Charge Transfer in Dynamical Biosystems, or The Treachery of (Static) Images

Beratan, David N.; Liu, Chaoren; Migliore, Agostino; Polizzi, Nicholas F.; Skourtis, Spiros S.; Zhang, Peng; Zhang, Yuqi

doi:10.1021/ar500271d

Cited by 151 publications

(192 citation statements)

References 66 publications

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“…At a cellular level, CT is responsible for a range of chemical and biochemical transformations, and is essential for life on Earth to exist [1][2][3][4][5]. In addition to its vital role in living systems, CT resides at the heart of energy conversion, transduction and storage [6][7][8][9][10][11][12][13], and provides signal transduction for devices integral to our modern lifestyles [14,15].…”

Section: Introductionmentioning

confidence: 99%

Building blocks for bioinspired electrets: molecular-level approach to materials for energy and electronics

Larsen

Espinoza

Hartman

et al. 2015

Pure and Applied Chemistry

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In biology, an immense diversity of protein structural and functional motifs originates from only 20 common proteinogenic native amino acids arranged in various sequences. Is it possible to attain the same diversity in electronic materials based on organic macromolecules composed of non-native residues with different characteristics? This publication describes the design, preparation and characterization of non-native aromatic β-amino acid residues, i.e. derivatives of anthranilic acid, for polyamides that can efficiently mediate hole transfer. Chemical derivatization with three types of substituents at two positions of the aromatic ring allows for adjusting the energy levels of the frontier orbitals of the anthranilamide residues over a range of about one electronvolt. Most importantly, the anthranilamide residues possess permanent electric dipoles, adding to the electronic properties of the bioinspired conjugates they compose, making them molecular electrets.

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Section: Introductionmentioning

confidence: 99%

Building blocks for bioinspired electrets: molecular-level approach to materials for energy and electronics

Larsen

Espinoza

Hartman

et al. 2015

Pure and Applied Chemistry

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“…1B) between the electron donor and acceptor, facilitated by the protein medium, or by direct van der Waals (vdW) contact between redox species. V decays rapidly with distance, and the steepness of this decay depends on the structure of the intervening medium (9). ET pathways and relative donor/acceptor orientations influence wave function overlap, and thus determine V and the ET rate.…”

mentioning

confidence: 99%

Defusing redox bombs?

Polizzi

Migliore

Therien

et al. 2015

Proc. Natl. Acad. Sci. U.S.A.

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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.Since at least the 1960s, aromatic amino acids were postulated to play a special role in biological redox chemistry as electron hole carriers (2). Circadian rhythm photochemistry, photosynthetic water splitting, nucleic acid biosynthesis, and cell signaling are now well understood to engage redox-active Trp and Tyr residues as essential parts of their function (3). Could Tyr and Trp also play a protective role during enzymatic reactions (such as the oxidation of aliphatic C-H bonds) that require high-energy intermediates (4, 5)? The answer will be dictated by the set of time scales at play: Hole hopping from the activated redox cofactor to the first Trp/Tyr must be slower than catalysis (to avoid disabling the enzyme's valuable catalytic function) but faster than oxidative protein damage. Gray and Winkler's (1) query of the Protein Data Bank (e.g., they searched for Trp/Tyr pairs within a 5-Å edge-to-edge cutoff distance) provides a critical starting point for more detailed investigations of these hole-transfer chains.Electron-transfer (ET) rates in biochemical reactions are usually proportional to the square of the electronic coupling interaction energy (V, Fig. 1B) between the electron donor and acceptor, facilitated by the protein medium, or by direct van der Waals (vdW) contact between redox species. V decays rapidly with distance, and the steepness of this decay depends on the structure of the intervening medium (9). ET pathways and relative donor/acceptor orientations influence wave function overlap, and thus determine V and the ET rate. The relative Trp and Tyr orientations fine-tune the hole-hopping rates. Two orientations are common among protein aromatics (Fig. 1C), the so-called parallel-displaced (PD) and the T-shape (T) orientations, where ring interactions capture quadrupolar electrostatic stabilization (10). PD geometries may use strong stacking interactions (akin to sigma bonding between p-orbitals) to maximize V; however, the strength of such interactions depends on orbital symmetry, as shown in Fig. 1D for indole pairs. Indeed, the greater than 10-fold stronger V for Tyr90-Trp231 in Fig. 2 arises from its PD geometry, compared with the T geometry of the other pairs.Within a subset of orientations (e.g., T or PD), additional geometric effects between Fig. 1. The electronic coupling interaction energy (...

