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Microfluidic cell encapsulation has provided a platform for studying the behavior of individual cells and has become a turning point in single-cell analysis during the last decade. The engineered microenvironment, along with protecting the immune response, has led to increasingly presenting the results of practical and pre-clinical studies with the goals of disease treatment, tissue engineering, intelligent control of stem cell differentiation, and regenerative medicine. However, the significance of cell-substrate interaction versus cell-cell communications in the microgel is still unclear. In this study, monodisperse alginate microgels were generated using a flow-focusing microfluidic device to determine how the cell microenvironment can control human bone marrow-derived mesenchymal stem cells (hBMSCs) viability, proliferation, and biomechanical features in single-cell droplets versus multi-cell droplets. Collected results show insufficient cell proliferation (234 % and 329 %) in both single- and multi-cell alginate microgels. Alginate hydrogels supplemented with poly-l-lysine (PLL) showed a better proliferation rate (514 % and 780 %) in a comparison of free alginate hydrogels. Cell stiffness data illustrate that hBMSCs cultured in alginate hydrogels have higher membrane flexibility and migration potency (Young's modulus equal to 1.06 kPa), whereas PLL introduces more binding sites for cell attachment and causes lower flexibility and migration potency (Young's modulus equal to 1.83 kPa). Considering that cell adhesion is the most important parameter in tissue engineering, in which cells do not run away from a 3D substrate, PLL enhances cell stiffness and guarantees cell attachments. In conclusion, cell attachment to PLL-mediated alginate hydrogels is crucial for cell viability and proliferation. It suggests that cell-cell signaling is good enough for stem cell viability, but cell-PLL attachment alongside cell-cell signaling is crucial for stem cell proliferation and self-renewal., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier B.V. All rights reserved.)

The oral formulation design for colon-specific drug delivery brings some therapeutic benefits in the ulcerative colitis treatment. We recently reported the specific delivery of hemoglobin nanoparticles-conjugating 5-aminosalicylic acid (5-ASA-HbNPs) to the inflamed site. In the current study, the therapeutic effect of the 5-ASA-HbNPs formulation was confirmed in vivo. This evaluation of 5-ASA-HbNPs not only shows longer colonic retention time due to adhesive properties, also provides full support for it as compared with free 5-ASA. It was considered as a suitable bio-adhesive nanoparticle with mucoadhesive property to pass through the mucus layer and accumulate into the mucosa. In UC model mice, a two-fold decrease in the disease activity indexes and colon weight/length ratios was significantly observed in the group treated with 5-ASA-HbNPs. This group received one percent of the standard dosage of 5-ASA (50 μg/kg), while, a similar result was observed for a significant amount of free 5-ASA (5 mg/kg). Furthermore, microscopic images of histological sections of the extracted colons demonstrated that the 5-ASA-HbNPs and 5-ASA groups displayed instances of inflammatory damage within the colon. However, in comparison to the colitis group, the extent of this damage was relatively moderate, suggesting 5-ASA-HbNPs improved therapeutic efficacy with the lower dosage form., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 American Pharmacists Association. Published by Elsevier Inc. All rights reserved.)

Glucosamine (Glu) is a cartilage and joint fluid matrix precursor that modulates osteoarthritic joint changes. To improve the enzymatic stability, glucosamine was developed into nanoglucosamine by the ionic gelation method through sodium tripolyphosphate (TPP) as cross-linking agent. The optimized mass ratio of Glu:TPP was (3:1) with the particle size 163 ± 25 nm and surface charge -5 mV. Then Sinapic acid (SA) as a natural phenolic acid with strong antioxidant and antimicrobial activities has been grafted onto glucosamine nanoparticles (GluNPs) with grafting efficiency (73 ± 6 %). The covalent insertion of SA was confirmed by UV-Vis, FTIR, 1 HNMR, XRD, and FESEM analyses and the other physicochemical properties were also characterized. SA-g-GluNPs showed spherical shape with a mean diameter of 255 ± 20 nm and zeta potential +16 mV. The in vitro release profile of SA-g-GluNPs exhibited the sustained and pH-dependent drug release property. SA-g-GluNPs had a more pronounced effect on reducing the elevated levels of LPS-induced oxidative stress and pro-inflammatory cytokines than free SA in the human chondrocyte C28/I2 cell line. Furthermore, the antibacterial properties against E. coli and S. aureus were also improved by SA-g-GluNPs. This study demonstrated the potential of phenolic acid grafted GluNPs in therapeutic drug applications for chondroprotection and food industries., Competing Interests: Declaration of competing interest The authors declare that they have no conflict of interest., (Copyright © 2023 Elsevier B.V. All rights reserved.)

