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Molecular relational learning refers to forecasting the interaction performance between pairs of molecules. Graph neural networks (GNNs) enables the effective modeling of chemical molecules by transferring them as abstract structures of graph, thus considering node-level interactions instead of atom's. However, the abilities of modeling and predicting of classical GNN methods is restricted by edges' redundancy and insufficient process of interaction modeling in a pair of molecular graphs. Therefore, based on the novel hypergraph convolutional neural network and bi-view cross interaction message passing and updating, we propose a hypergraph-based neural network method named IE-HGNN (Internal-External Bi-view Hypergraph Neural Network). We evaluate our method on two real-world molecular datasets, i.e., LEP and ZhangDDI, demonstrating IE-HGNN achieves excellent performance for both macro and micro molecules, while maintaining high training efficiency. We believe that this study introduces a novel approach for exploring the field of molecular relational learning and interaction prediction. [ABSTRACT FROM AUTHOR]

The effect of the temperature and salt solution on the structural characteristics of the protein 1BBL was investigated by molecular dynamics simulations. The paper presents simulation results regarding the non-bonded energy and the structural stability of the protein immersed in salt solutions with different concentrations and temperatures. Our work demonstrates that the electrostatic potential energy and van der Waals energy of the system show the opposite changes with the influence of the external environment. Since the electrostatic potential energy changes more obviously, it is dominated in the non-bonding interactions. The structural parameters, such as the root mean square deviation and the radius of gyration, increased initially and decreased afterward with the increase of the salt concentration. The protein presented the loose structure with a relative low stability when it was immersed in a monovalent solution with a salt concentration of 0.8 mol/L. The salt concentration corresponding to the maximum value of structural parameters in the monovalent salt solution was double that in the divalent salt solution. It was also concluded that the protein presented a compact and stable structure when immersed in salt solutions with a high concentration of 2.3 mol/L. The analysis of the root mean square deviation and root mean square fluctuation of the protein sample also exhibited that the structural stability and chain flexibility are strongly guided by the effect of the temperature. These conclusions help us to understand the structural characteristics of the protein immersed in the salt solutions with different concentrations and temperatures. [ABSTRACT FROM AUTHOR]

Green synthesis of nanoparticles has fuelled the use of biomaterials to synthesise a variety of metallic nanoparticles. The current study investigates the use of xylanases of Aspergillus niger L3 (NEA) and Trichoderma longibrachiatum L2 (TEA) to synthesise silver nanoparticles (AgNPs). Characterisation of AgNPs was carried out using UV–Vis spectroscopy, Fourier transform infrared spectroscopy (FTIR), and transmission electron microscopy, while their effectiveness as antimicrobial, antioxidant, catalytic, anticoagulant, and thrombolytic agents were determined. The colloidal AgNPs was brownish with surface plasmon resonance at 402.5 and 410 nm for NEA‐AgNPs and TEA‐AgNPs, respectively; while FTIR indicated that protein molecules were responsible for the capping and stabilisation of the nanoparticles. The spherical nanoparticles had size of 15.21–77.49 nm. The nanoparticles significantly inhibited the growth of tested bacteria (63.20–88.10%) and fungi (82.20–86.10%), and also scavenged DPPH (37.48–79.42%) and hydrogen peroxide (20.50–96.50%). In addition, the AgNPs degraded malachite green (78.97%) and methylene blue (25.30%). Furthermore, the AgNPs displayed excellent anticoagulant and thrombolytic activities using human blood. This study has demonstrated the potential of xylanases to synthesise AgNPs which is to the best of our knowledge the first record of such. The present study underscores the relevance of xylanases in nanobiotechnology. [ABSTRACT FROM AUTHOR]

In the present study, silver nanoparticles (AgNPs) were synthesised by adding 1 mM Ag nitrate solution to different concentrations (1%, 2.5%, 5%) of branch extracts of Eurycoma longifolia, a well known medicinal plant in South–East Asian countries. Characterisation of AgNPs was carried out using techniques such as ultraviolet–visible spectrophotometry, X‐ray diffractrometry, Fourier transform infrared–attenuated total reflection spectroscopy (FTIR–ATR), scanning electron microscopy. XRD analysis revealed face centre cubic structure of AgNPs and FTIR–ATR showed that primary and secondary amide groups in combination with the protein molecules present in the branch extract were responsible for the reduction and stabilisation of AgNPs. Furthermore, antioxidant [2,2‐diphenyl‐1‐picrylhydrazyl and 2,2′‐Azino‐bis(3‐ethylbenzthiazoline‐6‐sulphonic acid)], antimicrobial and anticancer activities of AgNPs were investigated. The highest bactericidal activity of these biogenic AgNPs was found against Escherichia coli with zone inhibition of 11 mm. AgNPs exhibited significant anticancer activity against human glioma cells (DBTRG and U87) and human breast adenocarcinoma cells (MCF‐7 and MDA‐MB‐231) with IC50 values of 33, 42, 60 and 38 µg/ml. [ABSTRACT FROM AUTHOR]

