The effect of aqueous alcohol solutions on the thermal transition of ribonuclease

Unfolding action of alcohols on a highly negatively charged state of cytochrome C

It is well-known that hydrophobic effect play a major role in alcohol-protein interactions leading to structure unfolding. Studies with extremely alkaline cytochrome c (U(B) state, pH 13) in the presence of the first four alkyl alcohols suggests that the hydrophobic effect persistently overrides even though the protein carries a net charge of -17 under these conditions. Equilibrium unfolding of the U(B) state is accompanied by an unusual expansion of the chain involving an intermediate, I(alc), from which water is preferentially excluded, the extent of water exclusion being greater with the hydrocarbon content of the alcohol. The mobility and environmental averaging of side chains in the I(alc) state are generally constrained relative to those in the U(B) state. A few nuclear magnetic resonance-detected tertiary interactions are also found in the I(alc) state. The fact that the I(alc) state populates at low concentrations of methanol and ethanol and the fact that the extent of chain expansion in this state approaches that of the U(B) state indicate a definite influence of electrostatic repulsion severed by the low dielectric of the water/alcohol mixture. Interestingly, the U(B) ⇌ I(alc) segment of the U(B) ⇌ I(alc) ⇌ U equilibrium, where U is the unfolded state, accounts for roughly 85% of the total number of water molecules preferentially excluded in unfolding. Stopped-flow refolding results report on a submillisecond hydrophobic collapse during which almost the entire buried surface area associated with the U(B) state is recovered, suggesting the overwhelming influence of hydrophobic interaction over electrostatic repulsions.

Role of N-t-Boc group in helix initiation in a novel tetrapeptide

Protecting groups in N- and C-terminal positions play a decisive role in the conformational preference of smaller peptides. Conformational analysis of tetrapeptide derivatives containing Ala, Ile and Gly residues was performed. Peptide 1, Boc-Ala-Ile-Ile-Gly-OMe (Boc: tert-butyloxycarbonyl) has a predominantly helical turn conformation in all the alcoholic solvents studied, whereas in the solid state it has a beta-sheet conformation. In contrast, peptide 2, Ac-Ala-Ile-Ile-Gly-OMe (Ac: acetyl) has a random coil conformation in solution. The FTIR spectrum of peptide 1 shows a lower frequency of urethane carbonyl, indicating involvement of the carbonyl group in hydrogen bonding in the helical turn.

Molecular simulation of the effects of alcohols on peptide structure

The effects of alcohols on local protein structure have been simulated using computational approaches and model peptides. Molecular simulations were carried out on a 7-residue peptide created in both an extended conformation and an alpha-helix to explore alcohol-induced changes in peptide structure. It was assumed that alcohols hydrogen bond at peptide carbonyl groups with an optimum geometry and compete with water molecules at these site. Energy minimization of the peptide/alcohol assemblies revealed that alcohols induced a twist in the peptide backbone as a function of (1) the methylene chain length, (2) the hydrogen-bond geometry, (3) halogenation of the molecule, (4) concentration, and (5) the dielectric constant. The rank ordering of the potencies of the alcohols was hexafluoroisopropanol > trifluoroethanol approximately pentanol > butanol > ethanol > methanol. Helix destabilization by cosolvent was measured by examining the hydrogen-bond lengths in peptide structures that resulted from a combination of energy minimization and molecular dynamics simulations. Destabilization was also found to be dependent upon the chemical nature of the alcohol and the hydrogen-bond geometry. The data suggest that alcohols at low concentrations affect protein structure mainly through a combination of hydrogen-bonding and hydrophobic interactions that are influenced by the properties of the solvent.

Heat denaturation of pepsinogen in a water-ethanol mixture

The effect of ethanol and pH on thermodynamic parameters and cooperativity of pepsinogen heat denaturation was studied by scanning microcalorimetry. Addition of 20% ethanol decreases the protein denaturation temperature by 10.7 degrees C at pH 6.4 and 15.8 degrees C at pH 8.0. It also decreases the denaturation heat capacity increment from 5.8 to 4.2 kcal/K.mol. The dependences of calorimetric denaturation enthalpy on denaturation temperature both in water and 20% ethanol are linear and intersect at about 95 degrees C. In 20% ethanol the pH shift from 5.9 to 8.0 results in a decreased number of cooperative domains in pepsinogen. This process causes no changes either in the secondary structure or in the local surroundings of aromatic amino acids. It is concluded that ethanol addition does not affect the cooperativity of pepsinogen denaturation substantially until the pH change provokes redistribution of charges in the protein molecule.

Effects of protein perturbants on phospholipid bilayers

Series of alcohols, amides, ureas, and sulfoxides with increasingly longer hydrocarbon chains have been shown to lower progressively the thermal denaturation temperature of proteins. This effect is presumably due to a hydrophobic interaction between the solute and nonpolar domains of the protein. Theoretically, these interactions should occur between the solute and any macromolecular structure having a nonpolar region to which the solute has access. A recent review by Arakawa et al. has summarized evidence for such an interaction between organic solutes and proteins and suggested that these interactions are favored at higher temperatures. The present study investigates the effects of several classes of compounds on the stability of phospholipid vesicles. The results show that many compounds that are known to perturb protein function also destabilize phospholipid bilayers as reflected by solute-induced loss of vesicle contents.

Alcohol induced conformational transitions of proteins and polypeptides. Thermodynamic studies of some model compounds

Integral enthalpies of solution of diglycine in tert.-butyl alcohol + water and of diglycine and beta-alanine in ethanol + water mixtures were measured at 298.15 K as a function of alcohol concentration. Enthalpies of transfer of the solutes from water to aqueous alcohol mixtures were evaluated from these data. Entropies of transfer of a peptide backbone unit (CH2CONH) and peptide group (CONH) from water to aqueous ethanol solutions were derived from the enthalpy of transfer data and the free energies of transfer of glycine, alpha-alanine, beta-alanine and diglycine. The thermodynamic transfer functions are discussed in terms of "water structure" mediated solute-solute interactions. The observed trends in the thermodynamic transfer functions have also been utilized to rationalize the effect of alcohols on the conformational stability of proteins and polypeptides in aqueous solutions.

