Download Energy Calculations for 4-Hydroxy-3

Elissa Williams
Modeling of Protein-Small Molecule Complexes;
The Protein Isopentenyl-Diphosphate Delta-Isomerase
And the Hetero Compound 4-Hydroxy-3-MethylButyl Diphosphate
Introduction
In the bacterium Escherichia coli, the protein Isopentenyl-Diphosphate Delta-Isomerase
(PDB ID Code: 1NFZ) is a catalytic enzyme which transforms the compound isopentenyl
pyrophosphate (IPP) into its isomer dimethylallyl pyrophosphate (DMAPP). IPP and DMAPP are
activated isoprenes, compounds which serve vital functions in bacteria. IPP and DMAPP are the
precursors to over 50,000 compounds in bacteria such as signaling molecules and components of
the plasma membrane. The IPP and DMAPP Isomerase protein is found in a variety of bacteria in
addition to E. coli. The hetero compound, 4-Hydroxy-3-MethylButyl Diphosphate (HET Code:
EIP), is an irreversible inhibitor of the protein Isopentenyl-Diphosphate Delta-Isomerase and
covalently binds to the protein when it is in an epoxy form. Experiments in which EIP is bound to
1NFZ and crystallized have lead researchers to believe that the key amino acid residues involved in
isomerization of IPP to DMAPP are Glu-116, Tyr-104, and Cys-67.
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Part I: Choosing a Protein-Hetero compound Complex and Extracting the Hetero compound
In Part I of the Protein Modeling Assignment, a protein and a hetero compound were
selected. The selected hetero compound and protein were complexed non-covalently to one
another. The hetero compound which was chosen for the Protein Modeling Assignment was 4Hydroxy-3-MethylButyl Diphosphate (HET Code: EIP). The protein chosen for the Protein
Modeling Assignment, which complexes with the hetero compound, was Isopentenyl-Diphosphate
Delta-Isomerase (PDB ID Code: 1NFZ). A PDB file of the complexed hetero compound and
protein was obtained from the RCSB Protein Data Bank website and downloaded using the
computer program DS Visualizer. The hetero compound was then extracted from the protein,
Figure 1, in DS Visualizer.
Figure 1: The Hetero compound. The Hetero compound 4-Hydroxy-3-MethylButyl Diphosphate
from Isopentenyl-Diphosphate Delta-Isomerase.
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Part II: Displaying the Protein-Hetero compound Complex
For Part II of the Protein Modeling Assignment, the PDB file downloaded in DS Visualizer
was displayed in a different format in order to obtain a more visually pleasing image of the hetero
compound complexed within the protein. As seen in Figure 2, the protein is in a solid ribbon format
in gray, blue, magenta, and green colors. The hetero compound is complexed in the right subunit of
the protein and is in ball and stick style colored by element.
Figure 2: The Protein-Hetero compound Complex. The Hetero compound 4-Hydroxy-3MethylButyl Diphosphate Complexed within Isopentenyl-Diphosphate Delta-Isomerase.
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Part III: Energy Calculations for 4-Hydroxy-3-MethylButyl Diphosphate
For Part III of the Protein Modeling Assignment, the extracted hetero compound file,
created in DS Visualizer, was imported into Chem3D Ultra. Chem3D Ultra was then used to
compute the steric energy calculations of the extracted hetero compound. These energy calculations
are titled “Single Point Energy Calculations” in Table 1. The extracted hetero compound, as seen in
Chem3D Ultra, is the left hand image in Figure 3. An energy minimization, or geometry
minimization, was performed on the hetero compound. An image of the resulting energy minimized
hetero compound is the right hand image in Figure 3. Chem3D Ultra was used to compute the steric
energy calculations of the energy minimized hetero compound. These energy calculations are titled
“Minimized Energy Calculations” in Table 1. A discussion was written which compares the steric
energy terms for the extracted hetero compound and the energy minimized hetero compound.
