Publications by authors named "Hossein Naderi-Manesh"

105 Publications

The influence of laser frequency and groove distance on cell adhesion, cell viability, and antibacterial characteristics of Ti-6Al-4V dental implants treated by modern fiber engraving laser.

Dent Mater 2021 Mar 16;37(3):547-558. Epub 2021 Jan 16.

Department of Nanobiotechnology/Biophysics, Faculty of Biological Science, Tarbiat Modares University, Tehran P.O. Box 14115-154, Iran.

Objective: Micro-nano scale surface modification of Ti-6Al-4V was investigated through the fascinated modern fiber engraving laser method. The process was performed at a high laser speed of 2000mm/s, under different laser frequencies (20-160kHz) and groove distances (0.5-50μm).

Methods: Topographic evaluations such as Atomic Force Microscopy (AFM) and Field Emission Scanning Electron Microscopy (FE-SEM) were used to identify the quality and regularity of patterns. The proliferation of human osteoblast-like osteosarcoma cells (MG63) was analyzed by MTT assay for up to 72h. Also, the plate counting method was used to quantify the viability potential of the modified surface against Escherichia coli bacteria.

Results: The cellular viability of the sample modified at the laser frequency of 20kHz and grooving distance of 50μm increased up to 35 and 10% compared to the non-treated and control samples, respectively. In the case of the surface modification at lower grooving distances range between 0.5-50μm, the maximum laser frequency (160kHz) applied leads to lower pulse's energies and less bacterial adhesion. Otherwise, at groove distances more than 50μm, the minimum laser frequency (20kHz) applied reduces the laser pulse overlaps, increases the cell adhesion and antibacterial properties.

Significance: Surface modification by the fiber engraving laser process significantly enhances the cell adhesion on the surface. As a result of such roughness and cell adhesion enhancement, the surface toxicity feature diminished, and its antibacterial properties improved.
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http://dx.doi.org/10.1016/j.dental.2020.12.007DOI Listing
March 2021

Morphometry and Modeling of Label-Free Human Melanocytes and Melanoma Cells.

Cell Biochem Biophys 2021 Jan 14. Epub 2021 Jan 14.

Department of Nanobiotechnology, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran.

A combination of light microscopy and image processing was applied to investigate morphology of label-free primary-melanocytes and melanoma cells. A novel methodological approach based on morphology of nuclear body was used to find those single cells, which were at the same phase of cell cycle. The area and perimeter of melanocytes and melanoma cells were quantified. We found that there was a significant difference between area and perimeter of adendritic-shaped melanocytes with melanoma cells and the reason(s) of this finding was speculated. Finally, a theoretical model based on losing dendrites was proposed, which was in agreement with our experimental data.
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http://dx.doi.org/10.1007/s12013-020-00963-wDOI Listing
January 2021

A novel iron quantum cluster confined in hemoglobin as fluorescent sensor for rapid detection of Escherichia coli.

Talanta 2020 Oct 11;218:121137. Epub 2020 May 11.

Department of Nanobiotechnology/Biophysics, Faculty of Biological Science, Tarbiat Modares University, 14115-154, Tehran, Iran. Electronic address:

A new method based on fluorescent probe of iron quantum cluster has been proposed for rapid detection of Escherichia coli (E. coli). The iron quantum cluster was synthesized using hemoglobin as both a source of iron and a protective agent (Hb-FeQCs). The investigation of the sensitivity of Hb-FeQCs towards metal ions showed a highly selective turn off fluorescence for Cu. It suggests that Cu can induce fluorescence quenching by binding to amino acids of Hb. The ability of E. coli bacteria to capture and reduce of Cu ions caused to efficient recovery of the fluorescence of Hb-FeQCs from Cu-caused quenching. This probe has a satisfactorily linear range of 0.35-35 μM for Cu under the optimal iron quantum cluster concentration (500 μg/mL) with an 85 nM detection limit. Rapid and facile detection of E.coli bacteria with the limit of detection around 8.3 × 10 CFU/mL was successfully achieved in the artificially contaminated urine, tap water, and DMEM samples within 30 min. The fluorescence recovery was investigated by different types of bacteria and only E. coli revealed 56% recovery which related to its capability to Cu reduction and the great potential of the fluorescent probe for rapid detection of pathogenic E. coli bacteria. Furthermore, the Hb-FeQCs can detect E. coli bacteria in an infected urine sample by retrieving up to 74% of its fluorescence which is helpful to accelerate the diagnosis and treatment of urinary tract infection (UTI).
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http://dx.doi.org/10.1016/j.talanta.2020.121137DOI Listing
October 2020

Imidazolium-based ionic liquid functionalized mesoporous silica nanoparticles as a promising nano-carrier: response surface strategy to investigate and optimize loading and release process for Lapatinib delivery.

Pharm Dev Technol 2020 Nov 9;25(9):1150-1161. Epub 2020 Aug 9.

Department of Biophysics/Nanobiotechnology, Faculty of Biological Science, Tarbiat Modares University, Tehran, Iran.

Imidazolium-based ionic liquid functionalized PEGylated mesoporous silica nanoparticles MCM-41 (denoted as [ImIL-PEGylated@MCM-41] NPs) is synthesized and evaluated as an efficient and reliable pH-sensitive nano-carrier for controlled release of cationic Lapatinib (Lap) drug. This nano-DDS was fully characterized by dynamic light scattering, scanning electron microscopy, X-ray powder diffraction, Fourier transform infrared spectroscopy, N adsorption-desorption measurement, and differential scanning calorimeter. Furthermore, the drug loading content and drug release profile were studied. The entrapment and loading efficiency of the optimized formulation for Lap were 91 ± 2.0% and 32.21 ± 2.70%, respectively. The results of cytotoxicity assay demonstrated that ImIL-PEG@MCM-41 has no significant toxicity on both cancerous and normal cell lines and the anticancer activity of Lap@ImIL-PEG@MCM-41 was comparable to free drug in case of human breast cells (SKBR3) and human embryonic kidney 293 cells (HEK-293). Meanwhile, three-dimensional (3D) cell culture was performed by multicellular tumor spheroids for understanding of cell response to drugs in physiologically 3D microenvironments. The results of Lap@ImIL-PEG@MCM-41 uptake during 48 hours showed a gradual release of the Lap through the multicellular tumor spheroids. This showed that the pH-responsive controlled release of Lapatinib leads to the satisfactory results in the breast cancer therapy.
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http://dx.doi.org/10.1080/10837450.2020.1803909DOI Listing
November 2020

Seed-mediated Electrochemically Developed Au Nanostructures with Boosted Sensing Properties: An Implication for Non-enzymatic Glucose Detection.

