Critique of the interpretation of the circular dichroism of unordered polypeptides and proteins

Efficient recovery of gamma-poly (glutamic acid) from highly viscous culture broth

An efficient strategy for the separation and recovery of gamma-polyglutamic acid (gamma-PGA) from highly viscous broth was developed. This strategy was divided into two processes: The first was to separate gamma-PGA from highly viscous culture broth; the second was to concentrate gamma-PGA solution by ultrafiltration for the reduction of the amount of alcohol required during recovery process with precipitation. By lowering the pH value of culture broth to 3, the viscosity of culture broth and the zeta potential of cell could be reduced to a sixth of the original value at 35 degrees C and a third, respectively. After the acidification of culture broth the energy demand for the separation of gamma-PGA from culture broth by centrifugation could be reduced to 17% of that without it when the centrifugal force was 22,000g. The amount of alcohol required for precipitation could be reduced to a fourth of that generally used without concentration by concentrating 20 g gamma-PGA/L solution to 60 g gamma-PGA/L at pH 5 by ultrafiltration with hollow-fiber membrane cartridge (MWCO 500,000).

On the helical conformation of un-ionized poly(gamma-D-glutamic acid)

The conformational preferences of the naturally occurring poly(gamma-D-glutamic acid) in the un-ionized state were investigated using a combination of molecular dynamics and quantum mechanical calculations. Results indicated that a left-handed helix with 19-membered ring hydrogen bonds set between the CO of the amide group i and the NH of amide group i + 3 is the most stable conformation for this poly(gamma-amino acid). Weak intramolecular interactions between the oxygens of the carboxyl side groups and the NH of the backbone amide groups were detected. They are assumed to be responsible for the unexpected handedness exhibited by the helix with regards to the stereochemistry of the compound.

Methylated poly(L-lysine): conformational effects and interactions with polynucleotides

Methylated lysine, arginine and histidine residues are found in a number of proteins (for example, histones, non-histone chromosomal proteins, ribosomal proteins, calmodulin, cytochrome C, etc.). We are studying the effects of methylation on the conformations of poly(lysine) and of the effects of methylation of poly(lysine) and poly(arginine) on interactions with polynucleotides. The conformational properties of epsilon-amino-methylated poly(lysine) differ from those of unmodified poly(lysine). Methylation increases resistance to thermally-induced and NaCl-induced changes in the CD spectrum. Guanidinium chloride increases (proportional to the degree of methylation) the extent of approach to the conformation in dispute as to its being a random coil or an extended helix. Methylation enhances aggregation in the helix-inducing solvent 0.5 M Ca(ClO4)2. With increasing methylation of poly(lysine), the conformation in dodecyl sulfate changes from beta, to 50% alpha, to random coil at the maximum methylation. Increasing methylation of poly(lysine) weakens the interaction with polynucleotides in respect to dissociation by salt, linearly with methyl content. Complexes of (dAdT)n.(dAdT)n with the polypeptides are increasingly stabilized to heat denaturation by progressive methylation. However, with a series of synthetic double-stranded RNA's and DNA's a more complex situation exists, Tm increasing or decreasing, depending on the base composition, sequence and type of sugar. Methylation of poly(lysine) and poly(arginine) can have opposite effects on Tm based on results with complexes with (dI)n.(dC)n. Methylated poly(lysine) affects the CD spectrum of polynucleotides, in a manner dependent on base composition and sequence. In some cases large positive or negative psi-spectra are induced, which, in the case of (dGdC)n.(dGdC)n, can be positive or negative depending on the degree of methylation of the polypeptide and the salt concentration. It is suggested that the biological effects of methylation proteins may be evoke by salt changes in the cell cycle, and that methylation can affect local interactions with nucleic acids and larger scale structure, and interactions with lipids.

Reasons for the occurrence of the twenty coded protein amino acids

Factors involved in the selection of the 20 protein L-alpha-amino acids during chemical evolution and the early stages of Darwinian evolution are discussed. The selection is considered on the basis of the availability in the primitive ocean, function in proteins, the stability of the amino acid and its peptides, stability to racemization, and stability on the transfer RNA. We conclude that aspartic acid, glutamic acid, arginine, lysine, serine and possibly threonine are the best choices for acidic, basic and hydroxy amino acids. The hydrophobic amino acids are reasonable choices, except for the puzzling absences of alpha-amino-n-butyric acid, norvaline and norleucine. The choices of the sulfur and aromatic amino acids seem reasonable, but are not compelling. Asparagine and glutamine are apparently not primitive. If life were to arise on another planet, we would expect that the catalysts would be poly-alpha-amino acids and that about 75% of the amino acids would be the same as on the earth.

Thermodynamic investigations of proteins. II. Calorimetric study of lysozyme denaturation by guanidine hydrochloride

The thermodynamic parameters of the denaturation of lysozyme are determined at various temperatures (25-60 degrees C) by isothermal calorimetric titrations with guanidine hydrochloride (GuHCl) and by scanning calorimetry in the presence of GuHCl. An approach for the determination of the enthalpy of preferential binding of GuHCl is proposed. It has been shown from GuHCl denaturation experiments that the net enthalpies of denaturation and the denaturational change in the heat capacity of protein can be obtained if preferential binding is taken into consideration. These results are nearly the same as in the case of thermal denaturation in the absence of denaturants. It is concluded that the states of both heat- and GuHCl-denatured lysozyme are thermodynamically indistinguishable.