Genomes and Genes
Experts and Doctors on amino acid sequence in Tehrān, Iran
Locale: Tehrān, Iran
Topic: amino acid sequence
- Rad S, Zahiri H, Noghabi K, Rajaei S, Heidari R, Mojallali L. Type 2 IDI performs better than type 1 for improving lycopene production in metabolically engineered E. coli strains. World J Microbiol Biotechnol. 2012;28:313-21 pubmed publisher..coli. In addition, the metabolic engineering of citrate pathway seems a promising approach to have more isoprenoid accumulation in E. coli. ..
- Oshaghi M, Ravasan N, Hide M, Javadian E, Rassi Y, Sadraei J, et al. Phlebotomus perfiliewi transcaucasicus is circulating both Leishmania donovani and L. infantum in northwest Iran. Exp Parasitol. 2009;123:218-25 pubmed publisher..Finding L. donovani infecting P. perfiliewi transcaucasicus in the area demands extensive and intensive typing of natural Leishmania infections in epidemiological investigations in Iran and the Mediterranean Basin in general. ..
- Karbalaei Heidari H, Ziaee A, Amoozegar M, Cheburkin Y, Budisa N. Molecular cloning and sequence analysis of a novel zinc-metalloprotease gene from the Salinivibrio sp. strain AF-2004 and its extracellular expression in E. coli. Gene. 2008;408:196-203 pubmed..8 kDa), electrospray-ionisation mass spectrometry revealed that the molecular mass of purified rSVP2 was only 34.2 kDa, which indicates a further cleavage site at the C-terminal. ..
- Younesi F, Pazhang M, Najavand S, Rahimizadeh P, Akbarian M, Mohammadian M, et al. Deleting the Ig-Like Domain of Alicyclobacillus acidocaldarius Endoglucanase Cel9A Causes a Simultaneous Increase in the Activity and Stability. Mol Biotechnol. 2016;58:12-21 pubmed publisher..This shows that Ig-like domain has a role in the increase of the enzyme stability by calcium in the wild-type enzyme. ..
- Zarrabi M, Dalirfardouei R, Sepehrizade Z, Kermanshahi R. Comparison of the antimicrobial effects of semipurified cyclotides from Iranian Viola odorata against some of plant and human pathogenic bacteria. J Appl Microbiol. 2013;115:367-75 pubmed publisher..This study is a part of our extended researches on finding new pharmaceutical potentials of plants and on developing new peptides for special purposes in a way that does not have harmful side effects or have the least side effects. ..
- Jazii F, Najafi Z, Malekzadeh R, Conrads T, Ziaee A, Abnet C, et al. Identification of squamous cell carcinoma associated proteins by proteomics and loss of beta tropomyosin expression in esophageal cancer. World J Gastroenterol. 2006;12:7104-12 pubmed..Our study not only supports the involvement of some of the formerly reported proteins in SCCE but also introduces additional proteins found to be lost in SCCE, including TMbeta. ..
- Seifinejad A, Taei A, Totonchi M, Vazirinasab H, Hassani S, Aghdami N, et al. Generation of human induced pluripotent stem cells from a Bombay individual: moving towards "universal-donor" red blood cells. Biochem Biophys Res Commun. 2010;391:329-34 pubmed publisher..Such specific stem cells provide an unprecedented opportunity to produce a universal blood group donor, in-vitro, thus enabling cellular replacement therapies, once the safety issue is resolved. ..
- Darabi M, Izadi Darbandi A, Masoudi Nejad A, Naghavi M, Nemat Zadeh G. Bioinformatics study of the 3-hydroxy-3-methylglotaryl-coenzyme A reductase (HMGR) gene in Gramineae. Mol Biol Rep. 2012;39:8925-35 pubmed publisher..Phylogenetic analysis indicated that there is a relationship among species of Gramineae and other organisms. According to these results, HMGRs should be derived from a common ancestor. ..
- Rahbar M, Rasooli I, Gargari S, Sandström G, Amani J, Fattahian Y, et al. A potential in silico antibody-antigen based diagnostic test for precise identification of Acinetobacter baumannii. J Theor Biol. 2012;294:29-39 pubmed publisher..Antigenicity of the region could also be explored for elicitation of antibody to protect the individuals exposed to A. baumannii. ..
