Overview of AlphaFold2 and breakthroughs in overcoming its limitations.

Predicting three-dimensional (3D) protein structures has been challenging for decades. The emergence of AlphaFold2 (AF2), a deep learning-based machine learning method developed by DeepMind, became a game changer in the protein folding community. AF2 can predict a protein's three-dimensional structure with high confidence based on its amino acid sequence. Accurate prediction of protein structures can dramatically accelerate our understanding of biological mechanisms and provide a solid foundation for reliable drug design. Although AF2 breaks through the barriers in predicting protein structures, many rooms remain to be further studied. This review provides a brief historical overview of the development of protein structure prediction, covering template-based, template-free, and machine learning-based methods. In addition to reviewing the potential benefits (Pros) and considerations (Cons) of using AF2, this review summarizes the diverse applications, including protein structure predictions, dynamic changes, point mutation, integration of language model and experimental data, protein complex, and protein-peptide interaction. It underscores recent advancements in efficiency, reliability, and broad application of AF2. This comprehensive review offers valuable insights into the applications of AF2 and AF2-inspired AI methods in structural biology and its potential for clinically significant drug target discovery.

Efficient Removal of Hexavalent Chromium (Cr(VI)) from Wastewater Using Amide-Modified Biochar.

The utilization of biochar, derived from agricultural waste, has garnered attention as a valuable material for enhancing soil properties and serving as a substitute adsorbent for the elimination of hazardous heavy metals and organic contaminants from wastewater. In the present investigation, amide-modified biochar was synthesized via low-temperature pyrolysis of rice husk and was harnessed for the removal of Cr(VI) from wastewater. The resultant biochar was treated with 1-[3-(trimethoxysilyl) propyl] urea to incorporate an amide group. The amide-modified biochar was characterized by employing Fourier transform infrared (FTIR) spectroscopy, scanning electron microscopy (SEM), and X-ray diffraction (XRD) techniques. During batch experiments, the effect of various parameters, such as adsorbent dosage, metal concentration, time duration, and pH, on Cr(VI) removal was investigated. The optimal conditions for achieving maximum adsorption of Cr(VI) were observed at a pH 2, an adsorbent time of 60 min, an adsorbent dosage of 2 g/L, and a metal concentration of 100 mg/L. The percent removal efficiency of 97% was recorded for the removal of Cr(VI) under optimal conditions using amide-modified biochar. Freundlich, Langmuir, and Temkin isotherm models were utilized to calculate the adsorption data and determine the optimal fitting model. It was found that the adsorption data fitted well with the Langmuir isotherm model. A kinetics study revealed that the Cr(VI) adsorption onto ABC followed a pseudo-second-order kinetic model. The findings of this study indicate that amide-functionalized biochar has the potential to serve as an economically viable substitute adsorbent for the efficient removal of Cr(VI) from wastewater.

Kinetics of Catalytic Oxidation of Methylene Blue with La/Cu Co-Doped in Attapulgite.

Methylene blue (MB) is a common pollutant in wastewater from the printing and dyeing industries. In this study, attapulgite (ATP) was modified with La3+/Cu2+, using the method of equivolumetric impregnation. The La3+/Cu2+ -ATP nanocomposites were characterized using X-ray diffraction (XRD) and scanning electron microscopy (SEM). The catalytic properties of the modified ATP and the original ATP were compared. At the same time, the influence of the reaction temperature, concentration of methylene blue and pH on the reaction rate were investigated. The optimal reaction conditions are as follows: MB concentration is 80 mg/L, the dosage of the catalyst is 0.30 g, the dosage of hydrogen peroxide is 2 mL, the pH is 10 and the reaction temperature is 50 °C. Under these conditions, the degradation rate of MB can reach 98%. The recatalysis experiment was carried out reusing the catalyst, and the experimental results showed that the degradation rate could reach 65% after three uses, indicating that the catalyst could be recycled many times and costs could be reduced. Finally, the degradation mechanism of MB was speculated, and the reaction kinetic equation was obtained as follows: -dc/dt = 14,044 exp(-3598.34/T)C(O)0.28.

TsOH-catalyzed acyl migration reaction of the Bz-group: innovative assembly of various building blocks for the synthesis of saccharides.

