Redox state and chain folding in cytochrome c

Structural basis of heme reactivity in myoglobin and leghemoglobin: thermal difference spectra

Thermal pertubation difference spectra of sperm whale myoglobin (Mb) and soybean leghemoglobin a (Lb a) in the near-ultraviolet reveal similarities in the tryptophan environment of the two proteins. Of the two tryptophans in each protein, one has its indolyl NH group fully exposed to aqueous solvent, while the other behaves as if it were surrounded by motile but nonpolar residues with little access to water. These environments are not significantly altered by removal of the heme group. Assuming conformational homology, the helix-spacing role of Trp-A12 in Mb (Kendrew, J.C. (1962), Brookhaven Symp. Biol. 15, 216-228) may be taken over, in Lb a, by Trp-H8 which, though remote in linear sequence, would occupy a suitable spatial location. Thermal difference spectra in the Soret and visible regions of pure high-spin (fluoroferric) and pure low-spin (cyanoferric) complexes showed a red shift on cooling Mb complexes, reflecting a predominantly nonpolar environment around the heme, but a blue shift on cooling Lb complexes, reflecting a more solvent-exposed environment. Thermal difference spectra using rose bengal as a probe of the heme pockets in the two apoproteins supported these conclusions. Thermal difference spectra for the high-spin complexes of both Mb and Lb are slightly larger in magnitude than in the low-spin complexes. This may reflect a more flexible heme pocket in the high-spin state, as suggested by recent circular dichroic results. A structural basis for the high oxygen affinity of Lb compared with Mb is proposed, based upon the observed differences in polarity and flexibility of the heme pocket and in amino acid substitutions.

The uptake and extrusion of monovalent cations by isolated heart mitochondria

The factors involved in the movement of monovalent cations across the inner membrane of the isolate heart mitochondrion are reviewed. The evidence suggests that the energy-dependent uptake of K+ and Na+ which results in swelling of the matrix is an electrophoretic response to a negative internal potential. There are no clear cut indications that this electrophoretic cation movement is carrier-mediated and possible modes of entry which do not require a carrier are examined. The evidence also suggests that the monovalent cation for proton exchanger (Na+ greater than K+) present in the membrane may participate in the energy-dependent extrusion of accumulated ions. The two processes, electrophoreti c cation uptake (swelling) and exchange-dependent cation extrusion (contraction) may represent a means of controlling the volume of the mitochondrion within the functioning cell. A number of indications point to the possibility that the volume control process may be mediated by the divalent cations Ca+2 and Mg+2. Studies with mercurial reagents also implicate certain membrane thiol groups in the postulated volume control process.

Hydrogen-isotope exchange of oxidized and reduced cytochrome c. A comparison of mass spectrometry and infrared methods

Hydrogen-deuterium exchange in 2H20 solutions of the two redox states of horse heart cytochrome c was investigated at 20 degrees C, pH 7, by mass spectrometry and infrared spectroscopy. Mass spectrometry indicates that ferricytochrome has 20 hydrogens unexchanged after 24 h, 28 hydrogens exchanging between 10 min and 24 h, and 156 hydrogens exchanging within 10 min; comparative values for ferrocytochrome are 45, 19 and 140. The displacement of the exchange curves obtained by infrared corresponds to 8 to 9 peptide hydrogens. These combined methods show many non-peptide hydrogens exchanging rapidly (87 and 79 for ferricytochrome c and ferrocytochrome c respectively), whereas others, probably buried inside the molecule and involved in hydrogen bonds, are not exchanged, even after 24 h (14 and 30 hydrogens respectively, which is relatively large for a small protein). Infrared results are given in terms of changes of standard free energy for the transconformational reaction which exposes the peptide hydrogens to solvent: in ferricytochrome c and ferrycoytochrome c, 30% and 40% respectively of the peptide hydrogens are protected by conformational transitions stabilized by more than 5 kcal/mol (21 kJ/mol), which implies a large increase in rigidity for the reduced form.

Hypothesis on the role of liganded states of proteins in energy transducing systems

In energy transducing systems the direction of energy transfer is proposed to be maintained by the synchronized turnovers of the conformational change of one protein coupling up to affect another. Catalysis by those systems implies, therefore, that under new space restrictions the groups of the transducing enzyme increase and decrease reactivity between themselves, with activatory and/or inhibitory ligands (H+, H2O, metals, etc.) and with the electron shells of the reactant molecules. The exergonic reaction-dependent turnover of the forms of the enzyme within the transition complexes would be maintained, therefore, under asymmetric phase angles of conformational-dependent reactivity that would effectively restrict the microscopic reversibility of transducing systems. Some well known reactions, such as hemoglobins Bohr effect, can be used to illustrate that microscopic (molecular) interactions subject to thermodynamic equilibria laws may similarly paricipate as driving forces in energy transducing sytems. This would allow the thermodynamic description of the role of proton translocation as that of a modificatory force of the structural parameters of proteins. Similarly, the relationship between the liganded states of hemoglobin and its change in conformation has been used to develop an illustrative model relating changes in oxido-reduction of electron carriers to induced-fit effects leading to a sequence of ATPase forms in transition complexes which become stabilized as high energy intermediates under the constraints imposed by the membrane of energy transducing organelles.

Conformational energy refinement of horse-heart ferricytochrome c

The reported X-ray structure of horse-heart ferricytochrome c has been refined by conformational energy calculations, using a three-stage computational procedure. In stage I, the atomic positions are adjusted to conform to idealized bond lengths and bond angles characteristic of small amino acid derivatives, while yet remaining as close as possible to the X-ray coordinates. In stage II, atomic overlaps are eliminated by adjusting the backbone and side-chain dihedral angles to minimize the nonbonded energy, hydrogen-bonded energy, and rotational energy contributions. In the final stage of refinement, the electrostatic energy and a more accurate hydrogen-bonded energy treatment are considered, in addition to the energy contributions of stage II. A "fitting potential" of gradually decreasing strength is imposed in both stages II and III, in order to keep the computed structure as similar to the x-ray structure as is consistent with a low-energy conformation. The final computed structure of cytochrome c exhibits a very low conformational energy (-504 kcal/mol) and also closely resembles the X-ray structure (RMS deviation = 0.77 A for all atoms). However, a special treatment was required in order to alter the location of the phenyl ring of phenylalanine-82. In contrast to the originally published X-ray structure, which shows the phenyl ring pointing away from the heme, the phenyl ring in the computed structure is tucked into the heme crevice, in a position similar to that observed in the reduced form of tuna cytochrome c, in the oxidized form of Rhodospirillum rubrum cytochrome c2, and also in the recently determined structure of oxidized tuna cytochrome c.

Energy transfer mechanisms in mitochondria

The problem of free energy transfer and transduction in mitochondria is reviewed from the point of view of conservative and dissipative mechanisms. Excited states are inherently dissipative and are not considered viable possibilities. If the free energy is already a local minimum and present in the form of potential energy, conservative transfer is possible within a properly designed medium. The design features are compatible with what is known about mitochondria.