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Table 2 Calculate the effect of single-point mutations on the binding affinity

From: Structural basis of RGD-hirudin binding to thrombin: Tyr3 and five C-terminal residues are crucial for inhibiting thrombin activity

Residues Mutation VDW Term Electrostatic Term Entropy Term Non-polar Term Weighted Mutation Energy Effect of Mutation
Tyr3 Ala 6.58 -1.92 0.12 0 2.2 destabilizing
Ser50 Ala 6.68 0.41 -0.58 0 2.71 destabilizing
Gln53 Ala 8.99 -0.47 -2.02 0 2.16 destabilizing
Asp55 Ala 8.7 3.15 -0.94 0 4.56 destabilizing
Glu57 Ala 0.72 1.78 -0.13 0 1.02 destabilizing
Ile59 Ala 3.19 -0.4 -0.58 0 0.78 destabilizing
  1. VDW Term: The van der Waals contribution to the binding energy differences.
  2. Electrostatic Term: The electrostatic contribution to the binding energy difference between wild type and mutated structures.
  3. Entropy Term: The side-chain entropy contribution to the binding energy differences.
  4. Non-polar Term: The non-polar (surface tension) contribution to the binding energy differences.
  5. Weighted Mutation Energy: The total free energy difference between the wild type and mutated structures. It is calculated as a weighted sum of the VDW, Electrostatic, Entropy and Non-polar terms.