Valproic acid (VPA) usage in high dose is teratogen with low bioavailability. Hence to improve its efficacy and reduce its side effect it was encapsulated by the Nano liposomes and stabilized by the chitosan at different concentrations. The cellular uptake, biocompatibility, loading and encapsulation efficiency of the six-different formulations (1:1, 2:1, and 4:1 of chitosan-phospholipids: VPA), PC12 differentiation to neuron cells assays (gene-expression level by qRT-PCR) were conducted for the efficacy assessment of the Nano carriers. The encapsulation efficiency (EE) results revealed that the encapsulation of the VPA corresponds to the phospholipids dose, where 2:1 formulations showed higher encapsulating rate (64.5% for non-coated and 80% for coated by chitosan). The time monitored released of VPA also showed that the chitosan could enhance its controlled release too. The cellular uptake exhibited similar uptake behavior for both the coated and the non-coated Nano carriers and cytoplasmic distribution. We witnessed no toxicity effects, at different concentrations, for both formulations. Moreover, the results indicated that the gene expression level of SOX2, NeuroD1, and Neurofilament 200 increased from 1 to 5 folds for different genes. The qRT-PCR data were confirmed by the immunofluorescence antibodies staining, where Neurofilament 68 and SOX2 cell markers were modulated during differentiation of PC12 cells. Finally, our findings suggest promising potential for the Lip-VPA-Chit Nano carrier in inducing the differentiation of PC12 into neuron for treating neurodegenerative disorders., (Copyright © 2022. Published by Elsevier B.V.)

Despite efforts to achieve a long-acting formulation for human growth hormone (hGH), daily injections are still prescribed for children with growth hormone deficiency. To grapple with the issue, acquiring a deep knowledge of the protein and understanding its interaction mechanism with the carrier can be beneficial. Herein, we designed and synthesized a novel chitosan-based copolymer and investigated its interaction with hGH using a combination of experimental and computational strategies. To construct the amphiphilic triblock copolymers (CDP), we grafted deoxycholic acid (DCA) and polyacrylic acid (PAA) onto the chitosan chains, and Fourier-transform infrared (FTIR) analysis confirmed the proper formation of CDP. Circular dichroism (CD) demonstrated the preservation of the secondary structure of hGH interacting with CDP, and, further, fluorescence spectroscopy proved the stability of the tertiary structure of the protein. Applying molecular dynamics simulation (MD), we examined the dynamics and integrity of hGH in the presence of the copolymer and compared its behavior with the protein in aquatic environments. Additionally, energy and contact analysis illustrated that the residues involved in the interaction were located predominantly in the connecting loops, and van der Waals (vdW) and electrostatic interactions were the main driving forces of the polymer-protein complex formation. This research's main aim was to trace the protein-polymer interaction's mechanism. We anticipate that the utility of the copolymer can address the challenges of fabricating a new sustained-release delivery platform for therapeutic proteins., (Copyright © 2021 Elsevier B.V. All rights reserved.)

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 2+ . It suggests that Cu 2+ 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 2+ -caused quenching. This probe has a satisfactorily linear range of 0.35-35 μM for Cu 2+ 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 3  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 2+ 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)., (Copyright © 2020 Elsevier B.V. All rights reserved.)

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., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2020 Elsevier B.V. All rights reserved.)

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., Competing Interests: Declaration of Competing Interest The authors declare that they have no conflict of interest., (Copyright © 2020 Elsevier B.V. All rights reserved.)

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 50 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., (Copyright © 2019 Elsevier B.V. All rights reserved.)

Hydrogen peroxide (H 2 O 2 ) 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 H 2 O 2 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., (Copyright © 2019 Elsevier B.V. All rights reserved.)

