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Biomedical subjects

Jay R Winkler

Publications and source records attributed to Jay R Winkler.

At least 19 recordsLinked to original sources

Site-specific collapse dynamics guide the formation of the cytochrome c' four-helix bundle.

The evolution of tryptophan-to-heme (W/heme) distance distributions extracted from analysis of fluorescence energy transfer kinetics during the refolding of Rhodopseudomonas palustris cytochrome c' reveals dramatic differences between two variants [W32 (Q1A/F32W/W72F) and W72 (Q1A)]. Both W32/heme and W72/heme distance distributions measured at the earliest time point attainable with a continuous-flow mixer (150 mus) confirm that the polypeptide ensemble is not uniformly collapsed and that native structure is not formed. Time-resolved fluorescence spectra indicate that W32 is sequestered from the aqueous solution during the first 700 mus of folding, whereas W72 remains exposed to solvent. The first moment of the W32/heme distance distribution evolves to its native value faster than that of W72, suggesting that the approach of W32 to the heme precedes that of W72.

Cytochromes c'↗

Probing folded and unfolded states of outer membrane protein a with steady-state and time-resolved tryptophan fluorescence.

Steady-state and time-resolved fluorescence measurements on each of five native tryptophan residues in full-length and truncated variants of E. coli outer-membrane protein A (OmpA) have been made in folded and denatured states. Tryptophan singlet excited-state lifetimes are multiexponential and vary among the residues. In addition, substantial increases in excited-state lifetimes accompany OmpA folding, with longer lifetimes in micelles than in phospholipid bilayers. This finding suggests that the Trp environments of OmpA folded in micelles and phospholipid bilayers are different. Measurements of Trp fluorescence decay kinetics with full-length OmpA folded in brominated lipid vesicles reveal that W102 is the most distant fluorophore from the hydrocarbon core, while W7 is the closest. Steady-state and time-resolved polarized fluorescence measurements indicate reduced Trp mobility when OmpA is folded in a micelle, and even lower mobility when the protein is folded in a bilayer. The fluorescence properties of truncated OmpA, in which the soluble periplasmic domain is removed, only modestly differ from those of the full-length form, suggesting similar folded structures for the two forms under these conditions.

Anisotropy↗

Stability and folding kinetics of structurally characterized cytochrome c-b562.

The four-helix-bundle protein fold can be constructed from a wide variety of primary amino acid sequences. Proteins with this structure are excellent candidates for investigations of the relationship between folding mechanism and topology. The folding of cytochrome b(562), a four-helix-bundle heme protein, is hampered by heme dissociation. To overcome this complication, we have engineered a variant of cytochrome b(562) (cyt c-b(562)) featuring a c-type linkage between the heme and the polypeptide chain. The replacement of the native cyt b(562) leader sequence in this protein with that of a c-type cytochrome (cyt c(556)) led to high yields of fully matured and correctly folded cyt c-b(562). We have determined the X-ray crystal structure of cyt c-b(562) at 2.25 A and characterized its physical, chemical, and folding properties. These measurements reveal that the c-type linkage does not perturb the protein fold or reduction potential of the heme group. The covalent attachment of the porphyrin to the polypeptide does, however, produce a substantial change in protein stability and folding kinetics.

Crystallography, X-Ray↗

Snapshots of cytochrome c folding.

Dansyl-to-heme distance distributions [P(r)] during folding have been determined in five variants of Saccharomyces cerevisiae iso-1 ferricytochrome c (labeled at mutant Cys residues 4, 39, 50, 66, and 99) by analysis of fluorescence energy-transfer kinetics. Moment analysis of the P(r) distributions clearly indicates that cytochrome c refolding is not a simple two-state process. After 1 ms of folding, the polypeptide ensemble is not uniformly collapsed and there are site variations in the relative populations of collapsed structures. P(r) distributions reveal structural features of the multiple intermediate species and evolution of the polypeptide ensemble.

