Solvent perturbation studies and analysis of protein and model compound data in denaturing organic solvents

Probing protein structure and dynamics by second-derivative ultraviolet absorption analysis of cation-{pi} interactions

We describe an alternate approach for studying protein structure using the detection of ultraviolet (UV) absorbance peak shifts of aromatic amino acid side chains induced by the presence of salts. The method is based on the hypothesis that salt cations (Li+, Na+, and Cs+) of varying sizes can differentially diffuse through protein matrices and interact with benzyl, phenyl, and indole groups through cation-pi interactions. We have investigated the potential of this method to probe protein dynamics by measuring high resolution second-derivative UV spectra as a function of salt concentration for eight proteins of varying physical and chemical properties and the N-acetylated C-ethyl esterified amino acids to represent totally exposed side chains. We show that small shifts in the wavelength maxima for Phe, Tyr, and Trp in the presence of high salt concentrations can be reliably measured and that the magnitude and direction of the peak shifts are influenced by several factors, including protein size, charge, and the local environment and solvent accessibility of the aromatic groups. Evaluating the empirical UV spectral data in light of known protein structural information shows that probing cation-pi interactions in proteins reveals unique information about the influence of structure on aromatic side chain spectroscopic behavior.

Penetration and interactions of the antimicrobial peptide, microcin J25, into uncharged phospholipid monolayers

Microcin J25 forms stable monolayers at the air-water interface showing a collapse at a surface pressure of 5 mN/m, 220 mV of surface potential, and 6 fV per squared centimeter of surface potential per unit of molecular surface density. The adsorption of microcin J25 from the subphase at clean interfaces leads to a rise of 10 mN/m in surface pressure and a surface potential of 220 mV. From these data microcin appears to be a poor surfactant per se. Nevertheless, the interaction with the lipid monolayer further increase the stability of the peptide at the interface depending on the mode in which the monolayer is formed. Spreading with egg PC leads to nonideal mixing up to 7 mN/m, with hyperpolarization and expansion of components at the interface, with a small excess free energy of mixing caused by favorable contributions to entropy due to molecular area expansion compensating for the unfavorable enthalpy changes arising from repulsive dipolar interactions. Above 7 mN/m microcin is squeezed out, leaving a film of pure phospholipid. Nevertheless, the presence of lipid at 10 and 20 mN/m stabilize further microcin at the interface and adsorption from the subphase proceeds up to 30 mN/m, equivalent to surface pressure in bilayers.

Solvent effects on the conformation and far UV CD spectra of gramicidin

Solvent effects on the far-uv CD spectra of the polypeptide gramicidin have been studied systematically in a series of alcohols of increasing chain length, ranging from methanol to dodecanol. The effects observed are of two types: primary, involving a change in the equilibrium mixture of conformers present, and secondary, involving a shift in the spectral peak positions as a function of solvent polarizability. To quantitate the primary effect, the ratio of the individual conformers present was estimated by deconvolution of the spectra into their component species. For short chain length alcohols, both parallel and antiparallel double helices are found in considerable abundance. As the solvent chain length is increased and its polarity is decreased, the left-handed antiparallel double helical species is favored. For all alcohols with chain lengths of four or more carbon atoms, the ratio of the conformers present remains relatively constant. To quantitatively examine the secondary effect, the magnitudes of the spectral shifts on the dominant conformer (species 3) have been correlated with the dielectric constants and refractive indices of the solvents, thereby indicating what underlying physical properties are responsible for these shifts. This work thus demonstrates that for gramicidin, a flexible polypeptide, the solvent effects on the CD spectra can be resolved into two types: changes due to the mixture of conformers present and shifts in the spectral characteristics. Both effects need to be considered when interpreting CD spectra in terms of secondary structure for this and other polypeptides in nonaqueous solutions.