Sci Rep 2020 04 29;10(1):7232. Epub 2020 Apr 29.

Department of Nanobiotechnology/Biophysics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, 14115-154, Iran.

A new approach has been developed to improve sensing performances of electrochemically grown Au nanostructures (AuNSs) based on the pre-seeding of the electrode. The pre-seeding modification is simply carried out by vacuum thermal deposition of 5 nm thin film of Au on the substrate followed by thermal annealing at 500 °C. The electrochemical growth of AuNSs on the pre-seeded substrates leads to impressive electrochemical responses of the electrode owing to the seeding modification. The dependence of the morphology and the electrochemical properties of the AuNSs on various deposition potentials and times have been investigated. For the positive potentials, the pre-seeding leads to the growth of porous and hole-possess networks of AuNSs on the surface. For the negative potentials, AuNSs with carved stone ball shapes are produced. The superior electrode was achieved from AuNSs developed at 0.1 V for 900 s with pre-seeding modification. The sensing properties of the superior electrode toward glucose detection show a high sensitivity of 184.9 µA mM cm, with a remarkable detection limit of 0.32 µM and a wide range of linearity. The excellent selectivity and reproducibility of the sensors propose the current approach as a large-scale production route for non-enzymatic glucose detection.
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http://dx.doi.org/10.1038/s41598-020-64082-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7190711PMC
April 2020

Capture and detection of rare cancer cells in blood by intrinsic fluorescence of a novel functionalized diatom.

Photodiagnosis Photodyn Ther 2020 Jun 17;30:101753. Epub 2020 Apr 17.

Department of Nanobiotechnology/Biophysics, Faculty of Biological Science, Tarbiat Modares University, 14115-154, Tehran, Iran. Electronic address:

The ability to identify and enrich target cells can play a significant role in biosensing in general. For the separation of rare cells; a biosilica structure was extracted from "Chaetoceros sp." diatoms as a novel natural source of mesoporous materials. These diatoms had special optical capabilities, especially in fluorescence emission. Biosilica surfaces of Chaetoceros sp. were chemically modified by iron oxide nanoparticles resulting in diatom silica magnetic particles functionalized with Trastuzumab antibody to separate the breast cancer cells from normal cells. The fully characterization of magnetic biosilica structure were studied by various spectroscopic techniques. The magnetic diatom conjugated with antibody displays strong absorption and two main types of fluorescence emission with peaks centered at 493 and 650 nm (photo-excited at 405 nm). As in vitro study, SKBR3 cells (HER2 positive cells) were selectively targeted and separated with this magnetic diatom structure from the mix of HER2 negative cells using a magnetic field. These results show that Chaetoceros silica shells are promising eco-friendly biomaterials suitable for biosensing chip and the targeted delivery of drugs to the specific sites.
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http://dx.doi.org/10.1016/j.pdpdt.2020.101753DOI Listing
June 2020

A novel fluorescent hydroxyapatite based on iron quantum cluster template to enhance osteogenic differentiation.

Mater Sci Eng C Mater Biol Appl 2020 Jun 24;111:110775. Epub 2020 Feb 24.

Department of Nanobiotechnology/Biophysics, Faculty of Biological Science, Tarbiat Modares University, 14115-154 Tehran, Iran. Electronic address:

Template-mediated self-assembly synthesis has produced a diverse range of biomimetic materials with unique physicochemical properties. Here, we fabricated novel fluorescent three-dimensional (3-D) hydroxyapatite (HAP) nanorod-assembled microspheres using iron quantum cluster (FeQC) as a hybrid template, containing three organic components: hemoglobin chains, piperidine, and iron clusters. The material characterization indicated that the synthesized HAP possessed a uniform rod-like morphology, ordered 3-D architecture, high crystallinity, self-activated fluorescence, and remarkable photostability. Our study proposed that this FeQC template is a promising regulating agent to fabricate fluorescent self-assembled HAP microspheres with a controlled morphology. The effect of HAP on stem cell fate and their osteogenic differentiation was investigated by culturing human bone marrow-derived mesenchymal stromal/stem cells (BMSCs) with HAP microspheres. Significant increases in collagen matrix production and gene expression of osteogenic markers, including osteocalcin (OCN), Runt-related transcription factor 2 (Runx2), bone sialoprotein (BSP) and alkaline phosphatase (ALP), were observed compared to the controls after 21 days of culture. Taken together, our data suggest that synthetic HAP nanorod-assembled microspheres represent a promising new biomaterial which exhibits enhanced fluorescent properties and osteoinductive effects on human BMSCs.
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http://dx.doi.org/10.1016/j.msec.2020.110775DOI Listing
June 2020

PDMS Nano-Modified Scaffolds for Improvement of Stem Cells Proliferation and Differentiation in Microfluidic Platform.

Nanomaterials (Basel) 2020 Apr 2;10(4). Epub 2020 Apr 2.

Department of Nanobiotechnology, Faculty of Biological Science, Tarbiat Modares University, Tehran 14115-154, Iran.

Microfluidics cell-based assays require strong cell-substrate adhesion for cell viability, proliferation, and differentiation. The intrinsic properties of PDMS, a commonly used polymer in microfluidics systems, regarding cell-substrate interactions have limited its application for microfluidics cell-based assays. Various attempts by previous researchers, such as chemical modification, plasma-treatment, and protein-coating of PDMS revealed some improvements. These strategies are often reversible, time-consuming, short-lived with either cell aggregates formation, not cost-effective as well as not user- and eco-friendly too. To address these challenges, cell-surface interaction has been tuned by the modification of PDMS doped with different biocompatible nanomaterials. Gold nanowires (AuNWs), superparamagnetic iron oxide nanoparticles (SPIONs), graphene oxide sheets (GO), and graphene quantum dot (GQD) have already been coupled to PDMS as an alternative biomaterial enabling easy and straightforward integration during microfluidic fabrication. The synthesized nanoparticles were characterized by corresponding methods. Physical cues of the nanostructured substrates such as Young's modulus, surface roughness, and nanotopology have been carried out using atomic force microscopy (AFM). Initial biocompatibility assessment of the nanocomposites using human amniotic mesenchymal stem cells (hAMSCs) showed comparable cell viabilities among all nanostructured PDMS composites. Finally, osteogenic stem cell differentiation demonstrated an improved differentiation rate inside microfluidic devices. The results revealed that the presence of nanomaterials affected a 5- to 10-fold increase in surface roughness. In addition, the results showed enhancement of cell proliferation from 30% (pristine PDMS) to 85% (nano-modified scaffolds containing AuNWs and SPIONs), calcification from 60% (pristine PDMS) to 95% (PDMS/AuNWs), and cell surface marker expression from 40% in PDMS to 77% in SPION- and AuNWs-PDMS scaffolds at 14 day. Our results suggest that nanostructured composites have a very high potential for stem cell studies and future therapies.
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http://dx.doi.org/10.3390/nano10040668DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7221996PMC
April 2020

