Team:ACIBADEM ISTANBUL/Model

• Home
• Project
• Team
• Lab
• Parts
• Human Practice
• Judging Form
• Attributions

Table of Contents

1. Homology Modelling
2. Modification PDB
3. Stability
4. Docking

Homology Modelling

For the in silico homology modelling I-Tasser program was used. Since, there wasn’t any reference template for our protein, homology modelling was done by similarity. However, confidince scores’ of the protein were very low. LTNF10 and LTNF 2.0 were modelled according to:

1) LTNF10
LKAMDPTPPL
2) C_GSx2_LTNF10+10_C
(N’_Cys + GSx2 + LTNF10 +10aa +Cys_C’)
CGGGGLKAMDPTPPLWIKTESPSTPC

These sequences.

Fig.1. LT10 homology model.(c –score : -0.55)	Fig.2. LTNF homology model.(c-score : -2.44)

Since the modelling scores were very low, repair process was applied to the proteins via FOLDX program. A function, RepairPDB, repaired the models and tried to lower their energy.

Modification PDB

The way it operates is the following: First it looks for all Asn, Gln and His residues and flips them by 180 degrees. This is done to prevent incorrect rotamer assignment in the structure due to the fact that the electron density of Asn and Gln carboxamide groups is almost symmetrical and the correct placement can only be discerned by calculating the interactions with the surrounding atoms. The same applies to His. We do a small optimization of the side chains to eliminate small VanderWaals’ clashes. This way we will prevent moving side chains in the final step. We identify the residues that have very bad energies and we mutate them and their neighbours to themselves exploring different rotamer combinations to find new energy minima. FoldX uses output-file as a tag to label different outputs from different commands in batch runs.

Fig.3. Repaired LT10	Fig.4. Repaired LTNF

Stability

Stability test were done on FOLDX program by calculating the average energy of the proteins. Results can be found below.

LT10 stability:

LTNF stability:

These results were obtained before the pdb repair.

LT10_Repaired stability:

LTNF_Repaired Stability:

It can be seen that energies of the proteins dropped dramatically. However, native ltnf is still more stable than circulized version. This is probably an error since experimental tests Show that circulized versions are more stable than the native one.

Docking