Structural basis for the antifolding activity of a molecular chaperone

Abstract

Molecular chaperones act on non-native proteins in the cell to prevent their aggregation, premature folding or misfolding. Different chaperones often exert distinct effects, such as acceleration or delay of folding, on client proteins via mechanisms that are poorly understood. Here we report the solution structure of SecB, a chaperone that exhibits strong antifolding activity, in complex with alkaline phosphatase and maltose-binding protein captured in their unfolded states. SecB uses long hydrophobic grooves that run around its disk-like shape to recognize and bind to multiple hydrophobic segments across the length of non-native proteins. The multivalent binding mode results in proteins wrapping around SecB. This unique complex architecture alters the kinetics of protein binding to SecB and confers strong antifolding activity on the chaperone. The data show how the different architectures of chaperones result in distinct binding modes with non-native proteins that ultimately define the activity of the chaperone.

Extended Data Figure 1. NMR characterization of SecB and unfolded MBP

a, SecB is enriched in hydrophobic amino acids, such as methyl-bearing (Ala, Ile, Leu, Met, Thr, and Val) and aromatic (Phe and Tyr). b, ¹H-¹⁵N TROSY HSQC (left) and ¹H-¹³C methyl HMQC (right) spectra of [U-²H; Ala-¹³CH₃; Met-¹³CH₃; Ile-δ1-¹³CH₃; Leu,Val-¹³CH₃/¹³CH₃; Thr-¹³CH3]-labeled SecB. SecB packing gives rise to two pairs of spectroscopically equivalent subunits: one pair is formed by subunits A and D, and the other pair by subunits B and C. Select assignment is included in the methyl spectrum with the asterisk indicating the other pair. c, ¹H-¹⁵N HSQC spectra of select MBP fragments spanning the entire sequence of MBP. d, Secondary structure propensity (SSP) values^, of unfolded MBP (extracted collectively from the fragments) plotted as a function of the amino acid sequence. A SSP score at a given residue of 1 or −1 reflects a fully formed α-helical or β-structure (extended), respectively, whereas a score of, for example, 0.5 indicates that 50% of the conformers in the native-state ensemble of the protein are helical at that position. The data show that several of the secondary structure elements in the folded MBP retain some transient secondary structure in the unfolded MBP fragments.

Extended Data Figure 2. NMR characterization of PhoA and MBP binding to SecB

a, To determine the SecB-recognition sites within PhoA and MBP ¹⁵N labeled PhoA and MBP fragments were titrated with unlabeled SecB. Due to the labeling scheme and the size of SecB, the intensity of the PhoA and MBP residues that are bound by SecB decreases dramatically or disappears. Several titration points were recorded but here only the spectra for the SecB:PhoA and SecB:MBP 1:1 are shown for two select fragments. The ¹H-¹⁵N HSQC spectra of PhoA or MBP are shown in the absence (blue) and presence (red) of SecB. b–c, PhoA (b) and MBP (c) refolding in the presence and absence of SecB monitored by ¹H-¹⁵N HSQC spectra. Spectra of the “refolded” state were recorded after rapid dilution of urea-treated MBP/PhoA in native buffer. Spectra of the “unfolded” state were recorded in urea. MBP and PhoA refolded in the their native structure in the absence of SecB but were retained in the unfolded state in the presence of SecB.

Extended Data Figure 3. Energetics of SecB interaction with PhoA and MBP

a, MALS of SecB–PhoA complex showing a stoichiometry of 1:1. b, ITC of SecB binding to PhoA and the energetics of binding. c, K_d values for complexes between select PhoA fragments encompassing the five (a through e) SecB-recognition sites and SecB. d, MALS of SecB–MBP complex showing a stoichiometry of 1:1. e, ITC of SecB binding to MBP and the energetics of binding. f, K_d values for complexes between select MBP fragments encompassing the seven (a through g) SecB-recognition sites and SecB. More than one of the smaller PhoA or MBP fragments (e.g. PhoA^c, PhoA^d-e, MBP^c-d) can be accommodated within SecB. Of note is the large favorable enthalpy of binding for the interaction of MBP and PhoA with SecB reflecting the large interacting surface. However, a large but unfavorable entropy diminishes the overall binding.

