Stable Conformers of the Alanine Dipeptide.
Methodology.
Molecular Mechanics (Force Field)
Techniques Used.
Building, optimization, bond constraints
Abstract. The alanine dipeptide contains many structural features
with a typical protein backbone. Among these are:
- flexible dihedral angles (j and y
).
- presence of multiple CO and NH units for H-bonding
- pendant side chain (methyl group) off of the main backbone.
This exercise is aimed at modeling this dimeric system and finding its
stable conformations, using the bio-specialized force fields AMBER and OPLS,
with comparison to a generic force field such as MM+/MMX/MM2.
Procedure. Build the alanine dipeptide in the conformation
shown above. Using an appropriate force field method and builder setting,
set dihedral constraints for one of the sets of angles j
/y as shown in the table below (D. J. Tobias
& C. L. Brooks III, J. Phys. Chem., 96, 3864 (1992)),
and optimize the structure with these constraints. Negative angles are counterclockwise
rotation of the bond, positive are clockwise. Record the energy at this
structure.
Next, optimize with the constraints removed, to see how much relaxation
occurs relative to the known angles. Record the new dihedral angles, and
the energy at this structure.
Repeat the above sequence at each of the three pairs of low energy minima
dihedrals in the table. How well does each method find the appropriate minima?
Results.
| Conformer |
Method |
j (degrees) |
y (degrees) |
Energy (kcal/mol) |
| C7eq |
CHARMM |
-77.5 |
89.9 |
0 |
| C5 |
CHARMM |
-134.8 |
145.9 |
1.78 |
| C7ax |
CHARMM |
60.6 |
-72.4 |
2.00 |