Bijan Ranjbar

Tarbiat Modares University, Teheran, Tehrān, Iran

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Publications (116)207.98 Total impact

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    ABSTRACT: G-quadruplexes are supramolecular structures of G-rich nucleic acid, formed by non-canonical base pairing in the presence of specific environmental inducers. These structures have been vastly considered in diagnostic and therapeutic applications. However, detailed information on structure, optical properties and thermal stability of G-quadruplex potent oligonucleotides is scarce. Herein, optical properties and thermodynamic stability of AS1411 quadruplex is reported for various concentrations of potassium and lead ions. Circular dichroism showed that AS1411 ss-DNA folds into parallel conformation in the presence of metal ions and molecular crowding condition. UV-Visible spectroscopy indicated formation of quadruplex and fluorescent spectroscopy revealed intercalation of PicoGreen in its structure, with enhancement of emission intensity upon increment of metal ion concentration. This investigation also proposes high-throughput and reliable analysis of AS1411 quadruplex's thermal stability by real-time PCR technique, which can be further applied for other quadruplex structures.
    International journal of biological macromolecules. 09/2014;
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    ABSTRACT: Co-deposition of RF-sputtering and RF-PECVD from acetylene gas and Au target were used to prepare sensor chip of gold nanoparticles (Au NPs). Deposition conditions were optimized to reach a Localized Surface Plasmon Resonance (LSPR) sensor chip of Au NPs with particle size less than 10 nm. The RF power was set at 180 W and the initial gas pressure was set at 0.035 mbar. Transmission Electron Microscopy (TEM) images and Atomic Force Microscopy (AFM) data were used to investigate particles size and surface morphology of LSPR sensor chip. The Au and C content of the LSPR sensor chip of Au NPs was obtained from X-ray photoelectron spectroscopy (XPS). The hydrogenated amorphous carbon (a-C:H) thin film was used as intermediate material to immobilize Au NPs on the SiO2 substrate. The interaction between two types of osmolytes, i.e. sorbitol and trehalose, with Pseudomonas cepacia lipase (PCL) were detected by the prepared LSPR biosensor chip. The detection mechanism is based on LSPR spectroscopy in which the wavelength of absorption peak is sensitive to the refractive index of the environment of the Au NPs. This mechanism eliminates the use of a probe or immobilization of PCL on the Au NPs of LSPR sensor chip. The interaction between PCL and osmolytes can change refractive index of the mixture or solution. We found that unlike to trehalose, sorbitol interacts with the PCL. This interaction increases refractive index of the PCL and sorbitol mixture. Refractive index of PCL in the presence of different concentration of sorbitol was obtained by Mie theory modeling of LSPR peaks. This modeling stated that the present LSPR sensor chip has sensitivity as high as wavelength shift of 175 nm per refractive index. Moreover, the detection of such weakly interaction between bio-molecules cannot be achieved by other analysis.
    Applied Surface Science 09/2014; 314:138–144. · 2.54 Impact Factor
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    ABSTRACT: Linker mediated self-assembly of gold nanoparticles is emerging as an interesting strategy for construction of hybrid nanoscale systems with enhanced plasmonic circular dichroism (PCD) signals. Herein, gold nanorods were assembled via DNA linker to investigate the possibility of signal enhancement. Assemblies were characterized by UV–visible, fluorescence, dynamic light scattering and circular dichroism (CD) spectroscopy. Hybridization of complementary strands resulted in PCD signal enhancement, which was further monitored by the increase of real time PicoGreen fluorescence intensity. Impressively, such changes in the real time fluorescence and plasmonic CD responses could be used as a new detection method for ultrasensitive sensors.