We developed an efficient method to achieve the regioselective acyl migration of benzoyl ester. In all the cases, the reactions required only the commercially available organic acid catalyst TsOH·H2O. This method enables the benzoyl group to migrate from secondary groups to primary hydroxyl groups, or from equatorial secondary hydroxyl groups to axial hydroxyl groups. The 1,2 or 1,3 acyl migration would potentially occur via five- and six-membered cyclic ortho acid intermediates. A wide range of orthogonally protected monosaccharides, which are useful intermediates for the synthesis of natural oligosaccharides, were synthesized. Finally, to demonstrate the utility of the method, a tetrasaccharide portion from a mycobacterial cell wall polysaccharide was assembled.

Ciprofloxacin removal by ultrasound-enhanced carbon nanotubes/permanganate process: In situ generation of free reactive manganese species via electron transfer.

Recently, free reactive manganese species (RMnS) generated via permanganate catalytic oxidation technology has been applied to contaminants abatement and sludge dewatering. This study proposed a novel free RMnS generation method in ultrasound enhanced carbon nanotube (CNTs)/permanganate process (UCP) for organics removal. Taking ciprofloxacin as a target contaminant, the removal efficiency in the UCP process (9.78 s-1) was remarkably higher than that of the permanganate (0.71 s-1) and CNTs/permanganate (2.57 s-1) processes. CNTs could enrich manganese compounds and ciprofloxacin, and act as an electronic platform for the electronic transfer from ciprofloxacin to manganese compounds for free RMnS generation, which was revealed by DFT calculation and spectrum analysis. Meanwhile, ultrasound further regulated the generation of RMnS as it could transform the inactive solid Mn(IV) into free RMnS. In the UCP process, non-free radical modes including RMnS oxidation (49.8%) and electron transfer (23.5%) were the dominant processes for ciprofloxacin removal in the UCP process, and hydroxyl radical oxidation (13.2%), CNTs adsorption (5.5%), and PM oxidation (8.0%) also contributed to ciprofloxacin removal. Interestingly, CNTs could be well reused in the UCP process as more than 88.75% of ciprofloxacin was removed after five times reuse of CNTs. The UCP process provides a novel strategy for rapid contaminants removal in water treatment via continuous generation of free RMnS.

4,6-Di-O-Benzylidenyl group-directed preparation of 2-deoxy-2-azido-α-d-galactopyranosides promoted by 3-O-TBDPS.

In this study, we designed a method to prepare 2-deoxy-2-azido-α-d-galactopyranosidic bonds using 4,6-di-O-benzylidenyl-3-O-t-butyldiphenylsilyl protected 2-deoxy-2-azido-1-thio-d-galactopyranoside 5 as donors. The donor 5 gives a good to excellent α-selectivity in the glycosylation with secondary alcohols, which was found to be associated with the benzylidenyl on 4,6-di-O and TBDPS on 3-O of the donor 5. Compared with results of the donor 6 and 7, the 3-O-TBDPS could increase the activity of the thioglycoside, and the lone pairs on 4,6-di-O-benzylidenyl group enhanced the gg-cofnormation, which plays a role in improving the stereoselectivity. Finally, this method was demonstrated through the synthesis of a α-galactosamine -containing pentasaccharide 26.

Origin of the Regioselectivity in the Aldol Condensation between Hydroxymethylfurfural and Levulinic Acid: A DFT Investigation.

Our previous work demonstrated that hydroxide ion (OH-) was able to catalyze aldol condensation reaction at room temperature between 5-hydroxymethylfurfural (HMF) and levulinic acid (LA). This work identified three primary reaction steps in this condensation reaction using density functional theory (DFT): (1) deprotonation of LA to generate LA ions, (2) LA ions addition at hydroxymethyl site of HMF, and (3) internal dehydration to form the condensation product. The reaction pathway through the C5 of LA forms a linear product that is favored with respect to both energy and configuration in all three elementary reaction steps. This is qualitatively consistent with the phenomenon observed in our previous experiment where the linear form is a main product. Further confirmation comes from the frontier orbital analysis of the transition states in the linear reaction route and explains the regioselectivity of product formation.

Synthesis, crystal structure and investigation of mononuclear copper(II) and zinc(II) complexes of a new carboxylate rich tripodal ligand and their interaction with carbohydrates in alkaline aqueous solution.

