Open Access Dissertation
Date of Award
Physics and Astronomy
The protein structures revealed by the crystallographic studies have provided the valuable information over the years regarding their biological functions. However, such snapshots of protein fluctuations averaged over time may not be enough to fully capture the underlying biological phenomena. A deeper understanding of the protein dynamics is crucial for elucidating the structural pathways or the transition mechanism from the initial state to the final state necessary for regulating the physical and chemical processes. Hence, the biological activities and functions are mainly governed by the protein conformational dynamics. However, the direct correlation of a wide range of protein dynamics to function still remains unclear, posing a major challenge to biophysical community. In this dissertation, the relationships among the protein's conformation, dynamics and function are investigated using the state-of-the-art neutron and X-ray scattering techniques. Taking the advantage of comparable wavelength and momentum transfer of neutron and X-ray to that of the atoms, we studied the protein dynamics at molecular level over the timescale of few femtoseconds to nanoseconds regime, which provides the information regarding the conformational flexibility of protein. Interestingly, we observed that the protein dynamic behavior is similar to that of glass forming liquids, where the relaxation process is non-exponential and the collective excitations are highly damped. Specifically, picosecond to nanosecond dynamics, also known as beta-relaxation process decays logarithmically over the time. Remarkably, such dynamic phenomena revealed the direct experimental evidences of structure-dynamics-function relationship of a large variety of protein family such as a large hyperthermophilic protein, a membrane protein, and the native and denatured globular proteins. Simultaneously, we successfully applied the idea of generic free-energy landscape based upon the dynamic behavior possessed by the proteins to explain their activities.
The dynamic behavior of a hyperthermophilic protein from the deep-sea is studied using the quasi-elastic neutron scattering (QENS). QENS results revealed that the dynamic property of a mesophilic protein is largely affected by the high pressure and temperature by distorting the protein energy landscape and therefore the activity. On the other hand, the hyperthermophilic protein restrains such effects. In addition, the mechanism of light activation of a G-protein-coupled receptor (GPCR), rhodopsin as a prototype is studied using small-angle neutron scattering (SANS) and QENS. The SANS data indicates the large conformational change in rhodopsin upon photoactivation. On the other hand, the QENS results show the significant difference in the intrinsic protein dynamics between the dark-state rhodopsin and the ligand-free apoprotein, opsin. These observed conformational and dynamical differences in rhodopsin activation are due to the influence of the covalently bound retinal chromophore.
The glass-like collective excitations in proteins are also investigated using inelastic neutron and X-ray scattering techniques. Such excitations correspond to the intrinsic protein dynamics necessary to overcome the conformational barriers, crucial for enzyme catalysis and ligand-binding. The data show the apparent softening of protein with rise in temperature, which reveals the protein conformational flexibility. Specifically, these results suggest that the native globular protein balances the protein conformational flexibility and rigidity for the biological activity.
Furthermore, the conformational change in periplasmic ligand-binding protein (PBP) upon bound to peptide is studied using the small-angle X-ray scattering (SAXS). The SAXS measurements from the ligand-free and the ligand-bound periplasmic protein, MppA do not show significant conformational change. It may be due to the low-resolution of the instrument such that a few angstrom of change in protein conformation is inaccessible. On the other hand, the three-dimensional shape reconstruction of MppA computed from SAXS intensity profile using ab-initio modeling matches perfectly its crystal structure.
Shrestha, Utsab Raj, "Exploring The Physics Of Proteins At Molecular Level By Neutron And X-Ray Scattering" (2017). Wayne State University Dissertations. 1743.