Inter-domain dynamics in the chaperone SurA and multi-site binding to its unfolded outer membrane protein clients

Abstract

<jats:title>Abstract</jats:title><jats:p>The periplasmic chaperone SurA plays a key role in outer membrane protein (OMP) biogenesis. <jats:italic>E. coli</jats:italic> SurA comprises a core domain and two peptidylprolyl isomerase domains (P1 and P2), but how it binds its OMP clients and the mechanism(s) of its chaperone action remain unclear. Here, we have used chemical cross-linking, hydrogen-deuterium exchange, single-molecule FRET and molecular dynamics simulations to map the client binding site(s) on SurA and to interrogate the role of conformational dynamics of the chaperone’s domains in OMP recognition. We demonstrate that SurA samples a broad array of conformations in solution in which P2 primarily lies closer to the core/P1 domains than suggested by its crystal structure. Multiple binding sites for OMPs are located primarily in the core domain, with binding of the unfolded OMP resulting in conformational changes between the core/P1 domains. Together, the results portray a model in which unfolded OMP substrates bind in a cradle formed between the SurA domains, with structural flexibility between its domains assisting OMP recognition, binding and release.</jats:p>

Structural Proteomics Methods to Interrogate the Conformations and Dynamics of Intrinsically Disordered Proteins

“…The models derived were globular in nature, whereas other evidence suggests that tau populates an ensemble of structures, including more elongated states ( Mylonas et al, 2008 ; Narayanan et al, 2010 ; Elbaum-Garfinkle and Rhoades 2012 ; Mirbaha et al, 2018 ). This suggests that XL-MS may be overrepresenting the abundance of globular states in solution as has been observed for other flexible systems ( Calabrese et al, 2020 ). A similar approach has also been used to derive a conformational ensemble for the protein aSyn.…”

“…One of the challenges when using XL-MS reagents to study dynamic proteins/assemblies with multiple copopulated states is that the experimentally derived distance restraints constitute a snapshot of interresidue distances spanning the ensemble ( Rappsilber 2011 ; Bonomi et al, 2017 ; Filella-Merce et al, 2020 ). In such cases, computational methods can be used to derive structural ensembles consistent with the data ( Ding et al, 2017 ; Webb et al, 2018 ; Calabrese et al, 2020 ). Alternatively, the distance restraints from XL-MS can be mapped onto previously determined ensembles ( Degiacomi et al, 2017 ; Bullock et al, 2018 ; Calabrese et al, 2020 ).…”

“…In such cases, computational methods can be used to derive structural ensembles consistent with the data ( Ding et al, 2017 ; Webb et al, 2018 ; Calabrese et al, 2020 ). Alternatively, the distance restraints from XL-MS can be mapped onto previously determined ensembles ( Degiacomi et al, 2017 ; Bullock et al, 2018 ; Calabrese et al, 2020 ). For IDPs, untangling and modeling these conformational families using restraints from XL-MS, and indeed using data from any technique, remains challenging.…”

“…A similar tag-transfer XL approach to study the interaction of dynamic proteins with folded proteins has also been developed. This method also exploits diazirine chemistry and uses MS to detect a mass tag left on the partner protein at the interaction site ( Horne et al, 2018 ; Calabrese et al, 2020 ). This approach was validated using a high-affinity regulatory peptide-protein complex MCL1 with BID, with the detected crosslinks mapping to the binding cleft of MCL1 ( Horne et al, 2018 ).…”

“…This approach was validated using a high-affinity regulatory peptide-protein complex MCL1 with BID, with the detected crosslinks mapping to the binding cleft of MCL1 ( Horne et al, 2018 ). This approach has been used to map interaction interfaces of unfolded outer membrane proteins with periplasmic chaperones Skp and SurA, revealing the primary sites on these chaperones which contact the unfolded clients ( Horne et al, 2018 ; Calabrese et al, 2020 ).…”