Shallow Distance Dependence for Proton-Coupled Tyrosine Oxidation in Oligoproline Peptides

Profiling charge transport: A new computational approach

To maintain life, charge transfer processes must be efficient to allow electrons to migrate across distances as large as 30-50 Å within a timescale from picoseconds to milliseconds, and the free-energy cost should not exceed one electron volt. By employing local ionization and local affinity energies, we calculated the pathway for electron and electron-hole transport, respectively. The pathway is then used to calculate both the driving force and the activation energy. The electronic coupling is calculated using configuration interaction procedure. When the charge acceptor is not known, as in oxidative stress, the charge transport terminals are found using Monte-Carlo simulation. These parameters were used to calculate the rate described by Marcus theory. Our approach has been elaborately explained using the famous androstane example and then applied to two proteins: electron transport in azurin protein and hole-hopping migration route from the heme center of cytochrome c peroxidase to its surface. This model gives an effective method to calculate the charge transport pathway and the free-energy profile within 0.1 eV from the experimental measurements and electronic coupling within 3 meV.

Modulation of proton-coupled electron transfer reactions in lysine-containing alpha-helixes: alpha-helixes promoting long-range electron transfer

The proton-coupled electron transfer (PCET) reaction plays an important role in promoting many biological and chemical reactions. Usually, the rate of the PCET reaction increases with an increase in the electron transfer distance because long-range electron transfer requires more free energy barriers. Our density functional theory calculations here reveal that the mechanism of PCET occurring in lysine-containing alpha(α)-helixes changes with an increasing number of residues in the α-helical structure and the different conformations because of the modulation of the excess electron distribution by the α-helical structures. The rate constants of the corresponding PCET reactions are independent of or substantially shallower dependent on the electron transfer distances along α-helixes. This counter-intuitive behavior can be attributed to the fact that the formation of larger macro-cylindrical dipole moments in longer helixes can promote electron transfer along the α-helix with a low energy barrier. These findings may be useful to gain insights into long-range electron transfer in proteins and design α-helix-based electronics via the regulation of short-range proton transfer.

Proton-Coupled Electron Transfer: The Engine of Energy Conversion and Storage

Proton-coupled electron transfer (PCET) underpins energy conversion in chemistry and biology. Four energy systems are described whose discoveries are based on PCET: the water splitting chemistry of the Artificial Leaf, the carbon fixation chemistry of the Bionic Leaf-C, the nitrogen fixation chemistry of the Bionic Leaf-N and the Coordination Chemistry Flow Battery (CCFB). Whereas the Artificial Leaf, Bionic Leaf-C, and Bionic Leaf-N require strong coupling between electron and proton to reduce energetic barriers to enable high energy efficiencies, the CCFB requires complete decoupling of the electron and proton so as to avoid parasitic energy-wasting reactions. The proper design of PCET in these systems facilitates their implementation in the areas of (i) centralized large scale grid storage of electricity and (ii) decentralized energy storage/conversion using only sunlight, air and any water source to produce fuel and food within a sustainable cycle for the biogenic elements of C, N and P.

A Mitochondria-Localized Iridium(III)-Chlorin E6 Conjugate for Synergistic Sonodynamic and Two-Photon Photodynamic Therapy Against Melanoma

While melanoma in its early stages can be successfully treated, the prognosis strongly worsens with an increasing depth of the tumor. Capitalizing on this, there is an urgent need for...

Towards practical applications in quantum computational biology

Fascinating progress in understanding our world at the smallest scales moves us to the border of a new technological revolution governed by quantum physics. By taking advantage of quantum phenomena, quantum computing devices allow a speedup in solving diverse tasks. In this Perspective, we discuss the potential impact of quantum computing on computational biology. Bearing in mind the limitations of existing quantum computing devices, we attempt to indicate promising directions for further research in the emerging area of quantum computational biology.

Theoretical Study of Shallow Distance Dependence of Proton-Coupled Electron Transfer in Oligoproline Peptides

Long-range electron transfer is coupled to proton transfer in a wide range of chemically and biologically important processes. Recently the proton-coupled electron transfer (PCET) rate constants for a series of biomimetic oligoproline peptides linking Ru(bpy)₃²⁺ to tyrosine were shown to exhibit a substantially shallower dependence on the number of proline spacers compared to the analogous electron transfer (ET) systems. The experiments implicated a concerted PCET mechanism involving intramolecular electron transfer from tyrosine to Ru(bpy)₃³⁺ and proton transfer from tyrosine to a hydrogen phosphate dianion. Herein these PCET systems, as well as the analogous ET systems, are studied with microsecond molecular dynamics, and the ET and PCET rate constants are calculated with the corresponding nonadiabatic theories. The molecular dynamics simulations illustrate that smaller ET donor-acceptor distances are sampled by the PCET systems than by the analogous ET systems. The shallower dependence of the PCET rate constant on the ET donor-acceptor distance is explained in terms of an additional positive, distance-dependent electrostatic term in the PCET driving force, which attenuates the rate constant at smaller distances. This electrostatic term depends on the change in the electrostatic interaction between the charges on each end of the bridge and can be modified by altering these charges. On the basis of these insights, this theory predicted a less shallow distance dependence of the PCET rate constant when imidazole rather than hydrogen phosphate serves as the proton acceptor, even though their pK_a values are similar. This theoretical prediction was subsequently validated experimentally, illustrating that long-range electron transfer processes can be tuned by modifying the nature of the proton acceptor in concerted PCET processes. This level of control has broad implications for the design of more effective charge-transfer systems.