Energy Term
Single Point Energy Calculations(kcal/mol)
Minimized Energy Calculations(kcal/mol)
Stretch
0.2573
1.0014
Bend
21.038
5.5746
Stretch-Bend
-0.0283
0.4464
Torsion
2.5847
2.152
Non-1,4 VDW
6.564
-0.3777
1,4 VDW
8.7138
9.4056
Charge/Charge
-94.5526
-103.3567
Charge/Dipole
12.2533
5.2264
Dipole/Dipole
-9.7998
-8.185
Total
-52.9698
-88.113
Table 1: Energy Calculations. Chem3D Energy Calculations for the extracted and energy
minimized forms of 4-Hydroxy-3-MethylButyl Diphosphate.
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Figure 3: The Hetero compound with and without Energy Minimization. The Structure of 4Hydroxy-3-MethylButyl Diphosphate when it is complexed within Isopentenyl-Diphosphate DeltaIsomerase (Left Figure) and Chem3D Energy Minimized 4-Hydroxy-3-MethylButyl Diphosphate
(Right Figure).
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Part III Discussion: Comparison of Steric Energy Terms before and After Energy
Minimization of the Hetero compound
All of the calculated energy terms for the hetero compound, 4-Hydroxy-3-MethylButyl
Diphosphate, changed when a MM2 energy minimization was performed on the hetero compound.
Not only do the values in Table 1 reflect the differences in energy of the two structures of the
hetero compound but also it is evident in Figure 3 that 4-Hydroxy-3-MethylButyl Diphosphate was
rotated, bent, and twisted after the energy minimization. The total energy of the hetero compound
decreased ~35kcal/mol after the energy minimization.
The stretch energy term, which represents the energy associated with any bonds that are
distorted from optimal length, increased ~0.7kcal/mol once the energy minimization was
performed. The bend energy, the energy associated with bond angles that are deformed from their
optimal values, was 21.038kcal/mol for the non-energy minimized hetero compound and
5.5746kcal/mol for the energy minimized hetero compound. The stretch-bend energy or the energy
required to stretch two bonds in a bond angle when the bond angle is compressed, increased
~0.4kcal/mol for the energy minimized structure of 4-Hydroxy-3-MethylButyl Diphosphate. The
torsion energy decreased ~0.4kcal/mol for the energy minimized hetero compound. Torsion energy
is the energy of deformed torsional angles in a compound. The through-space interactions between
atoms which are more than three bonds away from each other are referred to as non-1,4 van der
Waals energy. The non-1,4 van der Waals energy for 4-Hydroxy-3-MethylButyl Diphosphate
decreased ~6kcal/mol when the compound was energy minimized. The 1,4 van der Waals energy,
non-bonded interactions between atoms separated by two bonds, increased slightly less than
1kcal/mol for the energy minimized hetero compound. The charge/charge energy, interactions
between charged atoms, decreased ~9kcal/mol when the hetero compound was energy minimized.
The charge/dipole energy, interactions between charged atoms and transiently forming dipoles,
decreased from 12.2533kcal/mol for the non-energy minimized hetero compound to
5.2264kcal/mol for the energy minimized hetero compound. The dipole/dipole energy,
representative of the interactions between bond dipoles, decreased ~1kcal/mol when 4-Hydroxy-3MethylButyl Diphosphate was energy minimized.
For both the non-energy minimized form of 4-Hydroxy-3-MethylButyl Diphosphate and the
energy minimized form, the charge/charge energy term contributed the most to the total steric
energy of the hetero compound. The stretch-bend energy contributed least to the total steric energy
for the non-energy minimized hetero compound. The non-1,4 van der Waals energy contributed
least to the total steric energy of the minimized energy form of 4-Hydroxy-3-MethylButyl
Diphosphate.
