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Showing 1 to 11 of 11 for “"Protein Conformational Dynamics"”.
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Temperature-jump 2D IR spectroscopy to study protein conformational dynamics
… characterized, and applied to the study of protein folding and association. In solution, protein conformational changes span a wide range of timescale from nanoseconds to minutes. Ultrafast 2D IR spectroscopy measures time-dependent structural changes within the protein ensemble by probing …
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Efficient sampling of protein conformational dynamics and prediction of mutation effects.
Molecular dynamics (MD) simulation is a powerful tool enabling researchers to gain insight into biological processes at the atomic level. There have been many advancements in both hardware and software in the last decade to both accelerate MD simulations and increase their predictive accuracy; …
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Membrane protein conformational dynamics and ligand-binding interactions in bacterial glycoconjugate biosynthesis
Membrane associated proteins are an essential component of the complex biochemistry that is carried out at the membrane interface and perform essential functions for cellular life. Biophysical characterization of protein structure-function relationships faces a unique set of challenges due to the …
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Direct real-time correlation of protein conformation and substrate recognition
Conformational transitions in a protein and its interaction with the cognate substrate exemplify two important biomolecular processes that may be correlated, uncorrelated, or partially correlated. While the degree to which these processes are correlated may bear heavily on the mechanism and …
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Contributions to the analysis of proteins
Proteins are essential to organisms and play a central role in almost every biological process. The analysis of the conformational dynamics and mechanics of proteins using numerical methods, such as normal mode analysis (NMA), provides insight into their functional mechanisms. However, despite the …
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The Effects of DEAD-box Helicase Activity on Biomolecular Condensate Structure and Dynamics
… These bodies are composed of specific proteins and RNA which self-associate to drive condensate formation. The strengths, timescales, and valence of the biomolecular interactions which drive condensate formation also have consequences for the properties of these bodies. In the context …
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Ligand and Protein Dynamics of CYP3A4
… of the linkage between ligand binding and protein conformational dynamics with theoretical considerations of their impact on CYP3A4 catalysis using biophysical and theoretical methodologies. Specifically, the results herein demonstrate the complexity (requiring more than 2-states) in the …
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Inferring protein conformational ensemble using deep learning and evolutionary couplings
Submission published under a 24 month embargo labeled 'U of I Access', the embargo will last until 2024-05-01
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Computational methods to design biophysical experiments for the study of protein dynamics
… and data acquisition. In the field of protein biophysics, computational simulations such as molecular dynamics and spectroscopy-based experiments such as double electron-electron resonance and Fluorescence resonance energy transfer techniques have emerged as critical experimental tools …
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Insights into protein function from evolutionary and conformational dynamics
The volume of protein structure data has grown rapidly over the past 30 years, leaving a wake of facts that still require explanation. We endeavored to answer a few open questions on the structure-function relationship of intriguing mechanochemical protein systems. To this end this thesis work …
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Computational investigation of early events in plant growth signaling
… brassinosteroid signal transduction in terms of protein conformational dynamics. Focusing on the two primary brassinosteroid coreceptors, BRI1 and BAK1, we use a number of computational methods grounded in molecular dynamics simulations with the goal of understanding the physical mechanisms of …