Energy inputs model protein

Considering the highly processive mechanism of the protein degradation by the proteasome, a question naturally arises what is a mechanism behind such translocation rates Let us discuss one of the possible translocation mechanisms. In [52] we assume that the proteasome has a fluctuationally driven transport mechanism and we show that such a mechanism generally results in a nonmonotonous translocation rate. Since the proteasome has a symmetric structure, three ingredients are required for fluctuationally driven translocation the anisotropy of the proteasome-protein interaction potential, thermal noise in the interaction centers, and the energy input. Under the assumption that the protein potential is asymmetric and periodic, and that the energy input is modeled with a periodic force or colored noise, one can even obtain nonmonotonous translocation rates analytically [52]. Here we... 

Figure 2.4. The lefthand side shows a representative sheet of y-irradiation cross-linked elastic-contractile model protein, designed for the conversion of an input energy into the output of pumping iron, per-...

Figure 2.6. In general, the conversion from the extended state to the contracted state shown in Figure 2.5 is graphed here as a systematic family of sigmoid-shaped curves with a common dependence of oil-like character of the elastic-contractile model protein whether the energy input is thermal, chemi-...

Contraction of elastic matrices occurs as the temperature is raised through the temperature interval of Figure 5.5A this constitutes the input of thermal energy (TE), measurable as the heat of the transition seen in Figure 5.1C. Visible contraction also occurs as any of the independent variables move through the transition zone in Figure 5.5B. Depending on the composition of the model protein that consti-... 

Axiom S At constant temperature, an energy input that changes the temperature interval for thermally driven hydrophobic association in a model protein can drive contraction, that is, oillike folding and assembly, with the performance of mechanical work in other words, the energy input moves the system through the transition zone for contraction due to hydrophobic association. 

Increasing the concentration of acid, constitutes a particular chemical energy input. The addition of acid (H ), over the concentration range that protonates the carboxylate, lowers the temperature interval for the model protein, drives contraction, and defines the transition zone for this energy input indicated as c in Figure 5.18A. Figure 5.18B, 2a), represents the contraction and relaxation by reversible protonation and deprotonation of the carboxyl functional group, i.e., chemo-mechanical transduction. 

Another example is the Principle of Le ChStelier, which may be stated as follows For any system at rest (at equilibrium) the introduction of a stress (in our case an input energy) causes the system to react in such a way as to relieve the stress (in our case by an output energy). This principle reasonably describes protein-catalyzed energy conversion, that is, the function of protein-based machines. Under prescribed conditions, properly designed model protein-based machines exhibit a behavior where for each action there is a reaction. In section 5.4, regardless of the action, which was any one of several different input energies, the performance of mechanical work was the reac-... 

Figure 5.19. Demonstration of the similar form of the hydrophobic dependence of contractions independent of the form of energy used as long as the model protein is properly designed for the respective energy input. (A) Hiermally driven contraction due to hydrophobic association. (B) Protonation-driven...

A Changing the Oil-like Character of a Model Protein by Any Energy Input, %, That Moves the Transition Zone Can Be Used to Change the Energy of a Functional Group That Is Also Capable of Changing the Oil-like Character of the Model Protein... 

As shown in the hexagonal array in Figure 5.22, five different energy inputs can perform mechanical work by the consilient mechanism. The set of elastic-contractile model proteins capable of direct utilization of hydrophobic association for contraction are called protein-based molecular machines of the first kind. These are enumerated below with brief consideration of the reversibility of these machines. 

CaCl2 and NaCl as Chemical Energy Inputs to an Uncharged Model Protein to Drive Hydrophobic Association... 

For Model Protein i Using CaC as the Chemical Energy Input... 

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