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Chevron Plot
A chevron plot is a way of representing protein folding chemical kinetics, kinetic data in the presence of varying concentrations of Denaturation (biochemistry), denaturant that disrupts the protein's native tertiary structure. The plot is known as "chevron" plot because of the canonical ''v'', or Chevron (insignia), chevron shape observed when the logarithm of the observed relaxation rate is plotted as a function of the denaturant concentration. In a two-state system, folding and unfolding rates dominate the observed relaxation rates below and above the denaturation midpoint (Cm). This gives rise to the terminology of folding and unfolding arms for the limbs of the chevron. A priori information on the Cm of a protein can be obtained from equilibrium experiments. In fitting to a two-state model, the logarithm of the folding and unfolding rates is assumed to depend linearly on the denaturant concentration, thus resulting in the slopes mf and mu, called the folding and unfolding m-v ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Chevron Plot
A chevron plot is a way of representing protein folding chemical kinetics, kinetic data in the presence of varying concentrations of Denaturation (biochemistry), denaturant that disrupts the protein's native tertiary structure. The plot is known as "chevron" plot because of the canonical ''v'', or Chevron (insignia), chevron shape observed when the logarithm of the observed relaxation rate is plotted as a function of the denaturant concentration. In a two-state system, folding and unfolding rates dominate the observed relaxation rates below and above the denaturation midpoint (Cm). This gives rise to the terminology of folding and unfolding arms for the limbs of the chevron. A priori information on the Cm of a protein can be obtained from equilibrium experiments. In fitting to a two-state model, the logarithm of the folding and unfolding rates is assumed to depend linearly on the denaturant concentration, thus resulting in the slopes mf and mu, called the folding and unfolding m-v ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Phi Value Analysis
Phi value analysis, \phi analysis, or \phi-value analysis is an experimental protein engineering technique for studying the structure of the folding transition state of small protein domains that fold in a two-state manner. The structure of the folding transition state is hard to find using methods such as protein NMR or X-ray crystallography because folding transitions states are mobile and partly unstructured by definition. In \phi -value analysis, the folding kinetics and conformational folding stability of the wild-type protein are compared with those of point mutants to find ''phi values''. These measure the mutant residue's energetic contribution to the folding transition state, which reveals the degree of native structure around the mutated residue in the transition state, by accounting for the relative free energies of the unfolded state, the folded state, and the transition state for the wild-type and mutant proteins. The protein's residues are mutated one by one to ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Equilibrium Unfolding
In biochemistry, equilibrium unfolding is the process of unfolding a protein or RNA molecule by gradually changing its environment, such as by changing the temperature or pressure, pH, adding chemical denaturants, or applying force as with an atomic force microscope tip. If the equilibrium was maintained at all steps, the process theoretically should be reversible during equilibrium folding. Equilibrium unfolding can be used to determine the thermodynamic stability of the protein or RNA structure, i.e. free energy difference between the folded and unfolded states. Theoretical background In its simplest form, equilibrium unfolding assumes that the molecule may belong to only two thermodynamic states, the ''folded state'' (typically denoted ''N'' for "native" state) and the unfolded state (typically denoted ''U''). This "all-or-none" model of protein folding was first proposed by Tim Anson in 1945, but is believed to hold only for small, single structural domains of protei ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Denaturation Midpoint
Denaturation midpoint of a protein is defined as the temperature (Tm) or concentration of Denaturation (biochemistry), denaturant (Cm) at which both the Protein tertiary structure, folded and Denaturation (biochemistry), unfolded states are equally populated at equilibrium (assuming two-state protein folding). Tm is often determined using a thermal shift assay. If the widths of the folded and unfolded wells are assumed to be equal both these states will have identical free energies at the midpoint. However, for natural proteins this is not the case. There is an inherent asymmetry as evidenced by the difference in heat capacity, heat capacities between them - the folded ensemble has a lower heat capacity (in other words, lower Thermal fluctuations, fluctuations thus indicating a narrower well) than the unfolded ensemble. This would mean that the free energy of the folded state is lower at the denaturation midpoint than the unfolded state. In such a scenario, the temperature at which ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Protein Folding
Protein folding is the physical process by which a protein chain is translated to its native three-dimensional structure, typically a "folded" conformation by which the protein becomes biologically functional. Via an expeditious and reproducible process, a polypeptide folds into its characteristic three-dimensional structure from a random coil. Each protein exists first as an unfolded polypeptide or random coil after being translated from a sequence of mRNA to a linear chain of amino acids. At this stage the polypeptide lacks any stable (long-lasting) three-dimensional structure (the left hand side of the first figure). As the polypeptide chain is being synthesized by a ribosome, the linear chain begins to fold into its three-dimensional structure. Folding of many proteins begins even during translation of the polypeptide chain. Amino acids interact with each other to produce a well-defined three-dimensional structure, the folded protein (the right hand side of the figure), ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Debye–Hückel Equation
