Effect of axial ligand plane reorientation on electronic and electrochemical properties observed in the A67V mutant of rat cytochrome b5

Pseudocontact Shifts in Biomolecular NMR Spectroscopy

Paramagnetic centers in biomolecules, such as specific metal ions that are bound to a protein, affect the nuclei in their surrounding in various ways. One of these effects is the pseudocontact shift (PCS), which leads to strong chemical shift perturbations of nuclear spins, with a remarkably long range of 50 Å and beyond. The PCS in solution NMR is an effect originating from the anisotropic part of the dipole-dipole interaction between the magnetic momentum of unpaired electrons and nuclear spins. The PCS contains spatial information that can be exploited in multiple ways to characterize structure, function, and dynamics of biomacromolecules. It can be used to refine structures, magnify effects of dynamics, help resonance assignments, allows for an intermolecular positioning system, and gives structural information in sensitivity-limited situations where all other methods fail. Here, we review applications of the PCS in biomolecular solution NMR spectroscopy, starting from early works on natural metalloproteins, following the development of non-natural tags to chelate and attach lanthanoid ions to any biomolecular target to advanced applications on large biomolecular complexes and inside living cells. We thus hope to not only highlight past applications but also shed light on the tremendous potential the PCS has in structural biology.

Protein Engineering of Electron Transfer Components from Electroactive Geobacter Bacteria

Electrogenic microorganisms possess unique redox biological features, being capable of transferring electrons to the cell exterior and converting highly toxic compounds into nonhazardous forms. These microorganisms have led to the development of Microbial Electrochemical Technologies (METs), which include applications in the fields of bioremediation and bioenergy production. The optimization of these technologies involves efforts from several different disciplines, ranging from microbiology to materials science. Geobacter bacteria have served as a model for understanding the mechanisms underlying the phenomenon of extracellular electron transfer, which is highly dependent on a multitude of multiheme cytochromes (MCs). MCs are, therefore, logical targets for rational protein engineering to improve the extracellular electron transfer rates of these bacteria. However, the presence of several heme groups complicates the detailed redox characterization of MCs. In this Review, the main characteristics of electroactive Geobacter bacteria, their potential to develop microbial electrochemical technologies and the main features of MCs are initially highlighted. This is followed by a detailed description of the current methodologies that assist the characterization of the functional redox networks in MCs. Finally, it is discussed how this information can be explored to design optimal Geobacter-mutated strains with improved capabilities in METs.

Determination of the magnetic properties and orientation of the heme axial ligands of PpcA from Geobacter metallireducens by paramagnetic NMR

The rising interest in the use of Geobacter bacteria for biotechnological applications demands a deep understanding of how these bacteria are able to thrive in a variety of environments and perform extracellular electron transfer. The Geobacter metallireducens bacterium can couple the oxidation of a wide range of compounds to the reduction of several extracellular acceptors, including heavy metals, toxic organic compounds or electrode surfaces. The periplasmic c-type cytochrome PpcA from this bacterium is a member of a family composed of five periplasmic triheme cytochromes, which are important to bridge the electron transfer between the cytoplasm and the extracellular environment. To better understand the functional mechanism of PpcA it is essential to obtain structural data for this cytochrome. In this work, the geometry of the heme axial ligands, as well as the magnetic properties of the hemes were determined for the oxidized form of the cytochrome, using the ¹³C NMR chemical shifts of the heme α-substituents. The results were further compared with those previously obtained for the homologous cytochrome from Geobacter sulfurreducens. The orientations of the axial histidine planes and the magnetic properties of the hemes are conserved in both proteins. Overall, the results obtained allowed the definition of the orientation of the magnetic axes of PpcA from G. metallireducens, which will be used as constraints to assist the solution structure determination of the cytochrome in the oxidized form.

