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Annoucement on the First Scientific Meeting of Indonesian Protein Society

February 13, 2012

Indonesian Protein Society will hold its First Scientific Meeting at Jember city, East Java on July 6th to 8th, 2012. The first and second day will consist of  presentations from invited speakers and participants, while the third day will be social tour which include watching the largest fashion carnaval in Indonesia, Jember Fashion Carnaval. To register please send email to panitiaips@unej.ac.id and panitiaips@yahoo.com.

The first official circular (in Bahasa Indonesia) is as follow (released on February 14th, 2012).

Or download in PDF.



A simple way to visualize fibrinolysis in the classroom

January 15, 2012

A simple way to visualize fibrinolysis in the classroom

 

Zeily Nurachman*, Jatnika Hermawan, Yanti Rachmayanti, Lubna Baradja

 

Biochemistry and Molecular Biology Education Volume 31, Issue 1, pages 16–19, January 2003
Keywords:
Fibrinolysis;Lumbricus rubellus;lumbrokinase;protease;stroke
Abstract
Laboratory demonstration, as well as biochemistry lecture, has been used to complement explanation of biochemical processes. The laboratory demonstration is very useful in teaching biochemistry to students who lack background in biology. The experimental model of fibrinolysis described here presents a complex biological reaction in simplified manner, emphasizing specific terms related to enzymes, and triggers student interest in biochemistry.

 

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Identification a Novel Raw-Starch-Degrading-α-Amylase from a Tropical Marine Bacterium

January 15, 2012

Identification a Novel Raw-Starch-Degrading-α-Amylase from a Tropical Marine Bacterium

 

Zeily Nurachman , Alfredo Kono , Ocky K. Radjasa and Dessy Natalia

 

American Journal of Biochemistry and Biotechnology DOI: 10.3844/ajbbsp.2010.300.306 Volume 6, Issue 4 Pages 300-306
Abstract
Problem statement: Bacteria from the surface of the tropical marine hard coral Acropora sp. were screened for producing raw-starch-degrading-á-amylase. Approach: Based on its 16s rDNA sequence, a bacterium that produced the highest amylolitic activity was identified as Bacillus amyloliquifaciens ABBD. The bacterial isolate secreted a á-amylase extracellularly and then the enzyme was partially purified by ammonium sulfate precipitation followed by anion exchange chromatography. Results: Electrophoresis results both SDS-PAGE and native PAGE suggested that the enzyme was a heterodimeric protein (97 kDa) consisting of 45 and 55 kDa subunits. The á-amylase had an optimum pH of 7.0 and temperature of 60°C. More than 80% activity of the enzyme was retained under high salt conditions (up to 20% NaCl). The enzyme remained stable at 50°C for 1 h. Starch hydrolysis by the enzyme at 70°C yielded oligosaccharides (G2-G4) and at room temperature yielded glucose/maltose (G1 and G2). Conclusion: The B. amyloliquifaciens ABBD á-amylase was capable of degrading various raw starch granules from corn, rice, cassava and sago at room temperature.

 

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Cloning of the Endoglucanase Gene from a Bacillus amyloliquefaciens PSM 3.1 in Escherichia coli Revealed Catalytic Triad Residues Thr-His-Glu

January 15, 2012

Cloning of the Endoglucanase Gene from a Bacillus amyloliquefaciens PSM 3.1 in Escherichia coli Revealed Catalytic Triad Residues Thr-His-Glu

 

Zeily Nurachman , Sari DewiKurniasih , Ferra Puspitawati , Sarwono Hadi , Ocky KarnaRadjasa and Dessy Natalia

 

American Journal of Biochemistry and Biotechnology DOI: 10.3844/ajbbsp.2010.268.274 Volume 6, Issue 4 Pages 268-274

 

