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• W2549457756 abstract "A tremendous amount of evidence has accumulated in regards to the importance of intrinsically disordered proteins (IDPs) in the functioning of the cell and their role in human disease. However, understanding and modelling the physics of such proteins is one of the remaining challenges for the biophysics field. IDPs can present in a variety of forms, including flexible and extended structures, compact molten-globules, or mixtures of the two. Furthermore, many proteins which have regions with well-defined native states can have segments which are unfolded and disordered under physiological conditions. This thesis is an exploration of the physics of such IDPs, and the computational methodologies available for their study. The unfolded regions of intrinsically disordered proteins have long been described using the random coil model, which has been shown to successfully predict global properties such as the radius of gyration and intrinsic viscosities of IDPs and denatured proteins, alike. However, the two main axioms of the random coil model in regards to protein dynamics, (i) the ability of amino acid residues to sample the entire sterically allowed Ramachandran space, and (ii) the isolated pair hypothesis, which states that the conformations of residues are unaffected by nearest neighbour interactions, have been challenged through various lines of evidence. First, amino acid residues each have unique restrictions to their Ramachandran space. Second, many residues tend to have a strong bias for the pPII and beta-strand conformations. Third, the conformations of residues in protein sequences are strongly affected by nearest neighbour interactions. Part of this thesis explores the underlying causes of the distinct Ramachandran spaces of amino acid residues. In a recent experimental study of the thermodynamics of the pPII-beta equilibria of amino acid residues in GxG host-guest peptide systems (G: glycine, x: guest residue), a nearly exact enthalpy-entropy compensation at ∼300 K was revealed, suggesting a common mechanism for the intrinsic conformational preferences of amino acid residues. Motivated by these results and a number of studies linking water dynamics to the strong preference for the pPII conformation over the beta-strand conformation, a rigorous molecular dynamics (MD) study with explicit water molecules of 15 GxG peptides, along with trialanine and alanine dipeptide was performed. Several hydration properties were quantified, including a novel description of water orientation near protein surfaces, and correlated with experimental pPII propensities obtained from infrared (IR), Raman, vibrational circular dichroism (VCD), and NMR spectroscopy studies. Results revealed that the distributions of water orientations are more disordered in the beta-strand conformation than in the pPII conformation, in agreement with the entropic and enthalpic stabilization of the two conformations, respectively. Furthermore, the pPII to beta hydration differences and the solvent accessible surface areas of the Cbeta group correlate…" @default.
• W2549457756 created "2016-11-30" @default.
• W2549457756 creator A5086312275 @default.
• W2549457756 date "2021-07-16" @default.
• W2549457756 modified "2023-09-23" @default.
• W2549457756 title "Molecular Dynamics Studies of Intrinsically Disordered Peptides and Proteins" @default.
• W2549457756 doi "https://doi.org/10.17918/etd-7207" @default.
• W2549457756 hasPublicationYear "2021" @default.
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