This exercise will model the carboxylic acid-arginine portion of the arachidonic acid (substrate) cyclooxygenase (enzyme) complex interaction important in inflammation processes.

• Arachidonic acid will be modeled using a five carbon carboxylic acid, pentanoic acid, in its prevalent form at physiological pH.
• Arginine will be modeled using its side chain at physiological pH.
• The two will then be modeled together to view geometry that corresponds to the lowest energy for the pair and to view/better understand the specific noncovalent interactions that occur.

Save the arginine side chain file to your local drive, then open Spartan and load the saved file.

• Draw the molecular structure showing all atoms and the calculated charges displayed for the arginine side chain.  Use your understanding of charge distribution to explain these predicted charges.

• Measure the bond angles (Menu: Geometry, Angle, then select the 3 atoms in each angle) and view the geometry (use mouse to rotate molecule) about each of the three nitrogen atoms; identify the hybridization for each of these atoms

• Draw a Lewis structure for the arginine side chain at physiological pH conditions.  Be sure to show all lone electron pairs.  From the Lewis structure, what would you have predicted about the hybridization of the three nitrogen atoms?

• Now draw three Lewis resonance structures for the arginine side chain; be sure to show all appropriate charges.

• Measure and tabulate the three C-N bond distances (Menu: Geometry, Angle, then select 2 atoms); compare these to C-N and C=N bond distances.  Based upon these values and the three resonance structures, predict the average CN bond order.

• Display the electrostatic potential surface (Menu: Display, Surfaces, then check box).  What observations do you have concerning the electrostatic potential surface at the far end (away from the protein backbone) of the arginine side chain?  What role would arginine serve in terms of enzyme-substrate interactions.

Save the pentanoic acid spartan file to your local drive, then open Spartan and load the saved file.

• Draw the molecular structure showing all atoms and the calculated charges displayed for the pentanoic acid form (pentanoate) at physiological pH.  Use your understanding of charge distribution to explain these calculated results.

• Draw the resonance structures for a 5 carbon saturated carboxylic acid at physiological pH.

• Measure, tabulate and compare the two C-O bond distances (Menu: Geometry, Angle, then select 2 atoms); compare these to C-O and C=O bond distances.  Based upon these values and the two resonance structures, predict the average CO bond order.

• Measure the three bond angles (Menu: Geometry, Angle, then select the 3 atoms in each angle) about the carbon connected to the two oxygens and view the geometry (use mouse to rotate molecule); identify the hybridization of this carbon.

• Display the electrostatic potential surface (Menu: Display, Surfaces, then check box).  What observations do you have concerning the electrostatic potential surface at the carboxylic end of the acid?  What role would carboxylic acid functionalities serve in terms of enzyme-substrate interactions.

Save the arginine-acid complex file to your local drive, then open Spartan and load the saved file.

• Rotate the complex and identify the two specific interactions that hold this two moieties together.  Measure the distance between the two key pairs of atoms that hold this complex together.  Compare this distance to what would be observed if these two atoms were bonded together within a molecule.

• View the geometry of the arginine side chain in the complex and comment on any distortions you see (compared to the geometry of the side chain alone examined earlier).  Postulate why this distortion occurs.

• Measure the C-O distances in the complex and compare these to those observed in the acid alone.  Provide a plausible explanation for any observed distances.

• Display the complex in the "space-filling mode" (Menu: Model, Space Filling). Comment on your observations.

• Return to the "Ball and Wire mode."  (Menu: Model, Ball and Wire). Then display the electrostatic potential surface (Menu: Display, Surfaces, then check box).