Abstract

Problem statement: An Indonesian marine bacterial isolate, Bacillus amyloliquefaciens PSM 3.1 was isolated for hydrolyzing cellulose. A 1500-bp nucleotide fragment was amplified from the chromosomal DNA by the use of primers directed against the conserved sequence of Bacilli endoglucanase genes obtained from GenBank. Approach: The fragment was cloned and expressed in Escherichia coli. Results: The endoglucanase gene (eglII gene) had an open reading frame of 1500 nucleotides encoding a protein of 499 amino acids. The EglII protein belonged to Glycosyl Hydrolase family 5 (GH5) with a Cellulose Binding Module 3 (CBM 3). The structure model of the EglII protein revealed that the catalytic residues seemed to be Glu169 (as proton donor) and Glu257 (as nucleophile) and the catalytic triad residues were Thr256, His229 and Glu169. The EglII endoglucanase exhibited an optimum pH of 6.0 and temperature of 50°C and the enzyme tolerated to high salt concentration. Conclusion/Recommendations: This EglII endoglucanase is a promising candidate for many applications in biomass degradation.

 

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Biochemical characterization of a raw starch degrading α-amylase from the Indonesian marine bacterium Bacillus sp. ALSHL3

January 15, 2012

Biochemical characterization of a raw starch degrading α-amylase from the Indonesian marine bacterium Bacillus sp. ALSHL3

 

Keni Vidilaseris, Karina Hidayat, Debbie S. Retnoningrum, Zeily Nurachman, Achmad Saefuddin Noer and Dessy Natalia

 

BIOLOGIA Volume 64, Number 6, 1047-1052, DOI: 10.2478/s11756-009-0190-8

 

Abstract
An Indonesian marine bacterial isolate, which belongs to genus of Bacillus sp. based on 16S rDNA analysis and was identified as Bacillus filicolonicus according to its morphology and physiology, produced a raw starch degrading α-amylase. The partially purified α-amylase using a maize starch affinity method exhibited an optimum pH and temperature of 6.0 and 60°C, respectively. The enzyme retained 72% of its activity in the presence of 1.5 M NaCl. Scanning electron micrographs showed that the α-amylase was capable of degrading starch granules of rice and maize. This α-amylase from Bacillus sp. ALSHL3 was classified as a saccharifying enzyme since its major final degradation product was glucose, maltose, and maltotriose.

 

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Biochemical characterization of a glucoamylase from Saccharomycopsis fibuligera R64

January 15, 2012

Biochemical characterization of a glucoamylase from Saccharomycopsis fibuligera R64

 

Dessy Natalia, Keni Vidilaseris, Pasjan Satrimafitrah, Wangsa T. Ismaya, Purkan, Hjalmar Permentier, Guntur Fibriansah, Fernita Puspasari, Zeily Nurachman and Bauke W. Dijkstra, Soetijoso Soemitro.

 

Biologia Volume 66, Number 1, 27-32, DOI: 10.2478/s11756-010-0151-2

 

Abstract
Glucoamylase from the yeast Saccharomycopsis fibuligera R64 (GLL1) has successfully been purified and characterized. The molecular mass of the enzyme was 56,583 Da as determined by mass spectrometry. The purified enzyme demonstrated optimum activity in the pH range of 5.6–6.4 and at 50°C. The activity of the enzyme was inhibited by acarbose with the IC50 value of 5 μM. GLL1 shares high amino acid sequence identity with GLU1 and GLA1, which are Saccharomycopsis fibuligera glucoamylases from the strains HUT7212 and KZ, respectively. The properties of GLL1, however, resemble that of GLU1. The elucidation of the primary structure of GLL1 contributes to the explanation of this finding.

 

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Characteristics of raw starch degrading α-amylase from Bacillus aquimaris MKSC 6.2 associated with soft coral Sinularia sp.

January 15, 2012

Characteristics of raw starch degrading α-amylase from Bacillus aquimaris MKSC 6.2 associated with soft coral Sinularia sp.

