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

Abstract

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.

Rational design of metalloenzymes: From single to multiple active sites

“…While it is of difficulties in design of a functional dinuclear site, the design of metalloenzymes with a multinuclear site has more challenges, due to the combination of effective design of host proteins, synthesis and assembly of metal-clusters in protein, and characterization of structure and activity [51]. Fe-sulfur clusters, such as [115].…”

“…1) [2,. During this course, many approaches were developed, including metal substitution, metal cofactors replacement, and unnatural amino acids (UAAs) incorporation in native or de novo protein scaffolds, as well as with the help of computational designs [44][45][46][47][48][49][50][51].…”

Maquette Strategy for Creation of Light- and Redox-Active Proteins

“…In small proteins (for instance, ferredoxins; see also Figure 5B) they serve as electron transporters diffusing in the aqueous compartments between the larger oxidoreductases of respiratory and photosynthetic energy coupling ( Figure 5C). Early demonstrations showed iron sulfur clusters spontaneously assemble in maquettes 2 singly or in pairs, with or without heme(s); later singlechain variants were designed [Gibney et al, 1996;Mulholland et al, 1998;Musgrave et al, 2002;Nanda et al, 2005;Grzyb et al, 2010;Nanda et al, 2016]. Maquette frames of the kind in Figure 7 have also proved to offer a creative environment for metals alone and in clusters ( Figure 5C) [Dieckmann et al, 1997;Farrer et al, 2000;Calhoun et al, 2005;Geremia et al, 2005;Touw et al, 2007;Calhoun et al, 2008;Tegoni et al, 2012;Zastrow et al, 2012;Roy et al, 2014].…”

Green Rust: The Simple Organizing &lsquo;Seed&rsquo; of All Life?&nbsp;&nbsp;<strong> </strong>

“…[243,244] As it is the backbone amide hydrogen bonds that coordinate to the clusters, in these early times the side chains of amino acids played little part beyond, perhaps merely serving to bind two essential metal ions and orient substrates in the so-called "the two-metal-ion catalytic site". [35,189,245,246,247] The nesting itself renders the clusters more stable, more catalytically active and, in the case of the sulfides, significantly reduces their redox potential. These properties may have both quickened and directed the early evolution of metabolism.…”