    Journal of Physics D Applied Physics 07/2014; 47(31):315401. · 2.53 Impact Factor
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    ABSTRACT: We have previously reported an increase in the thermal stability of bacterial laccase from Bacillus sp. HR03 using site-directed mutagenesis. Three-dimensional model of this enzyme showed a negative patch in the connecting loop between domains 1 and 2. In the present study, the stability of laccase in organic solvents was improved by introducing nonpolar (E188 → A, I, L and V) and positively charged (E188 → K and R) residues in this region by site-directed mutagenesis. Irreversible thermoinactivation, C50 value, ∆∆G‡ and kinetic parameters of the wild type and its variants were calculated in the presence and absence of various organic solvents (ethanol, methanol, and 1-propanol). All variants showed higher C50 values when compared to the wild type. Nonpolar amino acid substitutions were found to be the most efficient mutants for their remarkable increase in C50 value and a decrease in thermoinactivation rate (ki) in the presence of mentioned solvents. Data showed that replacing a negative residue with hydrophobic residues on the surface of a protein could enhance thermoresistance as well as solvent stability. The stability of the resulting enzymes was dependent on the length of the alkyl chain. Results demonstrated that solvent tolerance was positively correlated with thermal stability. This article is protected by copyright. All rights reserved
    Engineering in Life Sciences 03/2014; · 1.63 Impact Factor
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    ABSTRACT: Introduction: Remarkable optical properties of gold nanorods (GNR) have been vastly used in biosensing and biomedical applications. In the light of sensing applicability, GNR based nanobiosensors are functionalized by various biomolecules such as peptides and oligonucleotides, that are known as nanoprobes. However, great sensitivity of GNRs to trace environmental changes and tendency to non-specific aggregation makes a crucial step in design and production of nanoprobe. Therefore, optimization of biorecognition element and stability investigations of nanoprobe is of great significance. Herein, stability of aged samples of oligonucleotide-functionalized GNRs has been studied at ambient temperature. Method: Gold nanorods were synthesized according to previously reported seed-mediated growth method. The nanostructure was purified by centrifugation and redispersed with a fixed concentration (1 OD). Surface of GNRs was biofunctionalized by a thiolated 22-mer oligonucleotide (1nM) after concentration optimization. Surface plasmon resonance (SPR) and Fourier transform infrared spectroscopy were used to monitor the bioconjugation via formation of Au-S bond. Samples of nanoprobe were then aged at ambient temperature (25 ºC) for different time intervals. Stability of the aged nanoprobe was investigated by monitoring the SPR bands of the nanostructure. Results: The characteristic SPR bands of GNRs along the short and long axis appeared at 520 nm and 724 nm, respectively. There was negligible shift in the wavelength maxima of nanoprobe after one week aging, with little decrease of intensity for both transverse and longitudinal surface plasmon resonance. Conclusions: The oligonucleotide-functionalized nanoprobe is stable at ambient temperature for biorecognition purposes. Keywords Gold Nanorod, Aging Process, Nanoprobe, SPR
    1st Tabriz International Life Science Conference and 12th Iran Biophysical Chemistry Conference; 05/2013
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    Mehdi Sadeqi, Bijan Ranjbar
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    ABSTRACT: The Cu 2+ dependent DNA cleavage DNAzyme is the unique example of known DNAzymes. The most established method for measuring the kinetics of deoxyribozyme reactions is based on the use of radiolabeled substrates. This method entails the cumbersome sampling, electrophoretic separation, and quantitation of the reaction products, as well as the continuous loss of substrate due to decay of the radioactive label. In this study we represent accurate, fast and inexpensive methods for kinetic study of the DNAzyme which is based on spectroscopic techniques. One of these methods is based on the SYBR gold extrinsic fluorescence. This probe has high affinity to double stranded DNA compared to single stranded DNA. Continuous Hyperchromicity assay (CHA) is used in second method which is a function of DNA hypercromicity that observed when double stranded DNA transformed to single stranded DNA. Using this methods can be traced DNAzyme substrate hybridization and product formation Simultaneously with reaction progress. Under conditions where the product release faster than enzymatic reaction, production release speed which is traced with these methods determined enzymatic reaction kinetic. These methods in addition to the kinetic study of the restriction DNAzyme can be used to study of other DNAzymes that has nucleic acid substrate. Comparison of the results show that the continuous hyperchromicity assay is more accurate than the extrinsic fluorescence method using SYBR gold because CHA method is DNA intrinsic physicochemical property result without interference of disturbing factors such as SYBR gold.