- Fasehee H, Westers H, Bolhuis A, Antelmann H, Hecker M, Quax W, et al. Functional analysis of the sortase YhcS in Bacillus subtilis. Proteomics. 2011;11:3905-13 pubmed publisher..Taken together, these novel findings show that B. subtilis has a functional sortase for anchoring proteins to the cell wall. ..
- Nazarian S, Mousavi Gargari S, Rasooli I, Amani J, Bagheri S, Alerasool M. An in silico chimeric multi subunit vaccine targeting virulence factors of enterotoxigenic Escherichia coli (ETEC) with its bacterial inbuilt adjuvant. J Microbiol Methods. 2012;90:36-45 pubmed publisher..Linear and conformational B-cell epitopes were identified. The identified T-cell epitopes are apt to bind MHC molecules. The epitopes in the chimeric protein are likely to induce both the B-cell and T-cell mediated immune responses. ..
- Azizian H, Bahrami H, Pasalar P, Amanlou M. Molecular modeling of Helicobacter pylori arginase and the inhibitor coordination interactions. J Mol Graph Model. 2010;28:626-35 pubmed publisher..In the absence of the experimental structure of H. pylori arginase we hope that our model will be useful to provide rational design of novel anti-H. pylori drugs. ..
- Jahangiri A, Rasooli I, Reza Rahbar M, Khalili S, Amani J, Ahmadi Zanoos K. Precise detection of L. monocytogenes hitting its highly conserved region possessing several specific antibody binding sites. J Theor Biol. 2012;305:15-23 pubmed publisher..monocytogenes. This protein sequence can serve as an antigen for designing a relatively cheap, sensitive, and specific diagnostic test for detection of L. monocytogenes. ..
- Salavatifar M, Amin S, Jahromi Z, Rasgoo N, Rastgoo N, Arbabi M. Green fluorescent-conjugated anti-CEA single chain antibody for the detection of CEA-positive cancer cells. Hybridoma (Larchmt). 2011;30:229-38 pubmed publisher..This strategy will likely allow the establishment of a rapid, single-step detection assay of CEA, which is considered to be one of the best predictors of malignancy among all other tumor markers. ..
- Behzadian F, Sabahi F, Karimi M, Sadeghizadeh M, Maghsoudi N, Forooshani R, et al. Molecular phylogenetic analysis of Iranian HDV complete genome. Virus Genes. 2005;30:383-93 pubmed..Data analysis confirmed genetic variability and heterogeneity of the HDV species isolated from different geographical areas. ..
- Mohammadpour H, Pourfathollah A, Nikougoftar Zarif M, Khalili S. Key role of Dkk3 protein in inhibition of cancer cell proliferation: An in silico identification. J Theor Biol. 2016;393:98-104 pubmed publisher..Dkk3 efficiently interacts with LRP, Kremen and EGF receptor and may be a promising protein in cancer therapy by blocking Wnt and EGFR downstream signaling. ..
- Jahangiri A, Rasooli I, Gargari S, Owlia P, Rahbar M, Amani J, et al. An in silico DNA vaccine against Listeria monocytogenes. Vaccine. 2011;29:6948-58 pubmed publisher..Vectors for checking the expression of constructs in mammalian cells and for harboring the foreign genes as DNA vaccine are suggested. ..
- Mirzarezaee M, Araabi B, Sadeghi M. Features analysis for identification of date and party hubs in protein interaction network of Saccharomyces Cerevisiae. BMC Syst Biol. 2010;4:172 pubmed publisher..If such a hypothesis is correct for other species as well, similar methods can be applied to predict the roles of proteins in those species. ..
- Rezaei Matehkolaei A, Makimura K, de Hoog G, Shidfar M, Satoh K, Najafzadeh M, et al. Multilocus differentiation of the related dermatophytes Microsporum canis, Microsporum ferrugineum and Microsporum audouinii. J Med Microbiol. 2012;61:57-63 pubmed publisher..The prevalence of M. ferrugineum in clinical samples in Iran appeared to be higher than suspected on the basis of routine phenotypic identification. ..
