A Structural Study on the Specificity of F1 Protease

Specificity studies of a thermostable alkaline serine protease F1 with its substrates were carried out through computational docking method. Structures of a series of synthetic peptide substrates were docked to the active site of the homology modelled F1 protease using AutoDock 3.0.5. The resulting clusters of the substrates that were docked were analysed by inspecting the energetic results and the orientation of each cluster to determine the arrangement of productive binding. The amino acids of the binding site that participated in the hydrophobic and hydrogen-bond interactions were also determined. Docking results showed that all substrates tested bound near the catalytic residues with SucAAPFpNA, the biggest substrate, showing the most negative docked energy value @docked = -18.75 kcal/mol). Smaller substrates such as GpNA and AApNA showed higher docked energy (Edocked = -7.77 kcal/mol and -8.77 kcal/mol, respectively). The best docked structure of each substrate was determined from the clusters. It was found that most of the lowest Edocked conformations display the best docked orientations with respect to the least distance calculated between the carbonyl carbon of the substrate PI residue and y-oxygen of the Ser226 catalytic triad. From the results, it also demonstrated that S1, S2 and S4 subsites of the enzyme play a critical role in determining the substrate specificity of F1 protease from the point of view that bigger-sized substrates such as SucAAPFpNA and SucAAPLpNA showed more favourable Edocked. This work also support the hypothesis that the catalytic serine and histidine residues were essential in catalysis as well as in stabilizing the enzymesubstrate complex for binding. Validation of computational study was carried out through biochemical assay. It was found that SucAAPFpNA was the most preferred substrate for the enzyme with specific activity of 3.079 U/mg followed by SucAAPLpNA at 1.016 U/mg. SucAAPFpNA was also observed to show the highest binding affinity towards the protease (Km = 1.26mM) and the highest catalytic ratio (1.226 min-l.rnM-1) compared to the other substrates tested. Similar to computational observations, smaller peptides showed lower specific activity and binding affinity towards the protease. Rank-order of the substrates tested for the docking and experimental methods were found to be similar for the top two substrates, with lesser agreement for the other substrates

Modal insan, daya saing dan prestasi usahawan wanita di Malaysia: analisis kualitatif usahawan wanita bumiputera di Melaka

Artikel ini membincangkan hasil dapatan kualitatif yang diperoleh daripada lima orang informan utama terhadap faktor yang mempengaruhi prestasi usahawan wanita Bumiputera yang yang berdaftar dengan Majlis Amanah Rakyat (MARA) di negeri Melaka. Institusi memainkan peranan penting dalam pembangunan sesebuah masyarakat, pembangunan sumber manusia dari sudut kemahiran, kebolehan, kreativiti, memberi bantuan kewangan dan bukan kewangan terutamanya dalam pembangunan prestasi dan kejayaan pengusaha. Justeru, penekanan terhadap pembangunan modal insan dan daya saing dilihat sebagai faktor penting dalam memastikan pengusaha mampu bersaing dalam pasaran masa kini. Dalam konteks pembangunan sosioekonomi negara, golongan wanita dilihat mampu untuk menyumbang ke arah peningkatan ekonomi dalam negara melalui perusahaan yang diceburi mereka. Lantaran, penekanan terhadap faktor modal insan dan daya saing dalam kalangan golongan wanita dilihat penting. Hal ini kerana, membolehkan usaha kerajaan dilakukan selaras dengan faktor yang paling mempengaruhi prestasi pengusaha. Bagi tujuan ini, temubual secara berstruktur telah dilakukan ke atas lima orang informan. Hasil temubual mendapati pengusaha wanita lebih memerlukan bantuan prasarana dan infrastruktur di samping aspek pendidikan dan latihan, pengalaman perniagaan, bantuan kewangan dan kreativiti

Knowledge, attitude and practice relating to food supplement intake among Universiti Teknologi MARA (UiTM) Terengganu students / Nur Athirah Muhamad Sobri dan Nurul Natasha Azira Shahrudin

The research study paper is about determine the level knowledge, attitude and practices relating to food supplement intake among Universiti Teknologi Mara (UiTM) Terengganu students. Food supplement which is also known as dietary supplements are popular in so many countries including Malaysia. The data is available by the target population which is university students on their food supplement intake. The result of the collecting data is obtained by 186 respondents and captured by using a set of questionnaire with four sections. Since the university students has variety habits, characteristics or lifestyle, their intake of food supplement may differ from the general population. The result reveal that the students have a lot of knowledge about the food supplement intake and only a few of them are not sure with the answer. They also have a good attitude and well practices towards food supplement intake. Food supplement also may be used in context of healthy lifestyle or as compensate for unhealthy lifestyle. The design of this research study is quantitative approach. This study investigate the effects of three independent variables which are knowledge, attitudes, practice and dependent variable which is food supplement intake

Solution structure and in Silico binding of a cyclic peptide with hepatitis B surface antigen

A specific ligand targeting the immunodominant region of hepatitis B virus is desired in neutralizing the infectivity of the virus. In a previous study, a disulfide constrained cyclic peptide cyclo S1,S9 Cys-Glu-Thr-Gly-Ala-Lys-Pro-His-Cys (S1, S9-cyclo-CETGAKPHC) was isolated from a phage displayed cyclic peptide library using an affinity selection method against hepatitis B surface antigen. The cyclic peptide binds tightly to hepatitis B surface antigen with a relative dissociation constant (KDrel) of 2.9 nm. The binding site of the peptide was located at the immunodominant region on hepatitis B surface antigen. Consequently, this study was aimed to elucidate the structure of the cyclic peptide and its interaction with hepatitis B surface antigen in silico. The solution structure of this cyclic peptide was solved using 1H, 13C, and 15N NMR spectroscopy and molecular dynamics simulations with NMR-derived distance and torsion angle restraints. The cyclic peptide adopted two distinct conformations due to the isomerization of the Pro residue with one structured region in the ETGA sequence. Docking studies of the peptide ensemble with a model structure of hepatitis B surface antigen revealed that the cyclic peptide can potentially be developed as a therapeutic drug that inhibits the virus–host interactions