    1st Tabriz International Life Science Conference & 12th Iran Biophysical Chemistry Conference; 05/2013
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    ABSTRACT: Structure-function relationships underlying laccases properties are very limited that makes these enzymes interesting for protein engineering approaches. Therefore in the current study, a thermostable laccase that was isolated from Bacillus sp.HR03 with the ability of bilirubin oxidation beside its laccase and tyrosinase activity is used. The extensive application of this enzyme is limited by its low expression level in Escherichia coli. Based on sequence alignments and structural studies, three single amino acid substitutions, D500G, D500E, D500S and a glycine insertion, are introduced using site-directed mutagenesis to evaluate the role of Asp(500) located in the C-terminal segment close to the T1 copper center. Substitution of aspartic acid with less sterically hindered, conserved residue such as glycine increase kcat (2.3 fold) and total activity (7.3 fold) which is accompanied by a significant increase in the expression level up to 3 fold. Biochemical characterization and structural studies using far-UV CD and fluorescence spectroscopy reveals the importance of C-terminal copper-binding loop in the laccase functional expression and catalytic efficiency. Kinetic characterization of the purified mutants toward 2, 2'-azino-bis (3-ethylbenzothiazoline-6-sulfonic acid) (ABTS), syringaldazine (SGZ) and bilirubin, shows that substrate specificity is left unchanged.
    International journal of biological macromolecules 05/2013; · 2.37 Impact Factor
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    ABSTRACT: در دهه هاي اخير، نانومواد گوناگوني پا به عرصه پژوهش در زمينه هاي پزشکي گزارده اند. نانوميله هاي طلا به دليل دارا بودن خواص اپتيکي منحصر به فرد، گزينه مناسبي جهت امر تشخيص شناخته شده و لذا در ساخت نانوبيوسنسور مورد توجه قرار مي گيرند. در اين راستا، پژوهش حاضر به بررسي پايداري نانوکاوشگر ميله اي طلا پس از اتصال به توالي اليگو نوکلئوتيدي در دماي محيط و دماي بالا پرداخته است. نتايج مطالعات نشان داد که نوسانات پلاسمونيک نانوپروب ميله اي در هر دو شرايط دمايي و در گستره غلظتي پيکومولار از اليگو نوکلئوتيد پايدار مانده و نانوساختارها متجمع نشده اند. دستاورد اين پژوهش، بر پايداري کانژوگه نانوساختار-اليگو نوکلئوتيد براي طراحي نانوبيوسنسورها مهر تأييد مي زند.
    اولین همایش ملی و کارگاه های تخصصی علوم و فناوری نانو; 05/2013
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    ABSTRACT: Laccases (benzenediol oxygen oxidoreductases, EC 1.10.3.2) are important multicopper enzymes that are used in many biotechnological processes. A recombinant form of laccase from Bacillus sp. HR03 was overexpressed in Escherichia coli BL-21(DE3). Inclusion body (IB) formation happens quite often during recombinant protein production. Hence, developing a protocol for efficient refolding of proteins from inclusion bodies to provide large amounts of active protein could be advantageous for structural and functional studies. Here, we have tried to find an efficient method of refolding for this bacterial enzyme. Solubilization of inclusion bodies was carried out in phosphate buffer pH 7, containing 8M urea and 4mM β-mercaptoethanol and refolding was performed using the dilution method. The effect of different additives was investigated on the refolding procedure of denaturated laccase. Mix buffer (phosphate buffer and citrate buffer, 100mM) containing 4mM ZnSO4 and 100mM sorbitol was selected as an optimized refolding buffer. Also Kinetic parameters of soluble and refolded laccase were analyzed.
    Enzyme and microbial technology. 05/2013; 52(6-7):325-30.
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    ABSTRACT: The effect of proline on refolding and unfolding kinetics as well as activity of Lipase from Pseudomonas fluorescens was determined using stopped-flow fluorescence and UV/Vis absorbance spectroscopy. Enzyme assay at different concentrations of proline revealed that activity of enzyme reaches maximum at 0.6M concentration of proline. Kinetic measurements showed that refolding rate is considerably accelerated in the presence of 0.6M proline. Unfolding kinetic traces were fitted to double exponential function, and it was revealed that lipase molecules were unfolded via two different pathways. Fast unfolding rate constant decreased, while slow one did not change significantly upon addition of proline.