Extended Data Figure 4. NMR characterization of the SecB–PhoA complex

a, ¹H-¹⁵N TROSY HSQC spectra of PhoA in the unfolded state (light blue) and in complex with SecB (grey). The unfolded state was induced by the addition of reducing agent or urea and assigned and characterized by NMR as shown before. Select resonance assignment of SecB-recognition sites in PhoA is included (the color is per the color code for each SecB-recognition site within PhoA; see Fig. 1b). There is an excellent correspondence between the PhoA residues identified to bind to SecB using the various PhoA fragments (Extended Data Fig. 2a) and the residues of full-length PhoA that are bound to SecB in the SecB–PhoA complex. All five SecB-recognition sites in PhoA (a through e) are engaged by SecB in the SecB–PhoA complex. The PhoA regions that are not bound to SecB (they retain their intensity in the complex) are all in an unfolded conformation as suggested by their essentially identical chemical shifts to the unfolded PhoA. b, Select strips from ¹³C-edited NOESY experiments highlighting inter-molecular NOEs in the SecB–PhoA complex. Owing to severe resonance overlap in the 120 kD SecB–PhoA complex, in order to identify specific inter-molecular NOEs we prepared samples wherein the two protein partners are labeled in different methyl-bearing type of amino acids. In this example, SecB was labeled in Leu, Met and Val residues and PhoA in Ile residues. Thus, all NOEs detected between Leu/Val/Met and Ile methyls are inter-molecular. c, ¹H-¹³C methyl HMQC spectra of SecB in complex with PhoA fragments carrying the individual PhoA sites: PhoA^a (green), PhoA^c (orange), PhoA^d (magenta) and PhoA^e (red). Both SecB and PhoA fragments are [U-²H; Ala-¹³CH₃; Met-¹³CH₃; Ile-δ1-¹³CH₃; Leu,Val-¹³CH₃/¹³CH₃; Thr-¹³CH₃]-labeled. d, Representative strips from ¹³C-edited NOESY-HSQC and HMQC-NOESY-HMQC NMR experiments. The NOE cross-peaks between SecB and residues of PhoA fragments are designated by a dashed-line red circle. e, Characteristic NOEs showing that the primary binding groove in SecA is enlarged by the displacement of helix α2 as shown in Figure 4a. For example, the NOE between SecB residues Ala95 and Phe137 is consistent with the closed conformation observed in apo SecB. This NOE is not present in the SecB–PhoA complex because the two SecB residues have moved apart as a result of the displacement of the helix α2.

Extended Data Figure 5. Strategy for the structure determination of the SecB–PhoA complex

The three main steps are briefly described here. More details can be found in Methods. The lowest-energy NMR structures of the SecB complexes with the individual PhoA sites a, c, d, and e are shown. The structural and NMR statistics for each structure are shown in Extended Data Table 1.

Extended Data Figure 6. Structures of SecB with MBP sites

a, Lowest-energy structure of SecB in complex with a MBP fragment encompassing site d (MBP^d, residues 105–152). b, Lowest-energy structure of SecB in complex with a MBP fragment encompassing site e (MBP^e, residues 165–210). SecB is shown as grey solvent-accessible surface (left) or as white cartoon (right). Expanded views (right) of the contacts between SecB and MBP. The SecB residues mediating contacts with MBP are shown as blue ball-and-stick. In both complexes an additional MBP molecule binds symmetrically to the opposite face of SecB but are not shown for clarity.