Isolation of bacteria from the acidic peat swamp forest soil and their lignin degradation potential

The tropical peat swamp forest in Malaysia has reduced significantly due to increasing pressure for development and demand for agricultural land. Pekan peat swamp forest is part of the 200,000 hectares of peat swamp forest located in Pahang, Peninsular Malaysia. While more extensive studies were done on flora and fauna, the study on microbial diversity in this habitat is very limited. The highly acidic environment, low concentrations of nutrients and anoxic condition of the peat are among challenges that hampered the cultivation of microorganism from this environment. In this study two types of agar-based medium, M1 minimal medium (M1) and peat water medium (PW) supplemented with glucose, methanol and lignin were used to isolate bacteria from the peat sediment. In comparison to M1, the use of PW has resulted with higher number of isolates with different morphologies. The PW mainly contains the acidic peat water that was collected from the sampling location. Based on the growth on medium supplemented with lignin, selected isolates were identified using 16s rDNA sequencing. At least three of the isolates showed sequence similarity to Burkholderia sp., which is one of the common species, studied on their ligninase-producing abilities. The results from this study serve as the preliminary data for further work on growth characteristics and enzymatic potential of isolates from acidic peat swamp soil

Recent advanced techniques in cysteine determination: a review

The utilization of cysteine in a wide variety of products especially bakery products has led to a huge concern of various groups of consumers especially those who restricted to religious-based dietary. It has become a major concern due to the raw materials are derived from arguable sources such as pig bristles and human hair. This review briefly elaborates cysteine as food additives with highlighted issues in halal perspective and toxicity in the food industry. This review also highlighted several analytical approaches used in direct determination of cysteine compound such as high performance liquid chromatography (HPLC), molecular imprinted polymers (MIPs), Raman spectroscopy, flow injection spectrophotometric, electrochemical biosensor and gold nanoparticles based calorimetric assa

Organic solvent tolerant proteases

The potential advantage of using organic solvents for enzymatic reactions was due to the shift of reaction equilibrium of hydrolytic enzymes towards completion of the synthetic reaction. However, the use of these solvents normally led to loss of most enzyme activities. Therefore, which were naturally stable in the presence organic solvents, were very useful for synthetic reactions. In our laboratory, several organic solvent-tolerant protease producers have been successfully isolated from benzyne-toluene-xylene-ethylbenzene (BTEX) tolerant bacteria. The formulation of physical and nutritional factors affecting the enzymes production have led to the optimizes production of proteases from both Pseudomonas aeruginosa strain K and Bacillus cereus 146, which were stable in organic solvents with Po/w values between4.0 and 8.8. Due to these remarkable properties, strain K protease with a molecular size of 51.0 kDa was further purified by two purification steps and characterized. Complete nucleotide sequences from Pseudomonas aeruginosa strain K and Bacillus pumilus 115b were also obtained and analyzed to gain better understanding of its nucleotides which responsible for the enzymes biocatalytic interaction with solvent environment

Imidazole-rich copper peptides as catalysts in xenobiotic degradation

Laccases, oxidative copper-enzymes found in fungi and bacteria were used as the basis in the design of nona- and tetrapeptides. Laccases are known to be excellent catalysts for the degradation of phenolic xenobiotic waste. However, since solvent extraction of laccases is environmentally-unfriendly and yields obtained are low, they are less preferred compared to synthetic catalysts. The histidine rich peptides were designed based on the active site of laccase extracted from Trametes versicolor through RCSB Protein Data Bank, LOMETS and PyMol software. The peptides were synthesized using Fmoc-solid phase peptide synthesis (SPPS) with 30–40% yield. These peptides were purified and characterized using LC-MS (purities >75%), FTIR and NMR spectroscopy. Synthesized copper(II)-peptides were crystallized and then analyzed spectroscopically. Their structures were elucidated using 1D and 2D NMR. Standards (o,m,p-cresol, 2,4-dichlorophenol) catalysed using laccase from Trametes versicolor (0.66 U/mg) were screened under different temperatures and stirring rate conditions. After optimizing the degradation of the standards with the best reaction conditions reported herein, medications with phenolic and aromatic structures such as ibuprofen, paracetamol (acetaminophen), salbutamol, erythromycin and insulin were screened using laccase (positive control), apo-peptides and copper-peptides. Their activities evaluated using GC-MS, were compared with those of peptide and copper-peptide catalysts. The tetrapeptide was found to have the higher degradation activity towards salbutamol (96.8%) compared with laccase at 42.8%. Ibuprofen (35.1%), salbutamol (52.9%) and erythromycin (49.7%) were reported to have the highest degradation activities using Cu-tetrapeptide as catalyst when compared with the other medications. Consequently, o-cresol (84%) was oxidized by Tp-Cu while the apo-peptides failed to oxidize the cresols. Copper(II)-peptides were observed to have higher catalytic activity compared to their parent peptides and the enzyme laccase for xenobiotic degradation