Prediksi Struktur Tiga Dimensi Protein β-NGF (Nerve Growth Factor) Burung Merpati (Columba livia)

Abstract

Protein β-NGF berperan dalam kelangsungan hidup sel neuron dan diferensiasi embrio aves yang diekspresikan oleh gen NGF. Informasi protein β-NGF telah diidentifikasi pada ayam dan masih terbatas dilaporkan pada merpati. Tujuan penelitian adalah memprediksi struktur tiga dimensi protein β-NGF merpati untuk menambah informasi karakter proteinnya. Protein target diperoleh dari server UniProt dengan kode akses B4ZE95. Prediksi struktur tiga dimensi dan karakterisasi protein β-NGF menggunakan server SWISS-MODEL dan program Chimera. Hasil analisis menunjukkan bahwa protein β-NGF merpati dan template memiliki nilai identity sebesar 89,91%, QMEAN 0,51 serta GMQE sebesar 0,44. Struktur tiga dimensi protein B4ZE95 memiliki asam amino hidrofobik (Ile, Leu, Trp, Phe, Val, Ala, Gly, Met, Cys); karboksil (Glu, Ser, Asp); amina (Lys, Thr) dengan 83 ikatan hidrogen.Kata kunci: columba livia, chimera, protein β-NGF, swiss-model Three Dimensional Protein Structure Prediction of β-NGF(Nerve Growth Factor) on Pigeon (Columba livia)ABSTRACTThe β-NGF protein plays a role in the survival of neuron cells and differentiation of avian embryo which is expressed by NGF gene. Information of β -NGF protein was identified in chicken and it is still limited reported in pigeon. The purpose of this study is to predict the three-dimensional structure of pigeon β-NGF protein to add information about its protein character. The target protein is obtained from UniProt server with access code B4ZE95. The prediction of three-dimensional structure and characterization of β-NGF protein were carried out using SWISS-MODEL server and Chimera program. The analysis showed that pigeon β-NGF protein and template had identity of 89,91%, QMEAN 0,51 and GMQE of 0,44. The three-dimensional structure of the B4ZE95 protein has hydrophobic amino acids namely (Ile, Leu, Trp, Phe, Val, Ala, Gly, Met, Cys); carboxyl namely (Glu, Ser, Asp); amine namely (Lys, Thr) with 83 hydrogen bonds.Keywords: columba livia, chimera, protein β-NGF, swiss model

Penentuan Struktur Tiga Dimensi dan Profil Hasil Hidrolisis Protein Alergen Arginin Kinase Secara in silico

“…Kualitas suatu model dapat dilhat dari persentase sequence identity target dan template. Persentase identity yang tinggi pada sekuens maka semakin mendekati yang sebenarnya dan dapat memperkecil nilai error dalam pembentukan struktur tiga dimensi (Alam et al, 2020). QMEAN adalah suatu penilaian struktur tiga dimensi pada satu kesatuan struktur atau biasa disebut dengan absolut global dan juga pada struktur per residu asam amino yang berdasarkan satu model tunggal.…”