Extended Data Figure 7. NMR-driven model structure of SecB–MBP complex

a, ¹H-¹⁵N TROSY HSQC spectra of MBP fragments (grey), MBP fragments in complex with SecB (blue) and full-length MBP in complex with SecB (magenta). The Gly (left) and Trp Nε (right) regions are shown as examples because of the excellent dispersion and lack of severe resonance overlap. The various MBP fragments covering the entire MBP sequence (Extended Data Fig. 1c) are colored grey and if they are located within a SecB-recognition site it is denoted in the superscript. The MBP residues that do not interact with SecB retain their intensity. These are residues located in regions that are not SecB-recognition sites (Fig. 1c). When these spectra are compared with the spectra of full-length MBP in complex with SecB (in magenta) a very good resonance correspondence is observed. Thus, two important observations can be made: first, all seven SecB-recognition sites (a through g) in MBP are engaged by SecB in the SecB–MBP complex; and, second, the MBP regions that do not interact with SecB in the SecB–MBP complex remain in an unfolded state. The Trp spectra (right) provide direct evidence in support of these observations: all Trp residues, with the exception of Trp155, are located in SecB-recognitions sites and they all interact with SecB in the SecB–MBP complex. In contrast, Trp155 does not bind to SecB when the corresponding MBP fragment was used, and this also the case for MBP. b, Modeled structure of the SecB–MBP complex. SecB is shown as a solvent-exposed surface and MBP as a pink ribbon. The seven MBP sites recognized by SecB are shown as sidechain surface and colored per the color code in the graphic of the MBP sequence at the top. The structure of the complex was modeled as detailed in Methods. Briefly, as mentioned above, NMR analysis demonstrated that all seven recognition sites in MBP (labeled a through g) are bound to SecB in the SecB–MBP complex. We have determined the high-resolution structure of MBP^d and MBP^e in complex with SecB (Extended Data Fig. 6). Because of their length and the short linker tethering the two sites, d and e sites most likely bind to the same side of SecB. MBP site f is the longest one, consisting of ~90 residues, and is thus entirely accommodated on the other side of SecB. With sites d, e and f occupying the primary binding sites, the other recognition sites (a, b, c and g) being much shorter can be accommodated within the secondary client-binding sites on SecB. The structure of MBP sites d and e in complex with SecB was determined using the experimental inter-molecular NOE data. The hydrophobic residues of the sites a, b, c, f, and g showing the strongest effect upon SecB binding, as determined by differential line broadening, were used to drive the docking of these sites to nonpolar residues on SecB. The modeled structure shows that the entire MBP sequence can be accommodated within one SecB molecule.

Extended Data Figure 8. Antiaggregation activity of SecB

a, A triple amino acid substitution in the SecB (V40A/L42A/L44A) client-binding site was prepared and is referred to as the triple mutant SecB (SecB™). ITC profile of the binding of PhoA to SecB™ to be compared with PhoA binding to wild type SecB (Extended Data Fig. 3b). The triple substitution causes a 40-fold reduction in the affinity of SecB for PhoA. b, Fluorescence-monitored MBP folding in the absence of SecB (blue), in the presence of wild-type SecB (green) and in the presence of SecB™ (red). The triple mutant diminishes significantly the antifolding activity of SecB. c, ¹H-¹⁵N TROSY HSQC spectra of MBP refolded in the absence (blue) and presence of SecB™ (red). In contrast to wild-type SecB (Extended Data Fig. 2c), SecB™ cannot hold MBP in the unfolded state. d, ¹H-¹³C methyl HMQC spectra of MBP^mut (blue) and in the presence of SecB (red) recorded at 22 °C. The MBP mutant (MBP^mut) carries two amino acid substitutions (G32D/I33P) that renders the protein prone to aggregation, especially at temperatures above 30 °C. No NMR signal of MBP^mut can be detected at temperatures above 30 °C and the protein precipitates in the NMR tube. At 22 °C, MBP^mut is folded, as evidenced by the resonance dispersion in the NMR spectra, and does not interact with SecB. e, ¹H-¹³C methyl HMQC spectrum of MBP^mut in the presence of SecB recorded at 50 °C. MBP^mut suffers heavy precipitation and aggregation at temperatures higher than 30 °C, but in the presence of SecB it is stable and folded even at temperatures as high as 50 °C. f, ¹H-¹⁵N TROSY HSQC spectra of SecB (blue) and in the presence of MBP^mut (orange) at 42 °C, indicating binding. Because of the elevated temperature, a significant unfolded population of MBP^mut is present, which binds to SecB (see main text). g, Mapping of the sites (orange) used by SecB to interact with MBP^mut, based on the chemical shift perturbation data from the spectra in (f).