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., (Copyright © 2018. Published by Elsevier B.V.)

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., (Copyright © 2018 Elsevier B.V. All rights reserved.)

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., (Copyright © 2017 Elsevier B.V. All rights reserved.)

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., (Copyright © 2017 Elsevier B.V. All rights reserved.)

Photoinactivation is a common phenomenon in bioluminescence ctenophore photoproteins (e.g mnemiopsin, berovin and BfosPP) with still unknown mechanism. The activity of coelenterate photoproteins (e.g aequorin), which has high structural similarity with ctenophore photoproteins, is not affected by light. Recently, we have characterized the effects of light on ctenophore photoprotein mnemiopsin, in different conformations, which has demonstrated light induced structural changes, uniquely secondary structures, of both apo and holo mnemiopsin. This paper is further expansion of our previous work, by applying molecular dynamics simulations to investigate photoinactivation related dynamics of berovin at atomistic level, in comparison with aequorin, under the influence of electric component of electromagnetic field. The results have indicated that the intense electric filed could influence structure of both berovin and aequorin but in different manner, whereas moderate electric field only effects on berovin's structure remarkably. In this case, increased helicity of residues E180-M193 and decreased helical contents of L38-D46 and L125-D138 segments are considerable in berovin as well as flexibility elevation of calcium binding loops. These changes cause structural expansion of berovin, especially at N-terminal domain, in direction of electric field. In conclusion, the induced structural changes of mentioned helical parts together with elevated fluctuation of their adjacent segments, N26-D46 and M193-Y206, indicate the influence of light on substrate stabilizing residues, Arg41 and Y204. This condition could presumably leads to inactivation of bioluminescence reaction due to separation of substrate from the cavity of the protein., (Copyright © 2017 Elsevier Inc. All rights reserved.)

Dextran sulfate-chitosan (DS-CS) nanoparticles, which possesses properties such as nontoxicity, biocompatibility and biodegradability have been employed as drug carriers in cancer therapy. In this study, DS-CS nanoparticles were synthesized and their sizes were controlled by a modification of the divalent cations cross-linkers (Ca 2+ , Zn 2+ or Mg 2+ ). Based on the optimized processing parameters, lapatinib encapsulated nanoparticles were developed and characterized by Dynamics Light Scattering (DLS) measurements, Fourier Transform Infrared Spectroscopy (FT-IR) and Scanning Electron Microscopy (SEM). Calcium chloride (CaCl 2 ) facilitated the formation of bare (100.3±0.80nm) and drug-loaded nanoparticles (134.3±1.3nm) with narrow size distributions being the best cross-linker. The surface potential of drug-loaded nanoparticles was -16.8±0.47mV and its entrapment and loading efficiency were 76.74±1.73% and 47.36±1.27%, respectively. Cellular internalization of nanoparticles was observed by fluorescence microscopy and MTT (3-(4, 5-dimethylthiazol-2-yl)-2, 5-diphenyltetrazolium bromide) assay was used to determine cytotoxicity of bare and drug-loaded nanoparticles in comparison to the free drug lapatinib. The MTT assay showed that drug-loaded nanoparticles had comparable anticancer activity to free drug within a duration of 48h. The aforementioned results showed that the DS-CS nanoparticles were able to entrap, protect and release the hydrophobic drug, lapatinib in a controlled pattern and could further serve as a suitable drug carrier for cancer therapy., (Copyright © 2016 Elsevier B.V. All rights reserved.)

