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:                                                                                     Figure 1b:

Protein and Hetero compound structure in Nature               Extracted Hetero compound 2C-Methyl-D-Erythritol

                                             2,4-Cyclodiphosphate

 

2C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase is a protein that contains the hetero-compound 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 2,4-cyclodiphosphate 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 hetero-compound 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 bonds play a large part in binding the protein and the hetero-compound. Structure of 2C-methyl-d-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.

 

 

 

 

 

 

Part III : Cyclodiphospate  Energy Calculations Performed in Chem3D

Table 1

Properties that contribute to total energy before and after Optimization of the Hetero compound.

 

 

                          

Figure 3a                                                                                         Figure 3b

CDI before energy minimization                              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 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 = ˝ V0 (1 + cos n w) where n is number of rotations and w 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-D-ERYTHRITOL 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 hetero-compounds

 

 

Figure 4

 Overlay view of extract and energy minimized hetero compound

 

 

 

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.

 

 

 

Figure 5b

Ligplot of  protein  2C-Methyl-D-Erythritol 2,4-Cyclodiphosphate  Synthase

 

 

 

 

 

 

 

 

 

 

 

 

 

 

              

 

Figure 5c                                                                               Figure 5d

       The protein 2C-Methyl-D-Erythritol                            The hetero compound CDI embedded within the protein

    2,4-Cyclodiphosphate Synthase                                      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.

 

 

 

 

 

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

 

 

 

 

 

 

                                                

                                                                                                                   

           Figure 5h

                    Hydrogen bond between the amino acid with the surrounding ribbon protein

 

 

 

 

 

 

 

 

 

 

 

 

 

     

      

   Figure 5i                                                                                 Figure 5j                

         Ligplot of Protein                                                         3D view of Ligplot of Protein

 

 

 

Part VI : Table of Residue-Ligand Interactions

 

Amino acid residue

Hetero compound atoms
Nature of interaction

Asp 8

Hydroxyl O

Hydrophobic

Asp 38

Hydroxyl O

Hydrophobic

Asp 46

Hydroxyl O

Hydrophobic

Asp 63

Hydroxyl H

Hydrogen Bond

Asp 65

Hydroxyl O

Hydrophobic

His 10

Hydroxyl O

Hydrogen Bond

His 34

Hydroxyl O

Hydrogen Bond

His 42

Hydroxyl O

Hydrogen Bond

Phe 61

Benzene Ring

Edge –to – Face, Hydrogen Bond.

Phe 68

Benzene Ring

Edge –to – Face, Hydrophobic Bond.

Pro 62

Cyclic ring

Hydrophobic

Leu 76

Hydrocarbon tail

hydrophobic

 

Table 2

Residue Ligand Interactions.

 

 

 

 

 

 

 

 

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 mevalonate-independent 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&list_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