Tuning Radical Relay Residues by Proton Management Rescues Protein Electron Hopping

Transient tyrosine and tryptophan radicals play key roles in the electron transfer (ET) reactions of photosystem (PS) II, ribonucleotide reductase (RNR), photolyase, and many other proteins. However, Tyr and Trp are not functionally interchangeable, and the factors controlling their reactivity are often unclear. Cytochrome c peroxidase (CcP) employs a Trp191^•+ radical to oxidize reduced cytochrome c (Cc). Although a Tyr191 replacement also forms a stable radical, it does not support rapid ET from Cc. Here we probe the redox properties of CcP Y191 by non-natural amino acid substitution, altering the ET driving force and manipulating the protic environment of Y191. Higher potential fluorotyrosine residues increase ET rates marginally, but only addition of a hydrogen bond donor to Tyr191^• (via Leu232His or Glu) substantially alters activity by increasing the ET rate by nearly 30-fold. ESR and ESEEM spectroscopies, crystallography, and pH-dependent ET kinetics provide strong evidence for hydrogen bond formation to Y191^• by His232/Glu232. Rate measurements and rapid freeze quench ESR spectroscopy further reveal differences in radical propagation and Cc oxidation that support an increased Y191^• formal potential of ∼200 mV in the presence of E232. Hence, Y191 inactivity results from a potential drop owing to Y191^•+ deprotonation. Incorporation of a well-positioned base to accept and donate back a hydrogen bond upshifts the Tyr^• potential into a range where it can effectively oxidize Cc. These findings have implications for the Y_Z/Y_D radicals of PS II, hole-hopping in RNR and cryptochrome, and engineering proteins for long-range ET reactions.

Constraints on the Radical Cation Center of Cytochrome c Peroxidase for Electron Transfer from Cytochrome c

The tryptophan 191 cation radical of cytochrome c peroxidase (CcP) compound I (Cpd I) mediates long-range electron transfer (ET) to cytochrome c (Cc). Here we test the effects of chemical substitution at position 191. CcP W191Y forms a stable tyrosyl radical upon reaction with peroxide and produces spectral properties similar to those of Cpd I but has low reactivity toward reduced Cc. CcP W191G and W191F variants also have low activity, as do redox ligands that bind within the W191G cavity. Crystal structures of complexes between Cc and CcP W191X (X = Y, F, or G), as well as W191G with four bound ligands reveal similar 1:1 association modes and heme pocket conformations. The ligands display structural disorder in the pocket and do not hydrogen bond to Asp235, as does Trp191. Well-ordered Tyr191 directs its hydroxyl group toward the porphyrin ring, with no basic residue in the range of interaction. CcP W191X (X = Y, F, or G) variants substituted with zinc-porphyrin (ZnP) undergo photoinduced ET with Cc(III). Their slow charge recombination kinetics that result from loss of the radical center allow resolution of difference spectra for the charge-separated state [ZnP(+), Cc(II)]. The change from a phenyl moiety at position 191 in W191F to a water-filled cavity in W191G produces effects on ET rates much weaker than the effects of the change from Trp to Phe. Low net reactivity of W191Y toward Cc(II) derives either from the inability of ZnP(+) or the Fe-CcP ferryl to oxidize Tyr or from the low potential of the resulting neutral Tyr radical.

Control of cyclic photoinitiated electron transfer between cytochrome c peroxidase (W191F) and cytochrome c by formation of dynamic binary and ternary complexes

Extensive studies of the physiological protein-protein electron-transfer (ET) complex between yeast cytochrome c peroxidase (CcP) and cytochrome c (Cc) have left unresolved questions about how formation and dissociation of binary and ternary complexes influence ET. We probe this issue through a study of the photocycle of ET between Zn-protoporphyrin IX-substituted CcP(W191F) (ZnPCcP) and Cc. Photoexcitation of ZnPCcP in complex with Fe(3+)Cc initiates the photocycle: charge-separation ET, [(3)ZnPCcP, Fe(3+)Cc] → [ZnP(+)CcP, Fe(2+)Cc], followed by charge recombination, [ZnP(+)CcP, Fe(2+)Cc] → [ZnPCcP, Fe(3+)Cc]. The W191F mutation eliminates fast hole hopping through W191, enhancing accumulation of the charge-separated intermediate and extending the time scale for binding and dissociation of the charge-separated complex. Both triplet quenching and the charge-separated intermediate were monitored during titrations of ZnPCcP with Fe(3+)Cc, Fe(2+)Cc, and redox-inert CuCc. The results require a photocycle that includes dissociation and/or recombination of the charge-separated binary complex and a charge-separated ternary complex, [ZnP(+)CcP, Fe(2+)Cc, Fe(3+)Cc]. The expanded kinetic scheme formalizes earlier proposals of "substrate-assisted product dissociation" within the photocycle. The measurements yield the thermodynamic affinity constants for binding the first and second Cc: KI = 10(-7) M(-1), and KII = 10(-4) M(-1). However, two-site analysis of the thermodynamics of formation of the ternary complex reveals that Cc binds at the weaker-binding site with much greater affinity than previously recognized and places upper bounds on the contributions of repulsion between the two Cc's of the ternary complex. In conjunction with recent nuclear magnetic resonance studies, the analysis further suggests a dynamic view of the ternary complex, wherein neither Cc necessarily faithfully adopts the crystal-structure configuration because of Cc-Cc repulsion.

