The identification of cation-binding domains on the surface of microsomal cytochrome b5 using 1H-NMR paramagnetic difference spectroscopy

Phospholipid membranes affect tertiary structure of the soluble cytochrome b5 heme-binding domain

The influence of charged phospholipid membranes on the conformational state of the water-soluble fragment of cytochrome b5 has been investigated by a variety of techniques at neutral pH. The results of this work provide the first evidence that aqueous solutions with high phospholipid/protein molar ratios (pH 7.2) induce the cytochrome to undergo a structural transition from the native conformation to an intermediate state with molten-globule like properties that occur in the presence of an artificial membrane surface and that leads to binding of the protein to the membrane. At other phospholipid/protein ratios, equilibrium was observed between cytochrome free in solution and cytochrome bound to the surface of vesicles. Inhibition of protein binding to the vesicles with increasing ionic strength indicated for the most part an electrostatic contribution to the stability of cytochrome b5-vesicle interactions at pH 7.2. The possible physiological role of membrane-induced conformational change in the structure of cytochrome b5 upon the interaction with its redox partners is discussed.

A further investigation of the cytochrome b5-cytochrome c complex

The interaction of reduced rabbit cytochrome b(5) with reduced yeast iso-1 cytochrome c has been studied through the analysis of (1)H-(15)N HSQC spectra, of (15)N longitudinal ( R(1)) and transverse ( R(2)) relaxation rates, and of the solvent exchange rates of protein backbone amides. For the first time, the adduct has been investigated also from the cytochrome c side. The analysis of the NMR data was integrated with docking calculations. The result is that cytochrome b(5) has two negative patches capable of interacting with a single positive surface area of cytochrome c. At low protein concentrations and in equimolar mixture, two different 1:1 adducts are formed. At high concentration and/or with excess cytochrome c, a 2:1 adduct is formed. All the species are in fast exchange on the scale of differences in chemical shift. By comparison with literature data, it appears that the structure of one 1:1 adduct changes with the origin or primary sequence of cytochrome b(5).

Molecular dynamics simulation of cytochrome b5: implications for protein-protein recognition

Cytochrome b5 participates in electron-transfer reactions with a variety of different proteins. To explore how this protein might discern between structurally varied proteins, we have performed a molecular dynamics simulation focusing on its structural stability and dynamic behavior in solution. The protein was simulated in water at 298 K and pH 6.9 for 2.5 ns. The protein deviated significantly from the crystal structure midway through the simulation, but ultimately the crystalline conformation was regained. The simulation was at all times well behaved as judged by comparison to structural NMR data obtained in solution. One region of the protein backbone that deviated from the crystal conformation contains acidic residues implicated in electrostatic-based protein-protein recognition. The mobility in this region caused the protein to display different patterns of residues at the surface with time, as well as the formation of a large cleft partially exposing the hydrophobic core lining the heme pocket. Furthermore, the position and cyclical formation of this cleft suggest that hydrophobic interactions may be important in protein-protein recognition events and possibly even electron transfer, as the cleft allows for easy access to the heme group. These results indicate that thermal motion could provide a low-energy mechanism for controlling recognition events. Thus, the dynamical behavior observed through the varying solution conformations sampled may be important in influencing the diverse range of protein-protein interactions in which cytochrome b5 participates.

Experimental and theoretical analysis of the interaction between cytochrome c and cytochrome b5

Experimental and theoretical investigation of the interaction of cytochrome c and cytochrome b5 performed over nearly twenty years has produced considerable insight into the manner in which these proteins recognize and bind to each other. The results of these studies and the experimental and theoretical strategies that have been developed to achieve these results have significant implications for understanding the behavior of similar complexes formed by more complex and less-well characterized electron transfer proteins. The current review provides a comprehensive summary and critical evaluation of the literature on which the current status of our understanding of the interaction of cytochrome c and cytochrome b5 is based. The general issues related to the study of electron transfer complexes of this type are discussed and some new directions for future investigation of such systems are considered.

The cytochrome b5-fold: an adaptable module

The family of b5-like cytochromes encompasses, besides cytochrome b5 itself, hemoprotein domains covalently associated with other redox proteins, in flavocytochrome b2 (L-lactate dehydrogenase), sulfite oxidase and assimilatory nitrate reductase. A comparison of about 40 amino acid sequences deposited in data banks shows that eight residues are invariant and about 15 positions carry strongly conservative substitutions. Examination of the location of these invariant and conserved positions in the light of the three-dimensional structures of beef cytochrome b5 and S cerevisiae flavocytochrome b2 suggests a strongly conserved protein structure for the b5-like heme-binding domain throughout evolution. Numerous NMR studies have demonstrated the existence of a positional isomerism for the heme, which involves both a 180 degree-rotation around the heme alpha,gamma-meso carbon atoms and a rotation through an axis normal to the heme plane at the iron. NMR studies did not detect significant differences in protein structure between reduced and oxidized states, or between species. The role of a number of side chains was probed by site-directed mutagenesis. Studies of complex formation and of electron transfer rates between cytochrome b5 and redox partners have led to the idea that complexation is driven by electrostatic forces, that it is generally the exposed heme edge which makes contact with electron donors and acceptors, but that there are multiple overlapping sites within this general area. For the bi- and trifunctional members of the family, extrapolation of available data would suggest a mobile heme-binding domain within a complex structure. In these cases the existence of a single interaction area for both electron donor and acceptor, or of two different ones, remains open to discussion.