Veera Andrade
Protein Modeling
2C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase:
2C-Methyl-D-Erythritol 2,4-Cyclodiphosphate
Part I : Introduction: Choosing a Hetero Compound
Figure 1a:
Protein and Hetero compound structure in Nature
Figure 1b:
Extracted Hetero compound 2C-Methyl-D-Erythritol
2,4-Cyclodiphosphate
2C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase is a protein that contains the heterocompound 2C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase. The PBD ID is 1JY8 and
the HET code for the hetero-compound is CDI421. Other proteins where this hetero-compound,
CDI, can be found are 2-C-Methyl- D-Erythritol 2,4-Cyclodiphosphate Synthase (ISPF) from E.
Coli involved in Mevalonate-Independent isoprenoid Biosynthesis, Complexed with
CMP/MECDP/MN2+ (PDB:1KNJ)
and The structure of 2c-methyl-D-erythritol 2,4cyclodiphosphate synthase in complex with CMP and product : SOURCE MOL_ID: 1;
escherichia coli (PDB: 1H48) . The protein is essential for cell survival, and reduced abundance
causes a severe growth defect with filamentous cell morphology and sensitivity to antibiotics that
target the cell wall. Subunit composition of 2-C-methyl-D-erythritol 2,4-cyclodiphosphate
synthase = [IspF]3 . Overall, for the whole molecule, the charge is –2 as it is a Phosphate.
The purpose of this project was to extract a hetero-compound from a protein, by using the
programs that were used throughout the class. To see how the hetero-compound is distorted
from its lowest energy conformation to bond with the protein. The energy minimized heterocompound and the extract hetero-compound were overlaid to show the exact difference between
the two. Moving deeper into the reaction between the protein and the hetero-compound the
amino acids that connect the two elements are displayed along with a ligplot to better show the
bonds in two-dimensions. The hydrogen bonds are specifically outlined, showing that hydrogen
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bonds play a large part in binding the protein and the hetero-compound. Structure of 2C-methyld-erythritol-2,4-cyclodiphosphate synthase involved in mevalonate-independent biosynthesis of
isoprenoids. Isoprenoids are biosynthesized from isopentenyl diphosphate and the isomeric
dimethylallyl diphosphate via the mevalonate pathway or a mevalonate-independent pathway
that was identified during the last decade. The non-mevalonate pathway is present in many
bacteria, some algae and in certain protozoa such as the malaria parasite Plasmodium falciparum
and in the plastids of higher plants.
Part II : Displaying the Protein-Hetero Compound Complex
Figure 2
Ribbon View of the protein and the CPK view of the Hetero compound
In the DS visualizer hetero compound was listed separately under "A" chain as CDI421. Other
amino acid residues were shown near the top of the expanded Hierarchy window listing. In the
above, Hetero compound can be seen embedded within the Protein Complex. Hetero compound
is shown in its proper CPK colors.
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Part III : Cyclodiphospate Energy Calculations Performed in
Chem3D
CDI Steric Energy Comparision
Component
Energy Terms
Stretch:
Bend:
Stretch-Bend:
Torsion:
Non-1,4 VDW:
1,4 VDW:
Dipole/Dipole:
Total:
Energy before
Energy after
minimization
minimization
93.5888
1.7626
1985.8006
7.783
3.8417
0.5338
2.1589
3.3315
-4.8154
-1.4553
7.4008
8.8734
-4.1687
-3.7301
2096.6803
11.7535
Table 1
Properties that contribute to total energy before and after Optimization of the Hetero compound.
Figure 3a
CDI before energy minimization
Figure 3b
CDI after energy minimization
The stretch term is the energy of the bond length that has been stretched or compressed beyond
its normal length between two atoms. Before the minimization, the hetero-compound’s stretch
value was 93.588 kcal/mol and after the minimization, the stretch value was 1.762 kcal/mol.
When these terms were compared to one another, the value before minimization shows a high
stretch energy value. This strain is caused by the hetero-compound either compressing bonds or
stretching bonds to be able to complex with the protein in a certain manner.
The Bend term reflects the energy due to the alteration of the bond angles from optimal bond
angles. The before minimization, the bend value was 1985.80 kcal/mol after the minimization;
the bend energy was 7.783 kcal/mol. This is due bending of angles which were caused by the
repelling forces due to satiric hindrance.
The Stretch-Bend term is the term that incorporates both the stretch and bend terms; combining
both the bond length and bond angles that are being altered from the optimal bond and length.
Before minimization, the energy was 3.8417 kcal/mol and was decreased after minimization to
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0.5388 kcal/mol. This indicates that the stretch-bend had little effect of the geometry
optimization or energy minimization of the hetero-compound. Thus, the stretch-bend term was a
minor contributor in the total energy during the rotation.
Torsional rotation is defined as the rotation between the atoms those are adjacent to each other
and the equation is given by V torsion = ½ V0 (1 + cos n ) where n is number of rotations and 
torsion angle. The energy minimization reduced the energy due to torsion from 2.1589 to 3.3315
kcal/mol.
The non-1, 4 van der waals energy changed from –4.8154 to –1.4553 kcal/mol during energy
minimization. The 1,4 van der waals energy is increased from 7.4008 to 8.8734 kcal/mol during
energy minimization. The dipole energy is changed from –4.1687 to –3.7301 kcal/mol during
energy minimization and is defined by energy associated with the interaction of bond poles.