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“…[139,140,141,142] Hydrogen is the sine qua non electron donor used by all life still in the form of NADH. [143,144] Indeed, in this way billions upon billions of electrons are transported to the vent in hydrothermal solutions exhaling at ~1000kg/sec in the present day. [145,146] Temperatures too were appropriate (30° to 100°C), as were pressures (≥100 bars), and longevity (~10 20 nanoseconds).…”

Section: The Disequilibria Imposed Across the Mineral Barriermentioning

confidence: 99%

Green Rust: The Simple Organizing ‘Seed’ of All Life?  <strong> </strong>

Russell

2018

Preprint

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The most important problem of synthetic biology is…the reduction of carbonic acid. and Without the idea of spontaneous generation and a physical theory of life, the doctrine of evolution is a mutilated hypothesis without unity or cohesion.[1] Leduc, [1]Abstract: Korenaga and coworkers present evidence to suggest that 4.3 billion years ago the Earth's mantle was dry and water filled the ocean to twice its present volume.[2] CO2 was constantly exhaled during the mafic to ultramafic volcanic activity associated with magmatic plumes that produced the thick, dense and relatively stable oceanic crust. In that setting two distinct major types of sub-marine hydrothermal vents were active: ~400°C acidic springs whose effluents bore vast quantities of iron into the ocean, and ~120°C, highly alkaline and reduced vents exhaling from the cooler, serpentinizing crust at some distance from the heads of the plumes. When encountering the alkaline effluents, the iron from the plume head vents precipitated out forming mounds likely surrounded by voluminous exhalative deposits similar to the banded iron formations known from the Archean. These mounds and the surrounding sediments likely comprising nanocrysts of the variable valence FeII/FeIII oxyhydroxide, green rust. The precipitation of green rust, along with subsidiary iron sulfides and minor concentrations of Ni, Co and Mo in the environment at the alkaline springs may have established both the key bio-syntonic disequilibria, and the means to properly make use of them -those needed to drive the essential inanimate-to-animate transitions that launched life. In the submarine alkaline vent model for the emergence of life specifically it is first suggested that the redox-flexible green rust microcrysts spontaneously formed precipitated barriers to the complete mixing of carbonic ocean and alkaline hydrothermal fluids, barriers that created and maintained steep ionic disequilibria; and second, that the hydrous interlayers of green rust acted as 'engines' that were powered by those ionic disequilibria and drove essential endergonic reactions. There, aided by sulfides and trace elements acting as catalytic promoters and electron transfer agents, nitrate could be reduced to ammonia and carbon dioxide to formate, while methane may have been oxidized to methyl and formyl groups. Acetate and higher carboxylic acids could then have been produced from these C1 molecules and aminated to amino acids, and thence oligomerized to offer peptide nests to phosphate and iron sulfides and secreted to form primitive amyloid-bounded structures, leading conceivably to protocells.

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Charge Transfer in Dynamical Biosystems, or The Treachery of (Static) Images

Cited by 151 publications

References 66 publications

Building blocks for bioinspired electrets: molecular-level approach to materials for energy and electronics

Building blocks for bioinspired electrets: molecular-level approach to materials for energy and electronics

Defusing redox bombs?

Green Rust: The Simple Organizing ‘Seed’ of All Life?  <strong> </strong>

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Charge Transfer in Dynamical Biosystems, or The Treachery of (Static) Images

Cited by 151 publications

References 66 publications

Building blocks for bioinspired electrets: molecular-level approach to materials for energy and electronics

Building blocks for bioinspired electrets: molecular-level approach to materials for energy and electronics

Defusing redox bombs?

Green Rust: The Simple Organizing &lsquo;Seed&rsquo; of All Life?&nbsp;&nbsp;<strong> </strong>

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Green Rust: The Simple Organizing ‘Seed’ of All Life? <strong> </strong>