Gold Nanowires/Fibrin Nanostructure as Microfluidics Platforms for Enhancing Stem Cell Differentiation: Bio-AFM Study.

Micromachines (Basel) 2019 Dec 30;11(1). Epub 2019 Dec 30.

Department of Nanobiotechnology, Faculty of Biological Sciences, Tarbiat Modares University, Tehran 14115-154, Iran.

Organ-on-a-chip technology has gained great interest in recent years given its ability to control the spatio-temporal microenvironments of cells and tissues precisely. While physical parameters of the respective niche such as microchannel network sizes, geometric features, flow rates, and shear forces, as well as oxygen tension and concentration gradients, have been optimized for stem cell cultures, little has been done to improve cell-matrix interactions in microphysiological systems. Specifically, detailed research on the effect of matrix elasticity and extracellular matrix (ECM) nanotopography on stem cell differentiation are still in its infancy, an aspect that is known to alter a stem cell's fate. Although a wide range of hydrogels such as gelatin, collagen, fibrin, and others are available for stem cell chip cultivations, only a limited number of elasticities are generally employed. Matrix elasticity and the corresponding nanotopography are key factors that guide stem cell differentiation. Given this, we investigated the addition of gold nanowires into hydrogels to create a tunable biointerface that could be readily integrated into any organ-on-a-chip and cell chip system. In the presented work, we investigated the matrix elasticity (Young's modulus, stiffness, adhesive force, and roughness) and nanotopography of gold nanowire loaded onto fibrin hydrogels using the bio-AFM (atomic force microscopy) method. Additionally, we investigated the capacity of human amniotic mesenchymal stem cells (hAMSCs) to differentiate into osteo- and chondrogenic lineages. Our results demonstrated that nanogold structured-hydrogels promoted differentiation of hAMSCs as shown by a significant increase in Collagen I and II production. Additionally, there was enhanced calcium mineralization activity and proteoglycans formation after a cultivation period of two weeks within microfluidic devices.
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http://dx.doi.org/10.3390/mi11010050DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7019962PMC
December 2019

Corrigendum to "Encapsulation of an endostatin peptide in liposomes: Stability, release, and cytotoxicity study" [Colloids Surf. B Biointerfaces 185 (October) (2019) 110552].

Colloids Surf B Biointerfaces 2020 02 10;186:110694. Epub 2019 Dec 10.

Department of Nanobiotechnology/Biophysics, Faculty of Biological Science, Tarbiat Modares University, 14115-154 Tehran, Iran. Electronic address:

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http://dx.doi.org/10.1016/j.colsurfb.2019.110694DOI Listing
February 2020

Tuning fluorophore excitation in a total-internal-reflection-fluorescence microscopy.

Appl Opt 2019 Oct;58(29):8055-8060

In a total-internal-reflection-fluorescence-microscopy method, there is anisotropy in the polarized evanescent wave. Since the evanescent wave is used as an excitation field, the mentioned anisotropy is a disadvantage in using the total-internal-reflection-fluorescence-microscopy technique. Therefore, by theoretical and analytical approaches, and based on the Fresnel coefficients, the effect of three dielectrics media on the anisotropy of the evanescent wave is investigated. Following that, a proper combination of the cover glass, oil immersion, and prism for both living and non-living samples is suggested that not only enhances the intensity of the evanescent wave, but also and importantly, decreases the essential anisotropy of the evanescent wave.
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http://dx.doi.org/10.1364/AO.58.008055DOI Listing
October 2019

Encapsulation of an endostatin peptide in liposomes: Stability, release, and cytotoxicity study.

Colloids Surf B Biointerfaces 2020 Jan 15;185:110552. Epub 2019 Oct 15.

Department of Nanobiotechnology/Biophysics, Faculty of Biological Science, Tarbiat Modares University, 14115-154 Tehran, Iran. Electronic address:

The endostatin protein is a potent inhibitor of angiogenesis and tumor growth. The anti-angiogenic and antitumor properties of full-length endostatin can be mimicked by its N-terminal segment, including residues 1-27. Therefore, our previous studies have shown that a mutant N-terminal peptide which the Zn-binding loop was replaced by a disulfide loop (referred to as the ES-SS peptide) has preserved antiangiogenic and antitumor properties compared to the native peptide. To increase stability and plasma half-life of the ES-SS peptide, the nano-sized liposomal formulations of the peptide with different ratio of phosphocholine (PC) were synthesized. The liposomal peptide formulations possessed an average size of around 100 nm with (-4 to -36 mv) in zeta potential. The encapsulation efficiency of the ES-SS peptide was in the range of 24-54% with different lipid: peptide molar ratios. In vitro release of the peptide from liposomes indicated a complete peptide release after 7 days. Cytotoxicity assay was evaluated using the human umbilical vein endothelial cells (HUVECs) for various concentrations of the liposomal peptide. The results depicted the gradual release of the peptide through liposomes. By comparing with the free peptide, the liposomal peptide formulations have indicated higher cell viability with IC value about 0.1 μM. The peptide-liposome interactions, as well as the peptide effect on the liposome structure, were also investigated through coarse-grained molecular dynamics (CG-MD) simulation. The results revealed that the peptides were assembled in the hydrophilic core of the liposome. The peptide behavior in liposome can stabilize the liposome structure and be a response to the observed low peptide release rate. The investigation is promising for designing a liposome-based anti-angiogenesis peptide delivery system.
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http://dx.doi.org/10.1016/j.colsurfb.2019.110552DOI Listing
January 2020

A novel aspect of functionalized graphene quantum dots in cytotoxicity studies.

