Bioinformatic Analysis Reveals Conservation of Intrinsic Disorder in the Linker Sequences of Prokaryotic Dual-family Immunophilin Chaperones

Abstract

The two classical immunophilin families, found essentially in all living cells, are: cyclophilin (CYN) and FK506-binding protein (FKBP). We previously reported a novel class of immunophilins that are natural chimera of these two, which we named dual-family immunophilin (DFI). The DFIs were found in either of two conformations: CYN-linker-FKBP (CFBP) or FKBP-3TPR-CYN (FCBP). While the 3TPR domain can serve as a flexible linker between the FKBP and CYN modules in the FCBP-type DFI, the linker sequences in the CFBP-type DFIs are relatively short, diverse in sequence, and contain no discernible motif or signature. Here, I present several lines of computational evidence that, regardless of their primary structure, these CFBP linkers are intrinsically disordered. This report provides the first molecular foundation for the model that the CFBP linker acts as an unstructured, flexible loop, allowing the two flanking chaperone modules function independently while linked in cis, likely to assist in the folding of multisubunit client complexes.

Dual-Family Peptidylprolyl Isomerases (Immunophilins) of Select Monocellular Organisms

“…Bioinformatic analysis showed that all CFBP linkers, in spite of their sequence dissimilarity, possess intrinsic disorder (ID), a hallmark of flexible protein linkers [16], as shown later with Flavobacterium johnsoniae CFBP (Figure 3). Thus, both classes of DFPPIs contain flexible linkers, serving as connector between the two classical PPI/immunophilin domains, which offered the first indication that the two domains may function as independent functional modules, able to freely bend against each other [14,16].…”

“…In analogy to the single family PPIases, it is safe to assume that the DFPPIs play a major role to facilitate folding of their client proteins, which also remain unidentified. Expanding on our previous suggestions [13,14,16], I propose a model (Figure 4), in which the bifunctional DFPPI is located, perhaps together with translating polyribosomes (polysomes), at specialized cellular sites that is tentatively named "translational co-folding centers" or TCCs.…”

“…All FCBPs contain three nonidentical repeats of TPR, referred as 3TPR [14]. In sharp contrast, the CFBPs do not contain TPR, but instead uses short peptide sequences, averaging ~50 amino acids in length, to serve as a linker between the CYN and FKBP domains [16].…”

“…collectively refer to these CFBP and FCBP sequences as DFPPIs, and summarize our current knowledge on these proteins along with a broader view of their potential function. More specialized reviews of DFPPI subsets and recent bioinformatic analysis of their structure can be found elsewhere [14][15][16].…”

“…(A) Intrinsic disorder in the linker peptide region (the central pink area), connecting the CYN and FKBP domains in FjCFBP39 (GenBank WP_012024434.1), computed with PrDOS, as previously described[16]. The red horizontal line is the baseline for disorder cutoff, set at 10% falsepositive rate.…”