Title: Balance between Protein Softness and Rigidity Assessed by Inelastic X-ray Scattering
Abstract: Collective excitations due to protein secondary structure have been of considerable interest in the past few years. Such excitations provide the notion of protein softness, and flexibility that are ultimately related to the activity of the protein. However, there has been a lack of evidence for the correlation between the protein structure, collective motions, and the flexibility. Here, we elucidate the protein activity from the perspective of protein softness and flexibility by studying the collective phonon-like excitations in proteins using a state-of-the-art inelastic x-ray scattering (IXS) technique. Both propagating and non-propagating modes of collective phonon-like excitations are observed in proteins on the length scale larger and shorter than the protein secondary structure, respectively. The longitudinal sound velocity of propagating mode of such excitations in protein samples is approximately 2,800 m/s, consistent with the previously reported results. The so-observed non-propagating localized phonon-like excitations give the measure of protein softness and flexibility. Such excitations suggest that protein becomes softer due to breakdown of weak non-covalent bonds (responsible for preserving the native conformation) upon thermal denaturation. In addition, it confirms that protein requires necessary rigidity along with flexibility for the enzyme activity. Furthermore, the drugs like warfarin and ibuprofen that have a strong binding affinity to specific binding sites of the protein, human serum albumin (HSA), do not affect the protein structure and collective excitations. Such results indicate that the efficiency of HSA upon binding to warfarin and ibuprofen in the plasma remains unaffected in carrying and transporting them to the specific targets.