Erica Kendrick
Modeling of Protein-Small Molecule Complexes
Protein-Hetero compound Complex
The first stage of this project was finding the protein-hetero compound complex. The
hetero compound had to be one of the major amino acids. My protein-hetero compound
complex is as follows:
Hetero compound: Leucine
het code: Leu
Protein: Leu/Ile/Val – binding protein with bound leucine
PDB ID: Iz16
Once the protein-hetero compound complex was found and downloaded [2], the next step
is to view and manipulate the complex using DS Visualizer.
Extracting the Hetero compound
The next step is to extract the hetero compound from the complex. This is done by
highlighting the hetero compound in the complex and then copying it and pasting it onto
a new 3D page in DS Visualizer.
Once the hetero compound is isolated, it can be manipulated in many different ways. For
this project, the charges and the hybridization had to be corrected.
Figure 1. Leucine hetero compound viewed with DS Visualizer
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Erica Kendrick
Once the structure of leucine was determined from viewing it in DS Visualizer, the next
step was to us ChemSketch to create a Lewis Structure of the zwitterions.
Figure 2. Leucine zwitterions
Displaying the Protein-Hetero compound Complex
The next step was to view the entire protein-hetero compound complex, so that both the
protein and the hetero compound could be easily seen. In order to see the complex, we
removed all the extra atoms, such as water. Then the protein is changed into a ribbon
conformation, while the hetero compound is in the CPK conformation. These
conformations provide visual details about the complex.
Figure 3. Leu/Ile/Val binding protein with bound Leucine viewed with DS Visualizer
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Steric Energy Calculations
For this section of the project, I used Chem3D Ultra to find the steric energy calculations.
The first step was to upload the extracted Leucine molecule into Chem3D Ultra. Then I
performed a single-point energy calculation. The single-point energy calculation gives
the steric energies of a specific conformation for a given molecule. The next step was to
perform the energy minimization (also known as geometry optimization). An energy
minimization provides us with the lowest energies that the molecule can have. A slight
change in conformation is seen when running an energy minimization.
Table 1 – Steric Energies
Types of Steric Energy
Pi System
Single Point Energy
4 3 9
Stretch
Bend
Stretch-Bend
Torsion
Non-1,4 VDW
1,4 VDW
Charge/Charge
Charge/Dipole
Dipole/Dipole
Energy Minimization
4 3 9
65.8955
2.2236
0.0688
1.8759
-0.7561
4.4337
-67.8149
0
0
0.4394
3.0214
0.1381
0.4706
-0.7223
5.3204
-78.2057
0
0
« Chem3D Embed »
Fig. 4. Leucine viewed with Chem3D Ultra
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Erica Kendrick
« Chem3D Embed »
Fig. 5. “Energy Minimized” Leucine viewed with Chem3D Ultra
From the above Excel spreadsheet, you can see that there are several types of steric
energies (column A). In order to understand the calculations that are provided by
Chem3D Ultra, you must first understand the meaning of each type of steric energy.
The first energy term in the table is Stretch. The stretch term represents the energy from
bonds that are “stretched” from their optimal bond length. From the data above, it is
obvious that the conformation of the extracted Leucine molecule has a significantly larger
stretch steric energy than the energy minimized conformation.
The next steric energy term is Bend. The bend term represents the energy from bond
angles that are “bent” at different angles than their optimal bond angle. This time, the
extracted conformation of Leucine has a lower steric energy than the energy minimized
conformation. This shows that the bond angles for the extracted conformation are closer
to their optimized angles than the bond angles for the energy minimization conformation.
The third steric energy term is Stretch-Bend. This term represents the energy that it takes
to stretch bonds in order to allow for the bond angle between them to be compressed.
The data for the two Leucine conformations shows that this steric energy is greater for
the energy minimized conformation.
Torsion is the fourth steric energy term from the table above. The torsion term represents
the energy required in changing the torsional (dihedral) angles from the optimal angles.
The torsion energies from the above table show that there is greater energy from the
extracted conformation of Leucine.
