The role of time in biological systems: a computational analysis ranging from molecular dynamics to biological network simulations.
Alessandro Masiero · Padua@research (University of Padova) · 2015
Time is the main character of this thesis, and it has been used in many ways. Starting from molecular dynamics simulations to biological networks, time has been analysed under different light and roles. The main subjects characterizing this work are Von Hippel-Lindau syndrome and circadian rhythm, although a method for molecular dynamics simulations trajectory analysis is presented at the end. Several works are presented here, analysing different aspects of protein dynamics as well as pathway alterations depending on the time coordinate. The first work analyses the interaction between protein Von Hippel-Lindau (pVHL) and its main interactor, Hipoxya Inducibe Factor 1α by means of molecular dynamics simulations, investigating on a non-conventional proline hydroxylation event. As a result, we obtained that a specific hydrogen bond network rearrangement and improved electrostatic energy for hydroxylated P567 appear to be compatible with an increase in HIF-1α binding affinity. Sequence analysis also confirms P567 to be vastly conserved during evolution, indicating a possible role for this alternative, PHD-3 driven, post translational modification in pVHL–HIF-1α complex formation. The second work dealt with the same main subject, but investigated through biological network simulations, particularly with Petri net models. In this work, we presented a novel manually curated Petri Net (PN) model of the main pVHL functional pathways. The model was built using functional information derived from the literature. It includes all major pVHL functions and is able to credibly reproduce VHL syndrome at the molecular level. The reliability of the PN model also allowed in silico knockout experiments, driven by previous model analysis. Interestingly, PN analysis suggests that the variability of different VHL manifestations is correlated with the concomitant inactivation of different metabolic pathways. In the third work, investigating the structural role of flavin-adenine-dinucleotide (FAD) through molecular dynamics simulations, we analyzed the Drosophila melanogaster Cryptochrome crystal structure, elucidating how this large co-factor within the receptor could be crucial for CRY structural stability. The co-factor appears indeed to improve receptor motility, providing steric hindrance. Moreover, multiple sequence alignments revealed that conserved motifs in the C-terminal tail could be necessary for functional stability. The fourth work focused on the sequence impact on the modern folds. We shuffled the sequences of 10 natural proteins and obtained 40 different and apparently unrelated folds. Our results suggest that shuffled sequences are sufficiently stable and may act as a basis to evolve functional proteins. The common secondary structure of modern proteins is well represented by a small set of permuted sequences, which also show the emergence of intrinsic disorder and aggregation-prone stretches of the polypeptide chain. The last work presented here is a method to quickly analyse molecular dynamics simulations trajectories. The complexity related to their interpretation and analysis is still one of the major challenges for most users. In this work we introduce RING MD, which is able to identify the most important frames (PDB structures) and key residues that cause different conformers transitions, providing a simple interpretation useful for non-expert users. Comparison with the classical analysis of three MD simulations, Ubiquitin, T4 Lysozyme and T4 Glutaredoxin, confirmed RING MD results and effectiveness. At the end, time should not be considered simply as something entraining the environment, it is what indeed modifies systems and environment. Different systems simply change in different ways, because of different mechanisms, but the main driving force should always be considered time.