 

Fernita Puspasari1, Zeily Nurachman1, Achmad Saefuddin Noer1,†, Ocky Karna Radjasa2, Marc J. E. C. van der Maarel3, Dessy Natalia1,*

 

Starch – Stärke, Volume 63, Issue 8, pages 461–467, August 2011

 

Keywords:
α-Amylase;B. aquimaris;Raw starch;Sinularia sp.

 

Abstract
Partially purified α-amylase from Bacillus aquimaris MKSC 6.2, a bacterium isolated from a soft coral Sinularia sp., Merak Kecil Island, West Java, Indonesia, showed an ability to degrade raw corn, rice, sago, cassava, and potato starches with adsorption percentage in the range of 65–93%. Corn has the highest degree of hydrolysis followed by cassaca, sago potato and rice, consecutively. The end products of starch hydrolysis were a mixture of maltose, maltotriose, maltotetraose, maltopentaose, maltohexaose, and small amount of glucose.

 

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Construction of synthetic open reading frame encoding human interferon alpha 2b for high expression in Escherichia coli and characterization of its gene product.

January 7, 2012

J Biotechnol. 2010 Jan 15;145(2):193-8. Epub 2009 Dec 1.

Construction of synthetic open reading frame encoding human interferon alpha 2b for high expression in Escherichia coli and characterization of its gene product.

Retnoningrum DS, Ningrum RA, Kurniawan YN, Indrayati A, Rachmawati H.

Source

School of Pharmacy, Institut Teknologi Bandung, Ganesha 10, Bandung 40132, Indonesia. retnoningrum@indo.net.id

Abstract

The aim of this research was to obtain recombinant human interferon alpha 2b (rhIFNalpha2b) from a synthetic open reading frame (ORF) overexpressed in Escherichia coli. For gene assembly, oligonucleotides were designed by Thermodynamically Balanced Inside Out (TBIO) method using the published synthetic codon optimized hIFNalpha2b ORF for high expression in E. coli. The synthetic ORF was assembled by a two-step Polymerase Chain Reaction (PCR) and cloned into a pGEM-T vector. The two-step PCR resulted in a DNA band of 522 base pairs (bp) corresponding to the size of hIFNalpha2b ORF. Fifteen recombinant pGEM-Ts were obtained and the sequencing results showed that the ORFs contained one to ten mutations with an error rate of 8.3 per kilo base. An ORF carrying one mutation was cloned into a pET32b vector and site-directed mutagenesis was performed to correct the mutation. The hIFNalpha2b ORF was overexpressed as a thioredoxin-his-tag fusion protein in E. coli BL21. The rhIFNalpha2b fusion protein was isolated from inclusion bodies (IB), renatured, and purified using Nickel columns, and all steps were monitored by Sodium Dodecyl Sulphate Polyacrylamide Gel Electrophoresis (SDS-PAGE). A rhIFNalpha2b fusion protein of 37kDa in size was produced in high expression levels relative to total protein, renatured and purified from IB with a yield of 3.46mg/l without any further optimization. The purified rhIFNalpha2b was confirmed by peptide analysis with nano-LC-MS/MS2 mass spectrometry. Our current research demonstrates for the first time that by using the TBIO method a synthetic ORF encoding hIFNalpha2b gene can be expressed at high levels in E. coli.

 

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Identification of sequence mutations affecting hemagglutinin specificity to sialic acid receptor in influenza A virus subtypes.

January 7, 2012

Bioinformation. 2010 Nov 27;5(6):244-9.

Identification of sequence mutations affecting hemagglutinin specificity to sialic acid receptor in influenza A virus subtypes.

Tambunan US, Ramdhan.

Source

Department of Chemistry, Faculty of Mathematics and Natural Science, University of Indonesia, Depok Campus, Depok 16424, Indonesia.

