(4 points) Click on the scene in PyMOL titled \"Ritonavir\" to show the structur
ID: 587005 • Letter: #
Question
(4 points) Click on the scene in PyMOL titled "Ritonavir" to show the structure of the HIV protease inhibitor ritonavir bound HIV protease. Ritonavir is a medication that is used to treat HIV by inhibiting HIV protease and thus preventing replication of the virus. Shown below is the structure of ritonavir. Two oxygen atoms in the structure are indicated with red arrows. 6. Briefly describe the intermolecular interactions that these atoms form with the water molecule shown with the stick representation (thick lines) in the PyMOL scene. How does this water help bind the drug to the protein? Answer in the space provided and limit your answer to one to two sentences. HOHExplanation / Answer
The water molecules bound by non-covalent intermolecular forces with the two oxygen atom of the Ritonavir and help to decrease the free energy of binding of Ritonavir with HIV-1 protease. In the crystal structure of HIV-1 protease complexed with Ritonavir there are four interfacial water molecules. The double-decoupling free energy molecular dynamics simulation method has been used to calculate the binding free energy contribution for each of water molecule, which shows that two of these water molecules contribute significantly to the binding free energy, the other two have close to zero contribution.
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