The non-1,4 VDW (van der Waals) steric energy term represents the energy that occurs
from the interaction between two atoms that are located more than three atoms apart. The
two conformations of Leucine that are compared above have similar amounts of non-1,4
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Erica Kendrick
VDW energy, with the energy minimized conformation being slightly larger than the
extracted conformation.
The next steric energy term is the 1,4 VDW term. This energy represents similar
energies as the previous term, however this time the atoms interacting are only separated
by two atoms. There is a larger difference in this term than the previous term, which
shows that more energy is required in the interactions of atoms that are closer together.
The energy minimization conformation of Leucine has a higher energy than that of the
extracted Leucine molecule.
The last steric energy term that will be discussed is the Dipole/dipole steric energy term.
This energy term represents the energy between interacting bond dipoles. As you can see
from the table above, both conformations of Leucine have no energy going toward this
type of steric energy.
Overlay
« Chem3D Embed »
Fig. 6. Overlaid extracted Leucine and energy minimized Leucine
In this portion of the project, I used Chem3D Ultra to overlay the extracted Leucine
conformation and the energy minimized Leucine conformation. By doing this, the subtle
differences between the two conformations can been easily seen. In order to do this, I
had to open both conformations within the same Chem3D Ultra tab. Once this was done,
the hydrogens were hidden from the structures; this allows a better view of the main
atoms of the Leucine molecule. Once the two models are oriented similarly, Chem3D
was used to overlay one conformation on the other. From the picture above, you can see
how must of the atoms line up, but there are some slight differences in conformation.
The main chain of carbon atoms line up nicely. The biggest difference in the overlay of
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Erica Kendrick
the conformations is the bonds with the oxygen atoms, they have slightly different angles.
Overall, the two conformations overlay well, with only a few very slight differences.
Protein-Ligand Interactions
Fig. 7. Wiring Diagram of Leu/Ile/Val binding protein with bound Leucine [1]
Above is a wiring diagram. A wiring diagram allows us to see the structure and amino
acid sequence of the entire protein from the protein-hetero compound complex. The lines
of purple images show the structure of the protein. The sections that resemble a curled
ribbon indicate the areas of the protein that form alpha helices and the arrows indicate
sections of beta sheets. The yellow bracket indicates a disulfide bond. The sequence of
letters represents the amino acid sequence of the protein, using the one letter
abbreviations for the amino acids. The red dots over some of the amino acids, such as
those over alanine (A) 100 and alanine 101, indicate the amino acids that come in contact
with the hetero compound. Other aspects and features of the wiring diagram, while very
informative, are not as important for this specific project.
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Erica Kendrick
Fig. 8. LIGPLOT of bound Leucine (Leu) [1]
The figure above is a LIGPLOT, which is a highly stylized view of the interactions
between the ligand (Leucine in this case) and individual amino acids within the protein.
All of the amino acids that were indicated earlier to be interacting directly with Leucine
by the wiring diagram are shown again on this LIGPLOT. The center structure is the
ligand, Leucine. The other structures surrounding it, which are labeled in a reddish color,
are amino acids that are interacting with Leucine at a very close range. The amino acids
that are indicated by what sort of look like reddish eyelashes are amino acids that are
farther from the amino acids or in a difficult position to indicate in another way, such as
behind the ligand, but still interact directly with the ligand.
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Erica Kendrick
Fig. 9. Leu/Ile/Val bind protein with bond Leucine, with interacting amino acid residues
shown in yellow.
As you can see, for this step of the project, I am illustrating the interactions between
amino acid residues and Leucine. In order to do this, using DS Visualizer, I took my
protein-hetero compound complex and manipulated it. The first step was to make the
protein a gray color, which would allow the amino acid residues to be seen easily. The
next step, using the wiring diagram from above, was to select all the amino acid residues
that were shown to be interacting with the bound Leucine. After they were all selected, I
put them into stick form and gave them a color that would make them stand out, yellow
in this case.
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Fig. 10. Interactions between Leucine and amino acid residues
The picture above shows a close view of the interactions between Leucine and the amino
acid residues without the rest of the protein present. In this case, all the amino acid
residues are labeled and the hydrogen bond interactions are shown by the green dashed
lines.
