By Enrico Di Cera, Frederic M. Richards, David S. Eisenberg, Peter S. Kim
This quantity commemorates the fiftieth anniversary of the looks in quantity four in 1948 of Dr. Jeffries Wyman's well-known paper during which he "laid down" the principles of linkage thermodynamics. specialists during this region give a contribution articles at the state of the art of this significant box and on new advancements of the unique thought. one of the themes lined during this quantity are electrostatic contributions to molecular unfastened energies in resolution; site-specific research of mutational results in proteins; allosteric transitions of the acetylcholine receptor; and decoding the molecular code of hemoglobin allostery.
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Additional resources for Linkage Thermodynamics of Macromolecular Interactions
To generate the extended structures, all side-chain dihedral angles were initially set to 180". The structures obtained after minimization are referred to as Beta-ml and Ex72ml, respectively. The pHdependent electrostatic free energy and the titration curve for the null model can thus be calculated using the analytical expressions in Eqs. (28) and (27). Since the electrostatic free energy of the fully unprotonated state is undefined in the null model, the free energy difference AGF(G) is set to 0 in Eq.
As explained above, the folding free energy AG? (8) of the unprotonated state is required to calculate the absolute pH stability from the relative stability. While the other charge states could, in principle, also be used as the reference states in the thermodynamic cycle in Fig. 1, their folding free energies are mainly of interest for comparison with the calculated pH-stability curves. The folding free energies in Table I11 are all in a range from about 0 to -20 kcal/mol. Even with the use of a relatively high dielectric TABLE 111 Electrostatic Free Enera DiJfmenct?
This results in 90, 88, and 90 titratable residues per protomer for types 0,A10, and A22, respectively. In the titration program of Beroza et al. (1991), 7500 Monte Carlo steps were performed to determine the average protonation of all sites at a given pH and the titration curves were calculated using 121 pH values evenly distributed in the interval from 0 to 12. , 1977). , 1996), and the empty capsid structure of A22 (called A22E), were provided by S. Curry, E. Fry, and D. 0 A resolution). 35 The protomers consist of 736, 736, and 737 residues, for OIBFS, A10, and A22, respectively.