Thermodynamics of the GTP-GDP-operated Conformational Switch of Selenocysteine-specific Translation Factor SelB. Alena Paleskava, Andrey L. Konevega and Marina V. Rodnina . The Journal of Biological Chemistry, 287, 27906-27912 (2012).  doi: 10.1074/jbc.M112.366120  .

3.  The main source of DCp changes on binding  arise from loss of water of interacting water from the surfaces of protein and ligand on binding, with the main contribution arising from the hydrophoboic effect.  Another less sizeable contribution to DCp would arise from burying polar residues with the ensuing changes in bound and bulk water interaction potentials.  The following equation has been used to show the contribution to ΔCp from dissolution of solids compounds in water:

 ΔCp = DcapDASAap + DcpDASAp,

where DASAap and DASAp are the apolar and polar solvent accessible surface areas changes, respectively.  Model compounds give values of Dcap = 0.45 and Dcp= -0.26 per mol of SA (angstroms squared). 

Table 2 below shows heat capacity changes and accessible surface area for SelB binding to guanine nucleotides.  ΔCp, heat capacity change; obtained as ΔH/dT; ΔASAap and ΔASAp, changes in apolar and polar solvent-accessible surface areas assuming that all the changes were conferred by either apolar (AAap) or polar (AAp) residues, respectively with no contribution from the other. (Ex:  for GTP in Hepes, 621/0.45=1380)  The values for the buried area were converted into the numbers of amino acids that were removed from the surface using the average ASA for apolar (34 Å2) and polar (56 Å2) amino acids. 

SelBGTPTable2

Figure 3 shows the heat capacity changes upon SelB interaction with guanine nucleotides. A, temperature dependence of binding enthalpy changes upon SelB interactions with GTP (●), GTPγS (○), GDPNP (■), and GDP (□). Standard deviations of measurements are given by error bars, which are smaller than the symbol size. B, bar representation of heat capacity changes upon SelB interactions with guanine nucleotides.

SelBGTPFig3

From graphs A and B and Table 2 above, compare the similarities and differences between the free and bound states of SelB with the different ligands.

 

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