Radiolytic Protein Footprinting with Mass Spectrometry to Probe the Structure...Keiji Takamoto
Structural proteomics approaches using mass spectrometry are in- creasingly used in biology to examine the composition and struc- ture of macromolecules. Hydroxyl radical–mediated protein foot- printing using mass spectrometry has recently been developed to define structure, assembly, and conformational changes of macro- molecules in solution based on measurements of reactivity of amino acid side chain groups with covalent modification reagents. Accurate measurements of side chain reactivity are achieved using quanti- tative liquid-chromatography-coupled mass spectrometry, whereas the side chain modification sites are identified using tandem mass spectrometry. In addition, the use of footprinting data in conjunc- tion with computational modeling approaches is a powerful new method for testing and refining structural models of macromolecules and their complexes. In this review, we discuss the basic chemistry of hydroxyl radical reactions with peptides and proteins, highlight various approaches to map protein structure using radical oxidation methods, and describe state-of-the-art approaches to combine com- putational and footprinting data.
Principles of RNA compaction : insights from equilibrium folding pathway of p...Keiji Takamoto
Counterions are required for RNA folding, and divalent metal ions such as Mg2+ are often critical. To dissect the role of counterions, we have compared global and local folding of wild-type and mutant variants of P4- P6 RNA derived from the Tetrahymena group I ribozyme in monovalent and in divalent metal ions. A remarkably simple picture of the folding thermodynamics emerges. The equilibrium folding pathway in mono- valent ions displays two phases. In the first phase, RNA molecules that are initially in an extended conformation enforced by charge–charge repulsion are relaxed by electrostatic screening to a state with increased flexibility but without formation of long-range tertiary contacts. At higher concentrations of monovalent ions, a state that is nearly identical to the native folded state in the presence of Mg2C is formed, with tertiary contacts that involve base and backbone interactions but without the subset of interactions that involve specific divalent metal ion-binding sites. The folding model derived from these and previous results provides a robust framework for understanding the equilibrium and kinetic folding of RNA.
Statistical Equilibrium Wealth Distributions in an Exchange Economy with Stoc...Keiji Takamoto
We describe an exchange market consisting of many agents with stochastic pref- erences for two goods. When individuals are indifferent between goods, statistical mechanics predicts that goods and wealth will have steady-state gamma distributions. Simulation studies show that gamma distributions arise for a broader class of pref- erence distributions. We demonstrate this mathematically in the limit of large numbers of individual agents. These studies illustrate the potential power of a statis- tical mechanical approach to stochastic models in economics and suggest that gamma distributions will describe steady-state wealths for a class of stochastic models with periodic redistribution of conserved quantities.
Radiolytic Protein Footprinting with Mass Spectrometry to Probe the Structure...Keiji Takamoto
Structural proteomics approaches using mass spectrometry are in- creasingly used in biology to examine the composition and struc- ture of macromolecules. Hydroxyl radical–mediated protein foot- printing using mass spectrometry has recently been developed to define structure, assembly, and conformational changes of macro- molecules in solution based on measurements of reactivity of amino acid side chain groups with covalent modification reagents. Accurate measurements of side chain reactivity are achieved using quanti- tative liquid-chromatography-coupled mass spectrometry, whereas the side chain modification sites are identified using tandem mass spectrometry. In addition, the use of footprinting data in conjunc- tion with computational modeling approaches is a powerful new method for testing and refining structural models of macromolecules and their complexes. In this review, we discuss the basic chemistry of hydroxyl radical reactions with peptides and proteins, highlight various approaches to map protein structure using radical oxidation methods, and describe state-of-the-art approaches to combine com- putational and footprinting data.
Principles of RNA compaction : insights from equilibrium folding pathway of p...Keiji Takamoto
Counterions are required for RNA folding, and divalent metal ions such as Mg2+ are often critical. To dissect the role of counterions, we have compared global and local folding of wild-type and mutant variants of P4- P6 RNA derived from the Tetrahymena group I ribozyme in monovalent and in divalent metal ions. A remarkably simple picture of the folding thermodynamics emerges. The equilibrium folding pathway in mono- valent ions displays two phases. In the first phase, RNA molecules that are initially in an extended conformation enforced by charge–charge repulsion are relaxed by electrostatic screening to a state with increased flexibility but without formation of long-range tertiary contacts. At higher concentrations of monovalent ions, a state that is nearly identical to the native folded state in the presence of Mg2C is formed, with tertiary contacts that involve base and backbone interactions but without the subset of interactions that involve specific divalent metal ion-binding sites. The folding model derived from these and previous results provides a robust framework for understanding the equilibrium and kinetic folding of RNA.
Statistical Equilibrium Wealth Distributions in an Exchange Economy with Stoc...Keiji Takamoto
We describe an exchange market consisting of many agents with stochastic pref- erences for two goods. When individuals are indifferent between goods, statistical mechanics predicts that goods and wealth will have steady-state gamma distributions. Simulation studies show that gamma distributions arise for a broader class of pref- erence distributions. We demonstrate this mathematically in the limit of large numbers of individual agents. These studies illustrate the potential power of a statis- tical mechanical approach to stochastic models in economics and suggest that gamma distributions will describe steady-state wealths for a class of stochastic models with periodic redistribution of conserved quantities.
