NAME: PUTERI NUR SARAH DIANA BINTI ENGKU BAHARUDDIN

DATE: 23/11/2014

SUBJECT: INTERNSHIP AT FACULTY OF BIOSCIENCE AND MEDICAL ENGINEERING.

TITLE: Homology modelling of Galactitol-1-phosphate 5-dehydrogenase (Peptoclostridium difficile)

OBJECTIVE:

Objective of this research is to create three-dimensional structure homology modelling of homologous protein from its templates homologous protein sequence of Galactitol-1-phosphate 5-dehydrogenase [Peptoclostridium difficile].

Target Sequences

Name: Galactitol-1-phosphate 5-dehydrogenase [Peptoclostridium difficile]

Sequences:

MKAAVLHGTNDMRFEDIEIKPCESDEVKIKVMAAGICGSDPPRVLKHWKYPVPAIPGHEFSGVIAEVGKDVKNVKVGDRVVAIPFIPCNECEYCKRGLFSLCDDHGMLGAKSFGAFAEYVNIKATNVLPIGDMDFEDAAMIEPLAVAMHGVLNIGVQVGDAVAVMGSGTMGQLVIQGLKIAGA

TIIAVDISDNKLRESKELGADIIINAKDIDPVEKIKELTGGKGVDIALECAGSKITQEQCLLITKKKSKIGFLGIAYSDITLSEEAFENIFRKELELKGFWNSYSAPFPGQEWTKGINLVNEGKIKLKEMVSHRFSLEDTYKAFEMIRDRKEEFNKILILPQGVEK

Template Sequences

Name: Chain B, Open State of Galactitol-1-phosphate 5-dehydrogenase From E. Coli, With Zinc in the Catalytic Site.

Sequences:

MKSVVNDTDGIVRVAESVIPEIKHQDEVRVKIASSGLCGSDLPRIFKNGAHYYPITLGHEFSGYIDAVGSGVDDLHPGDAVACVPLLPCFTCPECLKGFYSQCAKYDFIGSRRDGGFAEYIVVKRKNVFALPTDMPIEDGAFIEPITVGLHAFHLAQGCENKNVIIIGAGTIGLLAIQCAVALGAKSVTAIDISSEKLALAKSFGAMQTFNSSEMSAPQMQSVLRELRFNQLILETAGVPQTVELAVEIAGPHAQLALVGTLHQDLHLTSATFGKILRKELTVIGSWMNYSSPWPGQEWETASRLLTERKLSLEPLIAHRGSFESFAQAVRDIARNAMPGKVLLIP

Result

Retrieved Target sequence from NCBI

The target sequence of Galactitol-1-phosphate 5-dehydrogenase [Peptoclostridium difficile] were retrieved from NCBI database. By using the NCBI reference sequence, the reference numbers were pasted on the search tab and all databases were set as the search keywords. The FASTA format were downloaded and retrieved to be used as the target sequence of homology modelling.

Figure 1 Result of NCBI search of Galactitol-1-phosphate 5-dehydrogenase [Peptoclostridium difficile]

Retrieved template sequence from SWISS MODEL

The template sequences of Galactitol-1-phosphate-5-dehydrogenase [Peptoclostridium difficile] were retrieved from SWISS MODEL database. The SWISS MODEL contains three types of project mode that are automated mode, alignment mode and deep view project mode. For retrieving templates sequence, automated modes were selected and the FASTA sequences of target sequence were pasted on the blank box.

Figure 2 Retrieved template sequence by using SWISS MODEL.

The homology modelling of target and template sequences

The template and target sequence were used to create the homology modelling by using SWISS-MODEL server. The result showed the QMEAN Z-Score, estimate absolute model quality, Score of the model in high resolution X-ray structure, Residue error plot, Q-mean local score and model of the homology modelling of the sequences. From the homology modelling, the 3D structure homology modelling of target and template sequence were able to produce.

Figure 1 Local quality estimation of homology model target and template sequences

Figure 3 Result of template sequence and sequence similarity.

Figure 3 Z-score table of homology model target and template sequences

Figure 4 3D structure of homology modelling of target and template sequence.

Figure 2 Z score table of homology model target and template sequences

Model Evaluation and Quality Check

Discussion

The result has shown the Z score of homology model which contain, Local quality estimation of homology model target and template sequences, Z-score QMEAN4 value, Z-score QMEAN6 value and the three-dimensional structure of target and template sequence. The homology modelling of target and template sequence have QMEAN4 value of -6.96, all atom interaction value of -3.72, C-beta value of -4.65, solvation value of-6.02 and torsion value of -3.53. The result has shown the Z score of homology model which contain QMEAN6 value, all atom interaction value, C-beta value, solvation value, torsion value SS agree value and ACC agree value. The homology modelling of target and template sequence have QMEAN6 value of -5.02, all atom interaction value of -3.72, C-beta value of -4.65, solvation value of-6.02, torsion value of -3.53., SS Agree value of 0.90 and ACC Agree value of -0.86. The three dimensional structure of homology modelling of target and template sequence were able to produced.

For the model evaluation check, Ramachandran plot analysis were done and analysed. Based on the Ramachandran plot figure, red region represent the residue in the most favoured region, yellow region represent residue in additional allowed region, while light yellow represent generously allowed region. Finally, white region represent residues in disallowed region. From the Ramachandran analysis plot, it can be analysed that the total number of residues-690 with 83.7% residue in most favoured region, 11.7% residue in additional allowed region, 3.0% in generously allowed region and 1.5% residues in disallowed region. Number of glycine residue shown as triangle is 64 and number of proline residues is 28.

Conclusion

The homology models of three dimensional structure of Galactitol-1-phosphate 5-dehydrogenase (Peptoclostridium difficile) were successfully obtained.

References

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