    International journal of biological macromolecules 01/2013; · 2.37 Impact Factor
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    ABSTRACT: Like many other bacterial lipases Pseudomonas aeruginosa lipase has a very strong structure-function relationship. Herein, the effect of structural compactness of lipase has been investigated on its activity. Pseudomonas aeruginosa HR59 was isolated from burn infection as a new and inexpensive source. Bacterial lipase was extracted from this strain and purified by ion-exchange chromatography. Two divalent metal ions (calcium and magnesium) and three polar organic solvents (methanol, ethanol and iso- propanol) were used to study the structure-function relationship. Results of this study revealed that these additives activated enzyme by reducing the helix content of enzyme. Moreover, thermo stability of the enzyme decreased in the presence of calcium and magnesium ions; whereas it increased upon interaction with polar organic solvents under heat-induced denaturation. Results of this investigation encourage utilization of these activity enhancers for various medical and industrial applications.
    International journal of biological macromolecules 12/2012; · 2.37 Impact Factor
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    ABSTRACT: A sequence of 10 amino acids at the C-terminus region of methylglyoxal synthase from Escherichia coli (EMGS) provides an arginine, which plays a crucial role in forming a salt bridge with a proximal aspartate residue in the neighboring subunit, consequently transferring the allosteric signal between subunits. In order to verify the role of arginine, the gene encoding MGS from a thermophile species, Thermus sp. GH5 (TMGS) lacking this arginine was cloned with an additional 30 bp sequence at the 3´-end and then expressed in form of a fusion TMGS with a 10 residual segment at the C-terminus (TMGS(+)). The resulting recombinant enzyme showed a significant increase in cooperativity towards phosphate, reflected by a change in the Hill coefficient (nH) from 1.5 to 1.99. Experiments including site directed mutagenesis for Asp-10 in TMGS and TMGS(+), two dimentional structural survey, fluorescence and irreversible thermoinactivation were carried out to confirm this pathway. [BMB Reports 2012; 45(12): 748-753].
    BMB reports 12/2012; 45(12):748-53. · 1.63 Impact Factor
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    ABSTRACT: We investigated the possibility the active DNAzyme formation of particular Guanine-rich oligonucleotide with nonadiabatic tapered optical fiber (NATOF) sensor. These kinds of oligonucleotides can form stable four-stranded structure called G-quadruplex in the presence of particular metal ions. Structural change of immobilized oligonucleotide was detected by monitoring of transmission spectrum of the sensor. The formation of active DNAzyme formed was confirmed by verifying enzyme activity. Result shows that the NATOF sensor has capability to detect intramolecular structural changes and using this sequence as biorecognition molecule for fabricating fiber optic biosensor. © (2012) COPYRIGHT Society of Photo-Optical Instrumentation Engineers (SPIE). Downloading of the abstract is permitted for personal use only.
    OFS2012 22nd International Conference on Optical Fiber Sensors; 10/2012
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    ABSTRACT: Candida antarctica lipase B (CALB) belongs to psychrophilic lipases which hydrolyze carboxyl ester bonds at low temperatures. There have been some features reported about cold-activity of the enzyme through experimental methods, whereas there is no detailed information on its mechanism of action at molecular level. Herein, a comparative molecular dynamics simulation and essential dynamics analysis have been carried out at three temperatures (5, 35 and 50uC) to trace the dominant factors in the psychrophilic properties of CALB under cold condition. The results clearly describe the effect of temperature on CALB with meaningful differences in the flexibility of the lid region (a5 helix), covering residues 141–147. Open-closed conformations have been obtained from different sets of long-term simulations (60 ns) at 5uC gave two reproducible distinct forms of CALB. The starting open conformation became closed immediately at 35 and 50uC during 60 ns of simulation, while a sequential open-closed form was observed at 5uC. These structural alterations were resulted from a5 helical movements, where the closed conformation of active site cleft was formed by displacement of both helix and its side chains. Analysis of normal mode showed concerted motions that are involved in the movement of both a5 and a10 helices. It is suggested that the functional motions needed for lypolytic activity of CALB is constructed from short-range movement of a5, accompanied by long-range movement of the domains connected to the lid region.