Abstract

The attachment of the hemagglutinin protein of the H1N1 subtype of the pandemic influenza A virus to the sialic acid receptor Sia(α2-6)Gal has contributed to the ability of the virus to replicate in the human body and transmit among humans. In view of the pandemic caused by the replication and transmission of the H1N1 virus, more studies on the specificity of hemagglutinin towards sialic acid and how it affects the replication and transmission ability of this virus among humans are needed. In this study, we have applied sequence, structural and functional analyses to the hemagglutinin protein of the pandemic H1N1 virus, with the aim of identifying amino acid mutation patterns that affect its specificity to sialic acid. We have also employed a molecular docking method to evaluate the complex formed between hemagglutinin protein and the sialic acid receptor. Based on our results, we suggest two possible mutation patterns, namely (1) positions 190 and 225 from glutamic acid and glycine to aspartic acid (E190D in A/Brevig Mission/1/18 (H1N1), A/New York/1/18(H1N1) and A/South Carolina/1/1918(H1N1) and G225D in A/South Carolina/1/1918(H1N1), A/South Carolina/1/1918(H1N1), and A/Puerto Rico/8/34(H1N1)), and (2) positions 226 and 228 from glutamine and glycine to leucine and serine, respectively (Q226L and G228S in A/Guiyang/1/1957(H2N2), A/Kayano/57(H2N2), A/Aichi/2/1968(H3N2), A/Hong Kong/1/1968(H3N2) and A/Memphis/1/68(H3N2)) that can potentially contribute to the specificity of hemagglutinin to Sia(α2-6)Gal, thereby enabling the replication and transmission of virus within and among humans.

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Prediction of conformational changes by single mutation in the hepatitis B virus surface antigen (HBsAg) identified in HBsAg-negative blood donors.

January 7, 2012

Virol J. 2010 Nov 18;7:326.

Prediction of conformational changes by single mutation in the hepatitis B virus surface antigen (HBsAg) identified in HBsAg-negative blood donors.

Ie SI, Thedja MD, Roni M, Muljono DH.

Source

Eijkman Institute for Molecular Biology, Jl. Diponegoro 69, Jakarta, Indonesia.

Abstract

BACKGROUND:

Selection of hepatitis B virus (HBV) by host immunity has been suggested to give rise to variants with amino acid substitutions at or around the ‘a’ determinant of the surface antigen (HBsAg), the main target of antibody neutralization and diagnostic assays. However, there have never been successful attempts to provide evidence for this hypothesis, partly because the 3 D structure of HBsAg molecules has not been determined. Tertiary structure prediction of HBsAg solely from its primary amino acid sequence may reveal the molecular energetic of the mutated proteins. We carried out this preliminary study to analyze the predicted HBsAg conformation changes of HBV variants isolated from Indonesian blood donors undetectable by HBsAg assays and its significance, compared to other previously-reported variants that were associated with diagnostic failure.

RESULTS:

Three HBV variants (T123A, M133L and T143M) and a wild type sequence were analyzed together with frequently emerged variants T123N, M133I, M133T, M133V, and T143L. Based on the Jameson-Wolf algorithm for calculating antigenic index, the first two amino acid substitutions resulted in slight changes in the antigenicity of the ‘a’ determinant, while all four of the comparative variants showed relatively more significant changes. In the pattern T143M, changes in antigenic index were more significant, both in its coverage and magnitude, even when compared to variant T143L. These data were also partially supported by the tertiary structure prediction, in which the pattern T143M showed larger shift in the HBsAg second loop structure compared to the others.

CONCLUSIONS:

Single amino acid substitutions within or near the ‘a’ determinant of HBsAg may alter antigenicity properties of variant HBsAg, which can be shown by both its antigenic index and predicted 3 D conformation. Findings in this study emphasize the significance of variant T143M, the prevalent isolate with highest degree of antigenicity changes found in Indonesian blood donors. This highlights the importance of evaluating the effects of protein structure alterations on the sensitivity of screening methods being used in detection of ongoing HBV infection, as well as the use of vaccines and immunoglobulin therapy in contributing to the selection of HBV variants.

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