Many dissimilar protein domains switch between α-helix and β-sheet folds

Abstract

Fold-switching proteins challenge the one-sequence-one-structure paradigm by adopting multiple stable folds. Nevertheless, it is uncertain whether fold switchers are naturally pervasive or rare exceptions to the well-established rule. To address this question, we developed a predictive method and applied it to the NusG superfamily of >15,000 transcription factors. We predicted that a substantial population (25%) of the proteins in this family switch folds. Circular dichroism and nuclear magnetic resonance spectroscopies of 10 sequence-diverse variants confirmed our predictions. Thus, we leveraged family-wide predictions to determine both conserved contacts and taxonomic distributions of fold-switching proteins. Our results indicate that fold switching is pervasive in the NusG superfamily and that the single-fold paradigm significantly biases structure-prediction strategies.

Coevolution‐derived native and non‐native contacts determine the emergence of a novel fold in a universally conserved family of transcription factors

“…Altogether, our best TP for L contacts ( L = 162) with the highest number of ID contacts was achieved with the Metamorphics MSA and GREMLIN, obtaining 70 contacts for the NTD, 22 for the CTD in either fold, and 4 ID contacts (Figure 2 and Table S2). In comparison, a recent work on coevolutionary analysis on RfaH using EVcouplings 35 on sequences collected using iterative BLAST 36 and filtered by secondary structure propensity with JPred 28 led to the prediction of CTD and NTD contacts but did not report any correctly predicted ID contacts 27 …”

“…A recent work employed a secondary structure prediction approach to filter out potential non‐metamorphic RfaH homologs 27 . Based on this work, we used JPred 28 to identify which protein sequences from the Interpro + MG MSA exhibit both β‐strand and α‐helical propensity in a short section of the CTD, comprising residues 126–162 in the representative sequence of E. coli RfaH, that reports its metamorphic duality.…”

“…The retrieved sequences were also used to construct an HMM 32 profile that was employed to retrieve more RfaH sequences from the metaclust database, 26 using cutoff e‐values of 10 −30 , 10 −25 , and 10 −20 . Lastly, the sequences from Interpro and metaclust were combined and filtered based on the duality of their secondary structure propensity, similarly to previous works 27 . To do this, a region of the CTD sequence of each protein (starting from the residue pattern FQAIF, corresponding to residue number 126 in E. coli RfaH) was used as input for secondary structure prediction on the JPred4 webserver 28 (https://www.compbio.dundee.ac.uk/jpred/) using default settings.…”

“…The number of RfaH sequences was further increased by constructing a hidden Markov model (HMM) profile to use as input for a subsequent search of RfaH sequences in the metagenomic database metaclust 26 . Finally, in line with recent works, 27 all sequences were filtered using secondary structure prediction in JPred 28 to select only metamorphic candidates. This metamorphic enrichment protocol yielded an alignment of 3,570 nonredundant sequences that display four coevolving pairs of residues involved in interdomain interactions in the experimentally solved structure of αRfaH.…”

Global Fold Switching of the RafH Protein: Diverse Structures with a Conserved Pathway

“…58 For example, experimentally determined CD for full-length RfaH exhibits the characteristic α-helical configuration. 59 In contrast, the mixed components of secondary structures during conformational change complicate the CD spectra (Figure 6). Interestingly, we notice that the CD spectrum of S4, the compact core along the transition path, resembles that of the all-β fold.…”