Advances in Modeling the Stability of Noncovalent Complexes in Charged Droplets with Applications in Electrospray Ionization-MS Experiments

Inter-Domain Repulsion of Dumbbell-Shaped Calmodulin during Electrospray Ionization Revealed by Molecular Dynamics Simulations

The mechanisms whereby protein ions are released from nanodroplets at the liquid-gas interface have continued to be controversial since electrospray ionization (ESI) mass spectrometry was widely applied in biomolecular structure analysis in solution. Several viable pathways have been proposed and verified for single-domain proteins. However, the ESI mechanism of multi-domain proteins with more complicated and flexible structures remains unclear. Herein, dumbbell-shaped calmodulin was chosen as a multi-domain protein model to perform molecular dynamics simulations to investigate the structural evolution during the ESI process. For [Ca₄CAM], the protein followed the classical charge residue model. As the inter-domain electrostatic repulsion increased, the droplet was found to split into two sub-droplets, while stronger-repulsive apo-calmodulin unfolded during the early evaporation stage. We designated this novel ESI mechanism as the domain repulsion model, which provides new mechanistic insights into further exploration of proteins containing more domains. Our results suggest that greater attention should be paid to the effect of domain-domain interactions on structure retention during liquid-gas interface transfer when mass spectrometry is used as the developing technique in gas phase structural biology.

The fragmentation mechanism of gold nanoparticles in water under femtosecond laser irradiation

Plasmonic nanoparticles in aqueous solution have long been known to fragment under irradiation with intense ultrafast laser pulses, creating progeny particles with diameters of a few nanometers. However, the mechanism of this process is still intensely debated, despite numerous experimental and theoretical studies. Here, we use in situ electron microscopy to directly observe the femtosecond laser-induced fragmentation of gold nanoparticles in water, revealing that the process occurs through ejection of individual progeny particles. Our observations suggest that the fragmentation mechanism involves Coulomb fission, which occurs as the femtosecond laser pulses ionize and melt the gold nanoparticle, causing it to eject a highly charged progeny droplet. Subsequent Coulomb fission events, accompanied by solution-mediated etching and growth processes, create complex fragmentation patterns that rapidly fluctuate under prolonged irradiation. Our study highlights the complexity of the interaction of plasmonic nanoparticles with ultrafast laser pulses and underlines the need for in situ observations to unravel the mechanisms of related phenomena.

In Situ Observation of Coulomb Fission of Individual Plasmonic Nanoparticles

Reshaping plasmonic nanoparticles with laser pulses has been extensively researched as a tool for tuning their properties. However, in the absence of direct observations of the processes involved, important mechanistic details have remained elusive. Here, we present an in situ electron microscopy study of one such process that involves Coulomb fission of plasmonic nanoparticles under femtosecond laser irradiation. We observe that gold nanoparticles encapsulated in a silica shell fission by emitting progeny droplets comprised of about 10-500 atoms, with ejection preferentially occurring along the laser polarization direction. Under continued irradiation, the emitted droplets coalesce into a second core within the silica shell, and the system evolves into a dual-core particle. Our findings are consistent with a mechanism in which electrons are preferentially emitted from the gold core along the laser polarization direction. The resulting anisotropic charge distribution in the silica shell then determines the direction in which progeny droplets are ejected. In addition to yielding insights into the mechanism of Coulomb fission in plasmonic nanoparticles, our experiments point toward a facile method for forming surfaces decorated with aligned dual-gold-core silica shell particles.

Strengths and Weaknesses of Molecular Simulations of Electrosprayed Droplets

The origin and the magnitude of the charge in a macroion are critical questions in mass spectrometry analysis coupled to electrospray and other ionization techniques that transfer analytes from the bulk solution into the gaseous phase via droplets. In many circumstances, it is the later stages of the existence of a macroion in the containing solvent drop before the detection that determines the final charge state. Experimental characterization of small (with linear dimensions of several nanometers) and short-lived droplets is quite challenging. Molecular simulations in principle may provide insight exactly in this challenging for experiments regime. We discuss the strengths and weaknesses of the molecular modeling of electrosprayed droplets using molecular dynamics. We illustrate the limitations of the molecular modeling in the analysis of large macroions and specifically proteins away from their native states. Graphical Abstract ᅟ.

What factors determine the stability of a weak protein-protein interaction in a charged aqueous droplet?

Maintaining the interface of a weak transient protein complex transferred from bulk solution to the gaseous state via evaporating droplets is a critical question in the detection of the complex association (dissociation) constant by using electrospray ionization mass spectrometry (ESI-MS). Here we explore the factors that may affect the stability of a protein-protein interaction (PPI) using atomistic molecular dynamics (MD) modelling of a complex of ubiquitin (Ub) and the ubiquitin-associated domain (UbA) (RCSB PDB code ) and a non-covalent complex of diubiquitin (RCSB PDB code ) in aqueous droplets. A general method is presented to determine the protonation states of the complexes we investigate in particular, and that of a protein in general, under various pH conditions that an evaporating droplet acquires due to its change in size. We find that the combination of high temperature and high charge states of the protein complexes may destabilize the interface by creating new interfaces instead of a direct rupture of the initial stable interface. We provide evidence that highly charged protein complexes are found in droplets that form conical extrusions of the solvent on the surface due to charge-induced instability. This distinct droplet morphology leads to a higher solvent evaporation rate that assists in transferring the complex in the gaseous state without dissociation. The conical solvent protrusions expose on the droplet surface certain amino acids that otherwise would be solvated in a droplet with the protein complex of low charge states. The new vapor-protein interface does not have a direct effect on the stability of the PPI. A common way in experiments to stabilize the protein complexes in droplets is to reduce the protonation state of the proteins. Here we find that weakly bound protein complexes even at high protonation states can be stabilized by the presence of a small number of counterions, without affecting the protonation state of the protein. Our findings may provide guiding principles in ESI-MS experiments to stabilize weak transient PPIs.