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All Journal HAYATI Journal of Biosciences VALENSI CAKRA KIMIA (Indonesian E-Journal of Applied Chemistry) JURNAL KIMIA SAINS DAN APLIKASI Current Biochemistry Journal Jurnal Spektra Omega: Jurnal Fisika dan Pendidikan Fisika Indonesian Journal of Chemistry PROSIDING SEMINAR NASIONAL FISIKA (E-JOURNAL)
Sumaryada, Tony
Departemen Fisika, FMIPA, Institut Pertanian Bogor, Bogor 16680
Agriculture, Biological Sciences & Forestry Biochemistry, Genetics & Molecular Biology Chemical Engineering, Chemistry & Bioengineering Chemistry Earth & Planetary Sciences Education Electrical & Electronics Engineering Energy Engineering Physics Other

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FENOMENA HALO BERDASARKAN MODEL RELATIVISTIC MEAN FIELD (RMF) Nugraha, A.M.; Diningrum, J.P.; Sumaryada, T.; Sulaksono, A.
Jurnal Spektra Vol 16, No 2 (2015): Spektra: Jurnal Fisika dan Aplikasinya
Publisher : Jurnal Spektra

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Abstract

AbstrakHalo merupakan salah satu fenomena unik yang terjadi di inti atom, fenomena yang digambarkan adanya tambahan “ekor” dan adanya “ruang kosong” antara core dan ekor pada distribusi neutron. Metode analisa halo yang dikembangkan oleh V. Rotival dkk [Phys. Rev. C79, 054308 (2009)] pada isotop Cr, biasanya diaplikasikan pada model Hartree-Fock-Bogoliubov (HFB). Berbeda dengan Rotrival dkk, kami menggunakan model Relativistic Mean Field (RMF) pada penelitian ini. Berbeda dengan hasil perhitungan dengan model HFB, kami mengamati perilaku yang berbeda pada level  seiring dengan kemunculan halo. Selain itu, pada model RMF prediksi keberadaan halo pada isotop Cr lebih besar dibandingkan dengan prediksi berdasarkan model HFB . Pada penelitian ini kami juga mempelajari efek suku cross coupling meson-, tensor dan suku pertukaran elektromagnetik pada model RMF terhadap kemunculan halo pada isotop Cr. AbstractHalo is one of the unique phenomena that occur in atomic nucleus. In halo nucleus, the neutron density displays an unusually “tail” and “existing empty space” between the core and the tail of the nucleus. New analysis method to investigate halo was developed by V. Rotival, et al. [Phys. Rev. C79, 054308 (2009)]. The method was used to search the halo nuclei in the chain of Cr-isotopes within Hartree-Fock-Bogoliubov (HFB) model. Unlike the Rotival, et al, we use here the Relativistic Mean Field (RMF) model as the framework. We observed that the significant changing of  level behavior is in line with appearancing of halo. Moreover, we have also found that in the case of Cr isotopes, the neutron halo number prediction based RMF model is greater than that of HFB model  In this work we also study the effects of cross coupling meson -, tensor, and electromagnetic exchange terms in RMF model on the appearancing of halo in Cr-isotopes.     Keywords: Halo phenomena, RMF model, Cross coupling meson -, Tensor, Electromagnetic exchange.
Simulating the Aerodynamics Profiles of NACA 4312 Airfoil in Various Incoming Airspeed and Gurney Flap Angle Sumaryada, Tony; Jaya, Achmad Muharam; Kartono, Agus
Omega: Jurnal Fisika dan Pendidikan Fisika Vol 4 No 1 (2018)
Publisher : Program Studi Pendidikan Fisika UHAMKA

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.31758/OmegaJPhysPhysEduc.v4i1.1

Abstract

Simulations of the aerodynamics performance of NACA 4312 airfoil at various gurney flap angles and incoming airspeed (wind velocities) have been conducted. The gurney flaps size was set at 5.0% length of the chord line. Two airfoil models with gurney flap at 45° and 90° were simulated and compared with the results of plain airfoil (without gurney flap) model with the incoming airspeed of 10.0 m/s, 70.0 m/s and 200.0 m/s. The results have shown that increasing the value of gurney flap angle to 45° and 90° will increase the lifting force of the airfoil and decrease the drag force.
In-Silico Design of Novel Glucagon-Like Peptide 1 Mutants as Candidate for New Peptide Agonist Drugs Tony Sumaryada; Ajeng Widya Roslia; Alfi Afifah; Setyanto Tri Wahyudi; Agus Kartono
HAYATI Journal of Biosciences Vol. 28 No. 1 (2021): January 2021
Publisher : Bogor Agricultural University, Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.4308/hjb.28.1.92

