Papers by Fatemeh Ramezani
Staphylococcal protein A (SpA) is a major bacterial virulence factor of Staphylococcus aureus. S.... more Staphylococcal protein A (SpA) is a major bacterial virulence factor of Staphylococcus aureus. S. aureus is capable of escaping from immune system recognition by the surface display of protein A. The SpA protein is broadly used to purify immunoglobulin G (IgG) antibodies. This study investigates the ability of the fusion of Lpp’-OmpA (46 − 159) to anchor and display five repeat domains of protein A with 295 residues length (SpA295) of S. aureus on the Escherichia coli cell surface to develop a novel bioadsorbent. First, the binding between Lpp’-OmpA-SPA295 and IgGFc and anticipation of this structure was investigated using molecular dynamics simulation. Then high IgG recovery from human serum by the surface-displayed system of Lpp’-OmpA-SPA295 performed experimentally. In silico analysis showed the binding potential of SPA295 to IgG after surface expression on LPP-OmpA. Surface-engineered E. coli displaying SpA protein and IgG-binding assay with SDS-PAGE analysis exhibited the high ...
BMC Cardiovascular Disorders
Background: Myocardial ischemia-reperfusion (IR) injury is a leading cause of death all over the ... more Background: Myocardial ischemia-reperfusion (IR) injury is a leading cause of death all over the world, so developing practical approaches to promote cardioprotection against IR injury is essential. Exercise training is an effective strategy to improve cardioprotection. Hence, the purpose of this study was to investigate the effect of short-term preconditioning with two types of high-intensity interval training (HIIT) and moderate intensity continuous training (MICT) on klotho and TRPC6 mechanisms in cardioprotection. Methods: Eighty Male Wistar rats (250-300 g) were randomly divided into 7 groups, including Control, HIIT, MICT, Sham, IR, HIIT+IR, and MICT+IR. Training was performed in 5 consecutive days. HIIT protocol consisted of running on the treadmill at intervals 85-90% vo 2 max that separated by slow intensity periods at 50-60% vo 2 max. MICT program was performed at 70% VO 2 max at the same running distance with HIIT groups. The cardiac IR injury was induced by LAD occlusion followed by reperfusion. ELISA kit was used in order to measure the plasma levels of klotho, LDH and CK-MB, and TRPC6 expression was determined using the western blot technique. Data were analyzed using one way ANOVA and Tukey's post hoc tests. Results: The results of this study showed that both types of exercise training programs significantly increase plasma levels of klotho and reduce the infarct size and heart injury. In addition, the exercise training decreased the amount of TRPC6 channels expression during IR. However, the effect of HIIT on increasing the klotho and cardioprotection was greater compared to MICT. Conclusions: Based on the results, even a short-term of aerobic exercise training, especially HIIT, promotes cardioprotection against IR injury and decreases infarct size via an increase in klotho and attenuate of protein expression of myocardial TRPC6 during IR.
Materials Science and Engineering: C
AMB Express, Jan 30, 2018
Sortases are enzymes mostly found in Gram-positive bacteria which cleave proteins site-specifical... more Sortases are enzymes mostly found in Gram-positive bacteria which cleave proteins site-specifically. This feature makes them a promising tool in molecular biology and biotechnology. In this study, using bacterial surface display of recombinant proteins and ability of sortase A in site-specifically cleavage of the amino acid sequences, a novel method for one-step purification of recombinant proteins was developed. Using computational program tools, a chimeric protein containing a metallothionein (mt) and chitin binding domain (ChBD) was attached to the C-terminal domain of the truncated outer membrane protein A (Lpp'-ompA) using sortase recognition site (amino acid residues: LPQTG) as a separator. The structure of the chimeric protein was simulated using molecular dynamics to determine if the LPQTG motif is accessible to the sortase active site. The designed chimeric protein was expressed and purified. The purified chimeric protein was also displayed on the surface of E. coli cel...
