Evolving cellular automata schemes for protein folding modeling using the Rosetta atomic representation

Protein folding is the dynamic process by which a protein folds into its final native structure. This is different to the traditional problem of the prediction of the final protein structure, since it requires a modeling of how protein components interact over time to obtain the final folded structure. In this study we test whether a model of the folding process can be obtained exclusively through machine learning. To this end, protein folding is considered as an emergent process and the cellular automata tool is used to model the folding process. A neural cellular automaton is defined, using a connectionist model that acts as a cellular automaton through the protein chain to define the dynamic folding. Differential evolution is used to automatically obtain the optimized neural cellular automata that provide protein folding. We tested the methods with the Rosetta coarse-grained atomic model of protein representation, using different proteins to analyze the modeling of folding and the structure refinement that the modeling can provide, showing the potential advantages that such methods offer, but also difficulties that arise.

Structure Refinement and Fragmentation of Precipitates under Severe Plastic Deformation: A Review

During severe plastic deformation (SPD), the processes of lattice defect formation as well as their relaxation (annihilation) compete with each other. As a result, a dynamic equilibrium is established, and a steady state is reached after a certain strain value. Simultaneously, other kinetic processes act in opposite directions and also compete with each other during SPD, such as grain refinement/growth, mechanical strengthening/softening, formation/decomposition of solid solution, etc. These competing processes also lead to dynamic equilibrium and result in a steady state (saturation), albeit after different strains. Among these steady-state phenomena, particle fragmentation during the second phase of SPD has received little attention. Available data indicate that precipitate fragmentation slows down with increasing strain, though saturation is achieved at higher strains than in the case of hardness or grain size. Moreover, one can consider the SPD-driven nanocrystallization in the amorphous phase as a process that is opposite to the fragmentation of precipitates. The size of these crystalline nanoprecipitates also saturates after a certain strain. The fragmentation of precipitates during SPD is the topic of this review.

Molecular docking study on columbin isolated from Tinospora cordifolia as a cholinesterase inhibitor

Purpose: To investigate the acetylcholinesterase (AChE) inhibitory potential of columbin and also to assess its binding affinity against AChE protein. Methods: Crystals of columbin were isolated from the ethyl acetate fraction of Tinospora cordifolia using column chromatography and its structure was determined using x-ray crystallography. Ellman colorimetric assay was used to determine the AChE inhibitory effect in vitro while molecular docking was performed using the MOE 2015.010 software. The selected protein data bank (PDB) was modeled using PDB ID: 10CE (pacific electric ray). Results: The crystal and structure refinement data of columbin were: C20H22O6, Orthorhombic, P212121, a = 7.4951(2) Å (α = 90°), b = 11.6451(3) Å (β = 90°), c = 19.5882(5) Å (γ = 90°), V=1709.68(8) Å3, Z = 4, Density (calculated) = 1.392 Mg/m3, absorption coefficient = 0.851 mm-1, goodness-of-fit on F2 =1.091, T = 100(2) K. Columbin demonstrated good AChE inhibitory effect with half-maximal inhibitory concentration (IC50) of 1.2993 ± 0.17 mg/mL. Molecular docking data revealed that it exhibited hydrophobic and hydrogen bonding interactions with the surrounding residues, and this accelerated complexation between the ligands and the active site of the enzyme. Conclusion: Columbin may be useful in the management of neurodegenerative conditions such as Alzheimer’s disease.

Synthesis, crystal-structure refinement and properties of bastnaesite-type PrF[CO3], SmF[CO3] and EuF[CO3]

By adding a hot aqueous solution containing KF and K2[CO3] to another hot aquatic brine of Pr[NO3]3 ⋅ 5 H2O, Sm[NO3]3 ⋅ 5 H2O or Eu[NO3]3 ⋅ 5 H2O with a 1.3 times excess of the anion-providing solution, amorphous water-insoluble powders of PrF[CO3], SmF[CO3] and EuF[CO3] can be obtained. Through hydrothermal treatment at 210 °C for five days crystalline powders could be synthesized and their crystal structure was refined with Rietveld methods based on PXRD data. The named compounds crystallize in the bastnaesite-type structure with a = 710.912(12) pm, c = 976.811(6) pm for the praseodymium, a = 704.77(2) pm, c = 971.83(4) pm for the samarium and a = 700.734(6) pm, c = 969.066(8) pm for the europium compound, all hexagonal with Z = 6. Upon heating them, the compounds lose CO2 and fluoride oxides REFO emerge. Thermogravimetric experiments with crystalline samples show thermal stability up to 420 °C for PrF[CO3], 400 °C for SmF[CO3] and 340 °C for EuF[CO3], but decomposition below 200 °C for the amorphous ones. Infrared spectroscopy confirms only marginal portions of [OH]− instead of F− anions in all cases. The RE 3+ cations are coordinated by 9 + 2 anions at distances between 236 and 254 pm plus 326 pm to F− anions and oxygen atoms bonded to carbon as oxocarbonate anions [CO3]2−. Triggered by ultraviolet radiation, the bulk sample of EuF[CO3] shows a poor red luminescence.