    PLoS ONE 07/2012; 7(7):e40327. · 3.53 Impact Factor
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    M Sadeqi, B Ranjbar
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    ABSTRACT: Beyond the preservation of genetic information in the double helix structure in cells, DNA could also have catalytic role in the single stranded form taking different 3-D structures. This artificial catalytic biomolecule is known as DNAzyme or deoxyribozyme. The Cu 2+ dependent DNA cleavage DNAzyme is the unique example of known DNAzymes. It is introduced as a restriction DNAzyme due to the site specific cleavage of single strand DNA molecule. It is also used as Cu 2+ nanobiosensor in aqueous solutions by modification of DNAzyme molecule with florescence dye. Herein, we studied the structure and catalytic function of DNAzyme using Uv-visible and extrinsic fluorescence spectroscopy. Hyperchromic and hypochromic effects of DNA have been traced by Uv-visible spectroscopy to investigate structure, hybridization phenomenon and catalytic function. Absorbance intensity at 260 nm decreases upon hybridization of DNAzyme with substrate (hypochromic effect), which increased upon addition of cofactor and starting catalytic activity (hyperchromic effect). This result confirmed the efficiency of this spectroscopic technique for kinetic and function study of the DNAzyme compared with conventional methods. The optimum pH and thermal conditions for hybridization of restriction DNAzyme and its catalytic activity was also determined. The results are well in accordance with pervious findings reported by R. R Breaker. The extrinsic fluorescence study of the DNAzyme hybridization and its catalytic function by SYBR GOLD show consistency with Uv-visible experiment results, however this technique offers higher sensitivity compared to that of Uv-visible spectroscopy. Fluorescence intensity of DNAzyme-substrate increased upon hybridization, and decreased when the catalytic activity started. Our findings suggest that spectroscopic techniques, particularly extrinsic fluorescence spectroscopy using SYBR GOLD could be a good alternative to conventional methods for studying kinetic and catalytic activity of DNAzyme, being affordable and time saving.
    first international BiochemicalPhyisics congress; 06/2012
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    ABSTRACT: Bacillus licheniformis alpha-amylase (BLA), a thermophilic counterpart of Bacillus amyloliquefaciens alpha-amylase (BAA), is an appropriate model for the design of stabilizing mutations in BAA. BLA has 10 more histidines than BAA. Considering this prominent difference, in the present study, three out of these positions (I34, Q67, and P407; located in the thermostability determinant 1 region and Ca-III binding site of BAA) were replaced with histidine in BAA, using the site-directed mutagenesis technique. The results showed that the thermostability of P407H and Q67H mutants had increased, but no significant changes were observed in their kinetic parameters compared to that of the wild type. I34H replacement resulted in complete loss of enzyme activity. Moreover, fluorescence and circular dichroism data indicated a more rigid structure for the P407H variant compared with that of the wild-type BAA. However, the flexibility of Q67H and I34H mutants increased in comparison with that of wild-type enzyme.
    Journal of Microbiology and Biotechnology 05/2012; 22(5):592-9. · 1.40 Impact Factor
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    ABSTRACT: The unique morphology of anisotropic rod-shaped gold nanostructures has offered new prospects for biomedical and biosensing applications. This study investigates the interaction of two types of rod-shaped nanostructures, gold nanorods and gold nanorices with lysozyme as a model protein, comparing the probable structural, activity and kinetic stability alterations. Circular dichroism spectropolarimeter revealed that lysozyme retains high fraction of its native conformation in the presence of both nanostructures, with a slight increase in the helical and beta content. Upon the protein adsorption on both types of nanorods, kinetic studies showed maintenance of enzymatic activity, together with increase in the enzymatic affinity and kinetic stability at high temperature. Comparatively, gold nanorice induced better effect on the activity and stability of enzyme than that of gold nanorod. This study might open new insight into potential applications of gold nanorods as nanocarriers for genes and drugs; provided that the toxicological aspect of cationic surfactant-coated nanostructure is taken into consideration.