A new carboxylate rich asymmetric tripodal ligand, N-[2-carboxybenzomethyl]-N-[carboxymethyl]-ß-alanine (H3camb), and its di-copper(II), (NH4)2[1]2, and di-zinc(II), ((CH3)4N)2[2]2, complexes have been synthesized as carbohydrate binding models in aqueous solutions. The ligand and complexes have been fully characterized using several techniques, including single crystal X-ray diffraction. The interactions of (NH4)2[1]2 and ((CH3)4N)2[2]2 with D-glucose, D-mannose, D-xylose and xylitol in aqueous alkaline media were investigated using UV-Vis and (13)C-NMR spectroscopic techniques, respectively. The molar conductance, NMR and ESI-MS studies indicate that the complexes dissociate in solution to produce the respective complex anions, 1(-) and 2(-). Complexes 1(-) and 2(-) showed chelating ability towards the naturally abundant and biologically relevant sugars, D-glucose, D-mannose, D-xylose, and xylitol. The complex ions bind to one molar equivalent of the sugars, even in the presence of stoichiometric excess of the substrates, in solution. Experimentally obtained spectroscopic data and computational results suggest that the substrates bind to the metal center in a bidentate fashion. Apparent binding constant values, pK(app), between the complexes and the substrates were determined and a specific mode of substrate binding is proposed. The pK(app) and relativistic density functional theory (DFT) calculated Gibbs free energy values indicate that D-mannose displayed the strongest interaction with the complexes. Syntheses, characterizations, detailed substrate binding studies using spectroscopic techniques, single crystal X-ray diffraction and geometry optimizations of the complex-substrates with DFT calculations are also reported.

Molecular control of the nanoscale: effect of phosphine-chalcogenide reactivity on CdS-CdSe nanocrystal composition and morphology.

We demonstrate molecular control of nanoscale composition, alloying, and morphology (aspect ratio) in CdS-CdSe nanocrystal dots and rods by modulating the chemical reactivity of phosphine-chalcogenide precursors. Specific molecular precursors studied were sulfides and selenides of triphenylphosphite (TPP), diphenylpropylphosphine (DPP), tributylphosphine (TBP), trioctylphosphine (TOP), and hexaethylphosphorustriamide (HPT). Computational (DFT), NMR ((31)P and (77)Se), and high-temperature crossover studies unambiguously confirm a chemical bonding interaction between phosphorus and chalcogen atoms in all precursors. Phosphine−chalcogenide precursor reactivity increases in the order: HPTE < TOPE < TBPE < DPPE

Exocytosis of SH-SY5Y single cell with different shapes cultured on ITO micro-pore electrode.

Communication between cells by release of specific chemical messengers via exocytosis plays crucial roles in biological process. Catecholamines, like dopamine, epinephrine, and norepinephrine, which are types of neurotransmitters released from cells, can be oxidized and detected by the microelectrodes, and amperometric detection of exocytosis is an effective method for studying the communication between cells. The experimental results depend on many factors, among which the property of the microelectrode, cell states, and their positions to each other are particularly important. A type of indium tin oxide (ITO) micro-pore electrodes, which is characterized by its stability, has been developed with photolithography. SH-SY5Y cells can adhere and spread on ITO micro-pore electrodes. Therefore, it is possible to investigate the correlation between cell morphology and exocytosis. The results show that cells with clear process have higher release frequency of norepinephrine compared with cells in spherical shape. Combined with fluorescence observation, this technique provides a simple and convenient methodology for cell study.

[Determination of the eliminating ratio of TCM polysaccharide to hydroxyl radical by kinetic fluorescent spectrophotometry].

OBJECTIVE: To explore reaction dynamic of hydroxyl radical (*OH) and salicylic acid,and to determine the elimination ratios of TCM polysaccharide to *OH by kinetic fluorescent analysis. METHODS: The impact dynamics factors of this reaction were studied by fluorescent, such as the reaction of concentration, reaction time and temperature. The dynamical equation was built, a kinetic fluorescent spectrophotometry based on the reaction was developed to determine the elimination ratio. Repetitiveness and reliability of this method were tested by vitamin C. RESULTS: The dynamical equation of reaction rate to salicylic acid was gamma = 0. 9818x -1. 1801 under the condition of lambda ex = 295 nm, lambda em = 411 nm at room temperature, r approximately 1. The 50% elimination ratio (IC50) of TCM polysaccharide of Tangerine peel and Ganoderma lucidum to *OH was 78.01 mg/L and 232.5 mg/L, respectively. The IC50 of vitamin C was 24.52 microg/L, RSD was 0.23% (n = 5). CONCLUSIONS: The method is sensitive and reliable, it can be used to determine the elimination ratio of TCM polysaccharide to *OH.

