فهرست مطالب

Biomacromolecular Journal - Volume:3 Issue: 1, Summer 2017
  • Volume:3 Issue: 1, Summer 2017
  • تاریخ انتشار: 1396/07/11
  • تعداد عناوین: 9
  • Seied Abdolhamid Angaji * Pages 1-4
    Uncovering DNA sequence variations that correlate with phenotypic changes, e.g., diseases, is the aim of sequence variation studies. Common types sequence variations are Single nucleotide polymorphism (SNP, pronounced snip).SNPs are the third-generation molecular marker. SNP represents a DNA sequence variant of a single base pair with the minor allele occurring in more than 1% of a given population. There are an approximately 56,000,000 SNPs in the human genome. The broad field of applications for SNPs induced a pressing need for effective instruments for SNP detection. During the last decade a considerable number of methods for SNP discovery (search for new SNPs) and detection (recognition of already known SNPs) were developed. Studying the association between quantitative phenotype and SNPs is an important problem in biology. To understand underlying mechanisms of complex phenotypes, it is often necessary to consider joint genetic effects across multiple SNPs. In this article, SNPs and their role in association studies were reviewed.
    Keywords: Molecular markers, Candidate genes, Linkage
  • Hanieh Jafary * Pages 5-17
    Epigenetic alterations, including DNA acetylation, hypermethylation and hypomethylation, and the associated transcriptional changes of the affected genes are central to the evolution and progression of various human cancers, including pancreatic cancer. Cancer-associated epigenetic alterations are attractive therapeutic targets because such epigenetic alterations, unlike genetic changes, are potentially reversible. Several drugs that target epigenetic alterations, including inhibitors of histone deacetylase (HDAC) and DNA methyltransferase (DNMT), are currently approved for treatment of hematological malignancies and are available for clinical investigation in solid tumors. Histone deacetylases (HDACs) is well known to be associated with tumorigenesis through epigenetic regulation. HDACs comprise an ancient family of enzymes that play crucial roles in numerous biological processes and HDACs are found to be over expressed in many tumor types. Its inhibitors (HDACIs) induce differentiation and apoptosis of tumor cells. In addition, the activity of heat shock proteins (Hsps) can be regulated by HDACs. Hsps exist in many types of cells and these proteins can prevent aggregation and formation of toxic inclusion. Hsps are major molecular chaperones in prokaryotic and eukaryotic cells. This review summarizes mechanisms of histone deacetylase inhibitors action on Hsps and will describe the regulation of major cellular chaperones and heat shock factors by HDAC-mediated deacetylation.
    Keywords: HDAC, HDAC inhibitor, Chaperon, Hsp, Acetylation
  • Atiyeh Mahdavi *, Reza H. Sajedi, Mehdi Rassa Pages 18-25
    Extreme pHs, especially acidic pHs, are among the environmental stresses that some bacteria face. The most important strategies that bacteria employ for acid adaptation include either production of acidophilic proteins, or raising the pH of the microenvironment by secretion of basic compounds including ammonia produced by the action of urease. Considering the importance of acid-neutralizing bacteria, we previously isolated Bacillus sp. GUF8 from acidic soil of a tea plantation and identified it as Bacillus cereus using standard bacterial identification methods and 16S rDNA sequencing. Tea plantation soil is intrinsically acidic and so allows survival for only acidophilic or acid-tolerant bacteria. In the light of this fact, we investigated acid tolerance and/or adaptation property of B. cereus GUF8 in the present study. Our results showed that the isolate is an acid-tolerant and not acidophilic strain which neutralizes the acidic microenvironment by secreting urease. Urease production increases until the pH reaches to about 8.0-9.0, whilst the isolate grows optimally at around pHs 6.0-7.0 and there is a lag period of about two days prior to active growth on media at pH 4.0. The results suggest that the isolate has potential for use as a neutralizing agent in acidified environments.