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Part IV: Superimposing the Extracted and the Energy Minimized Hetero compound
For Part IV of the Protein Modeling Assignment, Chem3D Ultra performed an overlay of
the extracted hetero compound and the energy minimized hetero compound. The resulting image is
shown below (Figure 4). This image clearly demonstrates that the diphosphate and the hydroxyl
group of the energy minimized compound have been rotated and the four carbon chain is slightly
less bent in the energy minimized hetero compound.
Figure 4: Overlay of Extracted and Energy Minimized Hetero compound. A superimposed
image of 4-Hydroxy-3-MethylButyl Diphosphate in the Extracted and Energy Minimized Form.
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Part V: Protein-Ligand Interactions
In Part V of the Protein Modeling Assignment, the wiring diagram of the protein,
Isopentenyl-Diphosphate Delta-Isomerase, was obtained from the PDBSum website. The wiring
diagram displays all the amino acids in one subunit of the protein and indicates, with red dots,
which amino acid residues interact with the hetero compound. The wiring diagram is Figure 5
displayed below. The ligplot of the hetero compound, Figure 6, was also obtained from the
PDBSum website. The ligplot is a 2D visualization of the amino acid residues in the protein which
interact with the hetero compound. Figure 7, displayed next to Figure 6 for easy comparison, was
generated in DS Visualizer and also demonstrates the hetero compound and the interacting amino
acid residues. To obtain Figure 7, the interacting amino acid residues shown in the ligplot from the
PDBSum website were selected along with the hetero compound in the downloaded PDB file in DS
Visualizer. Only these amino acid residues and the hetero compound were displayed in a new tab in
DS Visualizer and the hydrogen bonds between the residues and the hetero compound were
generated using DS Visualizer. I had much trouble aligning Figure 7 to match the ligplot, Figure 6.
The hetero compound is closely aligned in both figures; however, some amino acid residues are not
in the same location in Figure 6 and 7. The PDB file in DS Visualizer was stylized to demonstrate
only the protein in gray solid ribbon format, Figure 8. The hetero compound was then displayed in
ball and stick format within the gray solid ribbon depiction of the protein, Figure 9. The protein,
hetero compound, and interacting amino acid residues, no hydrogen bonds are shown, were
obtained in DS Visualizer and is Figure 10 below. Also, the protein, hetero compound, and
interacting amino acid residues, including hydrogen bonds are depicted in Figure 11.
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Figure 5: The Wiring Diagram. An image of the primary and secondary structure of IsopentenylDiphosphate Delta-Isomerase complexed with the hetero compound 4-Hydroxy-3-MethylButyl
Diphosphate.
The above figure is the wiring diagram for the primary and secondary structure of IsopentenylDiphosphate Delta-Isomerase complexed with the hetero compound 4-Hydroxy-3-MethylButyl
Diphosphate. The red dots demonstrated on this figure represent the amino acid residues which
interact with the hetero compound. The blue dots in the figure represent the amino acid residues
which interact with a metal ion. The red rectangles demonstrate amino acid residues which are in
the protein’s catalytic site. This figure was obtained from the PDBSum website using the search
term “1NFZ.”
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Figure 6 (Left Figure): The Ligplot. An image of the Ligplot of the hetero compound 4-Hydroxy3-MethylButyl Diphosphate complexed within the protein Isopentenyl-Diphosphate DeltaIsomerase.
The above left figure is the “Ligplot” of 4-Hydroxy-3-MethylButyl Diphosphate complexed within
the protein Isopentenyl-Diphosphate Delta-Isomerase. This “ligplot” demonstrates the interactions
between the amino acids of the protein and the hetero compound. The following amino acids
interact with the hetero compound: Cys 118, Glu 116, Tyr 104, Lys 55, Ala 34, Glu 114, Arg 51,
Cys 67, Arg 83, Glu 87, Gly 68, Lys 21, and His 69. The green dashed lines in the figure represent
hydrogen bonds and the amino acids depicted as eyelashes interact hydrophobically with the hetero
compound. The “ligplot” was obtained from the PDBSum website.