- Aftabi Y, Colagar A, Mehrnejad F. An in silico approach to investigate the source of the controversial interpretations about the phenotypic results of the human AhR-gene G1661A polymorphism. J Theor Biol. 2016;393:1-15 pubmed publisher..However, the previously reported flexibility of the modular TAD could act as an intervening factor, moderate the SNP effects and causes distinct outcomes in different individuals and tissues. ..
- Shoja Z, Tagliamonte M, Jalilvand S, Ziaee A, Mokhtari Azad T, Hamkar R, et al. Molecular characterization analysis of the outer protein layer (VP7) from human rotavirus A genotype G1 isolate identified in Iran: implications for vaccine development. New Microbiol. 2012;35:415-27 pubmed..Indeed, the present study confirms that the A group G1 genotype is the most prevalent Rotavirus circulating in Iran and supports the development of G1 genotype-based rotavirus vaccine for this country. ..
- Raz A, Dinparast Djadid N, Zakeri S. Molecular characterization of the carboxypeptidase B1 of Anopheles stephensi and its evaluation as a target for transmission-blocking vaccines. Infect Immun. 2013;81:2206-16 pubmed publisher..stephensi is the main malaria vector, and this will broaden the scope for the potential wider application of CPBAs1 antigen homologs/orthologs...
- Rafiee M, Sokhansanj A, Yoosefi M, Naghizadeh M. Identification of salt-inducible peptide with putative kinase activity in halophilic bacterium Virgibacillus halodenitrificans. J Biosci Bioeng. 2007;104:178-81 pubmed..The sequence of the 16S rRNA gene was analyzed phylogenetically to classify strain XII. This organism was found to have the closest association with Virgibacillus halodenitrificans, which was proven by its phenotypic characteristics...
- Majdi M, Liu Q, Karimzadeh G, Malboobi M, Beekwilder J, Cankar K, et al. Biosynthesis and localization of parthenolide in glandular trichomes of feverfew (Tanacetum parthenium L. Schulz Bip.). Phytochemistry. 2011;72:1739-50 pubmed publisher..The high expression of TpGAS in glandular trichomes which also contain the highest concentration of parthenolide, suggests that glandular trichomes are the secretory tissues where parthenolide biosynthesis and accumulation occur...
- Mahmoudian M. The complex of human Gs protein with the beta 3 adrenergic receptor: a computer-aided molecular modeling study. J Mol Graph. 1994;12:22-8, 34 pubmed
- Molakarimi M, Mohseni A, Taghdir M, Pashandi Z, Gorman M, Parker M, et al. QM/MM simulations provide insight into the mechanism of bioluminescence triggering in ctenophore photoproteins. PLoS ONE. 2017;12:e0182317 pubmed publisher..This work also revealed that a hydrogen bonding network formed by a D158- R41-Y204 triad could be responsible for shuttling the proton from the 2- hydroperoxy group of the substrate to bulk solvent...
- Parvaneh N, Mamishi S, Rezaei A, Rezaei N, Tamizifar B, Parvaneh L, et al. Characterization of 11 new cases of leukocyte adhesion deficiency type 1 with seven novel mutations in the ITGB2 gene. J Clin Immunol. 2010;30:756-60 pubmed publisher..Definitive molecular diagnosis is valuable for genetic counseling and prenatal diagnosis. Regarding clinical presentations, it seems that omphalitis is the most consistent finding seen in LAD I infants. ..
- Khalaj Kondori M, Sadeghizadeh M, Khajeh K, Naderi Manesh H, Ahadi A, Emamzadeh A. Cloning, sequence analysis and three-dimensional structure prediction of DNA pol I from thermophilic Geobacillus sp. MKK isolated from an Iranian hot spring. Appl Biochem Biotechnol. 2007;142:200-8 pubmed..Predicted 3D structure and sequence alignments between MF and BF showed that all critical residues in the polymerase active site are conserved...
