Three-Dimensional Graph Matching to Identify Secondary Structure Correspondence of Medium-Resolution Cryo-EM Density Maps

Cryo-electron microscopy (cryo-EM) is a structural technique that has played a significant role in protein structure determination in recent years. Compared to the traditional methods of X-ray crystallography and NMR spectroscopy, cryo-EM is capable of producing images of much larger protein complexes. However, cryo-EM reconstructions are limited to medium-resolution (~4–10 Å) for some cases. At this resolution range, a cryo-EM density map can hardly be used to directly determine the structure of proteins at atomic level resolutions, or even at their amino acid residue backbones. At such a resolution, only the position and orientation of secondary structure elements (SSEs) such as α-helices and β-sheets are observable. Consequently, finding the mapping of the secondary structures of the modeled structure (SSEs-A) to the cryo-EM map (SSEs-C) is one of the primary concerns in cryo-EM modeling. To address this issue, this study proposes a novel automatic computational method to identify SSEs correspondence in three-dimensional (3D) space. Initially, through a modeling of the target sequence with the aid of extracting highly reliable features from a generated 3D model and map, the SSEs matching problem is formulated as a 3D vector matching problem. Afterward, the 3D vector matching problem is transformed into a 3D graph matching problem. Finally, a similarity-based voting algorithm combined with the principle of least conflict (PLC) concept is developed to obtain the SSEs correspondence. To evaluate the accuracy of the method, a testing set of 25 experimental and simulated maps with a maximum of 65 SSEs is selected. Comparative studies are also conducted to demonstrate the superiority of the proposed method over some state-of-the-art techniques. The results demonstrate that the method is efficient, robust, and works well in the presence of errors in the predicted secondary structures of the cryo-EM images

Amino acid-mPEGs: Promising excipients to stabilize human growth hormone against aggregation

Objective(s): Today, the non-covalent PEGylation methods of protein pharmaceuticals attract more attention and possess several advantages over the covalent approach. In the present study, Amino Acid-mPEGs (aa-mPEGs) were synthesized, and the human Growth Hormone (hGH) stability profile was assessed in their presence and absence.Materials and Methods: aa-mPEGs were synthesized with different amino acids (Trp, Glu, Arg, Cys, and Leu) and molecular weights of polymers (2 and 5 KDa). The aa-mPEGs were analyzed with different methods. The physical and structural stabilities of hGH were analyzed by SEC and CD spectroscopy methods. Physical stability was assayed at different temperatures within certain intervals. Molecular dynamics (MD) simulation was used to realize the possible mode of interaction between protein and aa-mPEGs. The cell-based method was used to evaluate the cytotoxicity.Results: HNMR and FTIR spectroscopy indicated that aa-mPEGs were successfully synthesized. hGH as a control group is known to be stable at 4 °C; a pronounced change in monomer degradation is observed when stored at 25 °C and 37 °C. hGH:Glu-mPEG 2 kDa with a molar ratio of 1:1 to the protein solution can significantly increase the physical stability. The CD spectroscopy method showed that the secondary structure of the protein was preserved during storage. aa-mPEGs did not show any cytotoxicity activities. The results of MD simulations were in line with experimental results.Conclusion: This paper showed that aa-mPEGs are potent excipients in decreasing the aggregation of hGH. Glu-mPEG exhibited the best-stabilizing properties in a harsh environment among other aa-mPEGs

Russian olive (Elaeagnus angustifolia) as a herbal healer

Introduction: Elaeagnus spp. is one in the family of riparian trees growing near the rivers or water corridors. In this family, Elaeagnus angustifolia (Russian olive) is famous because of its medical applications. Methods: A comprehensive review was performed to extract the related data from published literature. Results: Traditionally, it has been used as an analgesic, antipyretic and diuretic herbal medicine. A large number of compounds have been derived from Russian olive and made this plant a source of flavonoids, alkaloids, minerals and vitamins. Although the purpose of most studies is to use this plant for preparation of herbal medicines and as an ingredient for drug formulation, there is no available drug dosage form commercially. Conclusion: This review aimed to provide the most important documentary information on the active components of Elaeagnus spp. and their relation to the pharmacological properties and compare them with reported medicinal effects