Figure 7 (Right Figure): Interactions between the Hetero compound and the Amino Acids. An
image of the hetero compound, 4-Hydroxy-3-MethylButyl Diphosphate interacting with key Amino
Acid Residues.
The above right diagram demonstrates the amino acids, shown in yellow stick style, which interact
with the hetero compound, shown in ball and stick style. The green dashed lines represent hydrogen
bonds between the hetero compound and amino acids or between amino acids. This figure was
generated using DS Visualizer.
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Figure 8: The Protein. An image of the protein Isopentenyl-Diphosphate Delta-Isomerase.
The above picture is a solid ribbon representation of the protein Isopentenyl-Diphosphate DeltaIsomerase. This picture was generated in DS Visualizer.
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Figure 9: The Protein and the Hetero compound. An image of the protein IsopentenylDiphosphate Delta-Isomerase complexed with the hetero compound 4-Hydroxy-3-Methylbutyl
Diphosphate.
The above picture is a solid ribbon representation of the protein Isopentenyl-Diphosphate DeltaIsomerase complexed with the hetero compound 4-Hydroxy-3-MethylButyl Diphosphate which is
shown in ball and stick format. This picture was generated using DS Visualizer.
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Figure 10: The Protein, Hetero compound, and Interacting Amino Acids. An image of the
hetero compound, 4-Hydroxy-3-Methylbutyl Diphosphate, interacting with the amino acids of the
protein Isopentenyl-Diphosphate Delta-Isomerase.
The above picture is a solid ribbon representation of the protein Isopentenyl-Diphosphate DeltaIsomerase complexed with the hetero compound 4-Hydroxy-3-MethylButyl Diphosphate which is
shown in ball and stick format. The amino acids of the protein which interact with the hetero
compound are displayed in yellow. This picture was generated in DS Visualizer.
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Figure 11: The Hetero compound complexed within the Protein and Interacting with Amino
Acid Residues. An image of the protein Isopentenyl-Diphosphate Delta-Isomerase complexed with
the hetero compound 4-Hydroxy-3-MethylButyl Diphosphate and interacting with the amino acid
residues of the protein.
The above schematic shows the protein, Isopentenyl-Diphosphate Delta-Isomerase, complexed
with the hetero compound 4-Hydroxy-3-MethylButyl Diphosphate. The protein is shown in gray
ribbon and the hetero compound is the gray, orange, and red ball and stick figure on the left hand
side of the protein. The schematic demonstrates the key amino acids which interact with the hetero
compound (shown in yellow) and the hydrogen bonds between the hetero compound and the amino
acid residues are the green dashed lines. This figure was generated using DS Visualizer.
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Part VI: Table of Hetero Compound and Amino Acid Interactions
For Part VI of the Protein Modeling Assignment, the interacting amino acid residues, which
were identified in the ligplot in Part V of the assignment, were analyzed. The analysis was
constructed into a table, Table 2: Hetero compound and Amino Acid Interactions. The interacting
amino acids were defined along with the atoms in the hetero compound which interact with the
amino acid residues. The type of interaction is also explained in Table 2 below. It is important to
note that the ligplot, Figure 6 above, and the 3D ligplot generated in DS Visualizer, Figure 7, were
used and often referred to in order to complete this part of the assignment.
Table 2: Hetero compound and Amino Acid Interactions. A table defining the type of
interactions between the key amino acid residues of the protein and the hetero compound, 4Hydroxy-3-MethylButyl Diphosphate.
Amino Acid Residue
Atoms in the Hetero
Type of Interaction
Compound which interact
with the Residue
cys 118
- OH (alcohol group)
The sulfur group of the amino
acid interacts with the alcohol of
the hetero compound through
dipolar and hydrogen bonding
interactions.
glu 116
-OH (alcohol group)
The carboxylate group of the
amino acid is able to hydrogen
bond with the hetero compound’s
alcohol group.
tyr 104
- OH (alcohol group)
The alcohol group of the amino
acid is able to hydrogen bond
with the hetero compound’s
alcohol group.
lys 55
- Two oxygen atoms of the
The charged NH3+ group of the
terminal phosphate group
amino acid is able to form a
(PO4)-2
charged or electrostatic
interaction with two oxygen
atoms of the terminal phosphate
group of the hetero compound.