    International journal of biological macromolecules 04/2012; 51(1-2):91-6. · 2.37 Impact Factor
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    ABSTRACT: Ionic liquids (ILs) have gained increasing attention as solvents in chemical and biotechnological applications. Since alcohol dehydrogenases are of prime interest in industrial field, the present study has been conducted to study the influence of imidazolium based ionic liquids on kinetics, structure and stability of the thermophilic Thermoanaerobacter brockii (TBADH) alcohol dehydrogenase. Our results exhibited that the ionic liquids could affect kinetic parameters and stability, but not the tertiary structure. Through the determination of inhibition profile, which revealed mixed inhibition, Ki (affinity of IL for the enzyme) and KI (affinity of IL for enzyme–substrate complex) values were calculated. Structural analysis using crystallographic data from protein data bank elucidated the structural details responsible for different responses of alcohol dehydrogenases toward ionic liquids. Finally, enhanced stability in [MIm][Cl] was discussed.
    Journal of Molecular Liquids 03/2012; 170:66-71. · 2.08 Impact Factor
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    ABSTRACT: It is the common feature of α-amylases that calcium ion is required for their structural integrity and thermal stability. All amylases have at least one Ca(2+) per molecule; therefore amino acids involved in calcium binding are specific and conserved. In this study, sequence analysis revealed the presence of EF-hand-like motif in calcium-binding loop of Bacillus megaterium WHO (BMW)-amylase that was previously isolated from BMW. The EF-hand motif and its variants (EF-hand-like motif) are the most common calcium-binding motifs found in a large number of protein families. To investigate the effect of calcium ion on the thermal stability and activity of BMW-amylase, we used site-directed mutagenesis to replace histidine 58 with Asp (D), Ile (I), Tyr (Y), Phe (F), and Arg (R) at the seventh position of EF-hand-like motif. Upon the addition of an extra DX unit to the calcium-binding loop in H58D variant, thermal stability, catalytic activity, and chelating power of the enzyme improved due to higher affinity toward calcium. H58D variant demonstrated calcium independency compared to the wild type and other created mutants. Conformational changes in the presence and absence of Ca(2+) were monitored using fluorescence technique.
    Molecular Biotechnology 03/2012; · 2.26 Impact Factor
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    ABSTRACT: It has been lately proposed that the interaction between like-charged residues stabilizes the native state of proteins. To explore this, we created a histidine-histidine pair in the Ca-III binding site of the Bacillus amyloliquefaciens α-amylase (BAA) and then examined the impact of this pairing on the BAA. For this purpose, we used site-directed mutagenesis (SDM) to substitute Pro407 with His, Ala, Gln, Arg, and Glu in the BAA. Subsequently, thermostability, kinetic parameters and structural properties of these variants were measured. Moreover, His-His pairing effect on the BAA thermostability was examined by simultaneous mutation of two residues (P407H/H406A and P407H/H406N). The data exhibited a significant improve in thermostability and structural features of enzyme by His replacement instead of Pro407. Other substitutions in this site did not have a significant effect on the enzyme properties, except for P407R, which yielded a partial improvement. The results also showed that the thermostabilities of double mutants significantly decreased compared with that of the P407H mutant. Moreover, the thermostability of P407H remarkably increased compared with that of other variants even in the absence of Ca(2+). Our data clearly demonstrated that His406-His407 pairing was the major cause for improved thermal stability.
    International journal of biological macromolecules 01/2012; 50(4):1040-7. · 2.37 Impact Factor

Publication Stats

731 Citations
207.98 Total Impact Points

Institutions

  • 2001–2014
    • Tarbiat Modares University
      • • Department of Biochemistry
      • • Department of Biophysics
      • • Faculty of Sciences
      Teheran, Tehrān, Iran
  • 2012
    • Islamic Azad University
      • Department of Biology
      Tehrān, Ostan-e Tehran, Iran
  • 2009–2011
    • University of Guilan
      • Department of Biology
      Rasht, Ostan-e Gilan, Iran
  • 2001–2008
    • University of Tehran
      • • Institute of Biochemistry and Biophysics
      • • Department of Biotechnology
      Teheran, Tehrān, Iran
  • 2007
    • Stanford University
      Palo Alto, California, United States
  • 2006
    • Alzahra University
      Teheran, Tehrān, Iran
  • 2005–2006
    • National Institute of Genetic Engineering and Biotechnology
      Teheran, Tehrān, Iran