Nicholas F. Polizzi

Biochemistry and Theory of Proton-Coupled Electron Transfer

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Charge transfer in dynamical biosystems, or the treachery of (static) images.

Conspectus The image is not the thing. Just as a pipe rendered in an oil painting cannot be smoked, quantum mechanical coupling pathways rendered on LCDs do not convey electrons. The aim of this Account is to examine some of our recent discoveries regarding biological electron transfer (ET) and transport mechanisms that emerge when one moves beyond treacherous static views to dynamical frameworks. Studies over the last two decades introduced both atomistic detail and macromolecule dynamics to the description of biological ET. The first model to move beyond the structureless square-barrier tunneling description is the Pathway model, which predicts how protein secondary motifs and folding-induced through-bond and through-space tunneling gaps influence kinetics. Explicit electronic structure theory is applied routinely now to elucidate ET mechanisms, to capture pathway interferences, and to treat redox cofactor electronic structure effects. Importantly, structural sampling of proteins provides an understanding of how dynamics may change the mechanisms of biological ET, as ET rates are exponentially sensitive to structure. Does protein motion average out tunneling pathways? Do conformational fluctuations gate biological ET? Are transient multistate resonances produced by energy gap fluctuations? These questions are becoming accessible as the static view of biological ET recedes and dynamical viewpoints take center stage. This Account introduces ET reactions at the core of bioenergetics, summarizes our team’s progress toward arriving at an atomistic-level description, examines how thermal fluctuations influence ET, presents metrics that characterize dynamical effects on ET, and discusses applications in very long (micrometer scale) bacterial nanowires. The persistence of structural effects on the ET rates in the face of thermal fluctuations is considered. Finally, the flickering resonance (FR) view of charge transfer is presented to examine how fluctuations control low-barrier transport among multiple groups in van der Waals contact. FR produces exponential distance dependence in the absence of tunneling; the exponential character emerges from the probability of matching multiple vibronically broadened electronic energies within a tolerance defined by the rms coupling among interacting groups. FR thus produces band like coherent transport on the nanometer length scale, enabled by conformational fluctuations. Taken as a whole, the emerging context for ET in dynamical biomolecules provides a robust framework to design and interpret the inner workings of bioenergetics from the molecular to the cellular scale and beyond, with applications in biomedicine, biocatalysis, and energy science.

Zinc-binding structure of a catalytic amyloid from solid-state NMR

Significance Functional and pathological amyloid fibrils bind metal ions, but no metal-bound amyloid structures have been determined. Using solid-state NMR and structural bioinformatics, we have determined the oligomeric structure and coordination geometry of a Zn2+-mediated amyloid fibril that catalyzes ester hydrolysis. The peptide assembles into parallel β-sheets in which histidines bridge zinc ions to promote β-strand association in a geometry that mediates water activation for catalysis. The study demonstrates an approach for determining the structures of metalloamyloids. The resulting structure defines how metal ions can stabilize amyloids, lends support to the hypothesis that amyloids can serve as well-structured intermediates between amino acids and proteins during the evolution of life, and provides a framework for potential applications in material science. Throughout biology, amyloids are key structures in both functional proteins and the end product of pathologic protein misfolding. Amyloids might also represent an early precursor in the evolution of life because of their small molecular size and their ability to self-purify and catalyze chemical reactions. They also provide attractive backbones for advanced materials. When β-strands of an amyloid are arranged parallel and in register, side chains from the same position of each chain align, facilitating metal chelation when the residues are good ligands such as histidine. High-resolution structures of metalloamyloids are needed to understand the molecular bases of metal–amyloid interactions. Here we combine solid-state NMR and structural bioinformatics to determine the structure of a zinc-bound metalloamyloid that catalyzes ester hydrolysis. The peptide forms amphiphilic parallel β-sheets that assemble into stacked bilayers with alternating hydrophobic and polar interfaces. The hydrophobic interface is stabilized by apolar side chains from adjacent sheets, whereas the hydrated polar interface houses the Zn2+-binding histidines with binding geometries unusual in proteins. Each Zn2+ has two bis-coordinated histidine ligands, which bridge adjacent strands to form an infinite metal–ligand chain along the fibril axis. A third histidine completes the protein ligand environment, leaving a free site on the Zn2+ for water activation. This structure defines a class of materials, which we call metal–peptide frameworks. The structure reveals a delicate interplay through which metal ions stabilize the amyloid structure, which in turn shapes the ligand geometry and catalytic reactivity of Zn2+.