International journal of biological macromolecules, Jan 25, 2018
Lipases represent an important industrial biocatalysts group displaying enantioselectivity, high ... more Lipases represent an important industrial biocatalysts group displaying enantioselectivity, high stability in solvents and substrate specificity. A commonly used commercial enzyme for synthesis of organic materials is Candida antarctica lipase B (CALB). Its Industrial production involves cost-effective purification of large amounts of microbially-produced macromolecules. Hence, great focus is now placed on periplasmic secretion and storage. Accordingly, we designed and constructed a suitable signal peptide for secretion of lipase using a newly developed software. Molecular dynamic simulation was performed to compare structural states of native signal peptide of Staphylococcus aureus protein A (nSpA) and its modified counterpart (mSpA). Furthermore, the effect of these two peptides in binding to the signal peptidase I (SPase I) was studied. Simulation data confirmed experimental results showing that secondary structure of the mSpA binding region and the binding site of the SPase I cr...
New Cellular and Molecular Biotechnology Journal, Feb 15, 2013
While a large number of microbial species are capable of producing metal NPs, mechanism of nanopa... more While a large number of microbial species are capable of producing metal NPs, mechanism of nanoparticle biosynthesis is very important. The metabolic complexity of viable microorganisms complicates the analysis and identification of active species in the nucleation and growth of metal NPs. Strategies such as enzymatic oxidation or reduction, sorption on the cell wall and, in some cases, subsequent chelating with extracellular peptides or polysaccharides have been developed and used by microorganisms. Some species can control the membrane transport of heavy metals towards, or their active efflux from, the cell. Metal ion resistance via transport and passive mechanisms leading to extracellular precipitation is more characteristic for prokaryotes.[1,2] in this article we study several enzymes have important role in nanoparticle synthesis by microorganisms.
Upon entering biological systems such as the bloodstream, nanoparticles form molecular complexes ... more Upon entering biological systems such as the bloodstream, nanoparticles form molecular complexes with encountered proteins termed as the protein corona which shields the surface of the exogenous nanoparticle. Blood more abundant proteins such as albumin initially occupy the nanoparticle surface. Due to the high application of gold nanoparticle in medicine, in this study the docking of human serum albumin is performed to the gold nanoparticle and followed by investigating the changes in the structure of the protein by molecular dynamic simulation and GOLP force field. The results revealed that after the adsorption of albumin on the gold nanoparticle, human serum albumin was denatured and alpha-helix amount decreased significantly. Domain III that has a large cavity of fatty acid binding site, plays an important role in adsorption on the . enoit oaononan dlog Lys464, Thr504, Phe505 and Leu581 ang t lnildao amino acids doHSA adsorption on the GNP. After the adsorption of albumin on the...
Due to unusual optical, chemical and electrical properties of nanoparticles, making of them is ve... more Due to unusual optical, chemical and electrical properties of nanoparticles, making of them is very important. Nanoparticles are used in many respects in the biotechnology and industry, for example in the fields of catalysts, optics, life sciences, pharmacy, medicine, mechanics, magnetism and energy science. Variety of techniques for making of metal nanoparticles are chemical recovery using regenerative materials, aerosol technique, electrochemical deposition, photochemical recovery, laser exposure and ... . But as the term of green nanotechnology has emerged that a lot of attention has attracted and includes a wide range of processes that reduce or eliminate toxic substances to restore environment. Green Nanotechnology also seek more effective alternatives for energy production (e.g. solar and fuel cells). In green nanotechnology, for the synthesis of nanoparticles microorganisms are used. Well known that many microorganisms, aggregate inorganic material within or outside the cell ...
DARU Journal of Pharmaceutical Sciences, 2015
Background MMP-2 enzyme is a kind of matrix metalloproteinases that digests the denatured collage... more Background MMP-2 enzyme is a kind of matrix metalloproteinases that digests the denatured collagens and gelatins. It is highly involved in the process of tumor invasion and has been considered as a promising target for cancer therapy. The structural requirements of an MMP-2 inhibitor are: (1) a functional group that binds the zinc ion, and (2) a functional group which interacts with the enzyme backbone and the side chains which undergo effective interactions with the enzyme subsites. Methods In the present study, a QSAR model was generated to screen new inhibitors of MMP-2 based on L–hydroxy tyrosine scaffold. Descriptors generation were done by Hyperchem 8, DRAGON and Gaussian98W programs. SPSS and MATLAB programs have been used for multiple linear regression (MLR) and genetic algorithm partial least squares (GA-PLS) analyses and for theoretical validation. Applicability domain of the model was performed to screen new compounds. The binding site potential of all inhibitors was veri...
