Free energy protein formation

From tables of standard free energies of formation, we find AG,° = -2885 kj-mol-1. Therefore, the maximum nonexpansion work obtainable from 1.00 mol C6H1206(s) is 2.88 X 103 kj. About 17 kj of work must be done to build 1 mol of peptide links (a link between amino acids) in a protein, so the oxidation of 1 mol (180 g) of glucose can be used to build up to about 170 mol of such links. More visually the oxidation of one glucose molecule is needed to build about 170 peptide links. In practice, biosynthesis occurs indirectly, there are energy losses, and only about 10 such links can be built. A typical protein has several hundred peptide links, so several dozen glucose molecules must be sacrificed to build one protein molecule. 

How much energy is required to synthesize a single peptide bond in protein synthesis How does this compare with the free energy of formation of the peptide linkage, which is about 5 kcal/mole ... 

Although we have used the term bound water in this section, we have not used it generally elsewhere in this review. The word bound carries connotations of slow dynamics and large free energy of formation of a complex, which do not appropriately describe the water about a protein. The terms hydration shell and hydration water lack the above connotations and thus are preferred. 

The conception that the hydrophobicity of a protein is the property of its surface is used as the basis of the technique suggested by Melander and Horvath 30). This technique consists of an analysis of the effects of inorganic salts on the aqueous solubility of proteins30). According to the model considered by Melander et al.30), the free energy of solvation of a protein macromolecule in aqueous solution is described by Eq (3) (see above). The presence of a salt alters the protein solubility due to the concentration-dependent effect of the salt on the free energy of formation... 

Notwithstanding that the free energy of formation of peptide bonds from free amino acids corresponds to an equilibrium position in dilute solution beyond 99% hydrolysis, a number of authors have inclined to the view that peptide and protein synthesis may be catalyzed by proteases and peptidases. The free energy data indicate that, whether or not this is the case, the synthesis of small peptides from amino acids cannot, under physiological conditions, be a simple mass action reversal of hydrolysis. On the other hand, the condensation of large peptides may be promoted by proteases alone. 

Fig. 2b. The appearance of two crystal forms shows that the protein in the membrane exists in equilibrium between the protomeric aj8 unit and oligomeric (aj8>2 forms. The high rate of crystal formation of the protein in vanadate solution shows that transition to the E2 form reduces the difference in free energy required for self association of the protein. This vanadate-method for crystallization has been very reproducible [34-36] and it also leads to crystalline arrays of Ca-ATPase in sarcoplasmic reticulum [37] and H,K-ATPase from stomach mucosa [38]. 

It is not uncommon for protons to be taken up or released upon formation of a biomolecular complex. Experimental data on such processes can be compared to computational results based on, for example, Poisson-Boltzmann calculations.25 There is a need for methods that automatically probe for the correct protonation state in free energy calculations. This problem is complicated by the fact that proteins adapt to and stabilize whatever protonation state is assigned to them during the course of a molecular dynamics simulation.19 When the change in protonation state is known, equations are available to account for the addition or removal of protons from the solvent in the overall calculation of the free energy change.11... 

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