Energy Terms Steric Energy Energy Minimization
Stretch:
100.7771
174.1773
Bend:
4365.8746
525.8078
Stretch-Bend:
-12.389
5.6692
Torsion:
9.3069
98.4615
Non-1,4 VDW:
49.096
3.3126
1,4 VDW:
35.7321
50.1307
Charge/Charge:
0
0
Charge/Dipole:
17.4266
-14.6333
Dipole/Dipole:
0
-18.7167
Total:
4565.8243
824.2092
Vanillyl-Alcohol Oxidase before Minimization
Vanillyl-Alcohol Oxidase after Minimization
The steric energy of the Vanillyl-Alcohol Oxidase protein was calculated when
the heterocompound FAD is complexed with the protein. When the protein’s energy is
minimized, it represents the energy minimum of the compound in the gas phase.
Stretch is the energy related to energy of the bonds due to the stretching of the
bonds of the protein. The steric energy before the minimization was about 74 kcal/mol
lower than the energy after minimization. This is due to the bending of the oxidase
around the P-O bonds of the phosphate groups. Bend is the energy related to the bond
angles that keep the bonds from the most stable angle or conformation. The Bend for the
g was about 3840 kcal/mol less then the bend for the protein before minimization. This is
due to the high van der Waals forces between electron clouds in the protein before
minimization which causes the bend energy to be high. The bend contributed the most
energy to the steric energy of both compounds. The stretch-bend is the energy that
involves two bonds that form a bond angle and when that bond is strained. The heterocomplexed protein has about 17 kcal/mol less stretch-bend energy then the oxidase in the
gas phase. This is due to the bending of the energy minimized oxidase around the P-O
bonds. The stretch bend contributed little to the overall steric energy of both compounds.
The torsion is the energy from deviating dihedral angles from their most favorable
values. The torsion energy for the hetero-complexed protein was about 88 kcal/mol less
then the protein in the gas phase. This shows that the hetero-complexed compound has
more stability from angles that are closer to their optimial dihedral angle. The non-1,4
VDW is the energy related to the repulsive forces of the electron clouds between atoms
that are farther then three atoms apart. The protein in the gas phase had about 46
kcal/mol less non-1,4 VDW steric energy then the hetero-complexed compound. This is
due to the bending of the protein in the gas phase to produce more favorable interactions.
The 1,4 VDW is the energy from the repulsion of the electron clouds of the atoms that are
two atoms apart. The 1,4 VDW of the protein in the gas phase was about 15 kcal/mol
higher then the hetero-complexed protein since the bending caused the oxygens around
the phosphate groups to be closer together, causing more repulsions as the molecule bend
to its energy minimized conformation.
The charge/charge is the sum of the pairs of electrostatic interactions between
charged atoms. The charge/charge interactions in both of the phases of the protein turned
out to be zero. The electrostatic interactions between the two compounds did not change
from the minimization. The charge/dipole is the electrostatic energy from the interaction
of a charged group and of a group with a dipole. The charge/dipole of the protein in the
gas phase is about 31 kcal/mol lower in the protein in the gas phase. The protein in the
gas phase had more favorable dipole/charge interactions then the hetero-complexed
compound. Dipole/dipole is the energy of the interactions between two groups with
dipoles. The energy minimized compound had a dipole/dipole that was 18 kcal/mol
lower since it was in a conformation that allowed more dipole interactions between the
lone pairs of the oxygens and the hydrogens bonded to carbon. The total energy is the
sum of all the steric energies of the compound. The oxidase in the gas phase is much
more stable then the hetero-complexed oxidase since the oxidase in the gas phase had
about 5740 kcal/mol less of steric energy within the compound.
Information from PDBSum
The protein AHV1 complexes with FAD (flavin adenine dinucleotide).
Below is the wiring diagram of the protein. The red dots on the amino acids such as on
100 and 101 interact with the ligand FAD.
Below is the LIGPLOT for the amino acids that interact with Flavin Adenine
Dinucleotide.
The LIGPLOT shows the interactions between the amino actions of the protein such as
the hydrogen bonds (dotted green lines). The nitrogen of Arg 504 hydrogen bonds with
the lone electron pairs of the oxygen which is a part of a phosphate group.
The “eyelashes” are the hydrophobic interactions or other non-hydrogen bonding
interactions that occur between the amino acids and FAD. For example, the hydrophobic
amino acid Trp 413 interacts with the non-polar methylene group of FAD. Also the
oxygen of Glu 260 interacts with the lone pairs of electrons on the nitrogen of the adenine
of the FAD molecule.
Flavin adenine Dinucleotide (ball and stick) within the Vanillyl-Alcohol Oxidase.
The amino acids that inteact with FAD are shown in a pale yellow.
The amino acids that interact with FAD (amino acids that did not interact with FAD
where not shown)
The hetero-complex compound showing the interactions between FAD and the amino
acid side chains.
Amino acid
residue
Hetero
compound
atoms
Nature of interaction
Val 262
Adenine
nitrogens
The C-O and the N-H of the Val are hydrogen
bonding with the N-H and N respectively of the
heterocompound.
Lys 545
Ribose hydroxyl
Ser 101
Adenine
nitrogen and
The NH of Lys 545 is hydrogen bonding to the
two hydroxyls of the ribose in the adenylate
The O-H and the N-H of Ser in hydrogen bonding
to the nitrogen and the oxygen of the phosphate
Ile 102
phosphate group
ribose
respectively.
The –CH3 of Ile is hydrophobically interacting
with the –CH2 of the ribose.
Gly 103
Phosphate group
The N-H of Gly is hydrogen is bonding to the
oxygen of the phosphate in FAD
Asn 105
Phosphate group
The N-H of the amide group of Asn is hydrogen
bonding to the oxygen of the phosphate of FAD.
Glu 182
“
“
Asn 179
Amide group of
the fused
aromatic rings
Arg 504
Amide group of
the fused
aromatic rings
The amide group of Asn 179 is hydrogen bonding
to the C=O of the amide group of FAD and to the
hydroxyl group that is in between the nucleotide
and the fused aromatic rings.
The amide group of Asn 179 is hydrogen bonding
to the C=O of the amide group of FAD and to the
hydroxyl group that is in between the nucleotide
and the fused aromatic rings.
Val 185
The nitrogen in
the fused
aromatic rings
Fused Aromatic
rings
“
Pro 169
Gly 184
The C=O of Val in the peptide bond is hydrogen
bonding to the nitrogen in the fused aromatic rings
Hydrophobic interactions between the praline
methyl group and the fused aromatic rings
“
Tyr 187
C=O of the fused The hydroxyl group of the tyrosine is hydrogen
aromatic rings
bonding to the carbonyl of the fused aromatic
rings
Asp 170
C=O of the fused The N-H of the amide group of Asp is hydrogen
aromatic rings
bonding to the carbonyl of the fused aromatic
rings
Trp 413
aromatic ring
The aromatic Trp 413 is hydrophobically
interacting with one of the fused aromatic rings.
Arg 104
Phosphate group
Ser 175
Phosphate group
The N-H and the C=O of the peptide bond of Arg
are hydrogen bonding to the oxygen of the
phosphate group and the hydroxyl group that is in
between the nucleotide and the fused aromatic
rings.
The N-H of the peptide bond of Ser is hydrogen
bonding to the oxygen of the phosphate group
Phe 424
Fused aromatic
rings
The aromatic Phe 424 is hydrophobically
interacting with one of the fused aromatic rings.
Gly 184
Pro 169
“
Fused aromatic
rings
“
The methyl of Pro is hydrophobically interacting
with one of the fused aromatic rings.
Glu 182
“
“