Journal of Nanoparticle Research, 2014
ABSTRACT In recent years, there has been considerable progress in the design and study of gold na... more ABSTRACT In recent years, there has been considerable progress in the design and study of gold nanoparticles that geared toward biomedical applications. In most imaging and therapeutic applications, gold nanoparticles enter the bloodstream directly by intravenous administration forming molecular complexes with encountered proteins termed as the protein corona. Since albumin is the most abundant protein in human blood plasma, in this study, gold nanoparticle interactions and its shape effects on human serum albumin were studied by molecular dynamic simulation. These results revealed that in the interaction of albumin with any shapes of gold nanoparticle, human serum albumin unfolds and helix amount decreases. Cubic gold nanoparticles showed stronger unfolding effects on the albumin than the spherical gold nanoparticles.
Iranian Journal of Biotechnology, 2013
Eukaryotic expression of an important enzyme used in dairy industry. Background: Aqueous extract ... more Eukaryotic expression of an important enzyme used in dairy industry. Background: Aqueous extract of dried fourth stomach of unweaned bovine contains prochymosin, that subsequently is converted to active chymosin, a milk-coagulating enzyme in the cheese industry. Recombinant chymosin has been found to be a suitable replacement for natural bovine chymosin. Meanwhile it possesses several advantages to other plant, fungal and bacterial milk-clotting enzymes. Objectives: In present research we evaluate the expression of this critical enzyme in a eukaryotic system for future use in cheese industry. Materials and Methods: We have cloned bovine prochymosin gene in methylotrophic yeast, P. pastoris, using pPIC9K as an expression vector. The recombinant plasmid was transformed into the host by electroporation, and it was expressed in optimum conditions (temperature 29oC, 200 rpm, 2% methanol for induction, and 5 days of incubation). Transcription and expression of the recombinant prochymosin was evaluated by the reverse transcription polymerase chain reaction (RT-PCR), sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) analysis as well as western blotting and enzyme-linked immunosorbent assay (ELISA). Results: In optimum conditions, only a low level of this heterologous protein was detected using ELISA method and subsequently confirmed by RT-PCR. Conclusions: Since it has been reported that P. pastoris is an appropriate host for the expression of recombinant proteins, a low level of expression of prochymosin in this host should be explored in our future research.
Mol. BioSyst., 2015
Upon entering the blood stream, gold nanoparticles form molecular complexes with the encountered ... more Upon entering the blood stream, gold nanoparticles form molecular complexes with the encountered proteins such as albumin. Using molecular dynamics simulations, we have shown that with albumin exposure to the gold nanoparticles, the alpha helix amount reduced and ligand-binding sites altered by this structural change.
DARU Journal of Pharmaceutical Sciences, 2015
Background: Gold nanoparticles now command a great deal of attention for medical applications. De... more Background: Gold nanoparticles now command a great deal of attention for medical applications. Despite the importance of nano-bio interfaces, interaction between peptides and proteins with gold surfaces is not still fully understood, especially in a molecular level. Methods: In the present study computational simulation of adsorption of 20 amino acids, in three forms of mono-amino acid, homo di-peptide and homo tri-peptide, on the gold nanoparticles was performed by Gromacs using OPLSAA force field. The flexibility, stability, and size effect of the peptides on the gold nanoparticles were studied as well as the molecular structure of them. Results: According to our results, adsorbed homo tri-peptides on the gold surface had more flexibility, more gyration, and the farthest distance from the GNP in comparison with homo di-peptides and mono-amino acids. Conclusion: Our findings provide new insights into the precise control of interactions between amino acids anchored on the GNPs.
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Papers by Fatemeh Ramezani