Relationship between stability and flexibility in the most flexible region of Photinus pyralis luciferase.

Firefly luciferase is a protein with a large N-terminal and a small C-terminal domain. B-factor analysis shows that its C-terminal is much more flexible than its N-terminal. Studies on hyperthermophile proteins have been shown that the increased thermal stability of hyperthermophile proteins is due to their enhanced conformational rigidity and the relationship between flexibility, stability and function in most of proteins is on debate. Two mutations (D474K and D476N) in the most flexible region of firefly luciferase were designed. Thermostability analysis shows that D476N mutation doesn't have any significant effect but D474K mutation destabilized protein. On the other hand, flexibility analysis using dynamic quenching and limited proteolysis demonstrates that D474K mutation became much more flexible than wild type although D476N doesn't have any significant difference. Intrinsic and ANS fluorescence studies demonstrate that D476N mutation is brought about by structural changes without significant effect on thermostability and flexibility. Molecular modeling reveals that disruption of a salt bridge between D(474) and K(445) accompanying with some H-bond deletion may be involved in destabilization of D474K mutant.

Engineering a platelet-rich plasma-based multifunctional injectable hydrogel with photothermal, antibacterial, and antioxidant properties for skin regeneration.

Wound healing remains a significant challenge worldwide, necessitating the development of new wound dressings to aid in the healing process. This study presents a novel photothermally active hydrogel that contains platelet-rich plasma (PRP) for infected wound healing. The hydrogel was formed in a one pot synthesis approach by mixing alginate (Alg), gelatin (GT), polydopamine (PDA), and PRP, followed by the addition of CaCl2 as a cross-linker to prepare a multifunctional hydrogel (AGC-PRP-PDA). The hydrogel exhibited improved strength and good swelling properties. PDA nanoparticles (NPs) within the hydrogel endowed them with high photothermal properties and excellent antibacterial and antioxidant activities. Moreover, the hydrogels sustained the release of growth factors due to their ability to protect PRP. The hydrogels also exhibited good hemocompatibility and cytocompatibility, as well as high hemostatic properties. In animal experiments, the injectable hydrogels effectively filled irregular wounds and promoted infected wound healing by accelerating re-epithelialization, facilitating collagen deposition, and enhancing angiogenesis. The study also indicated that near-infrared light improved the healing process. Overall, these hydrogels with antibacterial, antioxidant, and hemostatic properties, as well as sustained growth factor release, show significant potential for skin regeneration in full-thickness, bacteria-infected wounds.

The optimal electrical stimulation for neural differentiation of conjunctiva mesenchymal stem cells.

AIMS: The combination of biomaterial conductive scaffolds and electrical stimulation (ES) dramatically promotes stem cell differentiation into electro-responsive cells like neural cells. In this study, we aimed to fabricate PCL/PPY nanofiber scaffolds through the electrospinning method and investigate the effect of ES duration on neural differentiation of Conjunctiva Mesenchymal Stem Cells (CJMSCs). METHODS: The topography of the fabricated scaffold was characterized using SEM and TEM microscopy, and its mechanical and other properties were determined by tensile, TGA, FTIR, and Contact angle tests. CJMSCs were seeded on the scaffolds and then subjected to electrical current (115 V m-1 at 100 Hz) with durations of 1, 3, and 7 min for 3 days. Then the effect of nanofiber scaffold and electrical currents on cell viability and expression of neural marker genes (Nestin, ß-tubulin, MAP-2) was investigated by MTT assay and qPCR analysis. RESULTS: Our results revealed the good biocompatibility of the PCL-PPy nanofiber scaffold, and according to q-PCR results, the electrical stimulation of 1 min day-1 for 3 days can induce neural differentiation of CJMSCs as indicated by the fold change of gene expression of Nestin (~127), B-tubulin (~30), and MAP-2 (~52). CONCLUSION: This study emphasizes that the utilization of an electrically conductive nanofibrous scaffold in conjunction with electrical current has potential applications in the field of neural tissue engineering.

Investigating the importance of Delaunay-based definition of atomic interactions in scoring of protein-protein docking results.