Toxicol In Vitro 2019 Dec 10;61:104649. Epub 2019 Sep 10.

Department of Nanobiotechnology/Biophysics, Faculty of Biological Sciences, Tarbiat Modares University, 14115-154 Tehran, Iran. Electronic address:

Graphene quantum dots (GQDs) represent a new generation of graphene-based nanomaterials with enormous potential for use and development of a variety of biomedical applications. However, up to now little studies have investigated the impact of GQDs on human health in case of exposure. GQDs were synthesized from citric acid as carbon precursor by hydrothermal treatment at 160 °C for 4 h. The synthesized GQDs showed strong blue emission under UV-Irradiation with fluorescence quantum yield of 9.8%. The obtained GQDs were further carbonized, activated and functionalized by nitric acid vapor method. Nitrogen adsorption/desorption isotherms were used to analyze the surface area and porous structures of GQDs. The results revealed that compared to GQDs, the specific surface area of functionalized graphene quantum dots (fGQDs) has been increased from 0.0667 to 2.5747 m/g and pore structures have been enhanced significantly. The potential cytotoxic effect of GQDs, fGQDs and GO suspensions was evaluated on HFF cell line using MTT assays and flow cytometry method after 24 h incubation. We have for the first time demonstrated that by carbonization, activation and functionalization of GQDs they still showed cytocompatible properties. We observed excellent biocompatibility of GQDs and fGQDs at low concentrations. Moreover, the results suggested that modification of GQDs yields product suspensions with high surface area, enhanced pore volume and loading capacities. Thus, fGQDs represent an attractive candidate for further use in drug delivery systems and bio-imaging application.
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http://dx.doi.org/10.1016/j.tiv.2019.104649DOI Listing
December 2019

Effects of natural compounds on conformational properties and hairpin formation of amyloid-β monomer: docking and molecular dynamics simulation study.

J Biomol Struct Dyn 2020 Jul 15;38(11):3371-3383. Epub 2019 Sep 15.

Faculty of Biological Sciences, Biophysics Department, Tarbiat Modares University, Tehran, Iran.

The β amyloid peptides (Aβ) are identified as a candidate target for Alzheimer's drugs. Phenolic compounds can bind to the Aβ and inhibit amyloid formation. However, the inhibitory mechanism of phenolic compounds remains unclear. In this study, the molecular dynamic simulation and docking program were used to characterize the molecular details of inhibitory mechanism of the phenolic compounds. Our Results show that the phenolic compounds can bind to hydrophobic region in Aβ monomer and alter hydrophobic interactions network at Aβ which play a key role in β-sheet formation. The cluster analysis and interactions network analysis were used to probe conformational changes in Aβ. In most populated clusters of Aβ-phenolic compounds complexes, the sheet structures were not observed or reduced. It seems that the binding of phenolic compounds can induce larger conformational diversity for amyloid peptide and changes conformational properties of amyloid peptide. The phenolic compounds can deform β-Hairpin structure of Aβ by destabilizing salt bridges E22-K28 and D23-K28 which can alter the conformation of Aβ in solution. These findings are in accordance with experimental results, to some extent give a molecular level interpretation for the inhibitory mechanism of phenolic compounds .In addition, this study may add important new details to the inhibitory mechanism of Alzheimer's drug.Communicated by Ramaswamy H. Sarma.
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http://dx.doi.org/10.1080/07391102.2019.1664934DOI Listing
July 2020

Activation of human insulin by vitamin E: A molecular dynamics simulation study.

J Mol Graph Model 2019 09 14;91:194-203. Epub 2019 Jun 14.

Biophysics Department, Faculty of Biological Sciences, Tarbiat Modares University, 14115-154, Tehran, Iran; School of Biological Science, Institute for Research in Fundamental Sciences (IPM), 19395-5746, Tehran, Iran. Electronic address:

Lack of perfect insulin signaling can lead to the insulin resistance, which is the hallmark of diabetes mellitus. Activation of insulin and its binding to the receptor for signaling process initiates via B-chain C-terminal hinge conformational change through an open structure to "wide-open" conformation. Observational studies and basic scientific evidence suggest that vitamin D and E directly and/or indirectly prevent diabetes through improving glucose secretion and tolerance, activating calcium dependent endopeptidases and thus improving insulin exocytosis, antioxidant effect and reducing insulin resistance. On the contrary, clinical trials have yielded inconsistent results about the efficacy of vitamin D supplementations for the control of glucose hemostasis. In this work, best binding modes of vitamin D and E on insulin obtained from AutoDock Vina were selected for Molecular Dynamic, MD, study. The binding energy obtained from Molecular Mechanics- Poisson Boltzman Surface Area, MM-PBSA method, revealed that Vitamins D and E have good affinity to bind to the insulin and vitamin E has higher binding energy (-46 kj/mol) by engaging more residues in binding site. Distance and angle calculation results illustrated that vitamin E changes the B-chain conformation and it causes the formation of wide-open/active form of insulin. Vitamin E increases the Val-Tyr distance to ∼15 Å and changes the hinge angle to ∼65°. Consequently, essential hydrophobic residues for binding to insulin receptor exposed to surface in the presence of vitamin E. However, our data illustrated that vitamin D cannot change B-chain conformation. Thus our MD simulations propose a model for insulin activation through vitamin E interaction for therapeutic approaches.
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http://dx.doi.org/10.1016/j.jmgm.2019.06.006DOI Listing
September 2019

Implicit solvent systematic coarse-graining of dioleoylphosphatidylethanolamine lipids: From the inverted hexagonal to the bilayer structure.

PLoS One 2019 5;14(4):e0214673. Epub 2019 Apr 5.

Department of Materials and Environmental Chemistry, Arrhenius Laboratory, Stockholm University, Stockholm, Sweden.

