Judul: Kestabilan Termal Asam Amino Enzim Lipase Bacillus subtilis Menggunakan Simulasi Dinamika Molekul
Abstrak: Bacillus subtilis lipase A (BsL) is extensively studied in enzymatic production of biodiesel, production of detergents, surfactants, food, pharmaceutical products, cosmetics, paper industry and nutrition. One drawback of using BsL is its relatively low optimum temperature at 37 oC (310 K). The objective of this research is to design BsL mutant more thermostable than the wild-type BsL by engineering mutations in residue stabilizer BsL. Molecular dynamic simulation was conducted to get better insight on the process of thermal denaturation or unfolding in BsL. Thermal denaturation of BsL was accelerated by conducting simulation at high temperature. Molecular dynamic simulation of BsL was performed with NAMD software package at 400-500 K. Selection of mutated residues was based on electrostatic interaction, disulfida bond, hidrofobic interaction analysis of BsL. From those analyses, three mutants were designed, which are Mutant-1 (Iso155Val), Mutant-2 (Ile135Cys/Hsd156Cys), and Mutant-3 (Glu65Asp). Parameters that were used to compare the thermostability of mutant with wild type enzyme were RMSD (Root Mean Square Deviation), SASA (Solvent Accessible Surface Area), Rg (Radius of Gyration), RMSF (Root Mean Square Fluctuation) and Secondary Structure. Molecular dynamics simulations were performed on all three mutants showed that the mutant-1 (Iso155Val) by giving the temperature of 525 K for 20 ns has a better thermostability compared to the wild type BSL. It concluded that hydrophobic interaction is important in improving the thermal stability of the enzyme lipase B. subtilis. Effect of mutation of hydrophobic interaction analysis results in an increase in the thermal stability of mutant-1 (Iso151Val) by giving a temperature of 500 K for 50 ns can improve thermal stability as evidenced by a decrease in the value of the parameter RMSD, Rg, RMSF, SASA and Secondary Structure is RMSD able lowered by 7.7 Å, the value of Rg able lowered by 3.41 Å and value SASA able lowered by 1504 Å2. For the beta-sheet structure, is able to retain about 16% compared to wild-type who did not have the beta-sheet structure. For the alpha-helix structure, mutan-1 did not influence alpa-helix composition. The resulted mutant design will be used as a suggestion to engineer BsL mutant in wet experiment.
Keyword: Bacillus subtilis lipase A, thermostability, molecular dynamic, NAMD, mutation, hydrofobic, interaction

Judul: Site-Directed Mutagenesis Lid Region Lipase Geobacillus stearothermophilus T1.2RQ Based on Dynamics Simulation Molecular
Abstrak: Lipase T1.2 dari Geobacillus stearothermophillus merupakan salah satu enzim termostabil yang mampu menghidrolisis ikatan ester karboksil pada komponen minyak menghasilkan gliserol dan asam lemak bebas. Struktur lipase T1.2 yang menarik terdapat pada bagian lid region yang berfungsi untuk aktivasi antarmuka dalam berbagai media pelarut. Penelitian ini bertujuan untuk memprediksi pergerakan molekul protein mutan menggunakan analisis komputasi yang dapat meningkatkan interaksi enzim dan substrat dalam pelarut. Pemilihan residu mutasi pada struktur lid region ditentukan berdasarkan stabilitas protein menggunakan simulasi dinamika molekuler. Konstruksi mutan lipase dalam plasmid pET-28a menggunakan metode quick change PCR untuk substitusi residu asam amino. Hasil simulasi dinamika molekuler menunjukan nilai RMSD protein mutan A190S dalam pelarut air memiliki pergerakan molekul yang lebih stabil dibandingkan mutan D182I. Pergerakan nilai RMSD mutan A190S dan D182I dalam pelarut campuran yang terdiri dari air, metanol, asam palmitat dan asam oleat memperlihatkan pergerakan molekul yang rendah. Aktivitas relatif hidrolitik mutan A190S dalam substrat minyak kelapa sawit mengalami peningkatan sebesar 9%, sedangkan mutan D182I mengalami penurunan yang signifikan sebesar 33%. Pada aktivitas relatif esterifikasi pembentukan ester asam lemak mutan D182I mengalami penurunan sebesar 53%. Stabilitas protein mutan sangat berkorelasi dengan aktivitas relatif lipase dalam interaksi dengan substrat. Simulasi dinamika molekul dalam sistem pelarut polar dapat memprediksi stabilitas molekul lipase yang dapat meningkatkan aktivitas hidrolitik untuk mendegradasi lipid., T1.2 lipase from Geobacillus stearothermophilus is a thermostable enzyme capable of hydrolyzing carboxyl ester bonds of lipids to produce glycerol and free fatty acids. One important feature of the T1.2 lipase structure is the lid region, which plays role in interfacial activation in various solvents. This study aims to investigate the association between the in-silico molecular dynamics of mutant T1.2RQ lipase harboring subsequent point mutations in the lid region and their enzymatic activities. Selection of mutation residues in the lid region structure was determined based on protein structure stability using molecular dynamics simulations. Lipase mutant construction in pET-28a plasmid using quick change PCR method for amino acid residue substitution. Molecular dynamics simulation from several parameters of RMSD, RMSF and radius of gyration showed that the mutant T1.2RQ-A190S protein in SOL-A (water solvent) had more stable molecular movement than the mutant T1.2RQ-D182I. Movement of mutant proteins T1.2RQ-A190S and T1.2RQ-D182I in a SOL-B consisting of water, methanol, palmitic acid and oleic acid showed low molecular movement. The relative hydrolytic activity of mutant T1.2RQ-A190S in palm oil substrate increased 9%, while the mutant D182I decreased significantly 33%. In relative activity of esterification, formation of mutant T1.2RQ-D182I fatty acid esters decreased 53%. The stability of mutant proteins is highly correlated with the relative activity of the lipase in the interaction with the substrate. Molecular dynamics simulations in polar solvent systems can predict the stability of lipase molecules that can increase hydrolytic activity for degrading lipids.
Keyword: Lid region, Lipase T1.2RQ, Modifikasi protein, Simulasi dinamika molekuler

Judul: Closed Knight’s Tour pada Papan Catur Berbentuk Persegi Panjang dengan Ukuran Maksimal 8 × 8
Abstrak: Closed Knight’s Tour merupakan langkah kuda yang mengunjungi setiap kotak pada papan catur tepat satu kali dengan langkah kuda berawal dan berakhir pada kotak yang sama. Graf yang terbentuk dari closed knight’s tour dinotasikan sebagai graf G(m,n), dengan m adalah banyaknya baris dan n adalah banyaknya kolom. Graf tersebut memuat Hamiltonian cycle. Sebuah graf terhubung G adalah graf bipartite jika dan hanya jika graf tersebut tidak memiliki cycle dengan panjang ganjil. Papan catur yang memenuhi syarat cukup untuk memiliki closed knight’s tour adalah papan catur berukuran 5 × 6, 5 × 8, 6 × 6, 6 × 7, 6 × 8, 7 × 8, dan 8 × 8.
Keyword: bipartite, closed knight’s tour, hamiltonian cycle, knight’s tour, teori graf