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"ABSTRAKThe interaction of cationic surfactant (CTAB, Cationic surfactant hexadecyltrimethyl ammonium bromide ((C₁₆H₃₃)N(CH₃)₃BR and TTAB, Tetradecyltrimethyl ammonium bromide ( )), a prevalent chemical in the industrialand natural processes, with water ( ) has been studied using GROMACSprogram and VMD program. In the following project, to simulate the CTAB andTTAB at air-water interface, GROMACS (Groningen Machine for ChemicalSimulations) software is used. GROMACS is a molecular dynamics packagedesigned for primary use of simulation of biochemical molecules like proteins,lipids, and nucleic acids that have a many complicated bonded interactions(GROMACS, 2010). Furthermore, to model and display the simulation, VMD(Visual Molecular Dynamics) program is used. VMD is intended for modeling,visualization and analysis of biological systems such as proteins, nucleic acids,lipid bilayer assemblies, etc. In this research project 13 simulations, 6 of these aresuccessive simulations and the other 7 simulations have been included in theappendix. The simulations have been simulated to prove the following 3hypotheses which are ssurfactants has an amphiphilic nature, surfactants adsorbon the interface between oil and water, lowering the interfacial tension andpromoting mixing and surface potential measurement at the air-water interfaceincreases surfactant-dependent manner in the air-water expanded transition region.Therefore with the addition of surfactant to the air-water interface, there will be asudden increase of surface potential. The first seven simulations that have beenincluded in the appendix were simulated to find the right charge distribution. Allthe observed results shown by these 13 simulations are not yet predictable orreliable; this is due to not the right amount of simulation time or the chargedistribution of the cationic surfactant. The three kinds of observations (the densityprofile of the cationic surfactant, the surface tension of the cationic surfactant withwater, and the surface potential of cationic surfactant with water) are veryuncertain and therefore many more simulations are required to be completed inthe future."

"Lipase B Candida antarctica (CALB) secara ekstensif dipelajari dalam produksi biodiesel, produk farmasi, deterjen, dan senyawa lainnya secara enzimatis. Salah satu kekurangan penggunaan CALB adalah suhu optimumnya yang relatif rendah pada 40oC (313 K). Tujuan penelitian ini adalah untuk merancang mutan CALB yang lebih termostabil dibanding CALB wild type dengan rekayasa penambahan ikatan disulfida. Simulasi dinamika molekul dilakukan untuk mengamati proses unfolding atau denaturasi termal CALB. Denaturasi termal CALB dipercepat dengan melakukan simulasi pada suhu tinggi. Simulasi dinamika molekul CALB dilakukan dengan perangkat lunak GROMACS pada suhu 300-700 K. Prediksi pasangan residu yang dapat dimutasi menjadi sistein dilakukan dengan perangkat lunak ?Disulfide by DesignTM?. Pemilihan residu yang dimutasi, didasarkan pada hasil analisis fleksibilitas CALB. Berdasarkan hasil analisis tersebut dirancang tiga mutan enzim CALB yaitu Mutan-1 (Leu73Cys/Ala151Cys), Mutan-2 (Trp155Cys/Glu294Cys), dan Mutan- 3 (Thr43Cys/Ser67Cys). Parameter yang digunakan untuk membandingkan termostabilitas enzim mutan dengan wild type adalah RMSD, SASA (solvent accessible surface area), jari-jari girasi (Rg), dan struktur sekunder. Simulasi dinamika molekul yang dilakukan pada ketiga mutan tersebut menunjukkan bahwa Mutan-1 memiliki termostabilitas yang lebih baik dibanding CALB wild type. Diharapkan hasil penelitian ini dapat memberikan saran rancangan mutasi yang dapat diimplementasikan ke dalam laboratorium basah (wet experiment).

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Candida antarctica lipase B (CALB) is extensively studied in enzymatic production of biodiesel, pharmaceutical products, detergents, and other chemicals. One drawback of using CALB is its relatively low optimum temperature at 313 K (40oC). The objective of this research is to design CALB mutant with improved thermostability by introducing extra disulfide bond. Molecular dynamic simulation was conducted to get better insight on the process of thermal denaturation or unfolding in CALB. Thermal denaturation of CALB was accelerated by conducting simulation at high temperature. Molecular dynamic simulation of CALB was performed with GROMACS software package at 300-700 K. Prediction of possible mutation was conducted using ?Disulfide by DesignTM? software. Selection of mutated residues was based on flexibility analysis of CALB.

From those analyses, three mutants were designed, which are Mutant-1 (73LeuCys/151AlaCys), Mutant-2 (155TrpCys/294GluCys), and Mutant-3 (43ThrCys/67SerCys). Parameters that were used to compare the thermostability of mutant with wild type enzyme were RMSD, SASA (solvent accessible surface area), radius of gyration (Rg), and secondary structure. Molecular dynamic simulation conducted on those three mutants showed that Mutant-1 have better thermostability compared to wild type CALB. The resulted mutant design will be used as a suggestion to engineer CALB mutant in wet experiment."