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.

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Research Project (R01)
Project #
5R01GM071628-07
Application #
8325517
Study Section
Special Emphasis Panel (ZRG1-BCMB-B (02))
Program Officer
Smith, Ward
Project Start
2004-08-01
Project End
2015-07-31
Budget Start
2012-08-01
Budget End
2013-07-31
Support Year
7
Fiscal Year
2012
Total Cost
$287,509
Indirect Cost
$55,590
Name
Duke University
Department
Chemistry
Type
Schools of Arts and Sciences
DUNS #
044387793
City
Durham
State
NC
Country
United States
Zip Code
27705
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
Brancolini, Giorgia; Migliore, Agostino; Corni, Stefano et al. (2013) Dynamical treatment of charge transfer through duplex nucleic acids containing modified adenines. ACS Nano 7:9396-406
Koo, Jaseung; Park, Jaehong; Tronin, Andrey et al. (2012) Acentric 2-D ensembles of D-br-A electron-transfer chromophores via vectorial orientation within amphiphilic n-helix bundle peptides for photovoltaic device applications. Langmuir 28:3227-38
Polizzi, Nicholas F; Skourtis, Spiros S; Beratan, David N (2012) Physical constraints on charge transport through bacterial nanowires. Faraday Discuss 155:43-62; discussion 103-14
Fry, H Christopher; Lehmann, Andreas; Saven, Jeffery G et al. (2010) Computational design and elaboration of a de novo heterotetrameric alpha-helical protein that selectively binds an emissive abiological (porphinato)zinc chromophore. J Am Chem Soc 132:3997-4005
McAllister, Karen A; Zou, Hongling; Cochran, Frank V et al. (2008) Using alpha-helical coiled-coils to design nanostructured metalloporphyrin arrays. J Am Chem Soc 130:11921-7
Lehmann, Andreas; Saven, Jeffery G (2008) Computational design of four-helix bundle proteins that bind nonbiological cofactors. Biotechnol Prog 24:74-9
Kang, Seung-gu; Saven, Jeffery G (2007) Computational protein design: structure, function and combinatorial diversity. Curr Opin Chem Biol 11:329-34
Bender, Gretchen M; Lehmann, Andreas; Zou, Hongling et al. (2007) De novo design of a single-chain diphenylporphyrin metalloprotein. J Am Chem Soc 129:10732-40

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