- Haghighi A, Rasti S, Nazemalhosseini Mojarad E, Kazemi B, Bandehpour M, Nochi Z, et al. Entamoeba dispar: genetic diversity of Iranian isolates based on serine-rich Entamoeba dispar protein gene. Pak J Biol Sci. 2008;11:2613-8 pubmed..dispar isolates based on the SREDP was more polymorphic in comparison of Serine-Rich Entamoeba histolytica Protein (SREHP) of the E. histolytica isolates as well as were different from a few known SREDP genes...
- Mehrizi A, Sepehri M, Karimi F, Djadid N, Zakeri S. Population genetics, sequence diversity and selection in the gene encoding the Plasmodium falciparum apical membrane antigen 1 in clinical isolates from the south-east of Iran. Infect Genet Evol. 2013;17:51-61 pubmed publisher..In conclusion, the low genetic diversity in PfAMA1 among Iranian isolates supports and provides valuable information for the development of a PfAMA1-based malaria vaccine. ..
- Rahmati S, Alijani N, Kadivar M. In vitro generation of glucose-responsive insulin producing cells using lentiviral based pdx-1 gene transduction of mouse (C57BL/6) mesenchymal stem cells. Biochem Biophys Res Commun. 2013;437:413-9 pubmed publisher..This new lentiviral vector could be suggested as an effective candidate for using in gene therapy of type-1 diabetes. ..
- Moradi A, Hosseinkhani S, Naderi Manesh H, Sadeghizadeh M, Alipour B. Effect of charge distribution in a flexible loop on the bioluminescence color of firefly luciferases. Biochemistry. 2009;48:575-82 pubmed publisher..Homology modeling reveals the appearance of a bulge in a flexible loop (T352-P359) upon mutation which shifts to the left side with a color change from green to red...
- Babaeekho L, Zakeri S, Djadid N. Genetic mapping of the duffy binding protein (DBP) ligand domain of Plasmodium vivax from unstable malaria region in the Middle East. Am J Trop Med Hyg. 2009;80:112-8 pubmed..It is suggested that to develop polyvalent vaccine against P. vivax infection, it is better to incorporate the common and high prevalent allelic variants of the antigen that were reported from different malaria endemic regions. ..
- Mardani A, Keshavarz H, Heidari A, Hajjaran H, Raeisi A, Khorramizadeh M. Genetic diversity and natural selection at the domain I of apical membrane antigen-1 (AMA-1) of Plasmodium falciparum in isolates from Iran. Exp Parasitol. 2012;130:456-62 pubmed publisher..The results obtained will have significant implications in the design and the development of an AMA-1-based vaccine against falciparum malaria...
- Hasani Ranjbar S, Amoli M, Ebrahim Habibi A, Haghpanah V, Hejazi M, Soltani A, et al. Mutation screening of VHL gene in a family with malignant bilateral pheochromocytoma: from isolated familial pheochromocytoma to von Hippel-Lindau disease. Fam Cancer. 2009;8:465-71 pubmed publisher..VHL type 2 presenting with both pheochromocytoma and retinal angioma in this family found to be associated with the new missense mutation (c499 C>T) of VHL gene. ..
- Adrangi S, Faramarzi M, Shahverdi A, Sepehrizadeh Z. Purification and characterization of two extracellular endochitinases from Massilia timonae. Carbohydr Res. 2010;345:402-7 pubmed publisher..Both enzymes were stimulated by Mn(2+) and inhibited by Hg(2+), and neither showed exochitinase activity. The N-terminal sequences of Chi-56 and Chi-64 were determined to be Q-T-P-T-Y-T-A-T-L and Q-A-D-F-P-A-P-A-E, respectively. ..
- Behdani M, Zeinali S, Khanahmad H, Karimipour M, Asadzadeh N, Azadmanesh K, et al. Generation and characterization of a functional Nanobody against the vascular endothelial growth factor receptor-2; angiogenesis cell receptor. Mol Immunol. 2012;50:35-41 pubmed publisher..These data show the potential of Nanobodies for the blockade of VEGFR2 signaling and provide a basis for the development of novel cancer therapeutics. ..
- Zakeri S, Raeisi A, Afsharpad M, Kakar Q, Ghasemi F, Atta H, et al. Molecular characterization of Plasmodium vivax clinical isolates in Pakistan and Iran using pvmsp-1, pvmsp-3alpha and pvcsp genes as molecular markers. Parasitol Int. 2010;59:15-21 pubmed publisher..6% for Pakistani and Iranian P. vivax isolates, respectively. These results indicate an extensive diversity in the P. vivax populations in both studies. ..