Lamellar and hexagonal lipid structures are of particular importance in the biological processes such as membrane fusion and budding. Atomistic simulations of formation of these phases and transitions between them are computationally prohibitive, hence development of coarse-grained models is an important part of the methodological development in this area. Here we apply systematic bottom-up coarse-graining to model different phase structures formed by 1,2-dioleoylphosphatidylethanolamine (DOPE) lipid molecules. We started from atomistic simulations of DOPE lipids in water carried out at two different water/lipid molar ratio corresponding to the lamellar Lα and inverted hexagonal HII structures at low and high lipid concentrations respectively. The atomistic trajectories were mapped to coarse-grained trajectories, in which each lipid was represented by 14 coarse-grained sites. Then the inverse Monte Carlo method was used to compute the effective coarse-grained potentials which for the coarse-grain model reproduce the same structural properties as the atomistic simulations. The potentials derived from the low concentration atomistic simulation were only able to form a bilayer structure, while both Lα and HII lipid phases were formed in simulations with potentials obtained at high concentration. The typical atomistic configurations of lipids at high concentration combine fragments of both lamellar and non-lamellar structures, that is reflected in the extracted coarse-grained potentials which become transferable and can form a wide range of structures including the inverted hexagonal, bilayer, tubule, vesicle and micellar structures.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0214673PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6450619PMC
December 2019

Chemiluminescent liposomes as a theranostic carrier for detection of tumor cells under oxidative stress.

Anal Chim Acta 2019 Jun 2;1059:113-123. Epub 2019 Feb 2.

Department of Nanobiotechnology/Biophysics, Faculty of Biological Science, Tarbiat Modares University, PO Box, 14115-154, Tehran, Iran. Electronic address:

Hydrogen peroxide (HO) is one of the main source of oxidative stress and a typical marker of reactive oxygen species (ROS)-associated diseases. Therefore, selective detection and scavenging of overproduced HO provide enormous benefits to the successful treatment of ROS-related diseases. The authors took advantage of this property to detect cancer cells using chemiluminescent peroxyoxalate reaction. Here, a new contrast agent presented for hydrogen peroxide, termed peroxyoxalate liposomes, which detect hydrogen peroxide through chemiluminescence reaction, and have the physical/chemical properties needed for imaging applications. The peroxyoxalate liposomes are composed of Bis (2, 4, 6-trichlorphenyl) oxalate (TCPO) and curcumin as fluorophore. Experimental factors such as TCPO, imidazole, hydrogen peroxide and curcumin concentration were optimized. Moreover, application of curcumin makes it possible to design a system for selective tumor destruction. In the reaction of peroxyoxalate, it acts as an oxalate activator with intracellular hydrogen peroxide and experiences excitation as a result of the reaction. In addition, curcumin also acts as a photosensitizer (PS) causing cell damage. In the optimum conditions, the measurable concentration range of 0.86-220 μM of hydrogen peroxide were evaluated from the linear calibration curve with satisfactory RSD% and corresponding detection limits of 650 nM. Therefore, it has the sensitivity needed to detect physiological concentrations of hydrogen peroxide. Moreover, cellular uptake experiments showed that the liposomes enhance extravasation into permeable membranes and significantly increased the bioavailability of curcumin.
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http://dx.doi.org/10.1016/j.aca.2019.01.045DOI Listing
June 2019

A cyclic peptide reproducing the α1 helix of VEGF-B binds to VEGFR-1 and VEGFR-2 and inhibits angiogenesis and tumor growth.

Biochem J 2019 02 19;476(4):645-663. Epub 2019 Feb 19.

Department of Biology, Faculty of Sciences, University of Guilan, 41335-19141 Rasht, Iran

Vascular endothelial growth factors (VEGFs) and their receptors (VEGFRs) are pivotal regulators of angiogenesis. The VEGF-VEGFR system is therefore an important target of anti-angiogenesis therapy. Based on the X-ray structure of VEGF-B/VEGFR-1 D2, we designed a cyclic peptide (known as VGB1) reproducing the α1 helix and its adjacent region to interfere with signaling through VEGFR-1. Unexpectedly, VGB1 bound VEGFR-2 in addition to VEGFR-1, leading to inhibition of VEGF-stimulated proliferation of human umbilical vein endothelial cells and 4T1 murine mammary carcinoma cells, which express VGEFR-1 and VEGFR-2, and U87 glioblastoma cells that mostly express VEGFR-2. VGB1 inhibited different aspects of angiogenesis, including proliferation, migration and tube formation of endothelial cells stimulated by VEGF-A through suppression of extracellular signal-regulated kinase 1/2 and AKT (Protein Kinase B) phosphorylation. In a murine 4T1 mammary carcinoma model, VGB1 caused regression of tumors without causing weight loss in association with impaired cell proliferation (decreased Ki67 expression) and angiogenesis (decreased CD31 and CD34 expression), and apoptosis induction (increased TUNEL staining and p53 expression, and decreased Bcl-2 expression). According to far-UV circular dichroism (CD) and molecular dynamic simulation data, VGB1 can adopt a helical structure. These results, for the first time, demonstrate that α1 helix region of VEGF-B recognizes both VEGFR-1 and VEGFR-2.
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http://dx.doi.org/10.1042/BCJ20180823DOI Listing
February 2019

Reaction mechanism of the bioluminescent protein mnemiopsin1 revealed by X-ray crystallography and QM/MM simulations.

J Biol Chem 2019 01 12;294(1):20-27. Epub 2018 Nov 12.

the Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Victoria 3010, Australia, and

Bioluminescence of a variety of marine organisms, mostly cnidarians and ctenophores, is carried out by Ca-dependent photoproteins. The mechanism of light emission operates via the same reaction in both animal families. Despite numerous studies on the ctenophore photoprotein family, the detailed catalytic mechanism and arrangement of amino acid residues surrounding the chromophore in this family are a mystery. Here, we report the crystal structure of Cd-loaded apo-mnemiopsin1, a member of the ctenophore family, at 2.15 Å resolution and used quantum mechanics/molecular mechanics (QM/MM) to investigate its reaction mechanism. The simulations suggested that an Asp-156-Arg-39-Tyr-202 triad creates a hydrogen-bonded network to facilitate the transfer of a proton from the 2-hydroperoxy group of the chromophore coelenterazine to bulk solvent. We identified a water molecule in the coelenteramide-binding cavity that forms a hydrogen bond with the amide nitrogen atom of coelenteramide, which, in turn, is hydrogen-bonded via another water molecule to Tyr-131. This observation supports the hypothesis that the function of the coelenteramide-bound water molecule is to catalyze the 2-hydroperoxycoelenterazine decarboxylation reaction by protonation of a dioxetanone anion, thereby triggering the bioluminescence reaction in the ctenophore photoprotein family.
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http://dx.doi.org/10.1074/jbc.RA118.006053DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6322872PMC
January 2019

Contribution of osteocalcin-mimetic peptide enhances osteogenic activity and extracellular matrix mineralization of human osteoblast-like cells.