How to measure and predict the molar absorption coefficient of a protein

The molar absorption coefficient, epsilon, of a protein is usually based on concentrations measured by dry weight, nitrogen, or amino acid analysis. The studies reported here suggest that the Edelhoch method is the best method for measuring epsilon for a protein. (This method is described by Gill and von Hippel [1989, Anal Biochem 182:319-326] and is based on data from Edelhoch [1967, Biochemistry 6:1948-1954]). The absorbance of a protein at 280 nm depends on the content of Trp, Tyr, and cystine (disulfide bonds). The average epsilon values for these chromophores in a sample of 18 well-characterized proteins have been estimated, and the epsilon values in water, propanol, 6 M guanidine hydrochloride (GdnHCl), and 8 M urea have been measured. For Trp, the average epsilon values for the proteins are less than the epsilon values measured in any of the solvents. For Tyr, the average epsilon values for the proteins are intermediate between those measured in 6 M GdnHCl and those measured in propanol. Based on a sample of 116 measured epsilon values for 80 proteins, the epsilon at 280 nm of a folded protein in water, epsilon (280), can best be predicted with this equation: epsilon (280) (M-1 cm-1) = (#Trp)(5,500) + (#Tyr)(1,490) + (#cystine)(125) These epsilon (280) values are quite reliable for proteins containing Trp residues, and less reliable for proteins that do not. However, the Edelhoch method is convenient and accurate, and the best approach is to measure rather than predict epsilon.

Alpha-helical assembly of biologically active peptides and designed helix bundle protein

The formation of alpha-helical assembly by complexing biologically active peptides with de novo designed protein is described. The de novo designed protein described here is a cystine-linked 4-helix bundle protein constructed with 80 amino acid residues and forms a hydrophobic core region surrounded by 4 helices in an aqueous solution. The biologically active peptides, such as melittin and human growth hormone releasing factor, contain the sequences that are able to form amphiphilic helices. These peptides alone do not form the alpha-helix structure in a diluted solution with low ion strength. But on mixing with the designed helix bundle protein, the peptides are strongly bound to the protein with the induction of alpha-helical structure in the biologically active peptides. The content of induced alpha-helix is in accord with that estimated from the amphiphilic sequence. The results mean that a novel architecture composed of alpha-helices is formed. Fluorescent and temperature-scanning measurement revealed that the alpha-helical assembly is constructed with hydrophobic interaction. Also, it is shown by means of fluorescence depolarization that the assembly has a compact globular form corresponding to 1:1 complex.

Fluctuation and rotation of human growth hormone-releasing factor in the presence and the absence of phospholipid bilayer analyzed by time-resolved fluorescence depolarization

Time-resolved fluorescence depolarization measurements were carried out for human growth hormone-releasing factor analog ([Trp10]-hGRF (1-29) NH2), where the Trp10 residue was incorporated as a fluorescent probe, in the presence and the absence of 1,2-dimyristoyl-sn-glycero-3-phospho-rac- glycerol(DMPG) liposome and in aqueous 2,2,2-trifluoroethanol (TFE) solution. The fluorescence lifetimes and the rotatory correlation times of the peptide in each medium were determined. The apparent volumes of the rotatory Brownian motion unit calculated from these fluorescent parameters indicate the different mode of the fluctuation and/or the rotation of the peptide in each medium, such as: (i) In the aqueous solution, several segments of the peptide fluctuate individually. (ii) In the DMPG bilayer, both the local fluctuation of Trp residue alone and the rotation of the whole molecule exist. (iii) In the aqueous TFE solution, the monomeric peptide rotates as a rigid ellipsoid.

Solution structure of human growth hormone-releasing factor fragment (1-29) by CD: characteristic conformational change on phospholipid membrane

The conformations of synthetic human growth hormone-releasing factor fragment (1-29) in the presence and the absence of 1,2-dimyristoyl-sn-glycero-3-phosphorylglycerol liposome as well as in aqueous 2,2,2-trifluoroethanol solution were investigated by CD spectroscopy. The secondary structure of the peptide in each solution was analyzed by two methods. Both results show that the peptide has an unordered structure in the aqueous solution, whereas it folds into helical structure in the aqueous alcohol and in the phospholipid solution. In addition, although the peptide exists as almost complete helix in the 50 vol% aqueous alcohol (80-90% helicity), it does not reach full helicity even in the solution containing excess amount of phospholipid liposome (maximum 65-70% helicity). The conformational difference is explained by the characteristic amphipathy of the peptide, i.e., the necessity to twist the separated amphipathic helical parts in the interaction with the phospholipid membrane probably makes the helicity of the peptide decrease.

Determination of tryptophan, tyrosine, and phenylalanine by second derivative spectrophotometry

Second derivative spectrophotometry has been useful for the determination of aromatic amino acids. However, published methods produce erroneous results, because those methods measure second derivative values by the vertical distance between peak and trough which is subject to variation according to the aromatic amino acid composition of proteins. This paper presents a method of second derivative spectrophotometry which measures second derivative absorbance values by means of the vertical distance from baseline to the derivative curve at a wavelength specifically assigned to each aromatic amino acid, and makes corrections for the interference from other amino acids at the same wavelength. The Appendix describes a computational method for obtaining absolute values of second derivative absorbances directly from normal absorbance values without using the spectrophotometer's derivative mode, because most commercial instruments produce completely arbitrary second derivative values which make comparison of data obtained on two different instruments impossible.

