David L. Beveridge
Molecular Biology & Biochemistry
Proteins are dynamic in nature, sampling different conformational states while performing their specific functions in the cell. The dynamical behavior of proteins, ranging from fast time scales of pico-nanoseconds to slower micro-milliseconds, is due to thermal motions which facilitate specific functions through different, functionally relevant conformational states. The amplitude of the fluctuations in motion is always changing due to interacting forces and energies acting on each atom in the protein. Thus, it is important to understand how these motions play critical roles in protein dynamics and to determine the structure-function dynamics relationship. Furthermore, proteins possess a cooperative property called allostery such that perturbation or mutation at distal sites can affect the function of the active site. Therefore, there is a need for advancement in theoretical methods to account for these dynamic changes, such as monitoring the motion or energy in a quantitative, correlated manner between all residue pairs of the protein. Another requirement is to decipher a way to analyze these correlated motions, as well as energy, in a systematic manner that treats the positions as a collective property to account for the largest variance in the motion or energy correlation. The field would benefit from advancement in the understanding of structure-function relationship.
Lakhani, Bharat, "Spectral Analysis of Protein Dynamics Based on All-atom MD Simulations" (2017). Dissertations. 74.
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