Abstract

The binding of glucagon-like peptide 1 (GLP-1) incretin hormone and its receptor GLP-1R plays an important role in the human body. The GLP-1 acts as the insulin secretion stimulator through a GLP-1R agonist activation to avoid the type 2 diabetes mellitus problem. A recent development in computational sciences has enabled us to design a new GLP-1 mutant which has a better binding stability to GLP-1R. In this paper, we have conducted an in-depth analysis of protein-protein docking of GLP-1 and GLP-1R receptor to determine the responsible factors affecting the binding stability. The protein-protein binding stability was analyzed by performing the point mutations on the GLP-1 structure and running the molecular dynamics simulation of the docked structures. Five mutants, Lys20Arg, Lys20His, Lys20Ser, Lys20Gly, and Lys20Ala, has been created computationally and docked with GLP-1R and tested via a molecular dynamics simulation and the free energy perturbation calculation to search for the best-binding mutant. Our results have shown that the Lys20His mutant design has the best potential to be developed as a new peptide agonist drug based on its binding affinity and structural integrity as compared to other mutants and the peptide agonist drugs available in the market exenatide, and liraglutide.
In Silico Analysis of Glucose Oxidase H516r and H516d Mutations for an Enzymatic Fuel Cell Puspa Julistia Puspita; Laksmi Ambarsari; Adrian Adiva; Tony Ibnu Sumaryada
Jurnal Kimia Valensi Jurnal Kimia VALENSI Volume 7, No. 2, November 2021
Publisher : Syarif Hidayatullah State Islamic University

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.15408/jkv.v7i2.20733

Abstract

Glucose oxidase (GOx) is an oxido-reductase enzyme that catalyzes glucose into hydrogen peroxide and glucono delta-lactone (GDL). GOx has the potential to be used in the medical field. Numerous research concerning the usage of GOx to create enzymatic biofuel cells have been done, nevertheless the results obtained have not been optimal. This research aims to increase the Km values of GOx in order to increase its potential as a material for an enzymatic fuel cell. The amino acid histidine in position 516 is a residue in the active site that plays an important part in the process of glucose oxidation. In this research we mutated H516 by in silico twice resulting in the mutants R516 and D516. The mutations resulted in a change of the docking area for both mutants and in the docking affinity for H516D resulting in higher Km values. This shows that the H516 residue plays an important part in the functions of glucose oxidase and mutation into aspartate could improve glucose oxidase based enzymatic fuel cells.
Molecular Interaction Analysis of COX-2 against Curcuminoid and Xanthorizol Ligand as Anti Breast Cancer using Molecular Docking Ridho Pratama; Laksmi Ambarsari; Tony Ibnu Sumaryada
Current Biochemistry Vol. 2 No. 3 (2015)
Publisher : IPB University

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Abstract

Breast cancer is one of the most common cancer in the world that occurs in women. Thedevelopment process of cancer is regulated by a variety of pathways that involve various enzymes. COX-2 is an enzyme involved in the inflammatory process in further stages that will play importantroles in breast cancer cells progression. The uses of natural compound from plants give new hope forbreast cancer treatment with minimal side effects. Temulawak is a potential breast cancer drugs because it contains curcuminoid and xanthorizol. Curcumin and xanthorizol has been reported to have chemopreventive effect on colon cancer development. The drug that has same functions of these compounds needed to be examined with various approaches. One of the approach used in this research is molecular docking. Based on ligand analysis with Lipinski and toxicity test using ADMET, curcuminoid and xanthorizol met criteria as medicinal compounds. Curcumin had the highest binding affinity(?G) with the value -9.3 kcal/mol but still under commercial drug celecoxib binding affinity (?G) = -12,5. There were three hydrogen bonds in amino acid Arg106 and Tyr341 His75 which were amino acids in the active side of COX-2. There were 15 amino acids that have similar ties with commercial drug celecoxib. Based on the binding affinity and binding similiarity, curcuminoid and xanthorizol were predicted as compounds that have potential as competitive inhibitor of COX-2 enzyme.
Simulasi Docking Senyawa Kurkumin dan Analognya Sebagai Inhibitor Reseptor Androgen pada Kanker Prostat Arwansyah Arwansyah; Laksmi Ambarsari; Tony I Sumaryada
Current Biochemistry Vol. 1 No. 1 (2014)
Publisher : IPB University

