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Articles by Cahyo Budiman
Total Records ( 6 ) for Cahyo Budiman
  Norsirah Abu Sari and Cahyo Budiman
  Background and Objective: A 35 kDa of FK506-binding protein of Plasmodium knowlesi (Pk-FKBP35) is a member of peptidyl prolyl cis-trans isomerase (PPIase) consisting of an N-terminal catalytic domain (FKBD) and C-terminal tetratricopeptide repeat domain (TPRD). This study aimed to investigate the thermal stability of full-length Pk-FKBP35 and its domains. Materials and Methods: Full-length Pk-FKBP35 and its isolated domain (Pk-FKBD and Pk-TPRD) were overexpressed in Escherichia coli BL21(DE3) and purified. Thermal stability of purified protein was measured based on the fluorescence signal of 8-anilino-1-naphthalenesulfonic acid (ANS) at the temperature ranging from 25-95°C. Results: The thermal denaturation curve for Pk-FKBP35 shows a cooperative transition with a Tm of 56.49±3.05°C, whereas calculated Tm for Pk-FKBD and Pk-TPRD were 60.67±2.81 and 53.64± 4.21°C, respectively. Higher stability of Pk-FKBD might be due to the high content of β-sheet secondary structure. Thermal unfolding profiles of Pk-FKB35 and Pk-FKBD in the presence of PPIase substrate were considerably different as compared to that of in the absence of the substrate, which might be due to structural stabilization by the substrate. Conclusion: The thermal stability property of Pk-FKBP35 is characterized by two events of interdomain destabilization and substrate-mediated stabilization.
  Wan Nur Shuhaida Wan Mahadi , Clemente Michael Wong Vui Ling , Kenneth Francis Rodrigues and Cahyo Budiman
  Background and Objective: Endo-1,4-β-mannanase (β-mannanase, EC is an industrially important enzyme which catalyses the hydrolysis of mannan-based polysaccharides. This enzyme is produced by psychrophilic and mesophilic groups of Arthrobacter sp., yet none of them were structurally characterized. This study aims to decipher the structural features of Arthrobacter β-mannanases that might responsible for their cold adaptation. Material and Methods: Thirty amino acid sequences encoding β-mannanases from Arthrobacter sp. were retrieved from GenBank and subjected to series of analysis of amino acid profiling and structural homology modelling using Phyre2 and SWISS-MODEL. Results: Structural alignment showed the catalytic residues (2 glutamic acids) were conserved among β-mannanase suggesting that they might shares catalytic mechanism. Psychrophilic β-mannanases showed remarkable differences from the mesophilic ones in the content of hydrophilic, particularly negatively charged, residues and proline, which were thought to be important for its cold adaptation. Three-dimensional model of all Arthrobacter β-mannanases forms a classic α/β barrel motif consisting of 8 helices and 9 β-sheets structures, except for psychrophilic ones, which having 8 helices and 8 β-sheets. Conclusion: Adaptation of Arthrobacter β-mannanases towards cold temperature involves structural adjustment particularly on structural flexibility and amino acid distribution.
  Isyana Khaerunnisa , Muhammad Pramujo , Irma Isnafia Arief , Cahyo Budiman , Asep Gunawan , Jakaria and Cece Sumantri
  Myostatin, or growth and differentiation factor-8 (GDF-8), is a member of the Transforming Growth Factor (TGF)-β superfamily. This family functions as a negative regulator of skeletal muscle. Mutations in exon 2 have been reported to convert Thymine into Guanine (T4842G) that alters the amino acid leucine into arginine, which is associated with body weight in chickens. The objectives of this study were to identify the polymorphism of T4842G mutation in the myostatin gene in Indonesian chickens and evaluate their effects on carcass characteristics. The gene polymorphism was identified with the Polymerase Chain Reaction-Restriction Fragment Length Polymorphism (PCR-RFLP) method using the BsrI restriction enzyme. The effect of genotype on carcass and meat quality was analyzed using the SAS General Linear Model (GLM) procedure. Genotyping was performed on 332 chickens from 7 Indonesian chicken populations (Kampung, Merawang, Sentul, Cobb broiler, F1 crossbreed of Kampung x layer, F1 crossbreed of Kampung x Cobb broiler and F2 crossbreed of Kampung x Cobb broiler). The product of amplification was 247 bp. The myostatin|BsrI locus was polymorphic in all populations, producing two alleles (G and T) and three genotypes (GG, GT, TT). Results from the analysis of the allele and genotype frequency showed that the T allele had a higher frequency than the G allele in all populations, except for the F1 crossbreed of the Kampung x Cobb broiler chicken population, which had equal allele frequencies. A significant effect was found between genotype and carcass characteristics in the F2 crossbreed Kampung x Cobb broiler chickens. A SNP in the coding region of myostatin in exon 2 was associated with live weight, carcass weight, breast weight, thighs weight, drum sticks weight, wings weight, breast muscle weight, thighs muscle weight, drum sticks muscle weight and free water. Here, the association of myostatin|BsrI gene polymorphism with chicken carcass characteristics in Indonesian chickens has been demonstrated, providing evidence that myostatin might be an important candidate gene for chicken carcass characteristics.