The approaches taken to represent and describe structural features of the macromolecules are of major importance when developing computational methods for studying and predicting their structures and interactions. This study attempts to explore the significance of Delaunay tessellation for the definition of atomic interactions by evaluating its impact on the performance of scoring protein-protein docking prediction. Two sets of knowledge-based scoring potentials are extracted from a training dataset of native protein-protein complexes. The potential of the first set is derived using atomic interactions extracted from Delaunay tessellated structures. The potential of the second set is calculated conventionally, that is, using atom pairs whose interactions were determined by their separation distances. The scoring potentials were tested against two different docking decoy sets and their performances were compared. The results show that, if properly optimized, the Delaunay-based scoring potentials can achieve higher success rate than the usual scoring potentials. These results and the results of a previous study on the use of Delaunay-based potentials in protein fold recognition, all point to the fact that Delaunay tessellation of protein structure can provide a more realistic definition of atomic interaction, and therefore, if appropriately utilized, may be able to improve the accuracy of pair potentials.

Docking, Molecular Dynamics Simulation and Synthesis of New Fenobam Analogues as mGlu5 Receptor Antagonists.

BACKGROUND: Fenobam is a non-competitive mGluR5 antagonist as an anxiolytic agent. OBJECTIVE: In this research a new series of fenobam analogues containing thiazole moiety instead of imidazole ring were designed and synthesized. METHODS: The ureido-substituted products were synthesized from reaction of amino thiazole derivatives and isocyanate derivatives in dichloromethane solvent under microwave and ultrasonic irradiation condition. The synthesized compounds structures were established by means of IR, 1HNMR, 13CNMR spectroscopic data. Then, docking calculations were performed on the active site of mGLuR5 and compared to Fenobam as a reference drug by using AutoDock program. The molecular dynamics (MD) simulations were done using GROMACS 5.0.5. RESULTS: Docking studies suggested that all of the compounds possess better binding energy when compared to fenobam. The results of MD simulations might offer the binding mode of ligand (3b), accuracy of docking and the reliability of active conformations which obtained by AutoDock. CONCLUSION: New derivatives of fenobam were designed and synthesized that have the better insilico results compared to fenobam and will evaluate in future studies.

Molecular Dynamics Simulation and Docking Studies of Selenocyanate Derivatives as Anti-Leishmanial Agents.

BACKGROUND: Selenocyanate derivatives have been recently presented as potent anti-leishmanial agents. OBJECTIVE: In this research, thirty five selenocyanate and diselenide compounds were subjected to docking studies and compared to Edelfosine and Miltefosine as reference drugs and then molecular dynamics (MD) simulation analysis. METHODS: Desired Selenocyanates were built using the HyperChem program and docking calculations were performed on the crystal structure of trypanothione reductase from Leishmania infantum. Then, MD simulation analysis was performed to explore the interaction stability of selected compound during structural motions of the interacting molecules. RESULTS: Based on the binding energy, all of the aryl rings were more potent than Edelfosine and Miltefosine as reference drug. The best compound base on hydrogen bonding, π-π interactions and orientation within the active site with high binding energy was selected for MD simulation analysis. The selected compound is known as high-affinity selective inhibitor for trypanothione reductase. CONCLUSION: These results can be used for future synthesis of new antileishmanial agents with better potency.

Evidence for the relationship between the regulatory effects of microRNAs and attack robustness of biological networks.

It has been previously suggested that microRNAs (miRNAs) have a tendency to regulate the important components of biological networks. The goal of the present study was to systematically test if one can establish a relationship between miRNA targets and the important components of biological networks (including human protein-protein interaction network, signaling network and metabolic network). For this analysis, we have studied the attack robustness of these networks. It has been previously shown that deletion of network vertices in descending order of their importance (e.g., in decreasing order of vertex degrees) can affect the network structure much more considerably. In the current study, we introduced three miRNA-based measures of importance: "miRNA count" (i.e., the number of miRNAs that regulate a given network component); average adjacent miRNA count, "AAmiC" (i.e., the average number of miRNAs regulating the targeted components adjacent to a given component); and total adjacent miRNA count, "TAmiC" (i.e., the total number of miRNAs regulating the targeted components adjacent to a given component). Our results suggest that "miRNA count" is only marginally capable of locating the important components of the networks, while TAmiC was the most relevant measure. By comparing TAmiC with the classical centrality measures (which are solely based on the network structure) when simultaneously removing vertices, we show that this measure is correlated to degree and betweenness centrality measures, while its performance is generally better than that of closeness and eigenvector centrality measures. The results of this study suggest that TAmiC which represents a measure based on both network structure and biological knowledge, can successfully determine the important network components indicating that miRNA regulation and network robustness are related.