De novo design of a hyperstable non-natural protein–ligand complex with sub-Å accuracy

Protein catalysis requires the atomic-level orchestration of side chains, substrates and cofactors, and yet the ability to design a small-molecule-binding protein entirely from first principles with a precisely predetermined structure has not been demonstrated. Here we report the design of a novel protein, PS1, that binds a highly electron-deficient non-natural porphyrin at temperatures up to 100 °C. The high-resolution structure of holo-PS1 is in sub-Å agreement with the design. The structure of apo-PS1 retains the remote core packing of the holoprotein, with a flexible binding region that is predisposed to ligand binding with the desired geometry. Our results illustrate the unification of core packing and binding-site definition as a central principle of ligand-binding protein design.

Where Is the Electronic Oscillator Strength? Mapping Oscillator Strength across Molecular Absorption Spectra

The effectiveness of solar energy capture and conversion materials derives from their ability to absorb light and to transform the excitation energy into energy stored in free carriers or chemical bonds. The Thomas-Reiche-Kuhn (TRK) sum rule mandates that the integrated (electronic) oscillator strength of an absorber equals the total number of electrons in the structure. Typical molecular chromophores place only about 1% of their oscillator strength in the UV-vis window, so individual chromophores operate at about 1% of their theoretical limit. We explore the distribution of oscillator strength as a function of excitation energy to understand this circumstance. To this aim, we use familiar independent-electron model Hamiltonians as well as first-principles electronic structure methods. While model Hamiltonians capture the qualitative electronic spectra associated with π electron chromophores, these Hamiltonians mistakenly focus the oscillator strength in the fewest low-energy transitions. Advanced electronic structure methods, in contrast, spread the oscillator strength over a very wide excitation energy range, including transitions to Rydberg and continuum states, consistent with experiment. Our analysis rationalizes the low oscillator strength in the UV-vis spectral region in molecules, a step toward the goal of oscillator strength manipulation and focusing.

Defusing redox bombs

Proteins catalyze crucial reactions via unstable, high-energy chemical intermediates. In the absence of physiological substrates, activated redox cofactors become ticking time bombs, capable of producing oxidative damage to the protein. In PNAS, Gray and Winkler (1) propose that chains of tryptophan (Trp) and tyrosine (Tyr) residues may serve as escape routes for potentially damaging, highly oxidizing electron holes (oxidizing equivalents) that are generated in enzymatic reactions. The aromatic residues are suggested to provide charge-shuttling pathways that lead out to the protein surface from buried active sites. Once outside the protein, the holes can be safely scavenged by cellular reductants.

Engineering High-Potential Photo-oxidants with Panchromatic Absorption

Challenging photochemistry demands high-potential visible-light-absorbing photo-oxidants. We report (i) a highly electron-deficient Ru(II) complex (eDef-Rutpy) bearing an E1/20/+ potential more than 300 mV more positive than that of any established Ru(II) bis(terpyridyl) derivative, and (ii) an ethyne-bridged eDef-Rutpy-(porphinato)Zn(II) (eDef-RuPZn) supermolecule that affords both panchromatic UV-vis spectral domain absorptivity and a high E1/20/+ potential, comparable to that of Ce(NH4)2(NO3)6 [E1/2(Ce3+/4+) = 1.61 V vs NHE], a strong and versatile ground-state oxidant commonly used in organic functional group transformations. eDef-RuPZn exhibits ∼8-fold greater absorptive oscillator strength over the 380-700 nm range relative to conventional Ru(II) polypyridyl complexes, and impressive excited-state reduction potentials (1E-/* = 1.59 V; 3E-/* = 1.26 V). eDef-RuPZn manifests electronically excited singlet and triplet charge-transfer state lifetimes more than 2 orders of magnitude longer than those typical of conventional Ru(II) bis(terpyridyl) chromophores, suggesting new opportunities in light-driven oxidation reactions for energy conversion and photocatalysis.

Mean First‐Passage Times in Biology

Many biochemical processes, such as charge hopping or protein folding, can be described by an average timescale to reach a final state, starting from an initial state. Here, we provide a pedagogical treatment of the mean first-passage time (MFPT) of a physical process, which depends on the number of intervening states between the initial state and the target state. Our aim in this tutorial review is to provide a clear development of the mean first-passage time formalism and to show some of its practical utility. The MFPT treatment can provide a useful link between microscopic rates and the average timescales often probed by experiment.