Judul: Simulasi Dinamika Molekul Protein 1GB1 Menggunakan Not Just Another Molecular Dynamcs Program (NAMD)
Abstrak: Protein 1GB1 helps Streptomyces griseus to avoid host defense by immunoglobulin binding site properties. The aim of this study are to learn the mechanism of unfolding and molecular dynamics of protein 1GB1 by temperature variance based on some parameters. Coordinate file of 1GB1 that given by NMR (Nuclear Magnetic Resonance) can be downloaded from Protein Data Bank, then it was processed by some steps such as minimization, heating, equilibration and production run using PBC (Periodic Boundary Condition) and PME (Particle Mesh Ewald) methods. Simulation running at 325K, 350K, 375K, 400K, 450K dan 500K. Except simulation 1 ns at 500K, all simulations running for 10 ns. Some parameters shown unfolding process of 1GB1 at 900 ps in 500 K simulation. Secondary structures that broke for the first time is alpha-helix that converted to turn and coil.
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Judul: Mekanisme Pelipatan Protein 1GB1 pada Temperatur Rendah Menggunakan Simulasi Dinamika Molekul
Abstrak: Protein 1GB1 (protein G domain B1) merupakan protein immunoglobulin dari Streptomyces griseus. Penelitian ini menggunakan metode simulasi dinamika molekul dan bertujuan untuk menentukan pengaruh penggunaan temperatur tinggi pada proses pembentangan protein (unfolding) dan temperatur rendah pada pelipatan (refolding) protein 1GB1. Simulasi unfolding dilakukan pada temperatur 500 K selama 16 ns. Koordinat akhir protein pada proses unfolding dijadikan masukan pada proses refolding dengan temperatur 225 K selama 30 ns. Langkahlangkah dalam simulasi ini meliputi proses preparasi, minimisasi, pemanasan dan ekuilibrasi serta production run. Protein 1GB1 akan unfolding pada temperatur 500 K dalam waktu 12 ns dengan tingkat kesamaan urutan asam amino hanya 7 % (hampir unfolding sempurna). Protein yang telah rusak ini kemudian kembali ke struktur awal melalui proses refolding pada suhu 225 K selama 30 ns dengan tingkat kesamaan urutan asam amino sebesar 72 % . Dari penelitian ini diperoleh bahwa proses pelipatan protein mengikuti mekanisme zipper model di mana α- helix terbentuk lengkap lebih dahulu dibandingkan struktur β-sheet.
Keyword: protein 1GB1, unfolding, refolding, hydrophobic collapse, zipper model, simulasi dinamika molekul

Judul: Etno-ornitologi Burung Kancilan Flores (Pachycephala nudigula nudigula Hartert 1897) pada Masyarakat Lio di Taman Nasional Kelimutu
Abstrak: Bare-throathed whistler is one of several wild birds in Kelimutu National Park (TNKL) that is believed to have correlation with Lio Community‟s belief. The estimation of Bare-throated whistler‟s population in Kelimutu National Park was about 186.41-1668.07 individual by the density about 0.0389-0.3481 ind/ha with the sex ratio 6.2:1 that spreaded on area with height of 1100 – 1600 masl. The characteristic of Bare-throated whistler‟s habitat is a natural forest with various canopy level, high plant species diversity and high density. The habitat characteristics related to the availability of food in the form of insects, cover, safety and a nesting site. Generally the most of Lio community knew the existence of Bare-throated whistler directly or from their parents‟ stories. The perceptions of Lio Community to the Bare-throated whistler‟s existence is generally support the conservation efforts. The perceptions construct the Lio Community‟s atitude that tend to be conservative to the existence of Bare-throated whistler. The attitude shown by their behavior that not cathing the Bare-throated whistler from the TNKL‟s area or the outside. The attitude have an important role to the existence of Bare-throated whistler in Kelimutu National Park‟s area.
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