Access Type

Open Access Dissertation

Date of Award

January 2015

Degree Type

Dissertation

Degree Name

Ph.D.

Department

Physics and Astronomy

First Advisor

Xiang Qiang Chu

Abstract

Neutron scattering has been proved to be a powerful tool to study the dynamics of biological systems under various conditions. This thesis intends to utilize neutron scattering techniques, combining with MD simulations, to develop fundamental understanding of several biologically interesting systems. Our systems include a drug delivery system containing Nanodiamonds with nucleic acid (RNA), and two specific model proteins, β-Casein and Inorganic Pyrophosphatase (IPPase).

RNA and nanodiamond (ND) both are suitable for drug-delivery applications in nano-biotechnology. The architecturally flexible RNA with catalytic functionality forms nanocomposites that can treat life-threatening diseases. The non-toxic ND has excellent mechanical and optical properties and functionalizable high surface area, and thus actively considered for biomedical applications. In this thesis, we utilized two tools, quasielastic neutron scattering (QENS) and Molecular Dynamics Simulations to probe the effect of ND on RNA dynamics. Our work provides fundamental understanding of how hydrated RNA motions are affected in the RNA-ND nanocomposites. From the experimental and Molecular Dynamics Simulation (MD), we found that hydrated RNA motion is faster on ND surface than a freestanding one. MD Simulation results showed that the failure of Stokes Einstein relation results the presence of dynamic heterogeneities in the biomacromolecules. Radial pair distribution function from MD Simulation confirmed that the hydrophilic nature of ND attracts more water than RNA results the de-confinement of RNA on ND. Therefore, RNA exhibits faster motion in the presence of ND than freestanding RNA.

In the second project, we studied the dynamics of a natively disordered protein β-Casein which lacks secondary structures. In this study, the temperature and hydration effects on the dynamics of β-Casein are explored by Quasielastic Neutron Scattering (QENS). We investigated the mean square displacement (MSD) of hydrated and dry β-Casein as a function of temperature, to study the effect of hydration on their flexibility. The Elastic Incoherent Structure Factor (EISF) in the energy domain reveals the fraction of hydrogen atoms participating in motion in a sphere of diffusion. In the time domain analysis, a logarithmic-like decay is observed in the range of picosecond to nanosecond (β-relaxation time) in the dynamics of hydrated β-Casein. Our temperature dependent QENS experiments provide evidence that lack of secondary structure in β-Casein results in higher flexibility in its dynamics and easier reversible thermal unfolding compared to other rigid biomolecules.

Lastly, we studied the domain motion of IPPase protein by Neutron Spin Echo Spectroscopy (NSE). We found that decrease in diffusion coefficient belongs to domain motion of IPPase. Moreover, Rg is varied by temperature and concentration.

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