Electronic Theses and Dissertation

Protein human epidermal growth factor (hEGF) diekspresikan di dalam tubuh dengan ukuran 6,12 kDa dan berperan dalam proliferasi dan deferensiasi sel tubuh. Makromolekul ini dikode oleh gen spesifik yang dapat diisolasi dari darah. Penelitian ini bertujuan untuk memperoleh sekuens hasil isolasi gen penyandi protein hEGF, menentukan hubungan kekerabatan antar organisme berdasarkan gen hEGF, membangun struktur 3D protein hEGF dan menemukan posisi pengikatan yang tepat antar protein target dengan salah satu protein motorik di dalam tubuh yaitu Miosin-9. Metode yang digunakan berupa ekstraksi DNA sampel darah yang diamplifikasi menggunakan primer spesifik. Hasil amplifikasi kemudian diidentifikasi melalui tahapan sekuensing sebagai informasi untuk konstruksi pohon filogenetik. Sekuen yang diperoleh dimodelkan secara in silico menggunakan Swiss model dan protein-protein docking. DNA berhasil teramplifikasi dengan ukuran 700 bp pada tiga sampel. Hasil konstruksi filogenetik menunjukkan tiga sampel gen hEGF berada pada clade yang sama. Sekuen hasil pensejajaran yang telah dimodelkan menggunakan Swiss model menghasilkan protein yang tidak homolog dengan identity seq 90%. Hasil simulasi docking yang diperoleh berupa nilai i-RMSD protein target 5.4 +/- 0.4, energi Van der Waals -29.3 +/- 1.7, dan Z-score -1,7. Hasil tersebut menunjukkan adanya interaksi antara protein EGF hasil isolasi dengan Miosin-9 yang diuji.

Kata kunci : hEGF, isolasi DNA, filogenetik, pemodelan protein, docking.

The 6,12 kDa human epidermal growth factor (hEGF) protein is expressed in the body and plays a role in cell proliferation and differentiation. This research aims to discover the isolated sequence of the gene encoding the hEGF protein, determine the phylogenetic relationship between organisms based on the hEGF gene, construct the 3D structure of the hEGF protein, and identify the precise binding position between the target protein and the motoric protein called Miosin-9. Blood samples are extracted of their DNA, which is then amplified using specified primers. Sequencing is utilized to identify the amplification results, which are then used to create phylogenetic trees. The retrieved sequences were modeled using the Swiss model and docking proteins in silico. In three samples, DNA was successfully amplified to 700 bp. The phylogenetic analysis revealed that the three hEGF gene samples belonged to the same clade. With a 30% identity seq, alignment result sequences that have been modeled using the Swiss model create proteins that are not homologous. The outcomes of this modeling were compared to the hEGF protein from the database, which had a sequence identity of greater than 90%. The i-RMSD value of the target protein (5.4 +/- 0.4), the Van der Waals energy (-29.3 +/- 1.7), and the Z-score were determined by simulation (-1.7). These results indicate a potential interaction between the isolated EGF protein and the miosin-9 tested. Keywords: docking, DNA isolation, hEGF, phylogenetics, protein modeling.