To bind or not to bind - dissociation equilibria studied by pulse dipolar EPR

Abstract

Pulse dipolar EPR is an appealing strategy for structural characterisation of complex systems in solution that complements other biophysical techniques. Significantly, the emergence of genetically encoded self-assembling spin labels exploiting exogenously introduced double-histidine motifs in conjunction with Cu^II -chelates offers high precision distance determination in systems non-permissive to thiol- directed spin labelling. However, the non‐covalent Cu^II coordination approach is vulnerable to low binding‐affinity. Here, an approach is outlined where dissociation constants (K_D) are investigated directly from the modulation depths of relaxation‐induced dipolar modulation enhancement (RIDME) EPR experiments applied to the model protein Streptococcus sp. group G. protein G, B1 domain (GB1). This reveals low‐ to sub‐μM Cu^II-chelate K_DS under RIDME conditions at cryogenic temperatures. We show the feasibility of exploiting the double‐histidine motif for EPR applications even at sub‐μM protein concentrations in orthogonally labelled Cu^II–nitroxide systems.

Additionally, modulation depth quantitation in Cu^II–Cu^II RIDME to simultaneously estimate a pair of non- identical independent K_DS is addressed. Furthermore, we develop a general speciation model to optimise Cu^II labelling efficiency, depending upon pairs of identical or disparate K_DS and total label concentration. We find the K_D estimates are in excellent agreement with previously determined values. We also investigated the vulnerability of binding to both competition from adventitious divalent metal ions, and pH sensitivity. A combination of room-temperature isothermal titration calorimetry (ITC) and Cu^II-nitroxide RIDME measurements are applied to GB1. Results demonstrate double-histidine spin labelling using Cu^II-nitrilotriacetic acid (Cu^II-NTA) is robust against the competitor ligand ZnII-NTA at >1000-fold excess, and high nM binding affinity is retained at acidic and basic pH, despite room-
temperature behaviour suggesting a stronger dependence.

Date of Award	15 Jun 2022
Original language	English
Awarding Institution	University of St Andrews
Supervisor	Bela Ernest Bode (Supervisor)