Redox- and pH-linked conformational changes in triheme cytochrome PpcA from Geobacter sulfurreducens

The periplasmic triheme cytochrome PpcA from Geobacter sulfurreducens is highly abundant; it is the likely reservoir of electrons to the outer surface to assist the reduction of extracellular terminal acceptors; these include insoluble metal oxides in natural habitats and electrode surfaces from which electricity can be harvested. A detailed thermodynamic characterization of PpcA showed that it has an important redox-Bohr effect that might implicate the protein in e^-/H⁺ coupling mechanisms to sustain cellular growth. This functional mechanism requires control of both the redox state and the protonation state. In the present study, isotope-labeled PpcA was produced and the three-dimensional structure of PpcA in the oxidized form was determined by NMR. This is the first solution structure of a G. sulfurreducens cytochrome in the oxidized state. The comparison of oxidized and reduced structures revealed that the heme I axial ligand geometry changed and there were other significant changes in the segments near heme I. The pH-linked conformational rearrangements observed in the vicinity of the redox-Bohr center, both in the oxidized and reduced structures, constitute the structural basis for the differences observed in the pK_a values of the redox-Bohr center, providing insights into the e^-/H⁺ coupling molecular mechanisms driven by PpcA in G. sulfurreducens.

Direct electrochemical analyses of human cytochromes b5 with a mutated heme pocket showed a good correlation between their midpoint and half wave potentials

Background

Cytochrome b₅ performs central roles in various biological electron transfer reactions, where difference in the redox potential of two reactant proteins provides the driving force. Redox potentials of cytochromes b₅ span a very wide range of ~400 mV, in which surface charge and hydrophobicity around the heme moiety are proposed to have crucial roles based on previous site-directed mutagenesis analyses.

Methods

Effects of mutations at conserved hydrophobic amino acid residues consisting of the heme pocket of cytochrome b₅ were analyzed by EPR and electrochemical methods. Cyclic voltammetry of the heme-binding domain of human cytochrome b₅ (HLMWb₅) and its site-directed mutants was conducted using a gold electrode pre-treated with β-mercarptopropionic acid by inclusion of positively-charged poly-L-lysine. On the other hand, static midpoint potentials were measured under a similar condition.

Results

Titration of HLMWb₅ with poly-L-lysine indicated that half-wave potential up-shifted to -19.5 mV when the concentration reached to form a complex. On the other hand, midpoint potentials of -3.2 and +16.5 mV were obtained for HLMWb₅ in the absence and presence of poly-L-lysine, respectively, by a spectroscopic electrochemical titration, suggesting that positive charges introduced by binding of poly-L-lysine around an exposed heme propionate resulted in a positive shift of the potential. Analyses on the five site-specific mutants showed a good correlation between the half-wave and the midpoint potentials, in which the former were 16~32 mV more negative than the latter, suggesting that both binding of poly-L-lysine and hydrophobicity around the heme moiety regulate the overall redox potentials.

Conclusions

Present study showed that simultaneous measurements of the midpoint and the half-wave potentials could be a good evaluating methodology for the analyses of static and dynamic redox properties of various hemoproteins including cytochrome b₅. The potentials might be modulated by a gross conformational change in the tertiary structure, by a slight change in the local structure, or by a change in the hydrophobicity around the heme moiety as found for the interaction with poly-L-lysine. Therefore, the system consisting of cytochrome b₅ and its partner proteins or peptides might be a good paradigm for studying the biological electron transfer reactions.

Structural propensities in the heme binding region of apocytochrome b5. II. Heme conjugates

In the absence of heme cofactor, the water-soluble domain of rat microsomal cytochrome b5 (cyt b5) contains a long flexible region within its 42-residue heme-binding loop. Heme capture induces this region to fold into a well-defined structure containing helices H3-H5, each separated by a turn, with His39 and His63 serving as axial ligands to the heme iron. We have shown that the H4 region of the apoprotein has the greatest tendency for disorder within the isolated binding loop. Here, the effect of the His63-iron bond and proximity of heme plane on the population of helical conformation in H4 and H5 was investigated by synthesis and characterization of a peptide-sandwiched mesoheme construct in which two H4-H5 peptides were covalently attached to a single cofactor. Spectroscopic data indicated that a holoprotein-like bis-histidine coordination state was achieved over a pH range from 7 to 9. Trifluoroethanol titrations of the construct and the analogous free peptide under these pH conditions revealed that heme proximity and iron ligation were insufficient to promote helix formation in H4 and H5. These observations were used to assess the role of disordered regions in heme capture and the loop-scaffold interface in holoprotein folding and stability.