Cytochromes c↗

Tertiary contact formation in alpha-synuclein probed by electron transfer.

To explore tertiary contact formation in alpha-synuclein, a natively unfolded protein implicated in Parkinson's disease, we have measured the rates of reaction between a powerful electron donor, the tryptophan (W) triplet excited state, and an acceptor, 3-nitro-tyrosine (Y(NO2)) in six different variants, probing loop sizes between 15 and 132 residues. Electron transfer rates decrease with loop size with the fastest contact time of 140 ns for the N-terminal pair and the slowest of 1.2 mus for the N- to C-terminal pair. Diffusion coefficients ranging from approximately 2 x 10-6 to approximately 10-5 cm2 s-1 were extracted from simultaneous fits of the W to Y(NO2) electron (triplet excited state) and energy transfer (singlet excited state) kinetics.

Electrons↗

Picosecond photoreduction of inducible nitric oxide synthase by rhenium(I)-diimine wires.

In a continuing effort to unravel mechanistic questions associated with metalloenzymes, we are developing methods for rapid delivery of electrons to deeply buried active sites. Herein, we report picosecond reduction of the heme active site of inducible nitric oxide synthase bound to a series of rhenium-diimine electron-tunneling wires, [Re(CO)3LL']+, where L is 4,7-dimethylphenanthroline and L' is a perfluorinated biphenyl bridge connecting a rhenium-ligated imidazole or aminopropylimidazole to a distal imidazole (F8bp-im (1) and C3-F8bp-im (2)) or F (F9bp (3) and C3-F9bp (4)). All four wires bind tightly (Kd in the micromolar to nanomolar range) to the tetrahydrobiopterin-free oxidase domain of inducible nitric oxide synthase (iNOSoxy). The two fluorine-terminated wires displace water from the active site, and the two imidazole-terminated wires ligate the heme iron. Upon 355-nm excitation of iNOSoxy conjugates with 1 and 2, the active site Fe(III) is reduced to Fe(II) within 300 ps, almost 10 orders of magnitude faster than the naturally occurring reduction.

Animals↗

Nature of the cytochrome c molten globule.

We have employed fluorescence energy transfer (FET) kinetics to probe unfolded and molten globule states of five dansyl (Dns) variants of Saccharomyces cerevisiae iso-1 cytochrome c. The covalently bound Fe(III) heme group quenches Dns fluorescence by energy transfer; measurements of FET kinetics yielded distributions of D-A distances (P(r)) for these states. The P(r) distributions and corresponding mean force potentials (U(r)) show that the cytochrome c molten globule is a highly structured state with a substantial number of native interactions. Wide P(r) distributions directly reflect the dynamic nature and conformational diversity of this molten globule. P(r) distributions for the "burst-phase" refolding intermediate suggest that the equilibrium cytochrome c molten globule is not a suitable model for early intermediates formed during protein refolding.

Cytochromes c↗

Electronic structures of trans-dioxometal complexes.

We have employed computational methods based on density functional theory to elucidate the effects of equatorial ligands on the electronic structures of trans-dioxometal complexes. In complexes with amine (sigma-only) equatorial donors, the (1)A(1 g)(b(2 g))(2)-->(1)E(g)(b(2 g))(1)(e(g))(1) excitation energy increases with metal oxidation state: Mo(IV) < Tc(V) < Ru(vi) and W(IV) < Re(V) < Os(VI). Increasing transition energies are attributed to enhanced oxometal pi-donor interactions in the higher valent central metals. But in complexes with cyanide equatorial donors, the (1)A(1 g)(b(2 g))(2)-->(1)E(g)(b(2 g))(1)(e(g))(1) energy remains roughly independent of metal oxidation state, likely owing to the compensating increased pi-donation from the pi(CN) orbitals to the metal d(xy) orbitals as the oxidation state of the metal increases.

Journal Article↗

Early events in the folding of four-helix-bundle heme proteins.

