Abstract
Electrospray ionization mass spectrometry (ESI-MS) has the potential to become a high-throughput robust experimental method for the detection of protein-protein equilibrium constants. Poorly understood processes that affect the stability of weak noncovalent protein complexes in the intervening droplet environment are a significant factor that precludes the advancement of the method. We use molecular dynamics to study the stability of a ubiquitin and ubiquitin-associated domain complex (RCSB PDB code 2MRO ) in an aqueous droplet with changing size and charge concentration. We present evidence that a weak protein complex changes conformation and may dissociate in shrinking droplets. Then, the droplets containing these dissociated proteins divide. Our findings suggest that in some cases ESI-MS does not measure the correct association constants. The study intends to stimulate research for systematic development of experimental protocols that stabilize weakly bound protein interfaces in droplets.
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