Colloids Surf B Biointerfaces 2019 Jan 17;173:662-671. Epub 2018 Oct 17.

Stem cell and regenerative medicine group, National Institute of Genetic Engineering and Biotechnology, Tehran, 14965/161, Iran. Electronic address:

A natural peptide motif in the first helix of osteocalcin (OCN) is used to promote nucleation and crystallization of hydroxyapatite (HA) in hard tissue. The capability of osteocalcin mimetic peptides to induce osteogenic activity of osteoblast cells leading to in-vitro mineralization is demonstrated. An osteocalcin-derived peptide consisting of thirteen amino acids is synthesized in both acidic (OSC) and amidic (OSN) forms and added into the human osteoblast-like cells (MG63) culture. The viability, proliferation, alkaline phosphatase activity, HA deposition and osteogenic gene expression by osteoblast cells are evaluated. It is revealed that the addition of 100 μg/ml of peptides enhances the proliferation rate and total protein content of osteoblast cells. Alkaline phosphatase activity is significantly higher in the presence of peptides which in turn stimulated RNA expression of collagen type I and osteopontin in a phosphate-dependent manner. Alizarin red staining and calcium content measurement show that mineral deposition is considerably increased. Ultrastructural characterization of MG63 cultures confirms the crystalline nature and chemical composition of HA mineral formation in the presence of peptides. It is confirmed that the osteocalcin-derived peptide, particularly in amidic form (OSN), is able to act as a bioactive inducer of mineralization process and hence accelerating bone tissue regeneration.
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http://dx.doi.org/10.1016/j.colsurfb.2018.10.035DOI Listing
January 2019

Synergistic effect of co-immobilized FGF-2 and vitronectin-derived peptide on feeder-free expansion of induced pluripotent stem cells.

Mater Sci Eng C Mater Biol Appl 2018 Dec 26;93:157-169. Epub 2018 Jul 26.

Stem Cell Technology Research Center, Tehran, Iran.

Expansion of human induced pluripotent stem cells (h-iPSCs) on mouse derived feeder layers or murine cells secretions such as Matrigel hamper their clinical applications. Alternative methods have introduced novel substrates as stem cell niches or/and optimized combinations of humanized soluble factors as fully defined mediums. Accordingly vitronectin as a main part of ECM have been commercialized significantly as a stem cell niche-forming substrate. In this work, we used a functional peptide derived from vitronectin (VTN) and co-immobilized it with FGF-2 (as an indisputable ingredient of defined culture mediums) on chitosan film surface. After chemical and physical characterization of the pristine chitosan surface as well as ones modified by VTN or/and FGF-2, h-iPS cells were cultured on them at the xeno/feeder-free conditions. Our results demonstrated that co-immobilization of these two biomolecules has a synergistic effect on adhesion and clonal growth of h-iPS cells with maintained expression of pluripotency markers in a FGF-2 density-dependent manner. This is the first report of co-immobilization of an ECM derived molecule and a growth factor for stem cell culture.
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http://dx.doi.org/10.1016/j.msec.2018.07.072DOI Listing
December 2018

A combination of bioactive and nonbioactive alkyl-peptides form a more stable nanofiber structure for differentiating neural stem cells: a molecular dynamics simulation survey.

J Biomol Struct Dyn 2019 08 18;37(13):3434-3444. Epub 2019 Jan 18.

a Department of Biological Science , Tarbiat Modares University , Tehran , Iran.

Self-assembling alkyl-peptides are important molecules due to their ability to construct nano-level structures such as nanofibers to be utilized as tissue engineering scaffolds. The bioactive epitope of FAQRVPP which acts as neural stem cells (NSCs) outgrowth inducing factor is used in nanofiber structures. Based on previous experimental studies the density and distribution pattern of the epitopes on the surface of the nanofibers plays an important role in the differentiation function efficiency. We decided to survey and compare the stability of two pre-constructed fiber structures in the forms of all-functionalized nanofiber (containing only bioactive alkyl-peptides) and distributed functionalized nanofiber (a combination of nonbioactive and bioactive alkyl-peptides with ratio 2:1). Our findings reveal that the all-functionalized fiber shows an unstable structure and is split into intermediate micelle-like structures to reduce compactness and steric hindrance of functional epitopes whereas the distributed functionalized fiber shows an integrated stable nanofiber with a more amount of beta sheets that are well-organized and oriented around the hydrophobic core. The hydrogen bonds and energy profiles of the structures indicate the role of hydrophobic interactions during the alkyl-chain core formation and the important role of electrostatic interactions and hydrogen bond network in the stability of the final structures. Finally, it seems that the possibility of the presence of intermediate structure is increased in the all-functionalized nanofiber environment, and it can reduce functional efficiency of the scaffolds. These findings can help to design more efficient nanofiber structures with different goals in scaffolds for tissue engineering. Abbreviations MD Molecular Dynamics NSCs Neural Stem Cells PME Particle mesh Ewald RDF Radial Distribution Function RG Radius of gyration RASA Relative Accessible Surface Area RMSD Root Mean Square Deviations SASA Solvent Accessible Surface Area. Communicated by Ramaswamy H. Sarma.
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http://dx.doi.org/10.1080/07391102.2018.1516571DOI Listing
August 2019

Poly-l-lysine-coated superparamagnetic nanoparticles: a novel method for the transfection of pro-BDNF into neural stem cells.

Artif Cells Nanomed Biotechnol 2018 22;46(sup3):S125-S132. Epub 2018 Jul 22.

d Division of Biotechnology , University of technology , Baghdad , Iraq ; Department of Biotechnology , University of technology , Baghdad , Iraq.

