Scope of Work We will elaborate new classes of de novo proteins that differ radically from natural photosynthetic systems and electron transfer proteins, that will ultimately enable us to decipher the essential engineering criteria important for the efficient conversion of photonic energy into electrochemical potential energy. Ultimately, we aim to establish rules, principles, and quantitative models that describe biological energy conversion by studying designed, well- controlled de novo proteins-systems that permit the logical dissection of structure-function relationships in molecular bioenergetics. Our efforts will include: (i) cofactor design and synthesis, (ii) protein expression, (iii) modern time-resolved spectroscopy, (iv) computational protein design, (v) molecular simulation, (vi) and theoretical analysis of fluctuating charge transport pathways, electronic coupling interactions, and charge migration dynamics.

Public Health Relevance

The design of protein function from scratch provides the ultimate test of our knowledge of proteins. To date, de novo protein design has achieved many basic protein functions. We propose to push de novo protein design to a new functional level, by fabricating proteins that will ultimately enable us to decipher the criteria required for the efficient conversion of the energy available from light and from charge separated states into stored electrochemical potential energy. Function-guided protein design will not only illuminate the roles that structure, conformation and dynamics play in biological energy transduction: deep understanding of fundamental protein structure-property relationships is a necessary prerequisite to realizing proteins that possess functions having no natural counterpart - such levels of insight from protein design will undoubtedly have tremendous impact upon human health.
The aims of this project are linked to sweeping challenges in molecular bioenergetics: (i) How do protein structure and response lead to effective energy transduction? (ii) What are the structural and energetic requirements for key energy transducing events, such as proton coupled electron transfer (PCET) and multi- step hole delivery in proteins? (iii) How are inherent protein thermal fluctuations coupled to energy harvesting, storage, and release? To address these broad challenges, we propose a collaborative project between investigators at Duke University and the University of Pennsylvania to build and interrogate de novo proteins that enable: (i) highly selective cofactor binding, (ii) modulation of the local environment about chromophores, donors, acceptors, and redox intermediates, (iii) control of H-bonding interactions that engender structure and proton transfer pathways in the constructs, and (iv) molecular-level tuning and modification of hole and electron transfer kinetics.
We aim to produce a microscopic description of ET-coupled structural dynamics germane to biology,16-21 to test emerging theories of protein-mediated charge transfer in fluctuating environments, and to examine models of macromolecular hole transfer (HT) near the tunneling/multi-step hopping transition point. The proteins described herein possess: (1) tailored environments for binding of cofactors with pre-organized donor-acceptor (D-A) geometries, designed cofactor connectivities, and optically triggered photo-oxidants and reductants;(2) theoretically designed and protein-based hole and electron transport pathways. Ultimately, we aim to establish rules, principles, and quantitative models that describe biological energy conversion by studying designed, well-controlled de novo proteins-systems that permit the logical dissection of structure- function relationships in molecular bioenergetics.

National Institute of Health (NIH)
National Institute of General Medical Sciences (NIGMS)
Research Project (R01)
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Special Emphasis Panel (ZRG1-BCMB-B (02))
Program Officer
Smith, Ward
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Duke University
Schools of Arts and Sciences
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Polizzi, Nicholas F; Wu, Yibing; Lemmin, Thomas et al. (2017) De novo design of a hyperstable non-natural protein-ligand complex with sub-Å accuracy. Nat Chem 9:1157-1164
Polizzi, Nicholas F; Therien, Michael J; Beratan, David N (2016) Mean First-Passage Times in Biology. Isr J Chem 56:816-824
Ulas, Gözde; Lemmin, Thomas; Wu, Yibing et al. (2016) Designed metalloprotein stabilizes a semiquinone radical. Nat Chem 8:354-9
Polizzi, Nicholas F; Eibling, Matthew J; Perez-Aguilar, Jose Manuel et al. (2016) Photoinduced Electron Transfer Elicits a Change in the Static Dielectric Constant of a de Novo Designed Protein. J Am Chem Soc 138:2130-3
Snyder, Rae Ana; Butch, Susan E; Reig, Amanda J et al. (2015) Molecular-Level Insight into the Differential Oxidase and Oxygenase Reactivities of de Novo Due Ferri Proteins. J Am Chem Soc 137:9302-14
Beratan, David N; Liu, Chaoren; Migliore, Agostino et al. (2015) Charge transfer in dynamical biosystems, or the treachery of (static) images. Acc Chem Res 48:474-81
Polizzi, Nicholas F; Migliore, Agostino; Therien, Michael J et al. (2015) Defusing redox bombs? Proc Natl Acad Sci U S A 112:10821-2
Snyder, Rae Ana; Betzu, Justine; Butch, Susan E et al. (2015) Systematic Perturbations of Binuclear Non-heme Iron Sites: Structure and Dioxygen Reactivity of de Novo Due Ferri Proteins. Biochemistry 54:4637-51
Migliore, Agostino; Polizzi, Nicholas F; Therien, Michael J et al. (2014) Biochemistry and theory of proton-coupled electron transfer. Chem Rev 114:3381-465
Fry, H Christopher; Lehmann, Andreas; Sinks, Louise E et al. (2013) Computational de novo design and characterization of a protein that selectively binds a highly hyperpolarizable abiological chromophore. J Am Chem Soc 135:13914-26

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