Topologically homologous four-helix-bundle heme proteins exhibit striking diversity in their refolding kinetics. Cytochrome b562 has been reported to fold on a sub-millisecond time scale, whereas cytochrome c' refolding requires 10 s or more to complete. Heme dissociation in cytochrome b562 interferes with studies of folding kinetics, so a variant of cytochrome b562 (cytochrome c-b562) with a covalent c-type linkage to the heme has been expressed in Escherichia coli. Early events in the electron transfer-triggered folding of Fe(II)-cytochrome c-b562, along with those of Fe(II)-cytochrome c556, have been examined by using time-resolved absorption spectroscopy. Coordination of S(Met) to Fe(II) occurs within 10 mus after reduction of the denatured Fe(III)-cytochromes, and shortly thereafter (100 micros) the heme spectra are indistinguishable from those of the folded proteins. Under denaturing conditions, carbon monoxide binds to the Fe(II)-hemes in approximately 15 ms. By contrast, CO binding cannot compete with refolding in the Fe(II)-cytochromes, thereby confirming that the polypeptide encapsulates the heme in <10 ms. We suggest that Fe-S(Met) ligation facilitates refolding in these four-helix-bundle heme proteins by reducing the conformational freedom of the polypeptide chain.

Carbon Monoxide↗

Luminescent ruthenium(II)- and rhenium(I)-diimine wires bind nitric oxide synthase.

Ru(II)- and Re(I)-diimine wires bind to the oxygenase domain of inducible nitric oxide synthase (iNOSoxy). In the ruthenium wires, [Ru(L)2L']2+, L' is a perfluorinated biphenyl bridge connecting 4,4'-dimethylbipyridine to a bulky hydrophobic group (adamantane, 1), a heme ligand (imidazole, 2), or F (3). 2 binds in the active site of the murine iNOSoxy truncation mutants Delta65 and Delta114, as demonstrated by a shift in the heme Soret from 422 to 426 nm. 1 and 3 also bind Delta65 and Delta114, as evidenced by biphasic luminescence decay kinetics. However, the heme absorption spectrum is not altered in the presence of 1 or 3, and Ru-wire binding is not affected by the presence of tetrahydrobiopterin or arginine. These data suggest that 1 and 3 may instead bind to the distal side of the enzyme at the hydrophobic surface patch thought to interact with the NOS reductase module. Complexes with properties similar to those of the Ru-diimine wires may provide an effective means of NOS inhibition by preventing electron transfer from the reductase module to the oxygenase domain. Rhenium-diimine wires, [Re(CO)3L1L1']+, where L1 is 4,7-dimethylphenanthroline and L1' is a perfluorinated biphenyl bridge connecting a rhenium-ligated imidazole to a distal imidazole (F8bp-im) (4) or F (F9bp) (5), also form complexes with Delta114. Binding of 4 shifts the Delta114 heme Soret to 426 nm, demonstrating that the terminal imidazole ligates the heme iron. Steady-state luminescence measurements establish that the 4:Delta114 dissociation constant is 100 +/- 80 nM. Re-wire 5 binds Delta114 with a K(d) of 5 +/- 2 microM, causing partial displacement of water from the heme iron. Our finding that both 4 and 5 bind in the NOS active site suggests novel designs for NOS inhibitors. Importantly, we have demonstrated the power of time-resolved FET measurements in the characterization of small molecule:protein interactions that otherwise would be difficult to observe.

Adamantane↗

Long-range electron transfer.

Recent investigations have shed much light on the nuclear and electronic factors that control the rates of long-range electron tunneling through molecules in aqueous and organic glasses as well as through bonds in donor-bridge-acceptor complexes. Couplings through covalent and hydrogen bonds are much stronger than those across van der Waals gaps, and these differences in coupling between bonded and nonbonded atoms account for the dependence of tunneling rates on the structure of the media between redox sites in Ru-modified proteins and protein-protein complexes.

Electron Transport↗

Many faces of the unfolded state: conformational heterogeneity in denatured yeast cytochrome C.