In order to get this image, I had to select that the protein not be showing, but the amino
acid residues of the protein that are interacting with the Leucine molecule still be visible.
After that was done by hiding the protein then selecting only the amino acid residues that
the wiring diagram indicated, I zoomed in so that these interactions could be seen easily.
Then I labeled them and added the lines that indicate the hydrogen bonding.
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Erica Kendrick
Fig. 11. Leu/Ile/Val binding protein with bound Leucine, showing interactions between amino
acid residues and the bound Leucine
This final image for this section of the project combines the views of the previous two
images, giving a comprehensive look at the protein-hetero compound complex. By
adding all of the steps that I have used for this section of the project, I end up with this
image. The steps that have been taken start off with making the protein a gray color.
Then the amino acids that interact with the bound Leucine are selected and given a stick
conformation and a yellow color. The interacting amino acid residues are labeled and the
hydrogen bond interactions are shown by the use of green dashed lines. While this view
can make the specific details hard to see, it gives a great indication of the interactions
happening within the protein-hetero compound complex.
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Erica Kendrick
Table 2 – Protein-Hetero compound Interactions
Amino Acid Residues
Hetero compound
atoms
Nature of Interactions
Tyr 18, 150, Side chain202
CH2Ph-OH
Tyr 202 interacts with
backbone- O
Leu 77
Side chainCH2CH2(CH3)
Unknown – both the
LIGPLOT and DS
Visualizer give no
indication of where the
interaction is taking place.
Backbond- O and OH
Hydrophobic interactions,
Tyr 202 is involved with
hydrogen bonding OH acts
as HBD
Hydrophobic interactions
Cys 78
Side chainCH2CH2(CH3)
Side chainCH2SH
Ser 79
Side chainCH2OH
Ala 100,
101
Thr 102
Side chainCH3
Side chainCHOHCH3
Side chainCH2CH2COO-
Ala 100 interacts with
backbone- OH and NH2
Backbone- OH and NH2
Gly 227
Side chain- H
Phe 276
Side chainCH2PH
Side chainCH2CH2(CH3)
Side chainCH2CH2(CH3)
Glu 226
Backbone- NH2
Can interact by weak
hydrogen bonding but the
H-bond monitor shows no
bonding
Hydrogen bonding at
multiple atoms of the
Leucine , acts as HBD and
HBA
Ala 100 is hydrogen
bonded and acts as HBA
Multiple hydrogen bonds,
acts as HBD and HBA
Hydrogen bonding,
negatively charged
carboxylate acts as HBA
Hydrophobic interactions
Hydrophobic interactions
Defined Terms:
“HBD” - is a hydrogen-bond donor (species has the H).
“HBA” - is a hydrogen-bond acceptor (species is attracted to the H).
"side chain" - the R group of the amino acid residue
"backbone" - part of the peptide bond, not the side chain atoms.
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Bibliography
1. PDB Sum. 1z16. Retrieved April 27, 2008.
http://www.ebi.ac.uk/thornton-srv/databases/pdbsum/
2. RCSB Protein Bank
Berman, H.M.; Westbrook, J.; Feng, Z.; Gilliland, G.; Bhat, T.N.; Weissig, H.;
Shindyalov, I.N.; Bourne P.E. : The Protein Data Bank. Nucleic Acids Research,
28 pp. 235-242 (2000).
http://www.rcsb.org/pdb/home/home.do
3. Slayden, Dr. Suzanne W. George Mason University.
http://classweb.gmu.edu/sslayden/Chem350/chem350.htm
4. Trakhanov, S.D., Vyas, N.K., Luecke, H., Kristensen, D.M., Ma, J., Quiocho, F.A.
Ligand-free and -bound structures of the binding protein (LivJ) of the Escherichia
coli ABC leucine/isoleucine/valine transport system: trajectory and dynamics of
the interdomain rotation and ligand specificity.
Biochemistry 44: 6597-6608 (2005)
DOI 10.2210/pdb1z16/pdb
http://www.ncbi.nlm.nih.gov/pubmed/15850393?dopt=Abstract
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