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  .

Summary

5.  The binding interactions between SelB and GTP are enthalpically favored and entropically disfavored and proceed with a negative - DCp. 

a.  List possible factors (not including buffer solution DH_ion) that could lead to enthalpy changes on binding

Answer: Enthalpy change accompany making and breaking IMFs among atoms in both species. These would include:

• loss of protein–solvent hydrogen bonds and van der Waals interactions,
• loss of ligand-solvent interactions,
• the formation of ligand-protein bonds, salt bridges and van der Waals contacts
•   reorganization of the intra-molecular hydrogen-bonding network of the protein,
• solvent reorganization near the protein surface, conformational changes at the binding site due to the binding even

b.  List possible factors (not including buffer solution DH_ion that could lead to enthalpy changes on binding

Answer: 

• release of confined or interfacial water molecules to the bulk (+ DS)
•  water molecules released from the complex surface (+ DS)
• reduction of conformational (rotational and vibrational) degrees of freedom of protein side-chains (- DS)
• loss of translational degrees of freedom upon binding in ligand (- DS)

c.  List possible factors that could lead to heat capacity changes on binding

• net decrease in hydrophobic groups exposure to water on complex formation (- DCp)

• net removal of surface area of the protein from contact with solvent (- ΔCp)  

• any process in which water is released from the surface (- ΔCp), including conformational changes in the protein which reduce the hydrodynamic radius and hence surface area of the protein on complex formation

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