- Raheb J, Naghdi S, Flint K. The effect of starvation stress on the protein profiles in Flexibacter chinensis. Iran Biomed J. 2008;12:67-75 pubmed..It is necessary to investigate the synthesis of these proteins during different stress conditions...
- Zahmatkesh A, Ansari Mahyari S, Daliri Joupari M, Rahmani H, Shirazi A, Amiri Roudbar M, et al. Expressional and Bioinformatic Analysis of Bovine Filia/Ecat1/Khdc3l Gene: A Comparison with Ovine Species. Anim Biotechnol. 2016;27:174-81 pubmed publisher..Our data suggests a difference in Filia expression pattern between cow and sheep, although the sequence is highly conserved. ..
- Said Alipour B, Hosseinkhani S, Ardestani S, Moradi A. The effective role of positive charge saturation in bioluminescence color and thermostability of firefly luciferase. Photochem Photobiol Sci. 2009;8:847-55 pubmed publisher..turkestanicus luciferase. On the other hand, pK(a) of amino acids in the flexible loop decreased upon introducing of positive charges. ..
- Ahmadian G, Ju W, Liu L, Wyszynski M, Lee S, Dunah A, et al. Tyrosine phosphorylation of GluR2 is required for insulin-stimulated AMPA receptor endocytosis and LTD. EMBO J. 2004;23:1040-50 pubmed
- Chitsazian F, Tusi B, Elahi E, Saroei H, Sanati M, Yazdani S, et al. CYP1B1 mutation profile of Iranian primary congenital glaucoma patients and associated haplotypes. J Mol Diagn. 2007;9:382-93 pubmed..Three SNP blocks determined the haplotypes. Comparison of haplotypes with those of other populations suggests a common origin for many of the mutations. ..
- Mehrizi A, Zakeri S, Salmanian A, Sanati M, Djadid N. Plasmodium falciparum: sequence analysis of the gene encoding the C-terminus region of the merozoite surface protein-1, a potential malaria vaccine antigen, in Iranian clinical isolates. Exp Parasitol. 2008;118:378-85 pubmed..In summary, result of this study indicates limited antigenic diversity, and thus support the potential utility of the C-terminal region of PfMSP-1 in designing polyvalent vaccine constructs. ..
- Mardani A, Keshavarz H, Heidari A, Hajjaran H, Raeisi A, Khorramizadeh M. Genetic polymorphism at the C-terminal domain (region III) of knob-associated histidine-rich protein (KAHRP) of Plasmodium falciparum in isolates from Iran. Parasitol Res. 2011;109:1647-52 pubmed publisher..falciparum strains exist in the malaria endemic areas of Iran. Our findings will be valuable in the design and the development of the molecular therapeutic reagents for falciparum malaria...
- Zahiri J, Yaghoubi O, Mohammad Noori M, Ebrahimpour R, Masoudi Nejad A. PPIevo: protein-protein interaction prediction from PSSM based evolutionary information. Genomics. 2013;102:237-42 pubmed publisher..They also reveal that the negative dataset selection could lead to an acute performance overestimation which is the principal drawback of the available methods. ..
- Shahhoseini M, Ziaee A, Ghaemi N. Expression and secretion of an alpha-amylase gene from a native strain of Bacillus licheniformis in Escherichia coli by T7 promoter and putative signal peptide of the gene. J Appl Microbiol. 2003;95:1250-4 pubmed..coli secretory system. This study recommends the use of this signal peptide for extracellular production of other foreign proteins in E. coli. ..
- Motavaze K, Namvar Z, Emami M, Noorbakhsh F, Rezaie S. Molecular characterization of a Squalene epoxidase gene in dermatophyte pathogen Trichophyton tonsurans. Iran Biomed J. 2008;12:55-8 pubmed..Sequences comparison in gene data banks (NCBI, NIH) for this part of DNA and its deduced amino acid revealed significant homology with members of the eukaryotic Squalene epoxidase. ..