This paper proposes a novel method for computing the cavities and channels/tunnels in a protein molecule in interactive time without significant user effort. A sphere tree structure is used to represent a protein molecule, which provides a parallel architecture to access a Graphic Processing Unit (GPU) memory. The use of CUDA programming with a GPU then allows the proposed system to work in parallel on either a sphere tree structure of a molecule or a set of voxels composing the space. A real-time performance is achieved for proximity queries on a protein molecule, and an interactive time performance is realized for finding all the cavities and channel/tunnels without user effort. The proposed system also provides a method for approximating a convex hull of a molecule in a discrete space, and then generates the shortest path from a user selected or automatically chosen cavity to the exterior of the protein molecule. Experimental results in comparison with previous methods confirm the time efficiency of the proposed system. [ABSTRACT FROM AUTHOR]

Abstract: Here we reported the assembly of horseradish peroxidase molecules mediated by the alternating magnetic field. The field can make quasi-one-dimensional assembly conformations. We proved the phenomenon was relative to the magnetic property of HRP molecules. Importantly, the electromagnetic field had little influence on the biological activity of HRP molecules. [Copyright &y& Elsevier]

The properties of absorption of infrared light for collagen, hemoglobin, bivine serum albumen (BSA) protein molecules with α- helix structure and water in the living systems as well as the infrared transmission spectra for person's skins and finger hands of human body in the region of 400-4000 cm (i.e., wavelengths of 2-20 μm) have been collected and determined by using a Nicolet Nexus 670 FT-IR Spectrometer, a Perkin Elmer GX FT-IR spectrometer, an OMA (optical multichannel analysis) and an infrared probe systems, respectively. The experimental results obtained show that the protein molecules and water can all absorb the infrared lights in the ranges of 600-1900 cm and 2900-3900 cm, but their properties of absorption are somewhat different due to distinctions of their structure and conformation and molecular weight. We know from the transmission spectra of person's finger hands and skin that the infrared lights with wavelengths of 2 μm-7 μm can not only transmit over the person's skin and finger hands, but also be absorbed by the above proteins and water in the living systems. Thus, we can conclude from this study that the human beings and animals can absorb the infrared lights with wavelengths of 2 μm-7 μm. [ABSTRACT FROM AUTHOR]

Combination effects of structure disorder of protein molecules containing the fluctuations of spring constant, dipole-dipole interaction constant and exciton-phonon coupling constant and diagonal disorder, resulting from nonuniform distribution of masses of amino acid residues and impurities, on the soliton transported the bio-energy in the proteins have been numerically simulated by fourth-order Runge–Kutta method in the improved model. The results obtained show that these structure disorders can change the states of solitons but as the solitons are quite robust against these disorder effects, they can only be dispersed or disrupted in the cases of quite large structure disorders. From these results and the properties of molecular structure of biological proteins we can conclude that the new soliton in the improved model is quite stable in normal conditions. Thus the soliton is possibly a carrier of bio-energy transport in the protein molecules. [ABSTRACT FROM AUTHOR]

The dynamic behaviors of the new soliton in the improved Davydov model in the protein molecules at biological temperature have been numerically simulated by utilizing the dynamic equations for the bio-energy transport and the Runge–Kutta way. In this simulation the influences of the temperature and structure disorders of the protein molecules on the soliton transporting the bio-energy have been completely considered. We find that the new soliton is quite stable in the cases of motion of a long time of 300 ps and of disorders of the structures of the proteins at biological temperatures of 300 K–320 K. The disorders of the structures contain the disorder of mass sequence of amino acids and the fluctuations of the coupling constant, force constant and dipole- dipole interaction constant and ground state energy of the proteins, designating the features of its structure and interactions between the particles in it. However, the soliton disperses in the cases of higher temperature of 325 K and larger structure disorders. The numerical results show that the new soliton is very robust against the influences of the thermal perturbation and structure disorders at biological temperature 300 K, its lifetime and critical temperature are at least 300 ps at 300 K and 320 K, respectively. These results are also consistent with analytical data. [ABSTRACT FROM AUTHOR]