A Comparison of the Effects of Ultrasonic Cavitation on the Surfaces of 45 and 40Kh Steels

The ultrasonic treatment of metal products in liquid is used mainly to remove various kinds of contaminants from surfaces. The effects of ultrasound not only separate and remove contaminants, they also significantly impact the physical–mechanical and geometric properties of the surfaces of products if there is enough time for treatment. The aim of this study was to compare the dynamics of ultrasonic cavitation effects on the surface properties of 45 (ASTM M1044; DIN C45; GB 45) and 40Kh (AISI 5140; DIN 41Cr4; GB 40Cr) structural steels. During the study, changes in the structure, roughness, sub-roughness, and microhardness values of these materials were observed. The results showed significant changes in the considered characteristics. It was found that the process of cavitation erosion involves at least 3 stages. In the first stage, the geometric properties of the surface slightly change with the accumulation of internal stresses and an increase in microhardness. The second stage is characterized by structure refinement, increased roughness and sub-microroughness, and the development of surface erosion. In the third stage, when a certain limiting state is reached, there are no noticeable changes in the surface properties. The lengths of these stages and the quantitative characteristics of erosion for the considered materials differ significantly. It was found that the time required to reach the limiting state was longer for carbon steel than for alloy steel. The results can be used to improve the cleaning process, as well as to form the required surface properties of structural steels.

Sequence Analysis and Preliminary X-ray Crystallographic Analysis of an Acetylesterase (LgEstI) from Lactococcus garvieae

A gene encoding LgEstI was cloned from a bacterial fish pathogen, Lactococcus garvieae. Sequence and bioinformatic analysis revealed that LgEstI is close to the acetyl esterase family and had maximum similarity to a hydrolase (UniProt: Q5UQ83) from Acanthamoeba polyphaga mimivirus (APMV). Here, we present the results of LgEstI overexpression and purification, and its preliminary X-ray crystallographic analysis. The wild-type LgEstI protein was overexpressed in Escherichia coli, and its enzymatic activity was tested using p-nitrophenyl of varying lengths. LgEstI protein exhibited higher esterase activity toward p-nitrophenyl acetate. To better understand the mechanism underlying LgEstI activity and subject it to protein engineering, we determined the high-resolution crystal structure of LgEstI. First, the wild-type LgEstI protein was crystallized in 0.1 M Tris-HCl buffer (pH 7.1), 0.2 M calcium acetate hydrate, and 19% (w/v) PEG 3000, and the native X-ray diffraction dataset was collected up to 2.0 Å resolution. The crystal structure was successfully determined using a molecular replacement method, and structure refinement and model building are underway. The upcoming complete structural information of LgEstI may elucidate the substrate-binding mechanism and provide novel strategies for subjecting LgEstI to protein engineering.

Influence of MHD - plasma melt processing on the structure and properties of cast aluminum alloy A390

Growth of production of cast products and the desire of enterprises to reduce the cost of manufacturing metal products led to a significant increase in requirements for the structure and properties of aluminum alloys. Increasing of physical and mechanical properties of alloys is most effectively at the stages of their preparation in liquid state. At that, it is possible to affect effectively on the quality of cast metal by external actions on alloys, deep refining from gases and harmful impurities, active modifying of alloy, reducing or eliminating the negative impact of heredity of charge materials. The main disadvantage of the processes of structure refinement of alloys by using modifiers is instability of their results, which depends on various reasons. One of the most important reasons is providing conditions for the formation and preservation of active modifier particles in the melt volume. They are assimilating by liquid alloy and acting on crystal nucleus at crystallization. It is known that only ~10% particles are active of the total number of particles added with the ligature into the melt. Other particles dissolve in the melt, take away by the crystallization front, or push back on to intergranular boundaries. The considered methods of electromagnetic, MHD and plasma actions on liquid metal allow to refine and modify alloys without use of special reagents. The paper presents studying of the structure and properties of supereutectic silumin A390 after treatment in casting magnetodynamic installation (MDI) by submerged into melt the plasma argon jet and alternating electromagnetic field & magnetohydrodynamic (MHD) effects, including simultaneous combination. There are developed the scientific and technological bases of MHD-plasma processing of liquid hypereutectic silumin A390 and original equipment for their realization. It provides dispersed structure of solidified alloy. Thus, there is a significant decreasing of sizes both particles of primary silicon and dendrites of α-solid solution of aluminium. Also, strength characteristics of alloys increased to 10%, and elongation rises up in 1.5-2 times. Keywords: plasma jet, magnetodynamic installation (MDI), aluminum alloy, mechanical properties.

Preparation, thermal analysis, and crystal structure refinement of the quaternary alloy (CuIn)2NbTe5

The quaternary alloy (CuIn)2NbTe5 was synthesized by solid-state reaction using the melt and annealing technique. The thermal analysis shows that this compound melts at 1026 K. The present alloy is isotypic with Cu2FeIn2Se5 and crystallizes in the space group P2c (Nº 112), with unit cell parameters a = 6.1964(2) Å, c = 12.4761(4) Å, c/a = 2.01, V = 479.02(3) Å3. (CuIn)2NbTe5, belonging to the system (CuInSe2)1-x(FeSe)x with x= ⅓, is a new adamantane compound with a P-chalcopyrite structure. This structure is characterized by a double alternation of anions-cations layers according to the Te-Te : Nb-In-Nb-In : Cu-In-Cu-In : Te-Te sequence, along the 010 direction.