Design principles for chlorophyll‐binding sites in helical proteins

Abstract

The cyclic tetrapyrroles, viz. chlorophylls (Chl), their bacterial analogs bacteriochlorophylls, and hemes are ubiquitous cofactors of biological catalysis that are involved in a multitude of reactions. One systematic approach for understanding how Nature achieves functional diversity with only this handful of cofactors is by designing de novo simple and robust protein scaffolds with heme and/or (bacterio)chlorophyll [(B)Chls]-binding sites. This strategy is currently mostly implemented for heme-binding proteins. To gain more insight into the factors that determine heme-/(B)Chl-binding selectivity, we explored the geometric parameters of (B)Chl-binding sites in a nonredundant subset of natural (B)Chl protein structures. Comparing our analysis to the study of a nonredundant database of heme-binding helical histidines by Negron et al. (Proteins 2009;74:400-416), we found a preference for the m-rotamer in (B)Chl-binding helical histidines, in contrast to the preferred t-rotamer in heme-binding helical histidines. This may be used for the design of specific heme- or (B)Chl-binding sites in water-soluble helical bundles, because the rotamer type defines the positioning of the bound cofactor with respect to the helix interface and thus the protein-binding site. Consensus sequences for (B)Chl binding were identified by combining a computational and database-derived approach and shown to be significantly different from the consensus sequences recommended by Negron et al. (Proteins 2009;74:400-416) for heme-binding helical proteins. The insights gained in this work on helix- (B)Chls-binding pockets provide useful guidelines for the construction of reasonable (B)Chl-binding protein templates that can be optimized by computational tools.

The Membrane- and Soluble-Protein Helix-Helix Interactome: Similar Geometry via Different Interactions

“…4). Upon further investigation, we found this was due to 26 helical pairs (18.4% of Anti left (int)) derived from chlorophyll binding proteins, which use His to coordinate metals (Braun et al, 2011). Meanwhile, a similar TM motif Anti left (int) contains only 3% of pairs from such proteins.…”

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

“…Understanding such metal-ligand effects can be useful in computational protein design to constrain sampling of amino acid conformations. Analyses of heme and chlorophyll binding sites in proteins uncovered significant constraints and context-dependent conformational preferences for these cofactors [35, 36]. In addition to rotation along the Cα-Cβ bond (the χ1 rotamer), bound cysteine has an additional χ2 rotamer along the Cβ-Sγ bond (Fig.…”

Ca2+-binding reduces conformational flexibility of RC–LH1 core complex from thermophile Thermochromatium tepidum

“…Braun et al 2011;Braun and Fiedor, 2009;Dezi et al 2007;Fowler et al 1994). The excitonically coupled BChl of purple bacterial LH1 complexes usually have their red-most transition at around 870-890 nm.…”