Structural and thermodynamic encoding in the sequence of rat microsomal cytochrome b(5)

The water-soluble domain of rat microsomal cytochrome b(5) is a convenient protein with which to inspect the connection between amino acid sequence and thermodynamic properties. In the absence of its single heme cofactor, cytochrome b(5) contains a partially folded stretch of 30 residues. This region is recognized as prone to disorder by programs that analyze primary structures for such intrinsic features. The cytochrome was subjected to amino acid replacements in the folded core (I12A), in the portion that refolds only when in contact with the heme group (N57P), and in both (F35H/H39A/L46Y). Despite the difficulties associated with measuring thermodynamic quantities for the heme-bound species, it was possible to rationalize the energetic consequences of both types of replacements and test a simple equation relating apoprotein and holoprotein stability. In addition, a phenomenological relationship between the change in T(m) (the temperature at the midpoint of the thermal transition) and the change in thermodynamic stability determined by chemical denaturation was observed that could be used to extend the interpretation of incomplete holoprotein stability data. Structural information was obtained by nuclear magnetic resonance spectroscopy toward an atomic-level analysis of the effects.

Electrochemical investigation of the effect of some organic phosphates on haemoglobin

The effects of DPG,IHP,GTP,GDP and GMP on the structure and stability of haemoglobin were electrochemically investigated with an iodide-modified silver electrode in 0.01 M KNO 3 at pH 7.0.Anodic and cathodic peaks of haemoglobin were observed at 250 mV and 12 mV with a formal potential value of 133 mV vs.Ag/AgCl.The effects of different concentrations of DPG,IHP,GTP,GDP and GMP on the anaerobic redox reaction were determined. The results showed that DPG and IHP can lead to a positive shift in the reduction peak of haemoglobin,indicating that the oxidation peak shift of haemoglobin was small as a result of stabilization of the reduced state and destabilization of the R-like state of haemoglobin.GTP elicited a more positive shift in the cathodic and anodic peaks of haemoglobin at a higher concentration,signifying that it has a low-affinity binding site on haemoglobin.The positive shift of the cathodic and anodic peaks revealed a slight variation in the structure and indicated the unfolding of haemoglobin in the presence of high concentrations of GTP.Our study also showed that GDP and GMP did not cause significant shift the cathodic and anodic peaks of haemoglobin even at high concentrations,refuting the existence of specific GDP-and GMP-binding sites on the protein.Moreover,the iodide-modified silver electrode method proved to be easy and useful in investigating the effects of ligands or other effectors on haemoglobin in solution.

Characterization of Heme-Coordinating Histidyl Residues of Cytochrome b5 Based on the Reactivity with Diethylpyrocarbonate: A Mechanism for the Opening of Axial Imidazole Rings

We investigated the reactivity of heme-coordinating imidazole with diethylpyrocarbonate using a soluble domain of cytochrome b(5). Analyses with various spectroscopic methods including MALDI-TOF-MS indicated that two axial His residues (His44 and His68) of cytochrome b(5) were protected from the modification by several factors, i.e., limited steric exposure of the axial imidazole to the solvent, the Fe-N(epsilon2) coordination bond, and protonation of the N(delta1) position by forming a hydrogen bond with its immediate surroundings. However, once N-carbethoxylation at the N(epsilon2) position of the axial His residues occurred with a higher concentration of diethylpyrocarbonate, displacement of heme prosthetic group from the protein moiety continued. Simultaneously, it facilitated the second N-carbethoxylation to take place at the N(epsilon1) position of the same imidazole ring, leading to a bis-N-carbethoxylated derivative and further to a ring-opened derivative. A similar mechanism seemed in operation for one non-axial His residue (His85), in which the N(delta1) atom works as a hydrogen acceptor in a strong hydrogen-bond and the other N(epsilon2) atom is in a protonated form, resulting in a formation of the ring-opened derivative upon treatment with a higher concentration of diethylpyrocarbonate. These results suggested that the use of diethylpyrocarbonate for MALDI-TOF-MS analysis might provide a unique method to characterize the protonation state of His residues and the strength of their hydrogen-bondings at the active site of enzymes.