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Abstract

Curcumin, the major compound of Curcuma longa L, has been proven to have the toxicity effect on prostate cancer cell. This research was aimed to study the affinity and interaction of curcumin and its analogs as compettitive inhibitor to androgen hormon before working in vitro/in vivo research. Curcumin and its analogs were transformed into 3D structure, then docked to androgen receptor (3B67). The data of Gibbs energy (?G) value showed stability interaction between ligand and androgen receptor residues. The docking results showed that curcumin and its analogs have potential as inhibitor on androgen receptor. Based on results ?G score, analog 4 (1,7-bis-(3,4-dihydroxy-phenyl)-hepta-1,6-diene-3,5-dione) has highest potential as the inhibitor for androgen receptor.
STUDI IN SILICO CONVERSE REGION ETOPOSITE BINDING DOMAIN Pada ISOZIM HUMAN DNA TOPOISOMERASE II Tirta Setiawan; Laksmi Ambarsari; Tony Ibnu Sumaryada
CAKRA KIMIA (Indonesian E-Journal of Applied Chemistry) Vol 4 No 1 (2016)
Publisher : Magister Program of Applied Chemistry, Udayana University, Bali-INDONESIA

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Abstract

ABSTRAK: DNA topoisomerase II (Top2) adalah enzim penting yang menangani permasalahan topologi pada DNA. Terdapat dua jenis Top2 pada manusia yaitu Top2A dan Top2B. Top2A diekspresikan pada sel yang aktif membelah seperti sel kanker sedangkan Top2B diekspresikan saat sel dalam fase istirahat. Peran penting inilah yang membuat DNA Top2A menjadi target  obat melawan kanker salah satunya obat etoposite. Sisi aktif pengikatan etoposite terhadap Top2B sudah dilakukan namun pada Top2A belum dilakukan. Studi pencarian area yang rapat dengan pensejajaran banyak sekuen pada Top2A dengan Top2B sebagai acuan bertujuan untuk pencarian sisi aktif pengikatan etoposite pada Top2A. Area yang rapat dengan kesamaan residu asam amino yang tinggi dapat digunakan untuk memprediksikan fungsi penting asam amino dalam enzim tersebut. Top2A dan Top2B memiliki kesamaan asam amino sebesar 80% dengan kesamaan struktur 71.81%. Asam amino aktif pengikatan etoposite pada Top2B Gly478, Asp479, Arg503, Met782 dan Gln778, dinyatakan mirip dan rapat terhadap residu Gly462, Asp463, Arg487, Met763 pada Top2A kecuali residu Gln778 dari Top2B namun penggantian ini tidak merubah struktur dari enzim tersebut karena sama-sama membentuk struktur alfa-heliks dan terletak pada posisi yang sama sehingga diprediksikan sisi aktif pengikatan etoposite pada enzim Top2B yaitu Gly478, Asp479, Arg503, Met782 dan Gln778memiliki fungsi yang sama dengan residu Gly462, Asp463, Arg487, Met763 dan Met767 dari Top2A. Hal ini menyebabkan etoposite juga dapat menghambat kerja enzim Top2A pada residu yang sama.   ABSTRACT: DNA topoisomerase II (Top2) is essential enzyme that solves the topological problems of DNA. Top2A and Top2B are two kind of Top2 in human. Top2A is expressed at differentiation active cells as cancer cells whereas Top2B is expressed at non differentiation cells or quiescent cells. Their critical role makes Top2B an attractive drug target against cancer as etoposite known as Top2 inhibitor. Active site for etoposite binding domain to Top2B has been done but in Top2A has not been done yet. Conserve region study by multiple sequence alignment between Top2A and Top2B as Top2B to be a template was aimed to search an active site for etoposite binding domain in Top2A. A conserve amino acid area with highest similarity was used to predict essential amino acid activity in the enzyme. Homology study shows that Top2A and Top2B have the same similarity of amino acids of 80% with  structure similarity of 71.81%. Active amino acids on Top2B for etoposite binding domain such as Gly478, Asp479, Arg503, Met782 dan Gln778 were found to be highly conserve with amino acid Gly462, Asp463, Arg487, Met763 on Top2A except Gln778 from Top2B but this does not change of structure of the enzyme because they have the same alfa-helix formations and positions so that it could be predicted that amino acids Gly478, Asp479, Arg503, Met782 and Gln778 on Top2B have similar activity and function with Gly462, Asp463, Arg487, Met763 and Met767 on Top2A.  This etoposite could inhibit the activity of the Top2A enzyme at same site.
The Role of E27-K31 and E56-K10 Salt-Bridge Pairs in the Unfolding Mechanism of the B1 Domain of Protein G Tony Ibnu Sumaryada; Kania Nur Sawitri; Setyanto Tri Wahyudi
Indonesian Journal of Chemistry Vol 18, No 1 (2018)
Publisher : Universitas Gadjah Mada

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (577.196 KB) | DOI: 10.22146/ijc.23934