These oxygen atoms have a
partial negative charge.
ala 34
- CH3 (methyl group)
The methyl group of the amino
acid interacts with the methyl
group of the hetero compound
through van der Waals forces.
glu 114
-OH (alcohol group)
The carboxylate group of the
amino acid is able to hydrogen
bond with the hetero compound’s
alcohol group.
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arg 83
glu 87
gly 68
lys 21
his 69
arg 51
cys 67
The NH2+ and the NH2 group of
the amino acid forms four
hydrogen bonds with three
oxygen atoms of the terminal
phosphate group in the hetero
compound.
- Two oxygen atoms of the
The carboxylate group of the
terminal phosphate group
amino acid interacts
(PO4)-2
electrostatically with two oxygen
atoms of the terminal phosphate
group of the hetero compound.
- The internal oxygen of the Two hydrogens of the amino acid
O3P - O - CH2 bond
form weak, polar interactions
with the internal oxygen of the
hetero compound.
- Two oxygen atoms of the
The charged NH3+ group of the
terminal phosphate group
amino acid is able to form a
(PO4)-2
charged or electrostatic
interaction with two oxygen
atoms of the terminal phosphate
group of the hetero compound.
These oxygen atoms have a
partial negative charge.
- Two oxygen atoms of the The two NH groups in the amino
terminal phosphate group
acid form hydrogen bonds with
(PO4)-2
the oxygen atoms of the terminal
phosphate of the hetero
compound.
+
- Two oxygen atoms of the The NH2 and the NH2 group of
internal phosphate group
the amino acid forms four
(PO4)-2
hydrogen bond with two oxygen
atoms of the internal phosphate
group in the hetero compound.
- OH (alcohol group), - The
The sulfur group of the amino
internal oxygen of the
acid interacts with the alcohol of
O3P - O - CH2 bond
the hetero compound through
dipolar and hydrogen bonding
interactions. The hydrogens of
the amino acid form weak polar
interactions with the internal
oxygen of the hetero compound.
- Three oxygen atoms of
the terminal phosphate
group (PO4)-2
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Part VII: Bibliographic Information
In order to complete Part I-VI of the Protein Modeling Assignment, the following sources of
information were used:
1. The RCSB Protein Data Bank was used to obtain the Protein-Hetero compound PDB File:
H.M. Berman, J. Westbrook, Z. Feng, G. Gilliland, T.N. Bhat, H. Weissig, I.N. Shindyalov,
P.E. Bourne: The Protein Data Bank. Nucleic Acids Research, 28 pp. 235-242 (2000).
2. Information regarding the Protein-Hetero compound complex was found in the journal
article which first reported the Protein-Hetero compound structure:
Wouters, J., Oudjama, Y., Barkley, S.J., Tricot, C., Stalon, V., Droogmans, L., Poulter,
C.D., Journal of Biological Chemistry, 2003, 278, 11903-11908. "Catalytic Mechanism of
Escherichia coli Isopentenyl Diphosphate Isomerase Involves Cys-67, Glu-116, and Tyr104 as Suggested by Crystal Structures of Complexes with Transition State Analogues and
Irreversible Inhibitors". http://www.jbc.org/cgi/reprint/278/14/11903
3. The PDBSum Website, http://www.ebi.ac.uk/thornton-srv/databases/pdbsum/, was used to
obtain the wiring diagram and Ligplot of the Protein-Hetero compound:
Laskowski R A, Chistyakov V V, Thornton J M (2005). PDBsum more: new summaries
and analyses of the known 3D structures of proteins and nucleic acids. Nucleic Acids Res.,
33, D266-D268.
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