Characterization of the heme–histidine cross-link in cyanobacterial hemoglobins from Synechocystis sp. PCC 6803 and Synechococcus sp. PCC 7002

The recombinant product of the hemoglobin gene of the cyanobacterium Synechocystis sp. PCC 6803 forms spontaneously a covalent bond linking one of the heme vinyl groups to a histidine located in the C-terminal helix (His117, or H16). The present report describes the (1)H, (15)N, and (13)C NMR spectroscopy experiments demonstrating that the recombinant hemoglobin from the cyanobacterium Synechococcus sp. PCC 7002, a protein sharing 59% identity with Synechocystis hemoglobin, undergoes the same facile heme adduct formation. The observation that the extraordinary linkage is not unique to Synechocystis hemoglobin suggests that it constitutes a noteworthy feature of hemoglobin in non-N(2)-fixing cyanobacteria, along with the previously documented bis-histidine coordination of the heme iron. A qualitative analysis of the hyperfine chemical shifts of the ferric proteins indicated that the cross-link had modest repercussions on axial histidine ligation and heme electronic structure. In Synechocystis hemoglobin, the unreacted His117 imidazole had a normal p K(a) whereas the protonation of the modified residue took place at lower pH. Optical experiments revealed that the cross-link stabilized the protein with respect to thermal and acid denaturation. Replacement of His117 with an alanine yielded a species inert to adduct formation, but inspection of the heme chemical shifts and ligand binding properties of the variant identified position 117 as important in seating the cofactor in its site and modifying the dynamic properties of the protein. A role for bis-histidine coordination and covalent adduct formation in heme retention is proposed.

1H NMR studies of the effect of mutation at Valine45 on heme microenvironment of cytochrome b5

1D and 2D (1)H NMR were employed to probe the effects on the heme microenvironment of cytochrome b(5) caused by the mutation from Val45 to Tyr45, His45 and Glu45. Compared with wild type (WT) cytochrome b(5), in all mutants the heme ring are CCW rotated relative to the imidazole planes of axial ligands and the angles beta between two axial ligand imidazole planes are not changed, being in agreement with the temperature dependence of the shifts of the heme protons. The ratios of heme isomers (major to minor) are smaller than that in WT. The 4-vinyl group of the heme in V45Y assumes cis-orientation, being similar to that of WT, while in V45E and V45H, both cis and trans orientation are found. The relationships between the structure and biological function of the mutants are discussed in terms of the geometry of heme and axial ligands, the hydrophobicity of heme pocket and the electrostatic potential of the heme-exposed area.

The effect of mutation at valine-45 on the stability and redox potentials of trypsin-cleaved cytochrome b5

In an attempt to elucidate the determinants of redox potential and protein stability in cytochrome b5, three mutants at a highly conserved residue Val45, which is a member of heme hydrophobic pocket residues have been characterized. The V45Y mutant was designed to introduce a bulkier residue and a hydroxyl group to the heme pocket. The mutants V45H and V45E were constructed to test the effect of positive and negative charge on the stability and redox potential of proteins. The influence of these mutants on the protein stability towards thermal, urea, acid, ethanol and on the redox potential were studied. It is concluded that the decrease of hydrophobic free energy and the larger volume of the tyrosine make the phenylhydroxyl group of tyrosine still sitting inside the hydrophobic pocket, while the side chain of the mutant V45E and V45H shift away from the heme pocket. The redox potentials of mutants V45Y, V45H, V45E and wild-type of cytochrome b5 are -35 mV, 8 mV, -26 mV and -3 mV, respectively. The bigger change of the V45Y on redox potential is due to the close contact between the hydroxyl group and the heme, while the changes of the V45E and V45H result from the alteration of charge density and distribution around the heme. Different relative stability of these mutants towards heat have been observed with the order: WT > V45Y-V45H > V45E being both in the oxidized and reduced state. The relative stability induced by addition of urea decreases in the order: WT > V45Y > V45H > V45E. These results suggest that the difference in the hydrophobic free energy is a major factor contributing to the stability of the Val45 mutants. Also the loose of the helix III in the mutant V45E makes it more unstable. These results indicate that residue Val45 plays an important role in the stability and redox potential of the protein.