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Structure And Stability Of Amyloid Fibrils Studied By Advanced Vibrational Spectroscopy, Marudachalam Shanmugasundaram
Structure And Stability Of Amyloid Fibrils Studied By Advanced Vibrational Spectroscopy, Marudachalam Shanmugasundaram
Legacy Theses & Dissertations (2009 - 2024)
Protein misfolding often leads to the formation of refractory protein aggregates like amyloid fibrils. These fibrils possess a highly ordered structure and are implicated in over 25 severe diseases including Alzheimer’s, Parkinson’s and prion diseases. This work was focused on understanding the morphology and conformation of amyloid fibrils and their stability after formation. The deconstruction of fibrils as well as other aggregates like inclusion bodies under mild conditions was also investigated using Archaeal chaperones.
Novel Nmr Based Technologies To Study Macromolecular Structures, Subhabrata Majumder
Novel Nmr Based Technologies To Study Macromolecular Structures, Subhabrata Majumder
Legacy Theses & Dissertations (2009 - 2024)
Nuclear Magnetic Resonance Spectroscopy (NMR) is one of the principle tools in structural biology to probe macromolecular structures and interactions. The atomic resolution afforded by this technique has been widely used to probe protein-protein, and protein-ligand interactions in-vitro. However, the natural milieu of the proteins is the living cell and the cellular cytoplasm is extremely heterogeneous. The NMR studies of folded protein in-cell, till now, have been limited by non-specific interactions of the cytosol. This thesis outlays a general methodology to study protein structure/interactions inside the living cells using NMR. In a closely related objective, it also describes the use …
Advanced Raman Spectroscopic Methods For Structural Characterization Of Amyloid Fibrils And Bionanotubes, Valentin Sereda
Advanced Raman Spectroscopic Methods For Structural Characterization Of Amyloid Fibrils And Bionanotubes, Valentin Sereda
Legacy Theses & Dissertations (2009 - 2024)
Amyloid aggregation is a specific form of protein misfolding and self-assembly related to several degenerative pathologies like Alzheimer's and Parkinson's diseases, type-II diabetes, etc. This association with deadly diseases has made amyloid fibrils the focus of intensive research for many decades. Most recently, a significant interest to protein fibrils was also due to the application of the remarkable self-assembling capabilities to form well-structured nano-biomaterials. Self-assembly of short peptide sequences into well-organized structures is another important strategy for bottom-up fabrications of nano-biomaterials. One of the most commonly used building blocks is diphenylalanine, a short dipeptide that has been identified as playing …
Molecular Dynamics Simulations Of Small Systems To Improve Base Pairing Parameters Of The Amber-99 Force Field, Angelo Christopher Setaro
Molecular Dynamics Simulations Of Small Systems To Improve Base Pairing Parameters Of The Amber-99 Force Field, Angelo Christopher Setaro
Legacy Theses & Dissertations (2009 - 2024)
Simulations of biochemical systems are being increasingly used to further our understanding of those systems. In broad strokes, chemical simulations can be broken into two categories, those that are rooted in a quantum mechanical approach and those that are classically rooted. Molecular dynamics is one such classical method, which propagates motion of a chemical system via repeatedly solving Newton’s Laws of motion. This approach is less computationally intensive than the quantum mechanical methods and allows for the simulation of systems of tens of thousands of atoms, if not more.