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Characterization of protein energy landscape and conformational ensembles isimportant for understanding mechanisms of protein folding and function. Westudied ensembles of bound and unbound conformations of six proteins to exploretheir binding mechanisms and characterize the energy landscapes in implicitsolvent. First, results show that bound and unbound spectra often significantlyoverlap. Moreover, the larger the overlap the smaller the RMSD between boundand unbound conformational ensembles. Second, the analysis of theunbound-to-bound changes points to conformational selection as the bindingmechanism for four of the proteins. Third, the center of the unbound spectrumhas a higher energy than the center of the corresponding bound spectrum of thedimeric and multimeric states for most of the proteins. This suggests that theunbound states often have larger entropy than the bound states consideredoutside of the complex. Fourth, the exhaustively long minimization, makingsmall intra-rotamer adjustments, dramatically reduces the distance between thecenters of the bound and unbound spectra as well as the spectra extent. Itcondenses unbound and bound energy levels into a thin layer at the bottom ofthe energy landscape with the energy spacing that varies between 0.8-4.6 and3.5-10.5 kcal/mol for the unbound and bound states correspondingly. At the sametime, the energy gap between the two lowest states in the full ensemble variesbetween 0.9 and 12.1 kcal/mol. Finally, the analysis of protein energyfluctuations showed that protein vibrations itself can excite the inter-statetransitions, thus supporting the conformational selection theory.

Ensemble-based characterization of unbound and bound states on protein energy landscape