Probing the interaction behavior of Nano-Resveratrol with α-lactalbumin in the presence of β-lactoglobulin and β-casein: spectroscopy and molecular simulation studies

The main purpose of this research was to evaluate the role of α-lactalbumin (α-LA), β-lactoglobulin (β-LG), and β-Caseins (β-CN) in the binding interaction between Nano Resveratrol (Nano Res), as binary and ternary systems. This investigation was fulfilled through the application of multi-spectroscopic, transmission electron microscopy (TEM), field emission scanning electron microscope (FE-SEM), conductometry, isothermal titration calorimetry (ITC), and molecular dynamics (MD) simulation techniques. Fluorescence spectroscopy observations illustrated the effectiveness of Nano Res throughout the quenching of α-LA, (α-LA-β-LG), and (α-LA-β-CN) complexes, confirming the occurrence of interaction through the combination of static and dynamic mechanisms. An enhancement in the temperature of all three complexes caused a decrease in their Ksv and Kb values, which indicates the static and dynamic behavior of their interactions. The obtained thermodynamic parameters proved the dominance of electrostatic interaction as the binding force of both binary and ternary systems. The observed properties of Tyr or Trp residues in proteins through the data of synchronous spectroscopy at Δλ = 15 and 60 nm, respectively, demonstrated the closer positioning of (α-LA-β-CN) complex to the proximity of Trp residues when compared to the two other cases. According to the resonance light scattering (RLS) measurements, the detection of a much greater RLS intensity in (α-LA-β-CN) Nano Res complex suggested the production of a larger complex. Furthermore, the conductometry outcomes displayed an increase in molar conductivity and therefore approved the occurrence of interaction between Nano Res and proteins in both binary and ternary systems. The spherical shape of Nano Res was confirmed through the results of FE-SEM and TEM analyses. The conformational changes of proteins throughout the binding of Nano Res was evaluated by circular dichroism (CD) technique, while molecular docking and MD simulations affirmed the binding of Nano Res to α-LA, (α-LA-β-LG), and (α-LA-β-CN) complexes as binary and ternary systems. These In Silico study data confirm the results of in vitro assessments. The occurrence of changes in the secondary structure of β-galactosidase was implied through the increased enzyme catalytic activity induced by the interaction of different lactose concentrations. Communicated by Ramaswamy H. Sarma</p

Use of Spectroscopic, Zeta Potential and Molecular Dynamic Techniques to Study the Interaction between Human Holo-Transferrin and Two Antagonist Drugs: Comparison of Binary and Ternary Systems

For the first time, the binding of ropinirole hydrochloride (ROP) and aspirin (ASA) to human holo-transferrin (hTf) has been investigated by spectroscopic approaches (fluorescence quenching, synchronous fluorescence, time-resolved fluorescence, three-dimensional fluorescence, UV-vis absorption, circular dichroism, resonance light scattering), as well as zeta potential and molecular modeling techniques, under simulated physiological conditions. Fluorescence analysis was used to estimate the effect of the ROP and ASA drugs on the fluorescence of hTf as well as to define the binding and quenching properties of binary and ternary complexes. The synchronized fluorescence and three-dimensional fluorescence spectra demonstrated some micro-environmental and conformational changes around the Trp and Tyr residues with a faint red shift. Thermodynamic analysis displayed the van der Waals forces and hydrogen bonds interactions are the major acting forces in stabilizing the complexes. Steady-state and time-resolved fluorescence data revealed that the fluorescence quenching of complexes are static mechanism. The effect of the drugs aggregating on the hTf resulted in an enhancement of the resonance light scattering (RLS) intensity. The average binding distance between were computed according to the forster non-radiation energy transfer theory. The circular dichroism (CD) spectral examinations indicated that the binding of the drugs induced a conformational change of hTf. Measurements of the zeta potential indicated that the combination of electrostatic and hydrophobic interactions between ROP, ASA and hTf formed micelle-like clusters. The molecular modeling confirmed the experimental results. This study is expected to provide important insight into the interaction of hTf with ROP and ASA to use in various toxicological and therapeutic processes