  Cahyo Budiman , Clement Angkawidjadja and Shigenori Kanaya
  Background and Objective: A 22 kDa FK506-binding protein from a psychrophilic bacterium Shewanella sp. SIB1 (SIB1 FKBP22) is a member of peptidyl prolyl cis-trans isomerase (PPIase). This protein is homodimer with a V-shaped form, consisting of N and C-domains, that are connected through a long α-helix, responsible for dimerization and PPIase activity, respectively. Understanding on structural mechanisms behind the function of SIB1 FKBP22 is limited by unsuccessful attempts on crystallization of the full length SIB1 FKBP22 homodimer due to its flexibility and low stability. Despite the isolated N-domain, with the absence of α-helix and C-domain was successfully crystallized and structurally solved, the comprehensive structural arrangement of SIB1 FKBP22 remains missing. The objective of this study is to construct a crystallizable SIB1 FKBP22 derivatives consisting of N and C-domains with its α-helix that reflect full length of SIB1 FKBP22 and a platform for comprehensive structural analysis. Materials and Methods: A monomeric mutant of SIB1 FKBP22 was constructed by combining two gene fragments encoding Met 8-Ile 205 and Met 1-Ala 60 of the first and second monomer of SIB1 FKBP22, respectively, with three glycine residues. This design yielded the mutant has tandemly repeated N-domain connected to C-domain through a long α-helix hence designated as NNC-FKBP22. Results: The NNC-FKBP22 was monomeric in solution implying that it did not form a V-shaped dimeric structure. The crystallization of NNC-FKBP22 was attempted under sitting-drop vapor diffusion. The crystals were obtained under 1.0 M sodium citrate with 10 mM CHES/sodium hydroxide at pH 9.5. The crystal was in the space group of P212121 with unit cell dimension a = 94.635, b = 92.479 and c = 337.327 Å. A complete native data was collected from a rotating anode source to a resolution of 3.5 Å at 100 K with an Rmerge value of 25.50. Conclusion: The NNC-FKBP22 was successfully crystallized implying that stabilization of SIB1 FKBP22 under protein engineering platform is promising approach to decipher its atomic structure. Protein engineering technique used in this study would also be applicable for other cold-adapted proteins with high structural flexibility and low stability.
  Jovi Silvester , Herman Umbau Anak Lindang , Lee Ping Chin , Lau Tiek Ying and Cahyo Budiman
  Background and Objective: The 35 kDa FK506-binding proteins (FKBP35) of plasmodium parasite is a member of peptidyl proly cis-trans isomerase consisting of FK506-binding domain (FKBD) and tetratricopeptide repeat domain (TPRD). A comprehensive understanding of structure and function relationship of this protein is needed as a platform for development of novel antimalarial drugs with no resistance effect. However, structural study of full-length FKBP35 is hampered by some issues on molecular size and dynamic due to its structural flexibility. Therefore, this study aimed to analyze full-length structure of FKBP35 from Plasmodium knowlesi (Pk FKBP35) and determine its dynamics using structural homology modeling and a transmission electron microscope (TEM). Methodology: Structural homology modeling was constructed using SWISS-MODEL and further validated using RAMPAGE, Global model quality estimation (GMQE), QMEAN statistical parameters and VERIFY3D. For electron microscopy analysis, purified Pk FKBP35 was placed on EM grid, negatively stained using 2% uranyl acetate and recorded under TEM. The image was then processed using ImageJ to classify the molecular shape of Pk FKBP35 based on circularity index. Flexibility analysis was conducted under PredyFlexy web server. Result: The 3D model of Pk FKBP35 was successfully built based on the template of 1p5q. The structure consists of 6 β-sheet and 10 α-helix secondary structures that dominates FKBD and TPRD, respectively, with high similarity to the domains of its homologous from P. falciparum and P. vivax. Negatively stained electron micrograph showed that Pk FKBP35 assumes in three conformations of elongated, hook and circular shapes, with preference conformation being circular shapes (72%). Meanwhile, flexibility prediction demonstrated that FKBD region is more flexible than TPRD. Conclusion: Three conformations concluded that Pk FKBP35 is a dynamic protein due to its flexibility properties. This dynamic might be important for acquiring the substrates. FKBD was found to modulate the flexibility of Pk FKBP35, probably due to the functional role of this catalytic domain and structurally dominated by β-sheet structure, which is more flexible than α-helix structure. Further, 3D model of Pk FKBP35 also suggested that the linker between the domains might involve in the structural dynamic.
  Rafida Razali , Vijay Kumar and Cahyo Budiman
  Background and Objective: The MD2 pineapple contains 14 various sizes of bromelain (MD2-bromelains) ranging from 19-200 kDa which are suspected to be structurally and enzymatically varied. This study aims to compare the enzymatic activity and structural features of small and medium-sizes of MD2-bromelains, designated as MD2-SBro (19 kDa) and MD2-MBro (38 kDa), respectively. Materials and Methods: Purified recombinant MD2-SBro and MD2-MBro obtained were used in this study. The enzymatic activity of both MD2-bromelain was determined using a plate agar system with casein as a substrate. Three-dimensional (3D) structures of both MD2-bromelains were constructed under SWISS-MODEL server-based structural homology modeling and verified stereo-chemically. Results: The MD2-SBro and MD2-MBro were shown to be enzymatically active toward casein with MD2-MBro exhibited higher enzymatic activity than MD2-SBro. The 3D structures revealed that Cys-His active site position of MD2-SBro was found to be located in the inappropriate location for catalysis. Besides, the substrate-binding pocket of MD2-SBro was found to be less hydrophobic than that of MD2-MBro. Conclusion: Unique structural features around the active site of MD2-SBro and MD2-MBro might account for the discrepancy in their enzymatic activities.
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