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Thermodynamic Properties of Water Molecules at a Protein-Protein Interaction Surface.

Huggins DJ, Marsh M, Payne MC - J Chem Theory Comput (2011)

Bottom Line: The simulations also highlight the importance of the restraints placed on the protein in determining the results.Finally, the results identify a correlation between the predicted entropy of water molecules at a given site and the solvent-accessible surface area and suggest that correlations between water molecules only need to be considered for water molecules separated by less than 3.2 Å.This is a vital aspect of molecular recognition and one which we believe must be developed.

View Article: PubMed Central - PubMed

Affiliation: Cambridge Molecular Therapeutics Programme, Hutchison/MRC Research Centre, University of Cambridge , Hills Road, Cambridge, CB2 0XZ, United Kingdom ; Department of Chemistry, University of Cambridge , Lensfield Road, Cambridge, UK CB2 1EW, United Kingdom ; TCM Group, Cavendish Laboratory, University of Cambridge , 19 J J Thomson Avenue, Cambridge CB3 0HE, United Kingdom.

ABSTRACT
Protein-protein interactions (PPIs) have been identified as a vital regulator of cellular pathways and networks. However, the determinants that control binding affinity and specificity at protein surfaces are incompletely characterized and thus unable to be exploited for the purpose of developing PPI inhibitors to control cellular pathways in disease states. One of the key factors in intermolecular interactions that remains poorly understood is the role of water molecules and in particular the importance of solvent entropy. This factor is expected to be particularly important at protein surfaces, and the release of water molecules from hydrophobic regions is one of the most important drivers of PPIs. In this work, we have studied the protein surface of a mutant of the protein RadA to quantify the thermodynamics of surface water molecules. RadA and its human homologue RAD51 function as recombinases in the process of homologous recombination. RadA binds to itself to form oligomeric structures and thus contains a well-characterized protein-protein binding surface. Similarly, RAD51 binds either to itself to form oligomers or to the protein BRCA2 to form filaments. X-ray crystallography has determined that the same interface functions in both interactions. Work in our group has generated a partially humanized mutant of RadA, termed MAYM, which has been crystallized in the apo form. We studied this apo form of MAYM using a combination of molecular dynamics (MD) simulations and inhomogeneous fluid solvation theory (IFST). The method locates a number of the hydration sites observed in the crystal structure and locates hydrophobic sites where hydrophobic species are known to bind experimentally. The simulations also highlight the importance of the restraints placed on the protein in determining the results. Finally, the results identify a correlation between the predicted entropy of water molecules at a given site and the solvent-accessible surface area and suggest that correlations between water molecules only need to be considered for water molecules separated by less than 3.2 Å. The combination of MD and IFST has been used previously to study PPIs and represents one of the few existing methods to quantify solvent thermodynamics. This is a vital aspect of molecular recognition and one which we believe must be developed.

No MeSH data available.


A plot of the change in SASA when a carbon atom is placed at each of the 56 hydration sites predicted by the restrained simulation against the calculated total −TΔS of that site with respect to bulk water.
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fig6: A plot of the change in SASA when a carbon atom is placed at each of the 56 hydration sites predicted by the restrained simulation against the calculated total −TΔS of that site with respect to bulk water.

Mentions: As a final test, we also calculated the change in solvent-accessible surface area (ΔSASA) of a carbon atom placed at the centroid of each hydration site. The ΔSASA upon binding is commonly employed as an estimate of the contribution of the hydrophobic effect to binding, so we were interested in how it correlates with the thermodynamic properties of the hydration sites. Figure 6 shows the plot of ΔSASA against the entropic contribution to the free energy (−TΔS) for all 65 hydration sites in the restrained simulation. The coefficient of determination between ΔSASA and −TΔS is 0.52, suggesting a reasonable correlation, with buried sites tending to have more negative entropies and thus more unfavorable contributions to the free energies. The coefficients of determination for ΔSASA with the interaction energy (0.06) and the total free energy (0.31) were not as high. The ΔSASA for a shape comprised of all 65 hydration spheres was 2167.46, and the sum of the entropic contributions to the free energies for the 65 sites was 62.14 kcal/mol. This corresponds to a value of 28.67 cal/mol/Å2, which is consistent with previous estimates used in MMPBSA (38) and MMGBSA(39) of between 5.0 and 50.0 cal/mol/Å2.