Density functional study of the catalytic cycle of nickel-iron [NiFe] hydrogenases and the involvement of high-spin nickel(II).

In light of recent experiments suggesting high-spin (HS) Ni(II) species in the catalytic cycle of [NiFe] hydrogenase, a series of models of the Ni(II) forms Ni-SI(I,II), SI-CO and Ni-R(I,II,III) were examined in their high-spin states via density functional calculations. Because of its importance in the catalytic cycle, the Ni-C form was also included in this study. Unlike the Ni(II) forms in previous studies, in which a low-spin (LS) state was assumed and a square-planar structure found, the optimized geometries of these HS Ni(II) forms resemble those observed in the crystal structures: a distorted tetrahedral to distorted pyramidal coordination for the NiS4. This resemblance is particularly significant because the LS state is 20-30 kcal/mol less stable than the HS state for the geometry of the crystal structure. If these Ni(II) forms in the enzyme are not high spin, a large change in geometry at the active site is required during the catalytic cycle. Furthermore, only the HS state for the CO-inhibited form SI-CO has CO stretching frequencies that match the experimental results. As in the previous work, these new results show that the heterolytic cleavage reaction of dihydrogen (where H2 is cleaved with the metal acting as a hydride acceptor and a cysteine as the proton acceptor) has a lower energy barrier and is more exothermic when the active site is oxidized to Ni(III). The enzyme models described here are supported by a calibrated correlation of the calculated and measured CO stretching frequencies of the forms of the enzyme. The correlation coefficient for the final set of models of the forms of [NiFe] hydrogenase is 0.8.

[Determination of cadmium, chromium and lead in Lycoris radiata with microwave digestion technique by graphite furnace atomic absorption spectrometry].

A new method using microwave digestion technique was developed for the determination of cadmium, chromium and lead in Lycoris radiata by graphite furnace atomic absorption spectrometry (GFAAS). Digestion solvents were discussed for sample preparation by microwave digestion technique. The optimum condition of determination by GFAAS was studied in the presence of NH4H2PO4 matrix modifier. The detection limits of Cd, Cr and Pb are 0.066 7, 1.22 and 0.810 microg x L(-1), respectively. The method was applied to the determination of Cd, Cr and Pb in Lycoris radiata samples with satisfactory results. The RSD of determination were lower than 3.1%. The recoveries were from 83.8% to 118%.

IR spectroelectrochemical study of the binding of carbon monoxide to the active site of Desulfovibrio fructosovorans Ni-Fe hydrogenase.

The binding of carbon monoxide, a competitive inhibitor of many hydrogenases, to the active site of Desulfovibrio fructosovorans hydrogenase has been studied by infrared spectroscopy in a spectroelectrochemical cell. Direct evidence has been obtained of which redox states of the enzyme can bind extrinsic CO. Redox states A, B and SU do not bind extrinsic CO; only after reductive activation of the hydrogenase can CO bind to the active site. Two states with bound extrinsic CO can be distinguished by FTIR. These two states are in redox equilibrium and are most probably due to different oxidation states of the proximal 4Fe-4S cluster. Vibrational frequencies and theoretical quantum mechanics studies (DFT) of this process preclude the possibility of strong bonding of extrinsic CO to the Fe or Ni atoms of the active site. We propose that CO inhibition is caused by weak interaction of the extrinsic ligand with the Ni atom, blocking electron and proton transfer at the active site. A calculated structure with a weakly bound extrinsic CO at Ni has relative CO frequencies in excellent agreement with the experimental ones.

High-spin Ni(II), a surprisingly good structural model for [NiFe] hydrogenase.

The first density functional calculations on high-spin (HS) Ni(II) models for the active site of the [NiFe] hydrogenases predict a ligand arrangement about Ni that is in better agreement with the crystal structures than previous predictions for low-spin (LS) Ni(II) models. With the crystal structures' geometry, the HS form is approximately 20 kcal/mol lower in energy than the LS one.