The chemists Peter Debye and Erich Hückel noticed that solutions that contain ionic solutes do not behave ideally even at very low concentrations. So, while the concentration of the solutes is fundamental to the calculation of the dynamics of a solution, they theorized that an extra factor that they termed gamma is necessary to the calculation of the activity coefficients of the solution. Hence they developed the Debye–Hückel equation and Debye–Hückel limiting law. The activity is only proportional to the concentration and is altered by a factor known as the activity coefficient \gamma. This factor takes into account the interaction energy of ions in solution. Debye–Hückel limiting law In order to calculate the activity a_C of an ion C in a solution, one must know the concentration and the activity coefficient: a_C = \gamma \frac\mathrm\mathrm, where * \gamma is the activity coefficient of C, * \mathrm is the concentration of the chosen ''standard state'', e.g. 1 mol ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Downhill Folding
Downhill folding is a process in which a protein folds without encountering any significant macroscopic free energy barrier. It is a key prediction of the folding funnel hypothesis of the energy landscape theory of proteins. Overview Downhill folding is predicted to occur under conditions of extreme native bias, i.e. at low temperatures or in the absence of denaturants. This corresponds to the ''type 0'' scenario in the energy landscape theory. At temperatures or denaturant concentrations close to their apparent midpoints, proteins may switch from downhill to two-state folding, the ''type 0'' to ''type 1'' transition. Global downhill folding (or ''one-state folding'') is another scenario in which the protein folds in the absence of a free energy barrier under all conditions. In other words, there is a unimodal population distribution at all temperatures and denaturant concentrations, suggesting a continuous unfolding transition in which different ensembles of structures pop ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Hammond Effect
Hammond's postulate (or alternatively the Hammond–Leffler postulate), is a hypothesis in physical organic chemistry which describes the geometric structure of the transition state in an organic chemical reaction. First proposed by George S. Hammond, George Hammond in 1955, the postulate states that: If two states, as, for example, a transition state and an unstable intermediate, occur consecutively during a reaction process and have nearly the same energy content, their interconversion will involve only a small reorganization of the molecular structures. Therefore, the geometric structure of a state can be predicted by comparing its energy to the species neighboring it along the reaction coordinate. For example, in an ''exothermic'' reaction the transition state is closer in energy to the reactants than to the products. Therefore, the transition state will be more geometrically similar to the reactants than to the products. In contrast, however, in an ''endothermic'' reaction ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Transition State
In chemistry, the transition state of a chemical reaction is a particular configuration along the reaction coordinate. It is defined as the state corresponding to the highest potential energy along this reaction coordinate. It is often marked with the double dagger ‡ symbol. As an example, the transition state shown below occurs during the SN2 reaction of bromoethane with a hydroxide anion: The activated complex of a reaction can refer to either the transition state or to other states along the reaction coordinate between reactants and products, especially those close to the transition state.Peter Atkins and Julio de Paula, ''Physical Chemistry'' (8th ed., W.H. Freeman 2006), p.809 According to the transition state theory, once the reactants have passed through the transition state configuration, they always continue to form products. History of concept The concept of a transition state has been important in many theories of the rates at which chemical reactions occ ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Temperature Jump
The temperature jump method is a technique used in chemical kinetics for the measurement of very rapid reaction rates. It is one of a class of chemical relaxation methods pioneered by the German physical chemist Manfred Eigen in the 1950s. In these methods, a reacting system initially at equilibrium is perturbed rapidly and then observed as it ''relaxes'' back to equilibrium.Atkins P. and de Paula J. ''Atkins' Physical Chemistry'' (8th ed., W.H.Freeman 2006) p.805, Steinfeld J.I., Francisco J.S. and Hase W.L., ''Chemical Kinetics and Dynamics'' (2nd ed., Prentice-Hall 1998) p.140-3, In the case of temperature jump, the perturbation involves rapid heating which changes the value of the equilibrium constant, followed by relaxation to equilibrium at the new temperature. The heating usually involves discharging of a capacitor (in the kV range) through a small volume (< 1 mL) of a conducting solution containing the molecule/reaction to be studied. In some versions of the apparatus use ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Pressure Jump
Pressure jump is a technique used in the study of chemical kinetics. It involves making rapid changes to the pressure of an experimental system and observing the return to equilibrium or steady state. This allows the study of the shift in equilibrium of reactions that equilibrate in periods between milliseconds to hours (or longer), these changes often being observed using absorption spectroscopy, or fluorescence spectroscopy though other spectroscopic techniques such as CD, FTIR or NMR can also be used. Historically, pressure jumps were limited to one direction. Most commonly fast drops in pressure were achieved by using a quick release valve or a fast burst membrane. Modern equipment can achieve pressure changes in both directions using either double reservoir arrangements (good for large changes in pressure) or pistons operated by piezoelectric actuators (often faster than valve based approaches). Ultra fast pressure drops can be achieved using electrically disintegrated ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