The mechanisms of glutaraldehyde-fixed sarcoma 180 ascites cell aggregation

Sediment height analysis was employed to investigate the mechanisms of cell aggregation by glutaraldehyde-fixed sarcoma 180 ascites cells. The aggregation of these cells proceeds by a polymer bridging mechanism in which the surface molecules of one cell associate directly with the surface molecules of adjacent cells by nonbonding interactions. The ability of adhesive surface macromolecules to serve as polymer bridges is regulated by hydrophobic and coulombic interactions. Hydrophobic interactions are not significantly involved in polymer bridging per se, but instead appear to operate either intramolecularly or between adjacent molecules of the same cell surface, and regulate the conformation and ability of such molecules to form stable intermolecular associations with the surface adhesive molecules of a nearby cell. A disruption of these intrasurface hydrophobic interactions generally promotes cell aggregation. Coulombic forces generated by the fixed charges of surface molecules inhibit aggregation; their diminution by charge neutralization promotes aggregation. It is likely that coulombic repulsive forces regulate intramolecular associations, interactions between adjacent molecules arising from the same cell surface, and interactions between macromolecules arising from different cell surfaces. The actual forces which serve to aggregate two fixed cells are not hydrophobic, but have characteristics commonly attributed to hydrogen bonding. Ion-pairing does not seem to play a role in the aggregation of fixed cells under physiological electrolyte conditions, nor does disulfide bridging.

Structure-affinity relationships of substrates for the neutral amino acid transport system in rabbit ileum

The apparent affinities of various amino acids for the neutral amino acid transport system in rabbit ileum were determined by measuring the inhibition of L-methionine-(14)C influx across the brush border membrane. The apparent affinity was very low for compounds lacking an alpha-amino group, compounds with the alpha-hydrogen substituted by a methyl group, D-compounds, compounds with tertiary branching in the side chain, compounds with either a positive or negative charge in the side chain, and in most cases, compounds with a hydrophilic moiety in the side chain. High apparent affinities were exhibited by compounds with unbranched carbon or carbon-sulfur side chains. Branched compounds such as valine and leucine exhibited affinities which correlate with binding of only the linear portion of the side chain. The calculated change in free energy of binding is 370 cal/mol/CH(2) group which suggests the binding region for the side chain is partially hydrophobic. The affinities of families of analogues, derivatives of cysteine, methionine, serine, alanine, valine, and phenylalanine, correlate with their calculated octanol/water partition coefficients and are also correlated with apparent structural and electronic differences between families. The data permit a preliminary description of the functional geometry of the neutral amino acid transport site. The site contains a region for binding the alpha-amino group, alpha-carboxyl group, and side chain. The regions about the alpha-amino group and alpha-hydrogen are quite sterically limited. The side chain binding region is hydrophobic in nature and appears to be shallow, binding only the linear portion of branched or ring compounds.

Effect of alcohols and neutral salt on the thermal stability of soluble and precipitated acid-soluble collagen

The effects of mono- and poly-hydric alcohols in the presence of KCl on the intrinsic stability of collagen molecules in dilute acid solution were compared with corresponding solvent and salt effects on the increased stability of the aggregated molecules in salt-precipitated fibrils. Salt addition decreased solubility and increased the thermal stability of fibrils, but progressively decreased the stability of collagen molecules in solution. In contrast, the alcohols enhanced solubility and decreased fibril stability, the effects increasing with solvent hydrocarbon chain length and with decreasing hydroxyl/methylene-group ratio. Molar destabilization of dissolved collagen by alcohols was lower than for fibrils, and at low salt concentration, both ethylene glycol and glycerol were structural stabilizers. Electron-micrograph studies indicated that salt-precipitated fibrils tended to adopt the native aggregation mode, and qualitatively similar solvent effects were observed in insoluble collagens. Implications of the experimental findings are discussed in terms of a model in which electrostatic and apolar interactions mainly govern the excess of stability in collagen fibrils whereas intrinsic stability of single molecules is a function of polar interactions and polypeptide-chain rigidity.

Study of the thermal denaturation of ribonuclease A by differential thermal analysis and susceptibility to proteolysis

1. The thermally induced change in conformation of ribonuclease A in solution was investigated by differential thermal analysis and the susceptibility of the enzyme to proteolytic digestion by ficin. 2. A transition with a mid-point of 60.5 degrees C at pH4.2 was observed directly by differential thermal analysis and shown to be a property of the native structure. 3. At pH4.2 ribonuclease A is susceptible to ficin digestion at 60 degrees C but not at 18 degrees C. 4. Chromatographic analysis of the digestion products reveals that transient active intermediates are produced during the digestion. 5. Three of these intermediates were purified and partially characterized. 6. The nature of those sections of the ribonuclease molecule that are involved in the thermal transition is discussed.

Structural stability and solvent denaturation of myoglobin

As judged from the midpoints of the denaturation transition of 31 water-miscible alcohols, ureas, and amides, the effectiveness of these denaturing agents on sperm-whale myoglobin increases with increasing chain length and hydrocarbon content, as expected in view of the disorganization of the hydrophobic interior of this protein. Increase in the hydroxyl content, blocking of the functional amino groups of the ureas and amides by alkyl substitution, and branching of the hydrocarbon portion of the denaturants are of less importance in determining the effectiveness of the denaturants.