    Keywords: Bacillus cereus GUF8, Acid, neutralizing, Urease, Acid tolerant
  • Yaser Fattahian, Ali Riahi-Madvar *, Reza Mirzaee, Masoud Torkzadeh-Mahani, Gholamreza Asadikaram Pages 26-37
    Peroxidase enzymes are vastly applicable in industry and diagnosiss. Recently, we introduced a new kind of peroxidase gene from Lepidium draba (LDP). According to protein multiple sequence alignment results, LDP had 93% similarity and 88.96% identity with horseradish peroxidase C1A (HRP C1A). In the current study we employed in silico tools to determine, to which group of peroxidase enzymes LDP belongs. The tertiary structure of protein was built using homology modeling method and the overall quality of predicted model was evaluated. The physicochemical and spatial properties of protein were measured. The binding site of protein which made a motif, was determined. The predicted tertiary structure possesses acceptable quality, based on several criteria. The predicted motif was also in agreement with previous studies. The isoelectric point (pI) of LDP was calculated as 8.25. Due to neutral pI of LDP and high similarity between structure of LDP and HRP C1A, it is assumed that LDP belongs to the neutral or neutral-basic isoenzymes.
    Keywords: Lepidium draba, Peroxidase, In silico, Bioinformatics, Binding site
  • Tahereh Taghavinejad, Ahmad Molaeirad *, Mahdi Alijanianzadeh, Maryam Khayati Pages 38-47
    Organophosphorus (OP) forms an important class of toxic compounds. They inhibit acetyl cholinesterase (AChE, EC that results in respiratory and myocardial malfunctions. Pesticides could be accumulated in vegetables and fruits, so detection of them is very important. The goals of this study are decreasing detection time and detection limit of methyl parathion bioprobe. In this research the methyl parathion bioprobe based on modified glassy carbon (GC) electrode-immobilized AChE is constructed. β-cyclodexterin (β-CD)/chitosan-multiwall carbon nanotube (CS-MCNT) composite, first by polymer wrapping method and then by layer-by-layer self-assembly technique, was prepared. Then different combination of β-CD, CS-MCNT and graphene was deposited on GC electrode. AChE solution (4mg/ml) was deposited on the modified GC electrode and dried in air at room temperature. The electrochemical measurement is based on AChE inhibition by methyl parathion (MPT) in the presence of acetyl choline iodide (ACTI) as substrate with cyclic voltammetry method. The results show that using graphene contributes to considerable increasing in current up to 27 µA. These measurements were done in phosphate buffer (pH = 7.5) and at 25°C. In another part the optimum pH and temperature were measured that were 7.5 and 55°C receptively. Detection limit for MPT was gained 5nM.
    Keywords: Biosensor, Detection limit, Organophosphorus, Cyclic voltammetry
  • Mojtaba Mortezavi *, Masoud Torkzadeh-Mahani, Navid Nezafat, Abdorrasoul Malekpour, Mohammad Zarenezhad, Roohullah Hemmati, Mahmood Maleki, Seyed Younes Hosseini, Reza Pazhoomand Pages 48-59
    Luciferase enzymes are involved in the bioluminescence reaction (light emission by living organisms). The bioluminescence process is a widespread phenomenon in the Nature. These enzymes are identified in some domains of life, but the luciferases from lampyrid genus are considered of for biological applications. The molecular cloning of a new type of firefly luciferase from Luciola lateralis was reported, previously. Here, we study its substrate binding site and rare codon with molecular docking and bioinformatics studies. By molecular modelling, some rare codons were identified that may have a critical role in structure and function of this luciferase. AutoDock Vina was used in the molecular docking that recognizes some residues that yield closely related with luciferin and AMP binding site. These types of studies help in the discovery of the light production reaction. Evaluation of these hidden information’s can improve the knowledge of luciferases folding and protein expression challenges and help in design of new drugs.
