Figure 1. Conservation of class-specific electrostatic potential distributions predict interclass J-protein complex formation in eukaryotes.

(A) Domain architecture of class A and class B J-proteins (shown as protomers). Class A J-proteins have an N-terminal J-domain (JD), a glycine/phenylalanine-rich flexible region (G/F), C-terminal β-sandwich domains (CTD-I and II) and a CTD-I inserted zinc-finger-like region (ZFLR). The Hsp70-interacting HPD motif is indicated in red. Protomer dimerization to form homodimers occurs at the dimerization domain (DD). The ZFLR in CTD-I is absent in the domain architecture of class B J-proteins. (B) Evolutionary tree ranking the kingdoms of organisms analyzed in this study. (C, D) Electrostatic isopotential contour maps (cyan + 1, red −1 kcal/mol/e) of CTD homodimers and of J-domains of class A (green cartoon diagrams) (C) and class B (blue cartoon diagrams) (D) J-proteins. Roman numerals show the four α-helices on class A JD. J-proteins from the following organisms are compared: Homo sapiens (DNAJA2, DNAJB1), Caenorhabditis elegans (DNJ-12, DNJ-13), Saccharomyces cerevisiae (Ydj1, Sis1), Arabidopsis thaliana (ATJ3, At5g25530), Pseudomonas oryzihabitans, Bordetella pertussis and Escherichia coli (DnaJ, CbpA). The dashed circles on the CTDs of DNAJA2 and DNAJB1 represent the spherical region used for local PIPSA analysis of electrostatic potential similarity. (E, F) Local PIPSA analysis results for class A CTD (E) and class B CTD (F) electrostatic potentials. The electrostatic potentials in the spherical regions (radius of 25 Å) indicated by the dashed black circles in (C) and (D) were clustered by similarity using Ward’s clustering. The heat maps show clustering of J-proteins by similarity (higher similarity indicated by a red shift).

DOI: http://dx.doi.org/10.7554/eLife.24560.003

Figure 1—figure supplement 1. Electrostatic isopotential contour maps of class A J-proteins from humans, fungi, nematodes and bacteria.

(A) Class A CTD dimers (cyan +1, red −1 kcal/mol/e). The protein structure is depicted in green cartoon representation. The J-protein name and corresponding Uniprot ID are given in parentheses for each organism. The human class A J-proteins are represented by DNAJA1 (P31689) and DNAJA2 (O60884). Saccharomyces cerevisiae (Ydj1, P25491) and Caenorhabditis elegans (DNJ-12, O45502) represent fungi and nematodes, respectively. Bacterial DnaJ are represented from the following subgroups: alphaproteobacteria (A0A063 × 4A7, Q1NCH5), betaproteobacterium (Q7VVY3), gammaproteobacteria (P08622, P0A1G8, C4T9C4, A0A0D7F716) and firmicute (M1ZGL1). (B) As in (A) Class A JDs.

DOI: http://dx.doi.org/10.7554/eLife.24560.004

Figure 1—figure supplement 2. Electrostatic isopotential contour maps of class B J-proteins from humans, fungi, nematodes and bacteria.

(A) Class B CTD dimers (cyan + 1, red −1 kcal/mol/e). CTD dimer structure depicted in blue cartoon representation. The J-protein name and corresponding Uniprot ID are given in parentheses for each organism. Human class B J-proteins are represented by DNAJB1 (P25685) and DNAJB4 (Q9UDY4). Saccharomyces cerevisiae (Sis1, P25294) and Caenorhabditis elegans (DNJ-13, Q20774) represent fungi and nematodes, respectively. Bacterial CbpA is represented by the following subgroups: alphaproteobacteria (A0A063XA16, Q1NEX3), betaproteobacterium (J7RE62), gammaproteobacteria (P36659, P63262, Q9BQH2, A0A0D7FE35) and firmicute (M1ZLZ3). (B) As in (A) Class B JDs.

DOI: http://dx.doi.org/10.7554/eLife.24560.005

Figure 1—figure supplement 3. Evaluation of JD interaction sites on CTDs of the opposite class J-proteins.

(A,B) Local PIPSA analysis of electrostatic potentials at (A) class B JD interaction sites on CTDs of class A J-proteins and (B) class A JD interaction sites on CTDs of class B J-proteins. Eukaryotic sequences are colored in black and prokaryotic ones in red. The electrostatic potentials in the spherical region (radius of 25 Å) indicated by the dashed black circles (Figure 1—figure supplement 1A and Figure 1—figure supplement 2A) were clustered by electrostatic distance using Average (a) and Ward’s (b) clustering. The heat map shows clustering of J-proteins according to electrostatic distance (high similarity indicated by a red shift). The color key and density plot is depicted on the top left.

DOI: http://dx.doi.org/10.7554/eLife.24560.006