Extended Data Figure 9. Kinetics of PhoA and MBP interaction with SecB and TF

(a–c) SPR analysis of the interaction of SecB with PhoA (a) and MBP at 20 °C (b) and 30 °C (c). Single-cycle and multiple-cycle procedures were used for the SPR analysis of SecB with PhoA and MBP, respectively. (d–f) BLI analysis of the binding of MBP to SecB (d), SecB™ (e) and TF (f). His-tagged PhoA or MBP (for SPR) or biotinylated MBP (for BLI) experiments was immobilized on an NTA chip (SPR) or streptavidin biosensor (BLI) and interactions were examined at different SecB or TF concentrations as indicated. Binding is reported in response units (RU) for SPR and wavelength shift (nm) for BLI as a function of time. (g–h) Effect of SecB on the kinetics of MBP folding. (g) Fluorescence-monitored folding of MBP (pre form) and mature MBP (h) in the absence (blue), and presence of 1- (green) and 4-fold (purple) excess of SecB. SecB does not appreciably delay folding of mature MBP. In fact, SecB excess appears to increase the yield of soluble, folded mature MBP (purple). i, ¹H-¹⁵N TROSY HSQC spectra of mature MBP refolded in the absence (blue) and presence of SecB (red). SecB cannot retain the mature MBP unfolded. j, Fluorescence-monitored folding of the slowly-folding MBP^Y283D variant in the absence (blue), and presence of 1- (green) and 5-fold (orange) TF. As elaborated in the main text, TF does not delay folding of pre-MBP (Fig. 5a). However, it does delay folding of an inherently slowly folding MBP mutant (MBP^Y283D) thus highlighting the importance of the intrinsic folding of the client protein and its association rate to the chaperone.

Figure 1. Recognition sites in SecB and client proteins

a, Structure of E. coli SecB (PDB ID 1QYN). The four subunits (A through D) are colored differently. The structural elements are labeled on subunit A. b–c, Hydrophobicity plot of PhoA (b) and MBP (c), as a function of their primary sequence. A hydrophobicity score (Roseman algorithm, window = 9) higher than zero denotes increased hydrophobicity. The sites identified by NMR to be recognized by SecB in PhoA (labeled a through e) and MBP (labeled a through g) are highlighted in blue and the residue range is shown at the bottom. d, The SecB residues identified by inter-molecular NOE data to interact with PhoA and MBP are shown in ball-and-stick and colored blue. e, Expanded view of the binding sites in SecB subunit A is shown and the residues interacting with client proteins are labeled. f, The hydrophobic residues in SecB are colored green, whereas all other residues are colored white. The primary (P) and secondary (S) client-binding sites in SecB are marked and their boundaries delineated.

Figure 2. Structure of the SecB–PhoA complex

Lowest-energy structure of the SecB–PhoA complex. SecB is shown as a space-filling model in grey. The five PhoA sites recognized by SecB are shown as space-filling models and colored per the color code in the graphic of the PhoA sequence at the top. The flexible regions of PhoA are shown as a pink ribbon. Four views of the complex are shown related by a rotation as indicated by the arrow. One PhoA molecule binds, which wraps around SecB. The NMR data show that the linkers tethering the binding sites in PhoA are flexible and do not interact with SecB (Extended Data Fig. 4a).

Figure 3. Recognition of non-native PhoA by SecB

Expanded views of the SecB–PhoA complex highlighting the binding details and contacts that mediate recognition of the four PhoA sites (a, c, d, and e) by SecB. The color code of the PhoA sites, shown as ball-and-stick, is as in Fig. 2. SecB in the expanded views is shown as white ribbon and residues contacting PhoA are displayed as blue ball-and-stick.

Figure 4. SecB structure adapts to client binding

a, Superposition of SecB structures (only subunit A is shown) in the unliganded state (blue) and bound to PhoA (pink). PhoA is not shown for clarity. The SecB helix α2 swings outward by ~50° upon PhoA binding. See also Extended Data Fig. 4e. b, Superposition of the structure of SecB subunits in complex with PhoA site c colored in orange and with PhoA site d colored in magenta. SecB is shown as a solvent-exposed surface in white.

Figure 5. Effect of chaperone-client binding mode on kinetics and chaperone activity

a, Folding of urea-denatured MBP (pre form) in the absence of a chaperone (blue) and in the presence of SecB (purple) or TF (orange). Folding was monitored by Trp fluorescence at 23 °C. SecB prevents the folding of MBP, whereas TF has a negligible effect. Both SecB and TF are in 4-fold excess over MBP. b, Kinetic analysis by BLI of the binding of MBP to SecB (left) and TF (right). c, Structure of SecB–PhoA and d, TF–PhoA complex. In both structures, the chaperone and PhoA are rendered as in Fig. 2. TF can only accommodate ~50 interacting PhoA residues per TF molecule, whereas one SecB molecule can accommodate the entire PhoA.