Poly-l-lysine-coated superparamagnetic iron oxide nanoparticles (SPIONs-PLL) were prepared and used as a novel-carrier for the transfer of brain-derived neurotrophic factor (BDNF) into neural stem cells (NSCs) under the beneficial influence of an external magnetic field. Pro-BDNF, a gene from human brain cDNA libraries, was obtained by polymerase chain reaction and constructed in a mammalian expression vector (PSecTag2/HygroB). The nanoparticles (NPs) were examined using Fourier transform infrared spectroscopy, zeta potential, and Transmission electron microscopy. From the results, the levels of BDNF among the transfected and untransfected cells were 30.326 ± 5.9 and 5.85 ± 3.11 pg/mL, respectively, as detected by an ELISA method. Moreover, the enhanced green fluorescent protein vector was used to evaluate the gene expression efficiency for SPIONs-PLL as a non-viral carrier in NSCs. This was performed under the influence of a magnetic field and the transfection reagents (such as Lipofectamine 2000), which served as a positive control. The histological analysis revealed that the concentration of intracellular NPs was significantly higher than intercellular NPs. These results suggest that SPIONs-PLL can serve as a novel alternative for the transfection of BDNF-NSCs and could be used in gene therapy.
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http://dx.doi.org/10.1080/21691401.2018.1489272DOI Listing
June 2019

Protein adsorption onto polysaccharides: Comparison of chitosan and chitin polymers.

Carbohydr Polym 2018 Jul 14;191:191-197. Epub 2018 Mar 14.

Department of Life Sciences Engineering, Faculty of New Sciences & Technologies, University of Tehran, Tehran, Iran.

Chitosan (CHS) and chitin (CHT) biopolymers have found many applications in the field of controlled-release drug delivery systems. Herein, molecular dynamics (MD) simulation and binding free energy calculations were used to investigate the potentials of CHS and CHT polymers for the controlled release of follicle-stimulating hormone (FSH). The results indicated that FSH conformation did not change in the presence of CHS and CHT. In addition, FSH-polymer interactions caused stability of the 3-helix structure of the alpha subunits of FSH (FSHα). Both the biopolymers interacted with the protein mainly through the hydrophobic forces. CHS has more affinity for FSH when compared with CHT. Furthermore, in both systems, the affinity of polymers for FSHα was more than that for beta subunits of FSH (FSHβ). The results suggested that the polysaccharides might improve the controlled-release FSH delivery.
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http://dx.doi.org/10.1016/j.carbpol.2018.03.034DOI Listing
July 2018

Monodisperse Rattle-Structured Gold Nanorod-Mesoporous Silica Nanoparticles Core-Shell as Sulforaphane Carrier and its Sustained-Release Property.

Drug Res (Stuttg) 2018 Sep 16;68(9):504-513. Epub 2018 Apr 16.

Department of Nanobiotechnology, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran.

Sulforaphane (SF) was loaded into the multi-functioned rattle-structured gold nanorod mesoporous silica nanoparticles core-shell to improve its stability and efficacy through its efficient delivery to tumors. The rattle-structured gold nanorod mesoporous silica nanoparticles (rattle-structured AuNR@mSiO core-shell NPs) were obtained by covering the surface of Au NPs with Ag and mSiO shell and subsequently selective Ag shell etching strategy. Then the surface of rattle-structured AuNR@mSiO NPs was decorated with thiolated polyethylene glycol-FITC and thiolated polyethylene glycol-folic acid to the designed form. The obtained FITC/FA@ [rattle-structured AuNR@mSiO] NPs was characterized by different techniques including energy dispersive X-ray spectroscopy (EDX), scanning and transmission electron microscopy (SEM & TEM), UV-visible spectrophotometer and dynamic light scattering (DLS). The FITC/FA@ [rattle-structured AuNR@mSiO] NPs has an average diameter around ~33 nm, which increases to ~38 nm after the loading of sulforaphane. The amount of the loaded drug was ~ 2.8×10-4 mol of SF per gram of FITC/FA@ [rattle-structured AuNR@mSiO] NPs. The rattle-structured AuNR@mSiO and FITC/FA@ [rattle-structured AuNR@mSiO] NPs showed little inherent cytotoxicity, whereas the SF loaded FITC/FA@ [rattle-structured AuNR@mSiO] NPs was highly cytotoxic in the case of MCF-7 cell line. Finally, Fluorescence microscopy and flow cytometry were used to demonstrate that the nanoparticles could be accumulated in specific regions and SF loaded FITC/FA@ [FeO@Au] NPs efficiently induce apoptosis in MCF-7 cell line Graphical Abstract.
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http://dx.doi.org/10.1055/a-0573-8966DOI Listing
September 2018

Hemoglobin-incorporated iron quantum clusters as a novel fluorometric and colorimetric probe for sensing and cellular imaging of Zn(II) and cysteine.

Mikrochim Acta 2017 12 18;185(1):60. Epub 2017 Dec 18.

Department of Nanobiotechnology/Biophysics, Faculty of Biological Science, Tarbiat Modares University, Tehran, 14115-154, Iran.

The authors describe a novel water-soluble, stable, biocompatible, and highly fluorescent probe consisting of iron quantum clusters incorporated into human adult hemoglobin (Hb-FeQCs). The Hb-FeQCs were characterized by various spectroscopic techniques. The probe displays strong absorption and yellow fluorescence with a peak centered at 567 nm (photo-excited at 460 nm). The Hb-FeQCs show excellent photostability over a wide range of pH values (5-12), even in the presence of high electrolyte concentrations. A colorimetric and a fluorometric method were worked out for the quantitation Zn(II) and cysteine in aqueous solution. Zinc ions induce a visible color change from brown to yellow. The sensitivity of Hb-FeQCs towards other metal ions was negligible, with the exception of Co and Cu, which caused a modest interference. The Hb-FeQCs were exploited in a sensitive and selective turn-on fluorescence assay for Zn. It is also found that cysteine quenches the fluorescence of the Hb-FeQCs/Zn(II) complex. Under the optimized conditions, the probe has a linear response in the 0.04 to 2.2 μM Zn(II) concentration range, with a 48 nM detection limit. Response to cysteine is linear in the 1-60 μM concentration range, with a 0.25 μM limit of detection. This fluorescent probe undergoes fluorescent emission intensity enhancement upon binding to zinc ions in living normal human fibroblast cells under visible lamp. The cellular imaging capability and very low cytotoxicity of this soluble iron quantum clusters can be potentially extended as an exciting sub-nanoplatform with promising biomaterial applications. Graphical abstract Schematic of yellow-emitting iron quantum clusters in hemoglobin matrix (Hb-FeQCs) were characterized and successfully applied for sensing zinc(II) and cysteine. The act as an on-off fluorescent probe and can be applied to image zinc ions in human fibroblast cells under visible light.
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http://dx.doi.org/10.1007/s00604-017-2600-xDOI Listing
December 2017

Peptide modified nanofibrous scaffold promotes human mesenchymal stem cell proliferation and long-term passaging.