Quantitation of aromatic residues in proteins: model compounds for second-derivative spectroscopy

The ultraviolet absorption spectrum of proteins in 6 M guanidine is approximately that of the sum of the spectra of the constituent aromatic amino acids, phenylalanine, tyrosine, and tryptophan, plus contributions from light scattering and disulfides. A multicomponent analysis of the spectrum would theoretically permit simultaneous quantitation of each aromatic amino acid in the protein. In practice, this has not been possible, because of the similarities of the spectra of the amino acids, large differences in molar absorptivity, variable absorption by the disulfides, light scattering, and wavelength shifts which occur when the amino acids are incorporated into proteins. We describe a method for the simultaneous quantitation of the aromatic amino acids in purified proteins. We used second-derivative ultraviolet spectroscopy coupled with a statistically weighted multicomponent analysis. Use of the second derivative virtually eliminated interference from light scattering and from cystine. Empirical selection of model compounds obviated the problem of wavelength shifts. The models are N-acetylphenylalanine ethyl ester in 6 M guanidine for phenylalanine, N-acetyltyrosine ethyl ester in 55% methanol for tyrosine, and mellitin in 6 M guanidine for tryptophan. This method permits accurate, rapid quantitation of phenylalanine, tyrosine, and tryptophan in intact, denatured proteins.

Estimation of state and amount of phenylalanine residues in proteins by second derivative spectrophotometry

The second derivative absorption spectra of serum albumin, insulin, ribonuclease and lysozyme were measured under various conditions to determine the state and amount of their phenylalanine residues. The second derivative spectra of these proteins were very similar to that of phenylalanine in the region between 245 and 270 nm where tryptophan and tyrosine residues caused no appreciable interference. Denaturation of proteins with urea or guanidine hydrochloride caused decrease in the intensity of the second derivative spectra, but scarcely affected the positions of peaks and troughs. The amounts of phenylalanine residues in proteins calculated from a second derivative spectra of denatured proteins coincided well with those reported in the literature. The states of the phenylalanine residues in the proteins could be deduced from the change in optical intensity on denaturation.

Second derivative spectrophotometry as an effective tool for examining phenylalanine residues in proteins

The second derivative absorption spectra of N-acetyl ethyl esters of phenylalanine, tyrosine and tryptophan, as models of the aromatic amino acid residues in proteins, were measured. The second derivative spectra of tyrosine and tryptophan were found to have no influence on the spectrum of phenylalanine over the range of 245 to 270 nm, where characteristic absorbance bands of phenylalanine were observed. Thus the second derivative spectrum is a good tool for examining the optical properties of phenylalanine residues in proteins.

Interaction between proteins and detergents which contain a hydrocarbon chain longer than 16 carbon atoms. II. Difference spectra of various proteins in cetyldimethyl-benzylammonium chloride

The detergents which contain a hydrocarbon side chain longer than 16 cabron atoms were used as a perturbant for the study of protein structure. ta low concentration of cetyldimethylbenzylammonium chloride (CDBA) caused difference spectra for Ac-Trp-OEt and AC-Tyr-OEt. The delta e values at their difference maxima became constant above 30 mM of cetyldimethylbenzylammonium chloride, 1430 at 294 nm for Ac-Trp-OEt and 450 at 288 nm for Ac-Tyr-OEt. These delta e values are higher than any other delta e values resulting from solvent effects by such a remarkably low concentration of organic reagents described in the literature so far. The absence of denaturation blue shift in the difference spectra and the fact that the optical rotatory dispersion of the proteins examined in the present study was not changed significantly by cetyldimethylbenzylammonium chloride indicate that the secondary and tertiary structures of the proteins were not destroyed by cetyldimethylbenzylammonium chloride. These characteristics, together with small overlapping of their difference spectra at 288 and 294 nm were advantageous in the determination of tryptophan and tyrosine residues exposed in glucagon, insulin and alcohol dehydrogenase from yeast. No tyrosine residues in ribonuclease A was accessible to cetyldimethylbenzylammonium chloride. Unusual difference spectrum with a peak at 298 nm was observed for lysozyme which is known to contain tryptophan residues in special environments. Ovalbumin gave a novel unusual difference spectrum with a peak at 290 nm and a shoulder at 298 nm, showing the existence of unusual tryptophan and probably tyrosine residues in the molecule.