Transferred nuclear Overhauser effect study of the C-terminal helix of yeast phosphoglycerate kinase: NMR solution structure of the C-terminal bound peptide

Role of hydrophobic interactions in yeast phosphoglycerate kinase stability

Cold denaturation of yeast phosphoglycerate kinase (yPGK) was investigated by a combination of far UV circular dichroism (CD), steady-state and time-resolved fluorescence, and small angle X-ray scattering. It was shown that cold denaturation of yPGK cannot be accounted for by a simple two-state process and that an intermediate state can be stabilized under mild denaturing conditions. Comparison between far UV CD and fluorescence shows that in this state the protein displays a fluorescence signal corresponding mainly to exposed tryptophans, whereas its CD signal is only partially modified. Comparison with spectroscopic data obtained from a mutant missing the last 12 amino-acids (yPGK delta404) suggests that lowering the temperature mainly results in a destabilization of hydrophobic interactions between the two domains. Small angle X-ray scattering measurements give further information about this stabilized intermediate. At 4 degrees C and in the presence of 0.45 M Gdn-HCl, the main species corresponds to a protein as compact as native yPGK, whereas a significant proportion of ellipticity has been lost. Although various techniques have shown the existence of residual structures in denatured proteins, this is one example of a compact denatured state devoid of its main content in alpha helices.

Conformations of peptide fragments from the FK506 binding protein: comparison with the native and urea-unfolded states

The helix-forming tendency of seven peptide fragments corresponding with the entire sequence of the FK506 binding protein (FKBP) has been investigated in aqueous buffer and in 2,2,2-trifluoroethanol (TFE) using CD and NMR spectroscopy. All fragments exhibited random coil conformations in aqueous buffer, whereas the amount of helix induced in the peptide fragments by TFE varied. The fragment with the highest degree of helicity in TFE corresponded with the single (alpha-helix in native FKBP. Fragments corresponding with beta-strands 2 and 3 also exhibited strong propensity towards helix formation. In contrast, the fragment corresponding with beta-strand 1 did not form helix in TFE. The inherent helix-forming tendencies are interpreted in light of the native structure to suggest possible folding nucleation sites. Conformational sampling in each peptide fragment was also compared with that observed in urea-denatured FKBP. With the exception of the fragment corresponding with beta-strand 2, the formation of helical structures in the peptide fragments in TFE was correlated with the observation of turn and/or helix conformers in urea-unfolded FKBP. Surprisingly, peptide fragments in aqueous solution were less structured than the corresponding regions in urea-denatured FKBP. The conformational differences between the peptide fragments and unfolded FKBP were not due to the urea buffer or to differences in their rotational correlation times. We conclude that local amino acid interactions are not generally sufficient to account for the formation of non-random conformations in unfolded FKBP. Formation of non-random structures in unfolded FKBP may require stabilization of incipient turn or helical conformations through transient contact with non-local non-polar residues.

A new metal-binding site for yeast phosphoglycerate kinase as determined by the use of a metal-ATP analog

Suicide substrate beta, gamma-bidentate Rh(III)ATP (RhATP) was used to map the metal ion-binding site in yeast phosphoglycerate kinase (PGK). Cleavage of the RhATP-inactivated enzyme with pepsin and subsequent separation of peptides by reverse-phase high-performance liquid chromatography gave two Rh-nucleotide bound peptides. One of the peptides corresponded to the C-terminal residues of PGK, and the other to a part of helix V. Of the four glutamates present in the C-terminal peptide, Glu 398 may be a likely metal coordination site. Therefore, importance of the C-terminal residues in PGK catalysis may be attributed, in part to the coordination of metal ion of the metal-ATP substrate. Metal coordination may then align the C-terminal peptide to extend toward the N-terminal domain and form the "closed" active site. Results presented in this paper suggest that one or more side chains of the enzyme may be coordinated to the metal ion in the PGK.3-phospho-D-glycerate-RhATP complex, and that exchange-inert metal-ATP analogs could be used to determine metal coordination sites on kinases and other metal-ATP-utilizing enzymes.