Surface modification of the substrate as a component of in vitro cell culture and tissue engineering, using bio-active molecules including extracellular matrix (ECM) proteins or peptides derived ECM proteins can modulate the surface properties and thereby induce the desired signaling pathways in cells. The aim of this study was to evaluate the behavior of human bone marrow mesenchymal stem cells (hBM-MSCs) on glass substrates modified with fibronectin (Fn), collagen (Coll), RGD peptides (RGD) and designed peptide (R-pept) as bio-active molecules. The glass coverslips were coated with fibronectin, collagen, RGD peptide and R-peptide. Bone marrow mesenchymal stem cells were cultured on different substrates and the adhesion behavior in early incubation times was investigated using scanning electron microscopy (SEM) and confocal microscopy. The MTT assay was performed to evaluate the effect of different bio-active molecules on MSCs proliferation rate during 24 and 72 h. Formation of filopodia and focal adhesion (FA) complexes, two steps of cell adhesion process, were observed in MSCs cultured on bio-active molecules modified coverslips, specifically in Fn coated and R-pept coated groups. SEM image showed well adhesion pattern for MSCs cultured on Fn and R-pept after 2 h incubation, while the shape of cells cultured on Coll and RGD substrates indicated that they might experience stress condition in early hours of culture. Investigation of adhesion behavior, as well as proliferation pattern, suggests R-peptide as a promising bio-active molecule to be used for surface modification of substrate in supporting and inducing cell adhesion and proliferation., (Copyright © 2016 Elsevier Inc. All rights reserved.)

The integrative and cooperative nature of protein structure involves the assessment of topological and global features of constituent parts. Network concept takes complete advantage of both of these properties in the analysis concomitantly. High compatibility to structural concepts or physicochemical properties in addition to exploiting a remarkable simplification in the system has made network an ideal tool to explore biological systems. There are numerous examples in which different protein structural and functional characteristics have been clarified by the network approach. Here, we present an interactive and user-friendly Matlab-based toolbox, PDB2Graph, devoted to protein structure network construction, visualization, and analysis. Moreover, PDB2Graph is an appropriate tool for identifying critical nodes involved in protein structural robustness and function based on centrality indices. It maps critical amino acids in protein networks and can greatly aid structural biologists in selecting proper amino acid candidates for manipulating protein structures in a more reasonable and rational manner. To introduce the capability and efficiency of PDB2Graph in detail, the structural modification of Calmodulin through allosteric binding of Ca(2+) is considered. In addition, a mutational analysis for three well-identified model proteins including Phage T4 lysozyme, Barnase and Ribonuclease HI, was performed to inspect the influence of mutating important central residues on protein activity., (Copyright © 2016 Elsevier Ltd. All rights reserved.)

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., (Copyright © 2012 Elsevier B.V. All rights reserved.)

The industrial utilization of savinase is mainly constrained by its stability limitations. In the present study, the irreversible thermoinactivation of savinase has been evaluated at 70 degrees C, and various possible mechanisms for irreversible thermoinactivation of savinase were examined. The main process seemed to be autodigestion of savinase at higher temperatures. To improve the thermal stability of the enzyme, the effect of two co-solvents (sorbitol and trehalose) on the enzyme's activity and stability was investigated. Both osmolytes prevented the autolysis of savinase at 70 degrees C without inactivating the enzyme; furthermore, the structural and kinetic stabilities of the enzyme increased in the presence of additives.

Molecular dynamics simulation method is used to assess the contribution of a disease-associated salt bridge in the early stages of the conformational rearrangement of human prion protein upon Arg208-->His mutation, which causes Creutzfeldt-Jakob disease. Previous investigations have suggested that the breakage of this putative salt bridge (D144/E146<-->Arg208) between helix 1 and helix 3 is responsible for such a mutation-driven process. So far, no experimental data has been reported in order to distinguish the contribution of this single salt bridge in the initial steps of amyloid formation. Consequently, we decided to investigate the role of this salt bridge in early conformational rearrangements. To remove the salt bridge without perturbations in the backbone structure, the neutralized states of the involved residues were used. Three 10-ns molecular dynamics simulations on three initial structures have been performed. The results revealed that the early stages of the conformational rearrangements, against common belief, are mainly associated with the mutation-induced global changes in the backbone dynamics but not with the breaking of the salt bridge.