Abstract

Molecular dynamics simulations of the B1 fragment of protein G (56 residues) have been performed at 325, 350, 375, 400, 450 and 500 K for 10 ns. An analysis of its structural and energetic parameters has indicated that the unfolding process of the GB1 protein begins at 900 ps of a 500-K simulation. The unfolding process is initiated when hydrogen bonds in the hydrophobic core region are broken; it continues with the α-helix transformation into coils and turns and ends with the destruction of the β-hairpins. These unfolding events are consistent with the hybrid model of the protein folding/unfolding mechanism, which is a compromise between the hydrophobic core collapse model and the zipper model. Salt-bridge pairs were found to play an important role in the unfolding process by maintaining the integrity of the tertiary structure of the protein. The breaking (or disappearance) of the salt-bridge pairs E27–K31 (in the α-helix) and E56–K10 (connecting β4 and β1) has resulted in the destruction of secondary structures and indicates the beginning of the unfolding process. Our results also suggest that the unfolding process in this simulation was not a complete denaturation of the protein because some β-hairpins remained
Desain dan Performansi Turbin Ventilator Angin Yang Dibuat dari Generator Sepedamotor M.N. Indro; T. Sumaryada; V.N.H. Lyjamil
PROSIDING SEMINAR NASIONAL FISIKA (E-JOURNAL) Vol 4 (2015): PROSIDING SEMINAR NASIONAL FISIKA (E-JOURNAL) SNF2015
Publisher : Program Studi Pendidikan Fisika dan Program Studi Fisika Universitas Negeri Jakarta, LPPM Universitas Negeri Jakarta, HFI Jakarta, HFI

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Abstract

In this paper we present our research on the design and performance of ventilator wind turbine. The generator for the wind turbine was taken from a used motorcycle’s generator. The weight of this generator has to be reduced almost a half from its previous weight (from 0.80 kg to 0.40 kg), otherwise the wind turbine will not rotate at all. The generator consist of 8 coils arrange in north-south pole adjacently. By varying the number of turns in each coils we could check the performance of the turbine in medium and fast wind speed. our results show that the output power of the ventilator wind turbine depend linearly on the number of turns and the wind speed. For medium wind speed (4 m/s), the highest efficiency is found to be 2.4 % with the output current and voltage are 24.33 mA and 6.00 Volt consecutively. For high wind speed (5 m/s), the highest efficiency is found to be 2.9 % with the output current and voltage 40.43 mA and 8.50 Volt. Some suggestions to increase the performance of the ventilator wind turbine were also given in this paper. Key words : motor cycle’s generator, output current-voltage, wind turbin ventilatur.
Molecular Docking Study of IPBCC.08.610 Glucose Oxidase Mutant for Increasing Gluconic Acid Production Shobiroh Nuur' Alimah; Tony Ibnu Sumaryada; Waras Nurcholis; Laksmi Ambarsari
Jurnal Kimia Sains dan Aplikasi Vol 25, No 5 (2022): Volume 25 Issue 5 Year 2022
Publisher : Chemistry Department, Faculty of Sciences and Mathematics, Diponegoro University

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (1286.493 KB) | DOI: 10.14710/jksa.25.5.169-178

Abstract

Glucose oxidase (GOD) is an oxidoreductase enzyme that catalyzes the oxidation of glucose to gluconolactone and hydrogen peroxide. Then, gluconolactone will be hydrolyzed to gluconic acid. The wide application of gluconic acid in various industries has increased production demand. However, glucose concentrations higher than 40% (w/w) inhibited the conversion of glucose to gluconic acid due to a decrease in the oxygen solubility concentration at pH 6, 30℃, and 1 bar pressure. Therefore, decreasing the value of Km is predicted to reduce saturation and enhance gluconic acid production. This study aimed to analyze the interaction between the IPBCC.08.610 GOD mutant with β-D-Glucose in improving gluconic acid production by decreasing the Km value. Mutations were performed in silico using Chimera and then docked using AutoDock Vina. The mutations resulted in distinct ligand poses in the binding pocket, different -OH conformations of the ligands, and changes in the T554M/D578P mutant’s hydrophobicity index (554 mutated from threonine to methionine, and 578 mutated from aspartate to proline), and decreased ΔG and Km values in the H559D mutant (559 mutated from histidine to aspartate), D578P and T554M/D578P. This decrease might strengthen the ligand-receptor interaction, increasing gluconic acid production. The H559D was the best mutant to increase production based on the ΔG, Km value, and stability due to the addition of hydrogen bonds.
Co-Authors A. Sulaksono, A. A.M. Nugraha, A.M. Adrian Adiva Agus Kartono Ajeng Widya Roslia Alfi Afifah Arwansyah Arwansyah Arwansyah Arwansyah, Arwansyah J.P. Diningrum, J.P. Jaya, Achmad Muharam Kania Nur Sawitri LAKSMI AMBARSARI M.N. Indro Puspa Julistia Puspita Ridho Pratama Setyanto Tri Wahyudi Shobiroh Nuur' Alimah Tirta Setiawan V.N.H. Lyjamil Waras Nurcholis