Selective site deuteration on the sugar ring as an efficient marker of conformation in nucleosides: The CD stretching mode of the (2′-R)-[2′-2H]-2′-deoxyuridine and its 3′,5′-O-(1,1,3,3-tetraisopropyldisiloxan-1,3-diyl)-derivative

Redox-Coupled Dynamics and Folding in Cytochrome c

Cytochrome c functions as an electron carrier in the mitochondrial electron-transport chain using the Fe(II)-Fe(III) redox couple of a covalently attached heme prosthetic group, and it has served as a paradigm for both biological redox activity and protein folding. On the basis of a wide variety of biophysical techniques, it has been suggested that the protein is more flexible in the oxidized state than in the reduced state, which has led to speculation that it is the dynamics of the protein that has been evolved to control the cofactor's redox properties. To test this hypothesis, we incorporated carbon-deuterium bonds throughout cytochrome c and characterized their absorption frequencies and line widths using IR spectroscopy. The absorption frequencies of several residues on the proximal side of the heme show redox-dependent changes, but none show changes in line width, implying that the flexibility of the oxidized and reduced proteins is not different. However, the spectra demonstrate that folded protein is in equilibrium with a surprisingly large amount of locally unfolded protein, which increases with oxidation for residues localized to the proximal side of the heme. The data suggest that while the oxidized protein is not more flexible than the reduced protein, it is more locally unfolded. Local unfolding of cytochrome c might be one mechanism whereby the protein evolved to control electron transfer.

Detecting protein-protein interactions by isotope-edited infrared spectroscopy: a numerical approach

We present a theoretical and numerical analysis of the vibrational coupling between isotope-edited amino acids in protein dimers. Depending on the presence and magnitude of coupling between 13Calpha=O peptide bond oscillators, characteristic level splittings of vibrational eigenstates are predicted. For the example of the Gramicidin A ion channel polypeptide, we observe typical IR fingerprints for the head-to-head and the antiparallel double-helical conformation of the dimer. We suggest that these findings can be used to clearly identify the structure of polypeptide aggregates using a particularly simple isotope substitution pattern.