No abstract

In the denatured states of Hydrogenobacter thermophilus cytochrome c(552) (HT) and Pseudomonas aeruginosa cytochrome c(551) (PA), and their mutants, the N-terminal amino group of the polypeptide chain is coordinated to heme Fe in place of the axial Met, the His-N(term) form being formed. The coordination of the N-terminal amino group to heme Fe leads to loop formation by the N-terminal stretch preceding the first Cys residue bound to the heme, and the N-terminal stretches of HT and PA are different from each other in terms of both the sequence and the number of constituent amino acid residues. The His-N(term) form was shown to be rather stable, and hence it can influence the stability of the denatured state. We have investigated the heme Fe coordination structures and stabilities of the His-N(term) forms emerging upon guanidine hydrochloric acid-induced unfolding of the oxidized forms of the proteins. The Fe-N(term) coordination bond in the His-N(term) form with a 9-residue N-terminal stretch of HT proteins was found to be tilted to some extent away from the heme normal, as reflected by the great heme methyl proton shift spread. On the other hand, the small heme methyl proton shift spread of the His-N(term) form with an 11-residue stretch of PA proteins indicated that its Fe-N(term) bond is nearly parallel with the heme normal. The stability of the His-N(term) form was found to be affected by the structural properties of the N-terminal stretch, such as its length and the N-terminal residue. With a given N-terminal residue, the stability of the His-N(term) form is higher for a 9-residue N-terminal stretch than an 11-residue one. In addition, with a given length of the N-terminal stretch, the His-N(term) form with an N-terminal Glu is stabilized by a few kJ mol(-1) relative to that with an N-terminal Asn. These results provide a novel insight into the stabilizing interactions in the denatured cyts c that will facilitate elucidation of the folding/unfolding mechanisms of the proteins.

No abstract

Living organisms have one-handed structures of L-amino acids in proteins and D-sugars in nucleic acids. Although the origins of each one-handed structure (or homochirality) have been discussed for many years, these discussions have been restricted to monomeric compounds, such as amino acids and monosaccharides, or their stereospecific condensation reactions. Oligomers of these compounds have to be considered in the accumulation processes of homochirality because of the differences in physical properties of the diastereomers. High-performance liquid chromatography (HPLC) and the calculation of the partition coefficient values showed that the peptides having heterochiral sequences like L-Ala-D-Ala or D-Ala-L-Ala were more hydrophobic than the peptides having homochiral ones (L-Ala-L-Ala and D-Ala-D-Ala). Similar results were given from the calculation of most linear dipeptides and all cyclic ones composed of Gly, Ala, Val, or Asp. In addition, longer homo-oligopeptides composed of Ala, Val, or Asp also gave similar results. This general tendency would be useful for the separation of diastereomeric oligopeptides in water. The results also suggest that the separation of the homochiral peptides from the heterochiral ones by their solubility in water could have progressed in a primitive hydrosphere.

Several types of L-amino acid residues (Ser, Asp) in proteins are sometimes converted to D-amino acid residues by posttranslational isomerization. This phenomenon leads to an increase in hydrophobicity and results in their deposition from aqueous media. This research involves the hydrophobicity of oligopeptides containing D-amino acid residues, which may be generated by posttranslational isomerization (racemization or epimerization), to clarify the relationship between normal peptide residues composed of L-amino acids and the peptides containing D-amino acid residues. Calculated log P (log P(calc), where P is the octan-1-ol/H(2)O partition coefficient) values for many amino acids and oligopeptide diastereoisomers have been obtained by a semiempirical calculation method based on the PM5 Hamiltonian and compared with the experimental values (log P(exp)) reported in the literatures. A linear correlation was found between log P(calc) and log P(exp) except for basic and aromatic amino acids, and peptides. Calculations on homo-oligopeptide diastereoisomers composed of alanine, valine, leucine, and aspartic acid showed differences in log P(calc) values between diastereoisomers. Pentapeptides containing Asp residues that are most racemized or even inverted in alpha A-crystallin were also calculated to show that log P(calc) values of pentapeptides differ depending on the configuration (D or L) and kinds of linkage (alpha or beta) to their C-terminal amino acid residues.