An ensemble of rapidly interconverting orientations in electrostatic protein-peptide complexes characterized by NMR spectroscopy

Abstract

Protein complex formation involves an encounter state in which the proteins are associated in a nonspecific manner and often stabilized by interactions between charged surface patches. Such patches are thought to bind in many different orientations with similar affinity. To obtain experimental evidence for the dynamics in encounter complexes, a model was created using the electron transfer protein plastocyanin and short charged peptides. Three plastocyanins with distinct surface charge distributions were studied. The experimental results from chemical shift perturbations, paramagnetic relaxation enhancement (PRE) NMR, and theoretical results from Monte Carlo simulations indicate the presence of multiple binding orientations that interconvert quickly and are dominated by long-range charge interactions. The PRE data also suggest the presence of highly transient orientations stabilized by short-range interactions.

Keywords: NMR spectroscopy; encounter complexes; molecular modeling; plastocyanins; tetralysine peptides.