case of ethanol/water mixtures. The reversing-pulse electric birefringence of this polypeptide has been studied in ethanol/water mixtures and in neutral aqueous solution. Upon rapid reversal of the pulse field, no transient could be observed. This confirms that the electric-field orientation of poly(l-ornithine hydrobromide) results predominantly from the contribution of the counterion-induced dipole moment, regardless of its molecular conformations. It is very probable that the backbone permanent dipole moment of the helical conformation is largely suppressed by the counterion-induced dipole moment in the ionized form.     

Purification and characterization of an oxygen-labile, NAD-dependent alcohol dehydrogenase from Desulfovibrio gigas.

A NAD-dependent, oxygen-labile alcohol dehydrogenase was purified from Desulfovibrio gigas. It was decameric, with subunits of M(r) 43,000. The best substrates were ethanol (Km, 0.15 mM) and 1-propanol (Km, 0.28 mM). N-terminal amino acid sequence analysis showed that the enzyme belongs to the same family of alcohol dehydrogenases as Zymomonas mobilis ADH2 and Bacillus methanolicus MDH.     

The complexation of aqueous metal ions relevant to biological applications: 2. Evaluation of simultaneous equilibria of poorly soluble zinc salts with select amino acids

Abstract

Simultaneous equilibria calculations were completed for seven aqueous zinc-ligand systems: zinc citrate plus either glycine, alanine, or serine, and zinc succinate plus either glycine, alanine, or serine, and zinc oxalate plus glycine. Mixed-ligand complexes were predicted for all but the zinc citrate-glycine system, and the proportion tends to peak around 5 molar equivalents of amino acid. Potential bioavailability of zinc appears to be increased by the inclusion of amino acids in solution, roughly in parallel with the increase in solubility of the zinc salt. Therefore, measurement of the change in solubility caused by addition of amino acids to aqueous solution gives qualitative insight to the potential increase in bioavailability of the metal ion, and mixed-ligand complexes are a significant proportion of the complexes present in solution.     

Pressurized solvent extraction of pure food grade starch

A commercial pressurized solvent extractor was used to remove lipid and non-lipid material from cornstarch using n-propanol/water and ethanol/water mixtures. Yields and chemical composition of the extract fractions were determined. Cornstarch samples were characterized using pasting properties and shear storage modulus measurements. The n-propanol/water extracted slightly higher amounts of both lipids and non-lipids. The lipid fractions contained mostly linoleic, palmitic and oleic free fatty acids. The non-lipid fraction contained mostly protein in the form of zein. The extracted starch had lower peak and setback viscosities than did the unextracted starch. The starch extracted with n-propanol/water had the lowest shear storage modulus values. Conversely, the samples extracted with ethanol/water had the highest shear storage modulus values. It is hypothesized that low amounts of zein present in conjunction with the starch is responsible for this observed effect.     

Enzymatic measurement of ethanol or NAD in acid extracts of biological samples

An enzymatic method for the measurement of ethanol has been developed to permit analyses with unneutralized acid extracts of blood, liver, cell suspensions, or other biological materials. Components of the assay mixture include NAD, yeast alcohol dehydrogenase, tris(hydroxymethyl)aminomethane (Tris), and lysine. Tris is a trapping agent for the reaction product, acetaldehyde. Lysine is used to maintain the pH at 9.7 where oxidation of ethanol is quantitative and most rapid, even when as much as 0.2 ml of 0.5 n HClO₄ is added. Lysine also causes the reaction to be 2 to 4 times faster than it is when either glycine or 2-amino-2-methyl-1-propanol is used as the buffer. The assay is linear up to an ethanol concentration of 0.125 mm in the reaction mixture and is complete by 4 min. By substituting ethanol for NAD in the reagents, the assay performs equally well in measuring NAD.     

Water Stress Induced Changes in the Amounts of Some Photosynthetic Assimilation Products and Respiratory Metabolites of Sunflower Leaves

Sunflower leaves, water-stressed under controlled conditions,contained greater amounts of amino acids as their water potentialdecreased, with glycine, serine, and glutamate increasing morethan alanine and aspartate. Proline accumulated only at severestress. Low O₂ concentration altered the amounts of amino acids,principally decreasing the amount of glycine and increasingserine. The changes in total pool size are related to previousresults on the accumulation of 14C and the specific activityof products. Photorespiration was large under water stress,where leaves accumulated carbon in glycine of low specific activity,and in 21% O₂, where both total amount and specific activityof glycine was greater than in 1.5% O₂. This suggests that thereare two pools of glycine, one controlled by O₂ and closely relatedto photosynthesis, the other non-photosynthetic and affectedby water stress. The organic acids suocinate, citrate, and fumarate increasedat small leaf-water potentials. Sucrose decreased in amountwith stress and was absent at the most severe stress; therewas less glucose and fructose. The amount of carbon lost fromsugars was similar to the amount accumulated in amino acidstogether with the carbon lost in respiration. It is concluded that stress decreased the flux of carbon fromphotosynthesis for the synthesis of amino acids and sugars butmore carbon from stored materials, principally sucrose, wasused in the production of organic acids and amino acids.     

Structural properties of human glycodelin A in water and in water-alcohol mixtures: a comparison with bovine beta-lactoglobulin A.

