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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.

 

FULL TEXT

 

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.

 

FULL TEXT

 

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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