Mapping molecular binding by means of conformational dynamics measurements

Abstract

Protein-protein interactions are key in virtually all biological processes. The study of these interactions and the interfaces that mediate them play a key role in the understanding of biological function. In particular, the observation of protein-protein interactions in their dynamic environment is technically difficult. Here two surface analysis techniques, dual polarization interferometry and quartz crystal microbalance with dissipation monitoring, were paired for real-time mapping of the conformational dynamics of proteinprotein interactions. Our approach monitors this dynamics in real time and in situ, which is a great advancement within technological platforms for drug discovery. Results agree with the experimental observations of the interaction between the TRIM21a protein and circulating autoantibodies via a bridging bipolar mechanism. This work provides a new chip-based method to monitor conformational dynamics of protein-protein interactions, which is amenable to miniaturized high-throughput determination.

Modeling the Dynamics of Protein–Protein Interfaces, How and Why?

“…SAXS [ 82 ] or mass spectrometry [ 83 ], on the other hand, can provide data about the stoichiometry and shape of the assembly. A recent work by do Nascimento et al combined a quartz crystal microbalance and dual polarization interferometry for the real-time investigation of the thermodynamics and conformational dynamics of the TRIM12 antibody–antigen complex [ 84 ]. All this information can be converted in spatial restraints that are used for sampling in integrative modeling platforms [ 85 , 86 , 87 ], in combination with modeling tools (docking, NMA, Monte Carlo, or MD simulations).…”

New structural insights into the role of TROVE2 complexes in the on-set and pathogenesis of systemic lupus erythematosus determined by a combination of QCM-D and DPI

“…Interactions between proteins and ligands are relevant for regulation of biological processes, because intrinsic conformational dynamics of proteins play crucial roles in ligand binding and dissociation [22,23].Accordingly, the conformational dynamics of the TROVE2 biorecognition was studied here by QCM-D, applying the novel function -∂f/∂D (∂f and ∂D are the time derivatives of the frequency and dissipation factor, see Supplementary Note 1) [24].This function provides a clear identification of the structural transitions of the adsorbed layer and allows the reaction path to be monitored in real time.…”

“…The joint use of both techniques provides important advantages, such as the determination of the mass of water within the adlayer, which plays a very important role in biochemical processes. Moreover, the use of two novel functions: -df/dD and h/molec, recently reported [24] allows the detection and characterization of reaction intermediates in situ, showing the effect of the hydrodynamic flow during the biomolecular interaction. These techniques have never previously been used to monitor reaction intermediates in this way.…”