Replacement of an electron transfer pathway in cytochrome c peroxidase with a surrogate peptide

A proposed electron transfer pathway in cytochrome c peroxidase was previously excised from the structure by design. The engineered channel mutant was shown to bind peptide surrogates without restoration of cyt c oxidation. Here, we report the 1.6 A crystal structure of (N-benzimidazole-propionic acid)-Gly-Ala-Ala bound within the engineered channel. The peptide retains many features of the native electron transfer pathway: placement of benzimidazole at the position of the Trp-191 radical, hydrogen bonding to Asp235, and positioning of the C-terminus near the point where wild type CcP makes closest contact to cyt c. The inability of this surrogate pathway to restore function supports proposals that electron transfer requires the Trp-191 radical.

EPR and ENDOR studies of cryoreduced compounds II of peroxidases and myoglobin. Proton-coupled electron transfer and protonation status of ferryl hemes

The nature of the [Fe(IV)-O] center in hemoprotein Compounds II has recently received considerable attention, as several experimental and theoretical investigations have suggested that this group is not necessarily the traditionally assumed ferryl ion, [Fe(IV)=O]2+, but can be the protonated ferryl, [Fe(IV)-OH]3+. We show here that cryoreduction of the EPR-silent Compound II by gamma-irradiation at 77 K produces Fe(III) species retaining the structure of the precursor [Fe(IV)=O]2+ or [Fe(IV)-OH]3+, and that the properties of the cryogenerated species provide a report on structural features and the protonation state of the parent Compound II when studied by EPR and 1H and 14N ENDOR spectroscopies. To give the broadest view of the properties of Compounds II we have carried out such measurements on cryoreduced Compounds II of HRP, Mb, DHP and CPO and on CCP Compound ES. EPR and ENDOR spectra of cryoreduced HRP II, CPO II and CCP ES are characteristic of low-spin hydroxy-Fe(III) heme species. In contrast, cryoreduced "globins", Mb II, Hb II, and DHP II, show EPR spectra having lower rhombicity. In addition the cryogenerated ferric "globin" species display strongly coupled exchangeable (1)H ENDOR signals, with A max approximately 20 MHz and a iso approximately 14 MHz, both substantially greater than for hydroxide/water ligand protons. Upon annealing at T > 180 K the cryoreduced globin compounds II relax to the low-spin hydroxy-ferric form with a solvent kinetic isotope effect, KIE > 6. The results presented here together with published resonance Raman and Mossbauer data suggest that the high-valent iron center of globin and HRP compounds II, as well as of CCP ES, is [Fe(IV)=O]2+, and that its cryoreduction produces [Fe(III)-O]+. Instead, as proposed by Green and co-workers, CPO II contains [Fe(IV)-OH]3+ which forms [Fe(III)-OH]2+ upon radiolysis. The [Fe(III)-O]+ generated by cryoreduction of HRP II and CCP ES protonate at 77 K, presumably because the heme is linked to a distal-pocket hydrogen bonding/proton-delivery network through an H-bond to the "oxide" ligand. The data also indicate that Mb and HRP compounds II exist as two major conformational substates.