A facile method for the formation of covalent bonds between protein molecules is zero-length cross-linking. This method enables the formation of cross-links without use of any chemical reagents. Here, the cross-linking is performed for lysozyme, peroxidase (a glycoprotein) and between lysozyme-peroxidase by the method of Simons et al. [B.L. Simons, M.C. King, T. Cyr, M.A. Hefford, H. Kaplan, Covalent cross-linking of protein without chemical reagents, Protein Sci. 2002, 11, 1558-1564]. Approximately one-third of the total lysozyme becomes cross-linked and the dimer form was the major product for both enzymes. This modification induced some changes in the kinetic properties of the dimer peroxidase, as evident by two-fold increasing of V(max) compared to the monomer but the enzymatic activity of cross-linked lysozyme dimer was the same as monomer. The activity of lysozyme dimer remained constant up to 10min at 80 degrees C, while peroxidase activity of both monomer and dimer began to decrease after heating. The structural changes of the enzymes were investigated by circular dichroism and intrinsic fluorescence techniques. Near UV result showed lysozyme possess a compact structure in the dimer form but disruption of tertiary structure of peroxidase dimer was observed. Also conformational changes were detected and discussed by intrinsic fluorescence experiments. Effect of several metals in the formation of lysozyme dimer showed that Co(2+) is the most effective one but its effect was marginal. At the end formation of heterogeneous dimer, peroxidase-lysozyme, was achieved using this method.

We decided to investigate the influence of the presence of disulfide bonds on the pattern of force distribution in the functional site of scorpion toxin BMK M1 in its functional state. Therefore, a series of short time molecular dynamics (MD) simulations were performed on this toxin in the native state and disulfide bond broken states. The comparison of disulfide bond broken states with the native state showed that the electrostatic potential energy of important functional residues in the reverse turn and C-terminal regions were modulated by the cooperative effect of all disulfide bonds in the molecule. Furthermore, our results revealed that disulfide bonds also play a cooperative role in modulating (1) the amplitude of the fluctuations of the functional segments and (2) the correlation of motions between important functional residue pairs in this toxin. Therefore, we can conclude that the disulfide bonds have cooperation to adjust the pattern of force distribution in the functional site of this toxin in its functional state.

The first cDNA from lampyridae encoding a glow-worm luciferase from lantern mRNA of Lampyris turkestanicus has been cloned, sequenced, the amino acid sequence predicted, and the sequence reported to GenBank. The cDNA was 1644 base pairs in length and coding a 547-residue protein. The deduced amino acid sequence of the luciferase gene of L. turkestanicus showed 98.7% and 95.8% identity to Lampyris noctiluca and Pyrocoelia rufa, respectively. Phylogenetic analysis further confirmed that the deduced amino acid sequences of L. turkestanicus luciferase gene belong to the same subfamily, Lampyrinae. The cDNA encoding the luciferase of L. turkestanicus was expressed as a 62kDa band in recombinant Escherichia coli and showed green luminescence in the presence of luciferin. Amongst amino acid differences of L. turkestanicus and L. noctiluca (its clade) there are two important substitutions. Signature amino-acid sequences and motifs found in the deduced sequence are CK2-phospho site, ASN-glycosylation, myristoylation site, PKC-phospho site, microbodies C-terminal targeting signal, and AMP-binding domain.

Detailed circular dichroism (CD), scattering and quenching studies, 1-anilinonaphthalene-8-sulfonate (ANS) binding, irreversible thermoinactivation, activity measurements and proteolytic digestion of bacterial alpha-amylases have been carried out to elucidate the effect of trifluoroethanol (TFE) on the structure of these enzymes. Under high concentrations of TFE both of the alpha-amylases, a thermostable alpha-amylase from Bacillus licheniformis (BLA) and its mesophilic counterpart from Bacillus amyloliquefaciens (BAA), acquire partially folded state characterized by an enhanced content of the secondary structure (helix) and reduced tertiary structures. According to ANS binding studies, we suggest that the TFE states induced by TFE/water mixture are not the molten globule state in the alpha-amylase folding pathway. In addition, data shows significant reversible aggregation of both enzymes in TFE/water mixtures with concentration between 10 and 60% (v/v). However, reversibility is more in case of BAA. As expected, in the absence of TFE, the thermophilic enzyme compared to mesophilic enzyme, shows a greater resistance to digestion by thermolysin. With respect to fluorescence quenching by acrylamide and potassium iodide, the thermophilic enzyme, BLA, is characterized by higher structural flexibility as compared to the BAA. On the other hand, in the presence of TFE, the enzymes are digested by protease to produce large protein fragments. It is proposed that highly helical secondary structures, acquired by BAA and BLA when dissolved in aqueous TFE, prevent binding and adaptation of the protein substrate at the active site of the protease.