We have measured fluorescence energy-transfer (FET) kinetics from a dansyl fluorophore (Dns) introduced by derivatization of a Cys side-chain to the Fe(III) heme covalently attached to unfolded yeast iso-1 cytochrome c (cyt). To gain a global picture of the unfolded state, we examined variants with the fluorophore attached on three different helices (K4C, E66C, K99C) and in three different loops (H39C, D50C, L85C). Analysis of the FET kinetics data gave distributions of distances between the fluorescent donor and acceptor; these distributions demonstrate that the guanidine hydrochloride (GuHCl)-denatured polypeptide ensemble is not a simple random coil. Although misligation imposes some constraints, it is not the only source of structural complexity in the unfolded protein. Our FET kinetics data reveal a high degree of heterogeneity in the unfolded ensemble of cytochrome c. We detect relatively large populations of compact structures in unfolded Dns(C50)cyt, Dns(C39)cyt, and Dns(C66)cyt. These structures likely play a role in forming a hydrophobic core during the folding process.

Cytochromes c↗

Electron tunneling through organic molecules in frozen glasses.

Reaction rates extracted from measurements of donor luminescence quenching by randomly dispersed electron acceptors reveal an exponential decay constant of 1.23 per angstrom for electron tunneling through a frozen toluene glass (with a barrier to tunneling of 1.4 electron volts). The decay constant is 1.62 per angstrom (the barrier, 2.6 electron volts) in a frozen 2-methyl-tetrahydrofuran glass. Comparison to decay constants for tunneling across covalently linked xylyl (0.76 per angstrom) and alkyl (1.0 per angstrom) bridges leads to the conclusion that tunneling between solvent molecules separated by approximately 2 angstroms (van der Waals contact) is 20 to 50 times slower than tunneling through a comparable length of a covalently bonded bridge. Our results provide experimental confirmation that covalently bonded pathways can facilitate electron flow through folded polypeptide structures.

Journal Article↗

Zinc-porphyrin Solvation in folded and unfolded states of Zn-cytochrome c.

After a brief review of the use of photochemical triggers and heme metal substitution to probe the folding dynamics of cytochrome c, we present new results on the photophysics and photochemistry of folded and unfolded states of the zinc-substituted protein (Zn-cyt c). Our measurements of Zn-cyt c triplet state decay kinetics reveal a systematic isotope effect on lifetimes: the decay in the folded protein (tau(H)2(O) approximately 10 ms) is only modestly affected by isotopically substituted buffers (k(H)2(O)/k(D)2(O) = 1.2), whereas a reduced triplet lifetime (approximately 1.3 ms) and greater isotope effect (1.4) were found for the chemically denatured, fully unfolded protein. The shortest lifetime (0.1-0.4 ms) and greatest isotope effect (1.5) were found for a fully exposed model compound, zinc-substituted N-acetyl-microperoxidase-8 (ZnAcMP8), implying that the unfolded protein provides some protection to the Zn-porphyrin group even under fully denaturing conditions. Further evidence for partial structure in unfolded Zn-cyt c comes from bimolecular quenching experiments using Ru(NH(3))(6)(3+) as an external Zn-porphyrin triplet state quencher. In the presence of quencher, partially unfolded protein at midpoint guanidinium chloride (GdmCl) and urea concentrations exhibits biphasic triplet decay kinetics, a fast component corresponding to an extended, solvent-exposed state (6.6 x 10(8) M(-1) s(-1) in GdmCl, 6.3 x 10(8) M(-1) s(-1) in urea) and a slow component attributable to a compact, relatively solvent-inaccessible, state (5.9 x 10(7) M(-1) s(-1) in GdmCl, 8.6 x 10(6) M(-1) s(-1) in urea). The variation in Zn-porphyrin solvation for the compact states in the two denaturants reveals that the cofactor in the partially unfolded protein is better protected in urea solutions.

Animals↗

Inner-sphere electron-transfer reorganization energies of zinc porphyrins.