The total energy is measured as the stretch, bend, stretch-bend, torsion, non-1, 4 VDW and 1, 4
VDW combined. Before energy minimization the steric energy of 2C-METHYL-DERYTHRITOL 2,4-CYCLODIPHOSPHATE was 2096.68 Kcal/mol and after energy
minimization the value was 11.7535 Kcal/mol.
Before and after energy minimization the term that contributed most to total steric energy was
the bend and the term that contributed the least was Non 1, 4 van der waals. The terms that
contributed the most and least to total satiric energy were found to be the same before and after
energy minimization steric forms.
Part IV : Overlaying of extracted and energy-minimized heterocompounds
Figure 4
Overlay view of extract and energy minimized hetero compound
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Part V : Protein – Ligand Interactions
Figure 4 shows a wiring diagram of 2C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase
showing the interactions from the amino acids to the protein and the hetero-compound. The
letters with the red dot above them shows an amino acid residue that is interacting with the
ligand (hetero-compound).
Figure 5a:
Wiring diagram of 2C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase
In the ligPlot not all the amino acids are shown interacting. The green dotted line symbolizes
hydrogen bonding, the hydrogen bond can be seen between hetero compound (CDI421) and
amino acids such as Asp63, Ser35, His34, His 42 etc.
Also, we can see the hydrogen bonding between two amino acids for example, Asp 65 with
His34 and Asp 38 with Asp 42.
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Figure 5b
Ligplot of protein 2C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase
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Figure 5c
The protein 2C-Methyl-D-Erythritol
2,4-Cyclodiphosphate Synthase
Figure 5d
The hetero compound CDI embedded within the protein
2C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase.
Figure 5e
The hetero compound CDI interacting with other amino acid (shown in yellow ) residues with in the protein.
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Figure 5f
The hetero compound CDI interacting with other amino acid (shown in yellow ) residues in the hidden protein
Figure 5g
The hetero compound CDI interacting via hydrogen bonds with other amino acids (shown in yellow ) residues
hidden in the hidden protein
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Figure 5h
Hydrogen bond between the amino acid with the surrounding ribbon protein
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Figure 5i
Ligplot of Protein
Figure 5j
3D view of Ligplot of Protein
Part VI : Table of Residue-Ligand Interactions
Amino acid residue Hetero compound atoms
Asp 8
Hydroxyl O
Asp 38
Hydroxyl O
Asp 46
Hydroxyl O
Asp 63
Hydroxyl H
Asp 65
Hydroxyl O
Nature of interaction
Hydrophobic
Hydrophobic
Hydrophobic
Hydrogen Bond
Hydrophobic
His 10
Hydroxyl O
Hydrogen Bond
His 34
His 42
Phe 61
Phe 68
Pro 62
Leu 76
Hydroxyl O
Hydroxyl O
Benzene Ring
Benzene Ring
Cyclic ring
Hydrocarbon tail
Hydrogen Bond
Hydrogen Bond
Edge –to – Face, Hydrogen Bond.
Edge –to – Face, Hydrophobic Bond.
Hydrophobic
hydrophobic
Table 2
Residue Ligand Interactions.
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Part VII: Bibliographic Information
1.Reference for Protein:
PDB file taken from the RCSB Protein Databank (http://www.pdb.org/). The Protein Data Bank.
Nucleic Acids Research, 28 pp. 235-242 (2000).
Steinbacher, S., Kaiser, J., Wungsintaweekul, J., Hecht, S., Eisenreich, W., Gerhardt, S., Bacher,
A., Rohdich, F. Structure of 2C-methyl-d-erythritol-2,4-cyclodiphosphate synthase involved in
mevalonate-independent biosynthesis of isoprenoids. J.Mol.Biol. v316 pp.79-88 , 2002
http://www.rcsb.org/pdb/explore.do?structureId=1JY8
Journal Article:
J Mol Biol. 2002 Feb 8;316(1):79-88.
Structure of 2C-methyl-d-erythritol-2,4-cyclodiphosphate synthase involved in mevalonateindependent biosynthesis of isoprenoids.
Steinbacher S, Kaiser J, Wungsintaweekul J, Hecht S, Eisenreich W, Gerhardt S, Bacher A,
Rohdich F.Abteilung fur Strukturforschung, Max-Planck-Institut fur Biochemie, Am
Klopferspitz 18a, Martinsried, D-82152, Germany. steinbac@biochem.mpg.de
PMID: 11829504 [PubMed - indexed for MEDLINE]
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&lis
t_uids=11829504
2. Reference for Hetero Compound:
J Biol Chem. 2002 Mar 8;277(10):8667-72. Epub 2002 Jan 10. (ref from Protein PDB: 1KNJ)
Structure and mechanism of 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase. An enzyme
in the mevalonate-independent isoprenoid biosynthetic pathway.
Richard SB, Ferrer JL, Bowman ME, Lillo AM, Tetzlaff CN, Cane DE, Noel JP.
http://www.jbc.org/cgi/content/full/277/10/8667
3. PDBSum citation.
S.Steinbacher et al. (2002). Structure of 2C-methyl-d-erythritol-2,4-cyclodiphosphate synthase
involved in mevalonate-independent biosynthesis of isoprenoids.J Mol Biol, 316, 79-88.
[PubMed id: 11829504] [DOI: http://dx.doi.org/10.1006/jmbi.2001.5341 ]
A. Yamaguchi, K. Iida, N. Matsui, S. Tomoda, K. Yura, M. Go: Het-PDB Navi. : A database for
protein-small molecule interactions. J. Biochem (Tokyo), 135, pp.79-84 (2004)
http://jb.oupjournals.org/cgi/content/abstract/135/1/79?etoc
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