Thermodynamic Properties of Water Molecules at a Protein-Protein Interaction Surface.

Huggins DJ, Marsh M, Payne MC - J Chem Theory Comput (2011)

A plot of the change in SASA when a carbon atom is placed at each of the 56 hydration sites predicted by the restrained simulation against the calculated total −TΔS of that site with respect to bulk water.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3924879&req=5

fig6: A plot of the change in SASA when a carbon atom is placed at each of the 56 hydration sites predicted by the restrained simulation against the calculated total −TΔS of that site with respect to bulk water.
Mentions: As a final test, we also calculated the change in solvent-accessible surface area (ΔSASA) of a carbon atom placed at the centroid of each hydration site. The ΔSASA upon binding is commonly employed as an estimate of the contribution of the hydrophobic effect to binding, so we were interested in how it correlates with the thermodynamic properties of the hydration sites. Figure 6 shows the plot of ΔSASA against the entropic contribution to the free energy (−TΔS) for all 65 hydration sites in the restrained simulation. The coefficient of determination between ΔSASA and −TΔS is 0.52, suggesting a reasonable correlation, with buried sites tending to have more negative entropies and thus more unfavorable contributions to the free energies. The coefficients of determination for ΔSASA with the interaction energy (0.06) and the total free energy (0.31) were not as high. The ΔSASA for a shape comprised of all 65 hydration spheres was 2167.46, and the sum of the entropic contributions to the free energies for the 65 sites was 62.14 kcal/mol. This corresponds to a value of 28.67 cal/mol/Å2, which is consistent with previous estimates used in MMPBSA (38) and MMGBSA(39) of between 5.0 and 50.0 cal/mol/Å2.

Bottom Line: The simulations also highlight the importance of the restraints placed on the protein in determining the results.Finally, the results identify a correlation between the predicted entropy of water molecules at a given site and the solvent-accessible surface area and suggest that correlations between water molecules only need to be considered for water molecules separated by less than 3.2 Å.This is a vital aspect of molecular recognition and one which we believe must be developed.

View Article: PubMed Central - PubMed

Affiliation: Cambridge Molecular Therapeutics Programme, Hutchison/MRC Research Centre, University of Cambridge , Hills Road, Cambridge, CB2 0XZ, United Kingdom ; Department of Chemistry, University of Cambridge , Lensfield Road, Cambridge, UK CB2 1EW, United Kingdom ; TCM Group, Cavendish Laboratory, University of Cambridge , 19 J J Thomson Avenue, Cambridge CB3 0HE, United Kingdom.

ABSTRACT
Protein-protein interactions (PPIs) have been identified as a vital regulator of cellular pathways and networks. However, the determinants that control binding affinity and specificity at protein surfaces are incompletely characterized and thus unable to be exploited for the purpose of developing PPI inhibitors to control cellular pathways in disease states. One of the key factors in intermolecular interactions that remains poorly understood is the role of water molecules and in particular the importance of solvent entropy. This factor is expected to be particularly important at protein surfaces, and the release of water molecules from hydrophobic regions is one of the most important drivers of PPIs. In this work, we have studied the protein surface of a mutant of the protein RadA to quantify the thermodynamics of surface water molecules. RadA and its human homologue RAD51 function as recombinases in the process of homologous recombination. RadA binds to itself to form oligomeric structures and thus contains a well-characterized protein-protein binding surface. Similarly, RAD51 binds either to itself to form oligomers or to the protein BRCA2 to form filaments. X-ray crystallography has determined that the same interface functions in both interactions. Work in our group has generated a partially humanized mutant of RadA, termed MAYM, which has been crystallized in the apo form. We studied this apo form of MAYM using a combination of molecular dynamics (MD) simulations and inhomogeneous fluid solvation theory (IFST). The method locates a number of the hydration sites observed in the crystal structure and locates hydrophobic sites where hydrophobic species are known to bind experimentally. The simulations also highlight the importance of the restraints placed on the protein in determining the results. Finally, the results identify a correlation between the predicted entropy of water molecules at a given site and the solvent-accessible surface area and suggest that correlations between water molecules only need to be considered for water molecules separated by less than 3.2 Å. The combination of MD and IFST has been used previously to study PPIs and represents one of the few existing methods to quantify solvent thermodynamics. This is a vital aspect of molecular recognition and one which we believe must be developed.

No MeSH data available.