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Showing 1 to 16 of 16 for “"protein motions"”.
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Unique Features of PTB RRMs: Insight into Protein Motions and RNA Binding
Polypyrimidine tract binding protein: PTB) is a highly conserved RNA binding protein comprised of four RRMs: RNA recognition motifs). RRMs are extremely prevalent in all kingdoms of life, and have been very well characterized in terms of structure and RNA binding properties. However, all four RRMs …
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Motions in myoglobin
… evidence of a pathway for ligands to enter the protein to bind at the heme iron. Motions within the protein are necessary for the protein to function. Pressure release and flash photolysis experiments help characterize some of these protein motions.
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Crystalline Protein Dynamics : A Simulation Analysis of Staphylococcal Nuclease
Understanding motions in protein crystals is likely to furnish insight into functional protein dynamics and will improve models for refinement against diffraction data. In this thesis, molecular dynamics (MD) simulations of crystalline Staphylococcal nuclease are reported and analysed in terms of …
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Conformational relaxation in heme proteins: Ligand rebinding above the glass transition
… temperature of the solvent, heme proteins are frozen into static conformations, and ligand rebinding is well described with a time- and temperature-independent distribution of enthalpic barriers, $g(H)$. This work addresses the relaxation of the enthalpic barriers that sets in near …
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Conserved Conformational Dynamics Control PTP1B Enzymatic Activity
… is changing. Namely, the emerging view is that protein function also depends on intrinsic protein dynamics. Further, while sequence conservation is well-correlated with conservation of structure, it is unknown if sequence also conserves protein dynamics. To understand the role of dynamics, 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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Conformational relaxation in heme proteins : ligand rebinding above the glass transition
… temperature of the solvent, heme proteins are frozen into static conformations, and ligand rebinding is well described with a time- and temperature-independent distribution of enthalpic barriers, g(H). This work addresses the relaxation of the enthalpic barriers that sets in near …
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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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Motions in myoglobin
… evidence of a pathway for ligands to enter the protein to bind at the heme iron. Motions within the protein are necessary for the protein to function. Pressure release and flash photolysis experiments help characterize some of these protein motions. Sperm whale carbonmonoxymyoglobin exhibits …
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The role of conformational motions in the control of ligand binding to myoglobin and hemoglobin
… hemoglobin are dioxygen storage and transport proteins. They bind small molecules (ligands) such as dioxygen (02) and carbon monoxide (CO) reversibly. The active site is the heme, a disc shaped molecule which sits in a pocket of the protein (heme pocket). At the center of the heme is an iron …
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The Effect of Hydration on Enzyme Activity and Dynamics
… the molecular basis of the role of water in protein function, several studies have established a correlation between enzyme activity and hydration level. While a threshold of hydration of 0.2 h (grams of water per gram of dried protein) is usually accepted for the onset of enzyme activity, …
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The activity and dynamics of enzymes
… flexibility, or the activation of anharmonic motions, for catalytic activity. However, in general, the timescales and forms of the functionally important motions coupled to progress along the reaction pathway remain poorly understood. A number of biophysical studies have shown that protein …
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Hydrogen-deuterium exchange studies by mass spectrometry: A method for obtaining conformational structures of proteins in solution
… has become an important method in the study of protein structure and dynamics. It provides an opportunity for obtaining conformational structures of protein motions in physiological conditions and offers unparalleled limits of detection. This method relies on the fact that the accessibility of …
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Protein and Ligand Dynamics in Drug Development and Resistance
<p>Biomolecules such as proteins are highly dynamic, and undergo a wide variety of motions at different timescales. Movements as small as a bond vibration or as large as a domain rearrangement can be critical for the function of a protein, making consideration and investigation of protein dynamics …
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Conformational Entropy in PEPCK Catalysis: Dynamic Motions Critical to Function
… years. Multiple studies have shown that dynamic motions of individual protein segments can play a role in enzyme function. Our enzyme of interest, phosphoenolpyruvate carboxykinase (PEPCK), has multiple dynamic motions that work in concert during the catalytic cycle. One of these mobile elements, …
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COMPUTATIONAL MULTISCALE INVESTIGATIONS OF BIOLOGICAL MOLECULES
… complex mechanisms that underlie Life itself. Proteins and RNA, two essential components of cellular structure and processes, exhibit remarkable structural and functional diversity. Traditional experimental techniques have provided valuable insights into their behaviors; however, they often …