- Iqbal Z, PÃ¼ttmann L, Musante L, Razzaq A, Zahoor M, Hu H, et al. Missense variants in AIMP1 gene are implicated in autosomal recessive intellectual disability without neurodegeneration. Eur J Hum Genet. 2016;24:392-9 pubmed publisher..Our findings indicate that the clinical spectrum for AIMP1 defects is broader than witnessed so far. ..
- Mansour A, Mousavi S, Rasooli I, Nazarian S, Amani J, Farhadi N. Cloning, high level expression and immunogenicity of 1163-1256 residues of C-terminal heavy chain of C. botulinum neurotoxin type E. Biologicals. 2010;38:260-4 pubmed publisher..In conclusion, availability of the recombinant protein provides an effective system to study the biochemical and physical interactions involved during BoNT binding to nerve cells and protection against its toxicity...
- Dezfouli M, Yadegari S, Nafissi S, Elahi E. Four novel C20orf54 mutations identified in Brown-Vialetto-Van Laere syndrome patients. J Hum Genet. 2012;57:613-7 pubmed publisher..The causative nucleotide variations were not observed in 200 control individuals. One of the patients harbored compound heterozygous mutations, but only one mutated allele was observed in each of the two remaining patients. ..
- Gholizadeh S, Djadid N, Basseri H, Zakeri S, Ladoni H. Analysis of von Willebrand factor A domain-related protein (WARP) polymorphism in temperate and tropical Plasmodium vivax field isolates. Malar J. 2009;8:137 pubmed publisher..This study presents the first large-scale survey on pvwarp polymorphism in the world, which provides baseline data for developing WARP-based TBV against both temperate and tropical P. vivax isolates. ..
- Ghollasi M, Ghanbari Safari M, Khajeh K. Improvement of thermal stability of a mutagenised ?-amylase by manipulation of the calcium-binding site. Enzyme Microb Technol. 2013;53:406-13 pubmed publisher..Further analysis suggested the H77E mutant as the most stable which increased the affinity of the enzyme for calcium ion and its optimum temperature was 5°C higher than the wild type. ..
- Sheari A, Kargar M, Katanforoush A, Arab S, Sadeghi M, Pezeshk H, et al. A tale of two symmetrical tails: structural and functional characteristics of palindromes in proteins. BMC Bioinformatics. 2008;9:274 pubmed publisher..Although palindromes frequently overlap with conserved Blocks, we suggest that palindromes overlap with Blocks only by coincidence, rather than being involved with a certain structural fold or protein domain. ..
- Momen Roknabadi A, Sadeghi M, Pezeshk H, Marashi S. Impact of residue accessible surface area on the prediction of protein secondary structures. BMC Bioinformatics. 2008;9:357 pubmed publisher..Thus, solvent accessibility can be considered as a rich source of information to help the improvement of these methods. ..
- Ebrahimi F, Rasaee M, Mousavi S, Babaeipour V. Production and characterization of a recombinant chimeric antigen consisting botulinum neurotoxin serotypes A, B and E binding subdomains. J Toxicol Sci. 2010;35:9-19 pubmed..We conclude that a significant correlation exists between the antigenic characteristics and protection capability of the chimeric protein prepared in this study. ..
- Asadi S, Javan M, Ahmadiani A, Sanati M. Alternative splicing in the synaptic protein interaction site of rat Ca(v)2.2 (alpha (1B)) calcium channels: changes induced by chronic inflammatory pain. J Mol Neurosci. 2009;39:40-8 pubmed publisher..Determining different Ca(v)2.2 splice variants in rat nervous system and the impact of inflammatory pain on the splicing pattern suggest a possible regulatory role for calcium channel alternative splicing. ..
- Rahban M, Salehi N, Saboury A, Hosseinkhani S, Karimi Jafari M, Firouzi R, et al. Histidine substitution in the most flexible fragments of firefly luciferase modifies its thermal stability. Arch Biochem Biophys. 2017;629:8-18 pubmed publisher..Based on our results we conclude that the MD simulation-based rational substitution of histidines by salt-bridge forming residues can modulate conformational dynamics in luciferase and shift its optimal temperature activity. ..