A major focus of scientific research is to understand biological phenomena and to explain our basic observations of life, however these phenomena have an underlying basis and are the result of many biophysical processes. The study of biophysical processes provides a more detailed examination of the components and actions involved, however many of these processes are not adequately understood and need further exploration. Experimental studies of biophysical processes such biomolecular dynamics, protein folding, molecular transport and enzymatic reactions provide a wealth of knowledge, however all these techniques have their limitations. To be able to adequately understand a biophysical process both spatial and temporal resolution is required and computational biophysical techniques such as molecular dynamics provides the atomic and temporal resolution to further understand these processes. Additionally, computational techniques allow us to be able to not see and observe the motions of biomolecules but to better define these states and motions through the systems free energy surfaces. As stated previously, all techniques have their limitations, including molecular dynamics, with limitations in atomic interaction descriptors or force fields as well as reaching timescales that are relevant to the target biophysical processes. The development of enhanced sampling techniques and more specifically the Orthogonal Space Sampling Scheme have been used to address this timescale issue. In this study of work, we aim to use this enhanced sampling technique to explore several biophysical processes of biomolecules. The first study investigates the reaction site dynamics and how long timescale protein dynamics are involved. By using the High Order Orthogonal Space Tempering technique, we explored a novel tRNA Methyltranferase TrmD which has an unusual fold that is used to bind a cofactor and the conformation of the cofactor when bound is unusual as well. Differences in the tRNA bound ternary complex and binary complex show differences in protein backbone collective motions as well as differing degree of coupling to the reaction site dynamics. The dynamics of binary complex reveal distant protein collective motions that are coupled to the cofactor internal dynamics, whereas the ternary complex shows coupling of methyl transfer distance and protein ligand stabilizing interactions which suggest when tRNA is bound motions are focused on those that are enzymatically productive. The second study investigates the long timescale protein dynamics and its involvement protein misfolding as well as how known perturbations that induce misfolding might change these dynamics. Murine prion protein or PrP is a protein that can undergo a misfolding event that leads to neurodegenerative diseases and has been established as an infectious agent which interactions with the misfolded protein can induce misfolding as well. Misfolding events have been observed in vivo and in vitro under low pH conditions, however the misfolded structure is still yet to be atomically resolved and the experimental data does not provide a defined process for the misfolding event. Simulations using the neutral and charged states of the PrP system and the perturbation of the β-sheet motif that has been suggested is involved in the misfolding process, we observe differences in dynamics of the β-sheet motif as well as overall protein collective motion. The protein in charged state where histidine 187 is protonated destabilizes the protein structure due to the buried charged making β-sheet dynamics easier where in the neutral state we see stronger hydrogen bonding interactions. Additionally, sites that have been implicated through experimental studies have shown correlated motions with the perturbed β-sheet motif. The final study investigates long timescale intrinsic DNA dynamics as well as the effects of 6mA methylation on DNA dynamics. DNA undergoes dynamics that span several levels from local base pair dynamics to global conformational changes. These levels of dynamics play a critical role for processes such as DNA transcription, repair, regulation and replication. Epigenetic regulation, typically, occurs through chemical modifications of the individual bases and methylation has been observed to control several processes. A shift in focus for an understudied methylation modification, 6mA, has found that it plays a more significant role in regulation of eukaryotes but the biophysical nature of the modification is unknown. Simulations of an 33 base pair fragment of DNA in the unmodified and 6mA methylated modification find significant differences in the dynamics across all levels. The unmodified DNA is considerably more flexible and is able to undergo base flipping events whereas the methylated DNA is more rigid and does not undergo any base flipping events in the simulated time. Further analysis shows coupling of the base flipping events and global DNA bending and coupling is loss in the methylated DNA. This loss in coupling is proposed to be caused by two sources: steric clashing of the added methyl groups and neighbor base steps as seen by the reduction in roll fluctuation and changes in water density distributions showing a loss of high water density in the major groove at the modification site and the formation of high water density across a stretch of associated DNA backbone. The results are consistent with previous and recent biophysical evidence which suggests that this fragment becomes more rigid and base pair lifetimes increase across the whole fragment. It is also consistent with biochemical data suggesting that the introduced rigidity prevents nucleosome wrapping. / A Dissertation submitted to the Institute of Molecular Biophysics in partial fulfillment of the requirements for the degree of Doctor of Philosophy. / Spring Semester 2019. / April 19, 2019. / Enhanced Sampling, Free Energy Simulations, Molecular Dynamics / Includes bibliographical references. / Wei Yang, Professor Directing Dissertation; Biwu Ma, University Representative; Hong Li, Committee Member; Branko Stefanovic, Committee Member; M. Elizabeth Stroupe, Committee Member.
| Identifer | oai:union.ndltd.org:fsu.edu/oai:fsu.digital.flvc.org:fsu_709061 |
| Contributors | Aitchison, Erick Wayne (author), Yang, Wei (Professor Directing Dissertation), Ma, Biwu (University Representative), Li, Hong (Committee Member), Stefanovic, Branko (Committee Member), Stroupe, M. Elizabeth (Margaret Elizabeth) (Committee Member), Florida State University (degree granting institution), College of Arts and Sciences (degree granting college), Institute of Molecular Biophysics (degree granting departmentdgg) |
| Publisher | Florida State University |
| Source Sets | Florida State University |
| Language | English, English |
| Detected Language | English |
| Type | Text, text, doctoral thesis |
| Format | 1 online resource (187 pages), computer, application/pdf |
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