Human glycodelin A (GdA) is a glycoprotein that is highly homologous to bovine beta-lactoglobulin A (beta-LgA) because the amino acid sequences are 50-60% identical. The structural characteristics of human GdA and beta-LgA were compared in water and 2-propanol/water solutions. Circular dichroism spectra reveal that in water the two proteins have a very similar beta-sheet secondary structure. In the presence of 2-propanol/water mixtures (up to 50% v/v) the alpha-helix structure of both proteins increases. A further increase in the alcohol percentage of the solvent (up to 80% v/v 2-propanol) causes the formation of a new folded tertiary structure containing mainly beta-sheet features. Synchrotron radiation small angle X-ray scattering indicates that, in a neutral pH aqueous solution, GdA is a dimer. Its radius of gyration value (Rg), 25.1+/-0.4 A, is greater than that of beta-LgA (21.1+/-0.3 A), probably because of the contribution of polysaccharides bound to Asn-28 and Asn-63 residues of GdA. Conversely, small angle X-ray scattering and gel permeation chromatography data on GdA in 2-propanol have revealed a massive aggregation of the protein.     

Imitating Prebiotic Homochirality on Earth

We show how the amino acids needed on prebiotic earth in their homochiral L form can be produced by a reaction of L-alpha-methyl amino acids—that have been identified in the Murchison meteorite—with alpha-keto acids under credible prebiotic conditions. When they are simply heated together they perform a process of decarboxylative transamination but with almost no chiral transfer, and that in the wrong direction, producing D-amino acids from the L-alpha-methyl amino acids. With copper ion a square planar complex with two of the reaction intermediates is formed, and now there is the desired L to L transformation, producing small enantioexcesses of the normal L-amino acids. We also show how these can be amplified, not by making more of the L form but by increasing its concentration in water solution. The process can start with a miniscule excess and in one step generate water solutions with L/D ratios in the over 90% region. Kinetic processes can exceed the results from equilibria. We have also examined such amplifications with ribonucleosides, and have shown that initial modest excesses of the D-nucleosides can be amplified to afford water solutions with D to L ratios in the high 90’s. We have shown that the homochiral compound has two effects on the solubility of the racemate. On one hand it decreases the solubility of the racemate by its role in the solubility product, as a theoretical equation predicts. On the other hand, it increases the solubility of the racemate by changing the nature of the solvent, acting as a cosolvent with the water. This explains why the amplification, while large, is not as large as the simple theoretical equation predicts. Thus when credible examples are produced where small enantioexcesses of D-ribose are created under credible prebiotic conditions, the prerequisites for the RNA world will have been exemplified.     

Nitrogen source and mineral optimization enhance d-xylose conversion to ethanol by the yeast Pichia stipitis NRRL Y-7124

Nutrition-based strategies to optimize xylose to ethanol conversion by Pichia stipitis were identified in growing and stationary-phase cultures provided with a defined medium varied in nitrogen, vitamin, purine/pyrimidine, and mineral content via full or partial factorial designs. It is surprising to note that stationary-phase cultures were unable to ferment xylose (or glucose) to ethanol without the addition of a nitrogen source, such as amino acids. Ethanol accumulation increased with arginine, alanine, aspartic acid, glutamic acid, glycine, histidine, leucine, and tyrosine, but declined with isoleucine. Ethanol production from 150 g/l xylose was maximized (61±9 g/l) by providing C:N in the vicinity of ∼57–126:1 and optimizing the combination of urea and amino acids to supply 40–80 % nitrogen from urea and 60–20 % from amino acids (casamino acids supplemented with tryptophan and cysteine). When either urea or amino acids were used as sole nitrogen source, ethanol accumulation dropped to 11 or 24 g/l, respectively, from the maximum of 46 g/l for the optimal nitrogen combination. The interaction of minerals with amino acids and/or urea was key to optimizing ethanol production by cells in both growing and stationary-phase cultures. In nongrowing cultures supplied with nitrogen as amino acids, ethanol concentration increased from 24 to 54 g/l with the addition of an optimized mineral supplement of Fe, Mn, Mg, Ca, Zn, and others.The mention of trade names or commercial products in this article is solely for the purpose of providing specific information and does not imply recommendation or endorsement by the U.S. Department of Agriculture.     

Interactions between taurine and ethanol in the central nervous system

Summary.  This purpose of this review will be to summarize the interactions between the endogenous amino acid taurine and ethyl alcohol (ethanol) in the central nervous system (CNS). Taurine is one of the most abundant amino acids in the CNS and plays an integral role in physiological processes such as osmoregulation, neuroprotection and neuromodulation. Both taurine and ethanol exert positive allosteric modulatory effects on neuronal ligand-gated chloride channels (i.e., GABA_A and glycine receptors) as well as inhibitory effects on other ligand- and voltage-gated cation channels (i.e., NMDA and Ca²⁺ channels). Behavioral evidence suggests that taurine can alter the locomotor stimulatory, sedating, and motivational effects of ethanol in a strongly dose-dependent manner. Microdialysis studies have revealed that ethanol elevates extracellular levels of taurine in numerous brain regions, although the functional consequences of this phenomenon are currently unknown. Finally, taurine and several related molecules including the homotaurine derivative acamprosate (calcium acetylhomotaurinate) can reduce ethanol self-administration and relapse to drinking in both animals and humans. Taken together, these data suggest that the endogenous taurine system may be an important modulator of effects of ethanol on the nervous system, and may represent a novel therapeutic avenue for the development of medications to treat alcohol abuse and alcoholism. Received November 21, 2001 Accepted January 4, 2002 Published online August 20, 2002 Acknowledgements This work was supported by funds from the State of California for medical research on alcohol and substance abuse through the University of California at San Francisco. The author wishes to thank Drs. C. W. Hodge and P. H. Janak for their support and helpful discussions. Author's address: Dr. M. Foster Olive, Ernest Gallo Clinic and Research Center, Department of Neurology, University of California at San Francisco, 5858 Horton Street, Suite 200, Emeryville, California, U.S.A., Fax +1/510/985 3101, E-mail: folive@itsa.ucsf.edu