Solvent Isotope Effects on Interfacial Protein Electron Transfer in Crystals and Electrode Films

D(2)O-grown crystals of yeast zinc porphyrin substituted cytochrome c peroxidase (ZnCcP) in complex with yeast iso-1-cytochrome c (yCc) diffract to higher resolution (1.7 A) and pack differently than H(2)O-grown crystals (2.4-3.0 A). Two ZnCcP's bind the same yCc (porphyrin-to-porphyrin separations of 19 and 29 A), with one ZnCcP interacting through the same interface found in the H(2)O crystals. The triplet excited-state of at least one of the two unique ZnCcP's is quenched by electron transfer (ET) to Fe(III)yCc (k(e) = 220 s(-1)). Measurement of thermal recombination ET between Fe(II)yCc and ZnCcP+ in the D(2)O-treated crystals has both slow and fast components that differ by 2 orders of magnitude (k(eb)(1) = 2200 s(-1), k(eb)(2) = 30 s(-1)). Back ET in H(2)O-grown crystals is too fast for observation, but soaking H(2)O-grown crystals in D(2)O for hours generates slower back ET, with kinetics similar to those of the D(2)O-grown crystals (k(eb)(1) = 7000 s(-1), k(eb)(2) = 100 s(-1)). Protein-film voltammetry of yCc adsorbed to mixed alkanethiol monolayers on gold electrodes shows slower ET for D(2)O-grown yCc films than for H(2)O-grown films (k(H) = 800 s(-1); k(D) = 540 s(-1) at 20 degrees C). Soaking H(2)O- or D(2)O-grown films in the counter solvent produces an immediate inverse isotope effect that diminishes over hours until the ET rate reaches that found in the counter solvent. Thus, D(2)O substitution perturbs interactions and ET between yCc and either CcP or electrode films. The effects derive from slow exchanging protons or solvent molecules that in the crystal produce only small structural changes.

Effects of interface mutations on association modes and electron-transfer rates between proteins

Although bonding networks determine electron-transfer (ET) rates within proteins, the mechanism by which structure and dynamics influence ET across protein interfaces is not well understood. Measurements of photochemically induced ET and subsequent charge recombination between Zn-porphyrin-substituted cytochrome c peroxidase and cytochrome c in single crystals correlate reactivity with defined structures for different association modes of the redox partners. Structures and ET rates in crystals are consistent with tryptophan oxidation mediating charge recombination reactions. Conservative mutations at the interface can drastically affect how the proteins orient and dispose redox centers. Whereas some configurations are ET inactive, the wild-type complex exhibits the fastest recombination rate. Other association modes generate ET rates that do not correlate with predictions based on cofactor separations or simple bonding pathways. Inhibition of photoinduced ET at <273 K indicates gating by small-amplitude dynamics, even within the crystal. Thus, different associations achieve states of similar reactivity, and within those states conformational fluctuations enable interprotein ET.

Electron transfer between cytochrome c and cytochome c peroxidase in single crystals

Cytochrome c (Cc) and cytochrome c peroxidase (CcP) form an important redox pair for understanding interprotein electron transfer (ET). Measurements of ET rates from photoexcited CcP substituted with Zn porphyrin to either yeast Fe(III)Cc or horse Fe(III)Cc in crystals reveal that the molecular associations found in the respective crystal structures determine solution reactivity. Similar forward rates for yeast isozyme-1 Cc (yCc) and yCc homologue horse Cc (hCc), despite different orientations relative to CcP, suggest small-amplitude conformational gating of ET even in the crystalline state; faster back ET in the yCc compared to the hCc complex agrees with the relative coupling between redox sites predicted by the structures.

Excision of a proposed electron transfer pathway in cytochrome c peroxidase and its replacement by a ligand-binding channel

A previously proposed electron transfer (ET) pathway in the heme enzyme cytochrome c peroxidase has been excised from the structure, leaving an open ligand-binding channel in its place. Earlier studies on cavity mutants of this enzyme have revealed structural plasticity in this region of the molecule. Analysis of these structures has allowed the design of a variant in which the specific section of protein backbone representing a previously proposed ET pathway is accurately extracted from the protein. A crystal structure verified the creation of an open channel that overlays the removed segment, extending from the surface of the protein to the heme at the core of the protein. A number of heterocyclic cations were found to bind to the proximal-channel mutant with affinities that can be rationalized based on the structures. It is proposed that small ligands bind more weakly to the proximal-channel mutant than to the W191G cavity due to an increased off rate of the open channel, whereas larger ligands are able to bind to the channel mutant without inducing large conformational changes. The structure of benzimidazole bound to the proximal-channel mutant shows that the ligand accurately overlays the position of the tryptophan radical center that was removed from the wild-type enzyme and displaces four of the eight ordered solvent molecules seen in the empty cavity. Ligand binding also caused a small rearrangement of the redesigned protein loop, perhaps as a result of improved electrostatic interactions with the ligand. The engineered channel offers the potential for introducing synthetic replacements for the removed structure, such as sensitizer-linked substrates. These installed "molecular wires" could be used to rapidly initiate reactions, trap reactive intermediates, or answer unresolved questions about ET pathways.