    Keywords: Luciola lateralis, Luciferase, Rare codon, Docking, Substrate binding site
  • Somaye Shahraki *, Hassan Mansouri-Torshizi, Zahra Ghanbari, Adeleh Divsalar, Ali Akbar Saboury Pages 60-74
    In many diseases such as cancer, simultaneous use of two or more pharmacologically active agents will be more effective and have fewer side effects. In this study a new palladium(II) complex with formula of [Pd(phen)(py-dtc)]NO3 (where is phen 1,10-phenanthroline and py-dtc is n-propyldithiocarbamate), was synthesized. The cytotoxic activity of this complex was tested against leukemia K562 cell lines. The cytotoxic concentration (Cc50) value of above Pd(II) complex was 53.06 μM. In the presence of vitamin K3, Cc50 value dramatically decreased to 32.95 μM and encouraged us to study DNA interaction of Pd (II) complex in the absence and presence of vitamin K3. Interaction of above Pd(II) complex in two modes (in the absence and presence of vitamin K3) with calf thymus DNA was evaluated using spectroscopic methods. UV-Vis results showed that in the presence of VK3, Pd(II) complex unexpectedly denatures CT-DNA at very low concentration. Fluorescence results showed that quenching of the intrinsic fluorescence of EBr-DNA system by Pd(II) complex is static quenching mechanism and type of mechanism does not change in the presence of vitamin. Also, in the absence and presence of vitamin, the mode of intercalation might play a major role in the interactions of Pd(II) complex with DNA. Several binding and thermodynamic parameters are also presented. We hope that these results provide a basis for additional studies and clinical use of combined anticancer drugs to be useful.
    Keywords: Anticancer, Pd(II) complex, Vitamin K3, Cytotoxicity, DNA binding
  • Zahra Amini-Bayat *, Nahid Bakhtiari Pages 75-82
    Creatinine amidohydrolase(EC catalyzes the reversible conversion of creatinine to creatine. Creatininase in combination with other enzymes is used for detection of creatinine in serum and urine which is of significant value for detection of renal, muscular and thyroid functions. The aim of this study was to produce recombinant creatininase enzyme in E.coli expression system to use it in creatinine assay kit. The pseudomonas pseudoalkaligene KF707 creatininase gene has been optimized and synthesized already. Subsequently, it has been subcloned into the pET28 expression vector then the expression vector has been transformed into the BL21 (DE3) cell and induced by IPTG, afterwards the expression has been evaluated using SDS-PAGE and western blot. The recombinant protein has been purified by Ni-NTA agarose resins and enzyme activity has been analyzed. A sharp 29kDa protein band has been observed on SDS-PAGE and confirmed by western blot. More than 40% of E.coli total protein was recombinant creatinase, The recombinant enzyme was purified with approximately 100% yield. The enzyme activity analysis showed that recombinant enzyme has 14 unit/ml activity. Recombinant p.pseudoalkaligene KF707 creatininase was produced for the first time and its good production yield confirmed that E.coli was an efficient expression system for its production.
    Keywords: Pseudomonas pseudoalkaligene KF707, Creatininase, Creatinine assay, Recombinant protein
  • Maryam Nourisefat, Ali Akbar Moosavi-Movahedi * Pages 83-92
    The Biophysical Chemistry Laboratory (BCL) was established in 1986 at Institute of Biochemistry and Biophysics (IBB), University of Tehran as the main base and the mother of biophysical chemistry in Iran. BCL is a famous worldwide research lab in the area of thermodynamics of protein denaturation and biomacromolecular interaction. The first student that joined BCL was MSc student in 1987, while the laboratory was in development. Despite the limited features, the results of his study on the thermodynamic analysis of the interaction between surfactants and H1 histone was published in Thermochimica Acta as the first outlet of the BCL in 1989 [1]. This was the initiate for internationalization of science in BCL with the support of thought, sacrifice, and perseverance. This way was led to achieving the main goal of the establishment of the laboratory with the big goals for the advancement of science, wisdom, and innovations. In the following, in 1990, because of the results of the student studies and international publications, BCL awarded the International Khawrazmi Prize entitled "Physical chemistry of the interaction of histone proteins with surfactant". A wide range of results on histone proteins were published in international journals (referred to ibb.ut.ac.ir/~moosavi[a]).
    Keywords: Biophysical Chemistry Laboratory (BCL), Protein thermodynamics, Artificial enzyme, Hydrophobic salts, UNESCO Chair on Interdisciplinary Research in Diabetes