Fundamental Limits on Wavelength, Efficiency and Yield of the Charge Separation Triad

In an attempt to optimize a high yield, high efficiency artificial photosynthetic protein we have discovered unique energy and spatial architecture limits which apply to all light-activated photosynthetic systems. We have generated an analytical solution for the time behavior of the core three cofactor charge separation element in photosynthesis, the photosynthetic cofactor triad, and explored the functional consequences of its makeup including its architecture, the reduction potentials of its components, and the absorption energy of the light absorbing primary-donor cofactor. Our primary findings are two: First, that a high efficiency, high yield triad will have an absorption frequency more than twice the reorganization energy of the first electron transfer, and second, that the relative distance of the acceptor and the donor from the primary-donor plays an important role in determining the yields, with the highest efficiency, highest yield architecture having the light absorbing cofactor closest to the acceptor. Surprisingly, despite the increased complexity found in natural solar energy conversion proteins, we find that the construction of this central triad in natural systems matches these predictions. Our analysis thus not only suggests explanations for some aspects of the makeup of natural photosynthetic systems, it also provides specific design criteria necessary to create high efficiency, high yield artificial protein-based triads

Targeting the substrate preference of a type I nitroreductase to develop antitrypanosomal quinone-based prodrugs.

Nitroheterocyclic prodrugs are used to treat infections caused by Trypanosoma cruzi and Trypanosoma brucei. A key component in selectivity involves a specific activation step mediated by a protein homologous with type I nitroreductases, enzymes found predominantly in prokaryotes. Using data from determinations based on flavin cofactor, oxygen-insensitive activity, substrate range, and inhibition profiles, we demonstrate that NTRs from T. cruzi and T. brucei display many characteristics of their bacterial counterparts. Intriguingly, both enzymes preferentially use NADH and quinones as the electron donor and acceptor, respectively, suggesting that they may function as NADH:ubiquinone oxidoreductases in the parasite mitochondrion. We exploited this preference to determine the trypanocidal activity of a library of aziridinyl benzoquinones against bloodstream-form T. brucei. Biochemical screens using recombinant NTR demonstrated that several quinones were effective substrates for the parasite enzyme, having K(cat)/K(m) values 2 orders of magnitude greater than those of nifurtimox and benznidazole. In tests against T. brucei, antiparasitic activity mirrored the biochemical data, with the most potent compounds generally being preferred enzyme substrates. Trypanocidal activity was shown to be NTR dependent, as parasites with elevated levels of this enzyme were hypersensitive to the aziridinyl agent. By unraveling the biochemical characteristics exhibited by the trypanosomal NTRs, we have shown that quinone-based compounds represent a class of trypanocidal compound

Foundations for Open Scholarship Strategy Development, Version 2.1 [Pre-print]

This document aims to agree on a broad, international strategy for the implementation of open scholarship that meets the needs of different national and regional communities but works globally. Scholarly research can be idealised as an inspirational process for advancing our collective knowledge to the benefit of all humankind. However, current research practices often struggle with a range of tensions, in part due to the fact that this collective (or “commons”) ideal conflicts with the competitive system in which most scholars work, and in part because much of the infrastructure of the scholarly world is becoming largely digital. What is broadly termed as Open Scholarship is an attempt to realign modern research practices with this ideal. We do not propose a definition of Open Scholarship, but recognise that it is a holistic term that encompasses many disciplines, practices, and principles, sometimes also referred to as Open Science or Open Research. We choose the term Open Scholarship to be more inclusive of these other terms. When we refer to science in this document, we do so historically and use it as shorthand for more general scholarship. The purpose of this document is to provide a concise analysis of where the global Open Scholarship movement currently stands: what the common threads and strengths are, where the greatest opportunities and challenges lie, and how we can more effectively work together as a global community to recognise and address the top strategic priorities. This document was inspired by the Foundations for OER Strategy Development and work in the FORCE11 Scholarly Commons Working Group, and developed by an open contribution working group. Our hope is that this document will serve as a foundational resource for continuing discussions and initiatives about implementing effective strategies to help streamline the integration of Open Scholarship practices into a modern, digital research culture. Through this, we hope to extend the reach and impact of Open Scholarship into a global context, making sure that it is truly open for all. We also hope that this document will evolve as the conversations around Open Scholarship progress, and help to provide useful insight for both global co-ordination and local action. We believe this is a step forward in making Open Scholarship the norm. Ultimately, we expect the impact of widespread adoption of Open Scholarship to be diverse. We expect novel research practices to accelerate the pace of innovation, and therefore stimulate critical industries around the world. We could also expect to see an increase in public trust of science and scholarship, as transparency becomes more normative. As such, we expect interest in Open Scholarship to increase at multiple levels, due to its inherent influence on society and global economics

Construction and in vivo assembly of a catalytically proficient and hyperthermostable de novo enzyme

Although catalytic mechanisms in natural enzymes are well understood, achieving the diverse palette of reaction chemistries in re-engineered native proteins has proved challenging. Wholesale modification of natural enzymes is potentially compromised by their intrinsic complexity, which often obscures the underlying principles governing biocatalytic efficiency. The maquette approach can circumvent this complexity by combining a robust de novo designed chassis with a design process that avoids atomistic mimicry of natural proteins. Here, we apply this method to the construction of a highly efficient, promiscuous, and thermostable artificial enzyme that catalyzes a diverse array of substrate oxidations coupled to the reduction of H2O2. The maquette exhibits kinetics that match and even surpass those of certain natural peroxidases, retains its activity at elevated temperature and in the presence of organic solvents, and provides a simple platform for interrogating catalytic intermediates common to natural heme-containing enzymes