Mater Sci Eng C Mater Biol Appl 2018 Mar 21;84:80-89. Epub 2017 Nov 21.

Department of Nanobiotechnology, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran; Department of Biophysics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran. Electronic address:

Long-term culture, passage and proliferation of human mesenchymal stem cells (hMSCs) cause loss of their stemness properties including self-renewal and multipotency. By optimizing the MSCs environment in vitro, maintaining the stemness state and better controlling the cell fate might be possible. We have recently reported the significant effects of bioactive Tat protein-derived peptide named R-peptide on hMSC adhesion, morphology and proliferation, which has demonstrated R-peptide enhanced MSC early adhesion and proliferation in comparison to other bioactive molecules including RGD peptide, fibronectin and collagen. In this study, R-peptide was used to evaluate stemness properties of MSCs after long-term passaging. R-peptide conjugated poly caprolactone (PCL) nanofibrous scaffold and unmodified nanofibrous scaffold were used to study the impact of R-peptide modified PCL nanofibers and PCL nanofibers on cell behavior. The results showed early formation of focal adhesion (FA) complex on R-peptide modified scaffolds at 30min after cell seeding. The rate of cell proliferation was significantly increased due to presence of R-peptide, and the MSCs marker analyses using flow cytometry and immunocytochemistry staining proved the ability of R-peptide to maintain mesenchymal stem cell properties (high proliferation, expression of multipotent markers and differentiation capacity) even after long-term passage culturing. Accordingly, our (The) results concluded that bioactive R-peptide in combination with nanofibrous scaffold can mimic the native ECM comprising micro/nano architecture and biochemical molecules in a best way. The designed scaffold can link extracellular matrix (ECM) to nucleus via formation of FA and organization of cytoskeleton, causing fast and strong attachment of MSCs and allowing integrin-mediated signaling to start.
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http://dx.doi.org/10.1016/j.msec.2017.11.017DOI Listing
March 2018

Proteomic features of delayed ocular symptoms caused by exposure to sulfur mustard: As studied by protein profiling of corneal epithelium.

Biochim Biophys Acta Proteins Proteom 2017 Nov 5;1865(11 Pt A):1445-1454. Epub 2017 Sep 5.

Department of Biophysics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran. Electronic address:

Exposure to mustard gas can lead to variations in the proteome of corneal epithelium cells and after a latency period produces delayed symptoms in the eyes of chemical victims. Hence, a comparative proteome analysis was conducted between the corneal epithelial cells of chemical victims from Iran-Iraq war (1980-1988) and healthy donors. To this end, corneal epithelium samples from victims and healthy individuals were collected, and the proteome of these samples were prepared for two-dimensional electrophoresis and the analysis of spots by statistical software. Selected spots were further analyzed by matrix-assisted laser desorption/ionization time-of-flight/time-of-flight mass spectrometry. Twenty four proteins were identified of which eighteen proteins showed downregulation while six proteins were upregulated in the victims in comparison to the normal individuals. Also, six protein spots were confirmed by western-blot analysis. In conclusion, all the twenty-four identified proteins are involved in pathways which their up- or down-regulation leads to the accumulation of undesired substrates, cell death and apoptosis. Bioinformatics' tools indicated that these identified proteins were involved in various metabolic processes, DNA damage response, immune response and etc. The present study provides a suitable platform for further clinical studies.
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http://dx.doi.org/10.1016/j.bbapap.2017.08.021DOI Listing
November 2017

QM/MM simulations provide insight into the mechanism of bioluminescence triggering in ctenophore photoproteins.

PLoS One 2017 4;12(8):e0182317. Epub 2017 Aug 4.

Department of Biochemistry, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran.

Photoproteins are responsible for light emission in a variety of marine ctenophores and coelenterates. The mechanism of light emission in both families occurs via the same reaction. However, the arrangement of amino acid residues surrounding the chromophore, and the catalytic mechanism of light emission is unknown for the ctenophore photoproteins. In this study, we used quantum mechanics/molecular mechanics (QM/MM) and site-directed mutagenesis studies to investigate the details of the catalytic mechanism in berovin, a member of the ctenophore family. In the absence of a crystal structure of the berovin-substrate complex, molecular docking was used to determine the binding mode of the protonated (2-hydroperoxy) and deprotonated (2-peroxy anion) forms of the substrate to berovin. A total of 13 mutants predicted to surround the binding site were targeted by site-directed mutagenesis which revealed their relative importance in substrate binding and catalysis. Molecular dynamics simulations and MM-PBSA (Molecular Mechanics Poisson-Boltzmann/surface area) calculations showed that electrostatic and polar solvation energy are +115.65 and -100.42 kcal/mol in the deprotonated form, respectively. QM/MM calculations and pKa analysis revealed the deprotonated form of substrate is unstable due to the generation of a dioxetane intermediate caused by nucleophilic attack of the substrate peroxy anion at its C3 position. 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.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0182317PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5544205PMC
October 2017

Evidence of Multi-Domain Morphological Structures in Living Escherichia coli.

Sci Rep 2017 07 18;7(1):5660. Epub 2017 Jul 18.

Department of Nanobiotechnology, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, P.O. Box 14115-111, Iran.

A combination of light-microscopy and image processing was used to elaborate on the fluctuation in the width of the cylindrical part of Escherichia coli at sub-pixel-resolution, and under in vivo conditions. The mean-squared-width-difference along the axial direction of the cylindrical part of a number of bacteria was measured. The results reveal that the cylindrical part of Escherichia coli is composed of multi-domain morphological structures. The length of the domains starts at 150 nm in newborn cells, and linearly increases in length up to 300 nm in aged cells. The fluctuation in the local-cell-widths in each domain is less than the fluctuation of local-cell-widths between different domains. Local cell width correlations along the cell body occur on a length scale of less than 50 nm. This finding could be associated with the flexibility of the cell envelope in the radial versus longitudinal directions.
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http://dx.doi.org/10.1038/s41598-017-05897-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5516040PMC
July 2017