Inner-sphere electron-transfer reorganization energies of Zn(protoporphyrin IX) and Zn(octaethylporphyrin) are determined from band-shape analyses of the first ionization obtained by gas-phase valence photoelectron spectroscopy. The experimentally determined total inner-sphere reorganization energies for self-exchange (120-140 meV) indicate that structural changes upon oxidation are largely confined to the porphyrin ring, and substituents on the ring or solvent and other environmental factors make smaller contributions. Computational estimates by different models vary over a wide range and are sensitive to numerical precision factors for these low reorganization energies. Of current computational models that are widely available and practical for molecules of this size, functionals that contain a mixture of Hartree-Fock exchange and DFT exchange-correlation appear to be the most applicable.

Metalloporphyrins↗

Alpha-synuclein structures from fluorescence energy-transfer kinetics: implications for the role of the protein in Parkinson's disease.

Parkinson's disease is associated with the deposition and accumulation of alpha-synuclein fibrils in the brain. A30P and A53T mutations have been linked to the early-onset familial disease state. Time-resolved tryptophan fluorescence energy-transfer measurements have been used to probe the structures of pseudo-wild-type and mutant (A30P) alpha-synucleins at physiological pH (7.4), in acidic pH (4.4) solutions, and in the presence of SDS micelles, a membrane mimic. Fluorescent donor-energy acceptor (DA) distance distributions for six different tryptophan/3-nitro-tyrosine pairs reveal the presence of compact, intermediate, and extended conformations of the protein. CD spectra indicate that the protein develops substantial helical structure in the presence of SDS micelles. DA distributions show that micelles induce compaction in the N-terminal region and expansion of the acidic C terminus. In acidic solutions, there is an increased population of collapsed structures in the C-terminal region. Energy-transfer measurements demonstrate that the average DA distances for the W4-Y19 and Y19-W39 pairs are longer in one of the two disease-related mutants (A30P).

Amino Acid Sequence↗

Electron tunneling in rhenium-modified Pseudomonas aeruginosa azurins.

Laser flash-quench methods have been used to generate tyrosine and tryptophan radicals in structurally characterized rhenium-modified Pseudomonas aeruginosa azurins. Cu(I) to "Re(II)" electron tunneling in Re(H107) azurin occurs in the microsecond range. This reaction is much faster than that studied previously for Cu(I) to Ru(III) tunneling in Ru(H107) azurin, suggesting that a multistep ("hopping") mechanism might be involved. Although a Y108 radical can be generated by flash-quenching a Re(H107)M(II) (M=Cu, Zn) protein, the evidence suggests that it is not an active intermediate in the enhanced Cu(I) oxidation. Rather, the likely explanation is rapid conversion of Re(II)(H107) to deprotonated Re(I)(H107 radical), followed by electron tunneling from Cu(I) to the hole in the imidazole ligand.

Azurin↗

Photoswitchable luminescence of rhenium(i) tricarbonyl diimines.

The synthesis, characterization, and X-ray crystal structures of [Re(diimine)(CO)(3)(dpe)](PF(6)) (dpe = 1,2-di(4-pyridyl)ethylene) compounds are reported. The cis-dpe complexes exhibit yellow luminescence after UV excitation, whereas the trans-dpe counterparts are nonluminescent. The luminescence quantum yields of the cis-dpe complexes are strongly dependent on the identity of the diimine ligand. Irradiation (350 nm) of the trans-dpe complexes induces trans --> cis dpe-ligand isomerization with quantum yields on the order of 0.2, and this process leads to an on-switching of yellow luminescence. After long 350-nm irradiation times, a steady state composed of roughly 70% cis- and 30% trans-dpe complexes is reached. The reverse cis --> trans photoisomerization reaction is induced by irradiating the cis-dpe complexes at 250 nm, switching off the yellow luminescence. For 250-nm excitation, photodecomposition of the [Re(diimine)(CO)(3)(dpe)](+) complexes competes efficiently with photoisomerization.

Journal Article↗