Using α-Helical Coiled-Coils to Design Nanostructured Metalloporphyrin Arrays

McAllister, Karen A.; Zou, Hongling; Cochran, Frank V.; Bender, Gretchen M.; Senes, Alessandro; Fry, H. Christopher; Nanda, Vikas; Keenan, Patricia A.; Lear, James D.; Saven, Jeffery G.; Therien, Michael J.; Blasie, J. Kent; DeGrado, William F.

doi:10.1021/ja800697g

Cited by 65 publications

(65 citation statements)

References 12 publications

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“…For many of these goals, appropriately designed helical scaffolds hold much promise as they can provide structural stability and both topological and helical symmetry to facilitate multi-cluster molecules. In de novo porphyrin containing proteins, the helical topology has allowed the design of multi-cofactor nanowires [72, 73] – and similar strategies could be imagined for incorporating iron-sulfur clusters. As seen with existing helical designs, minimizing conformational strain by accommodating low-energy first shell ligand rotamers may be key for producing robust metalloproteins that are stable to redox cycling.…”

Section: Future Directionsmentioning

confidence: 99%

Structural principles for computational and de novo design of 4Fe–4S metalloproteins

Nanda

Senn

Pike

et al. 2016

Biochimica et Biophysica Acta (BBA) - Bioenergetics

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Iron-sulfur centers in metalloproteins can access multiple oxidation states over a broad range of potentials, allowing them to participate in a variety of electron transfer reactions and serving as catalysts for high-energy redox processes. The nitrogenase FeMoCO cluster converts di-nitrogen to ammonia in an eight-electron transfer step. The 2(Fe4S4) containing bacterial ferredoxin is an evolutionarily ancient metalloprotein fold and is thought to be a primordial progenitor of extant oxidoreductases. Controlling chemical transformations mediated by iron-sulfur centers such as nitrogen fixation, hydrogen production as well as electron transfer reactions involved in photosynthesis are of tremendous importance for sustainable chemistry and energy production initiatives. As such, there is significant interest in the design of iron-sulfur proteins as minimal models to gain fundamental understanding of complex natural systems and as lead-molecules for industrial and energy applications. Herein, we discuss salient structural characteristics of natural iron-sulfur proteins and how they guide principles for design. Model structures of past designs are analyzed in the context of these principles and potential directions for enhanced designs are presented, and new areas of iron-sulfur protein design are proposed.

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Section: Future Directionsmentioning

confidence: 99%

Structural principles for computational and de novo design of 4Fe–4S metalloproteins

Nanda

Senn

Pike

et al. 2016

Biochimica et Biophysica Acta (BBA) - Bioenergetics

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“…A number of recent studies have reported the creation of symmetric, well-ordered assemblies composed of a few protein molecules (1)(2)(3)(4). Designing ordered assemblies of larger size and complexity has been a greater challenge.…”

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confidence: 99%

Structure of a 16-nm Cage Designed by Using Protein Oligomers

Lai

Cascio²,

Yeates

2012

Science

269

263

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Designing protein molecules that will assemble into various kinds of ordered materials represents an important challenge in nanotechnology. We report the crystal structure of a 12-subunit protein cage that self-assembles by design to form a tetrahedral structure roughly 16 nanometers in diameter. The strategy of fusing together oligomeric protein domains can be generalized to produce other kinds of cages or extended materials.

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“…Water-soluble proteins have been designed to selectively bind nonbiological porphyrin-based cofactors (Bender et al, 2007; Cochran et al, 2005; Fry et al, 2010; McAllister et al, 2008), and one of these complexes has been redesigned to yield a redox-active membrane protein (Korendovych et al, 2010). This membrane protein (PRIME) was designed to form an antiparallel D 2 symmetric homo-tetramer.…”

Section: Computational Design Of Membrane Proteinsmentioning

confidence: 99%

Computational Design of Membrane Proteins

Pérez-Aguilar

Saven

2012

Structure

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Summary Membrane proteins are involved in a wide variety of cellular processes, and are typically part of the first interaction a cell has with extracellular molecules. As a result, these proteins comprise a majority of known drug targets. Membrane proteins are among the most difficult proteins to obtain and characterize, and a structure-based understanding of their properties can be difficult to elucidate. Notwithstanding, the design of membrane proteins can provide stringent tests of our understanding of these crucial biological systems, as well as introduce novel or targeted functionalities. Computational design methods have been particularly helpful in addressing these issues and this review discusses recent studies that tailor membrane proteins to display specific structures or functions, and how redesigned membrane proteins are being used to facilitate structural and functional studies.

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Using α-Helical Coiled-Coils to Design Nanostructured Metalloporphyrin Arrays

Cited by 65 publications

References 12 publications

Structural principles for computational and de novo design of 4Fe–4S metalloproteins

Structural principles for computational and de novo design of 4Fe–4S metalloproteins

Structure of a 16-nm Cage Designed by Using Protein Oligomers

Computational Design of Membrane Proteins

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