Synopsis

• The Binding Affinity (∆G˚’ and K_d) of the 13 interfaces of CTF3, MCM21 and CTF19 was predicted using PRODIGY.

Based on the general log Kd frequency from Protein-Protein interaction database 2.0, the log Kd value of each interface is labelled as dash line with corresponding color. (https://bmm.crick.ac.uk/~bmmadmin/Affinity/)

•  Most of the concerned interfaces have their log K_d values within the average range (10^-12 M to 10^-6 M) of protein-protein interaction (PPI), indicating normal binding affinity; while four of them fall in the 10^-4 M range.

• Based on K_d data analysis:

Hydrogen bonds are essential for stable protein-protein binding, while it is doubtful whether salt bridges contributes to binding.

Van der Waals interaction contributes less to binding while could be essential in large numbers.

• Based on structural analysis:

Hydrogen bonds and salt bridges are highly conserved in complex with high binding affinity, indicating their key function in binding.

Conclusion of Van der Waals interaction contribution is similar to data analysis.

⭐Apart from non-covalent bonds, Entropy is another essential element that contributes to binding affinity which includes solvent effect, conformational changes and geometric complementarity. For further information see 👉Entropic Basis of Binding Affinity.

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