Acyl carrier protein structural classification and normal mode analysis

Abstract

All acyl carrier protein primary and tertiary structures were gathered into the ThYme database. They are classified into 16 families by amino acid sequence similarity, with members of the different families having sequences with statistically highly significant differences. These classifications are supported by tertiary structure superposition analysis. Tertiary structures from a number of families are very similar, suggesting that these families may come from a single distant ancestor. Normal vibrational mode analysis was conducted on experimentally determined freestanding structures, showing greater fluctuations at chain termini and loops than in most helices. Their modes overlap more so within families than between different families. The tertiary structures of three acyl carrier protein families that lacked any known structures were predicted as well.

Evolution of acyl-ACP thioesterases and β-ketoacyl-ACP synthases revealed by protein–protein interactions

“…However, Cr-cACP is unable to complement an EcACP knockout strain, suggesting that it cannot interact with all endogenous FAS enzymes, similar to spinach ACP (De Lay and Cronan 2007). The phylogeny of ACPs (Figure S2),(Cantu et al 2012b) shows –surprisingly- distinct families, even within the previously identified ACP1 family (Cantu et al 2012b), suggesting that the match between ACP and partner protein also depends on the evolutionary origin of the ACP itself.…”

“…Second, Predalgo (Tardif et al 2012) (currently the only targeting prediction tool for algae) predicts mitochondrial targeting for ACP1 and chloroplastic targeting for ACP2. Third, a phylogenetic tree of ACPs shows at least 16 families (Cantu et al 2012b) (Figure S2A) and subfamilies in FAS ACPs (Figure S2B), including the two C. reinhardtii ACPs: ACP1 clustering with mitochondrial ACPs and ACP2 with chloroplastic ACPs.…”

“…Type I synthases are present in eukaryotes and thought to be a fusion of the evolutionarily older type II synthases (McCarthy and Hardie 1984). The acyl carrier protein (ACP) (Crosby and Crump 2012; Cantu et al 2012b) is the central protein that carries the iteratively growing fatty acid on its phosphopantetheine arm, which is post-translationally added by dedicated phosphopantetheinyl transferases (PPTases) (Lambalot et al 1996). In type II synthases, ACP buries its attached cargo within its inner hydrophobic core, and protein-protein interactions with catalytic proteins induces the acyl chain to release from the inner core and into the active site of the catalytic protein (Zornetzer et al 2010).…”

Structural consequences of chromophore formation and exploration of conserved lid residues amongst naturally occurring fluorescent proteins

“…(68) The best correlation between the experimental and theoretical B-factors was obtained by systematically changing the cutoff distance (ranging from 15–21 Å) and distance weights (ranging from 0–3) for interactions between Cα atoms, Figure S1. (69) The cut-off distance and distance weight values were changed and their corresponding Pearson's correlation coefficient values were recorded. Since the wild-type FPs are composed of multiple chains that are structurally similar, only chain A for each of them was used in these studies.…”

Structural analysis of protein–protein interactions in type I polyketide synthases

“…In some structures an additional short helix (helix III) is found in the second loop depends on its helix-loop equilibrium conformations (Sharma et al, 2006; Cantu et al, 2012). The longer helix-I is positioned anti-parallel to helix II and helix IV, while helix I and helix IV are arranged at a small angle relative to each other (Figure 16-A).…”