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2022 ◽  
Vol 12 (2) ◽  
pp. 874
Author(s):  
Yao Wei ◽  
Francesco Macheda ◽  
Zelong Zhao ◽  
Terence Tse ◽  
Evgeny Plekhanov ◽  
...  

Hydrogen-rich superhydrides are promising high-Tc superconductors, with superconductivity experimentally observed near room temperature, as shown in recently discovered lanthanide superhydrides at very high pressures, e.g., LaH10 at 170 GPa and CeH9 at 150 GPa. Superconductivity is believed to be closely related to the high vibrational modes of the bound hydrogen ions. Here, we studied the limit of extreme pressures (above 200 GPa) where lanthanide hydrides with large hydrogen content have been reported. We focused on LaH16 and CeH16, two prototype candidates for achieving a large electronic contribution from hydrogen in the electron–phonon coupling. In this work, we propose a first-principles calculation platform with the inclusion of many-body corrections to evaluate the detailed physical properties of the Ce–H and La–H systems and to understand the structure, stability, and superconductivity of these systems at ultra-high pressure. We provide a practical approach to further investigate conventional superconductivity in hydrogen-rich superhydrides. We report that density functional theory provides accurate structure and phonon frequencies, but many-body corrections lead to an increase of the critical temperature, which is associated with the spectral weight transfer of the f-states.


2022 ◽  
Vol 23 (2) ◽  
pp. 888
Author(s):  
Żaneta Arciszewska ◽  
Sofia Gama ◽  
Monika Kalinowska ◽  
Grzegorz Świderski ◽  
Renata Świsłocka ◽  
...  

Caffeic acid (CFA) is one of the various natural antioxidants and chemoprotective agents occurring in the human diet. In addition, its metal complexes play fundamental roles in biological systems. Nevertheless, research on the properties of CFA with lanthanide metals is very scarce, and little to no chemical or biological information is known about these particular systems. Most of their properties, including their biological activity and environmental impact, strictly depend on their structure, stability, and solution behaviour. In this work, a multi-analytical-technique approach was used to study these relationships for the Eu(III)/CFA complex. The synthesized metal complex was studied by FT-IR, FT-Raman, elemental, and thermal (TGA) analysis. In order to examine the chemical speciation of the Eu(III)/CFA system in an aqueous solution, several independent potentiometric and spectrophotometric UV-Vis titrations were performed at different M:L (metal:ligand) and pH ratios. The general molecular formula of the synthesized metal complex in the solid state was [Eu(CFA)3(H2O)3]∙2H2O (M:L ratio 1:3), while in aqueous solution the 1:1 species were observed at the optimum pH of 6 ≤ pH ≤ 10, ([Eu(CFA)] and [Eu(CFA)(OH)]−). These results were confirmed by 1H-NMR experiments and electrospray-ionization mass spectrometry (ESI-MS). To evaluate the interaction of Eu(III)/CFA and CFA alone with cell membranes, electrophoretic mobility assays were used. Various antioxidant tests have shown that Eu(III)/CFA exhibits lower antioxidant activity than the free CFA ligand. In addition, the antimicrobial properties of Eu(III)/CFA and CFA against Escherichia coli, Bacillus subtilis and Candida albicans were investigated by evaluation of the minimum inhibitory concentration (MIC). Eu(III)/CFA shows higher antibacterial activity against bacteria compared to CFA, which can be explained by the highly probable increased lipophilicity of the Eu(III) complex.


2022 ◽  
Author(s):  
Yao Gong ◽  
Gaurav Behera ◽  
Luke Erber ◽  
Ang Luo ◽  
Yue Chen

Proline hydroxylation (Hyp) regulates protein structure, stability and protein-protein interaction and is widely involved in diverse metabolic and physiological pathways in cells and diseases. To reveal functional features of the proline hydroxylation proteome, we integrated various data sources for deep proteome profiling of proline hydroxylation proteome in human and developed HypDB (https://www.HypDB.site), an annotated database and web server for proline hydroxylation proteome. HypDB provides site-specific evidence of modification based on extensive LC-MS analysis and literature mining with 15319 non-redundant Hyp sites and 8226 sites with high confidence on human proteins. Annotation analysis revealed significant enrichment of proline hydroxylation on key functional domains and tissue-specific distribution of Hyp abundance across 26 types of human organs and fluids and 6 cell lines. The network connectivity analysis further revealed a critical role of proline hydroxylation in mediating protein-protein interactions. Moreover, the spectral library generated by HypDB enabled data-independent analysis (DIA) of clinical tissues and the identification of novel Hyp biomarkers in lung cancer and kidney cancer. Taken together, our integrated analysis of human proteome with publicly accessible HypDB revealed functional diversity of Hyp substrates and provides a quantitative data source to characterize proline hydroxylation in pathways and diseases.


Author(s):  
Nguyen Huu Tho ◽  
Pham Hong Cam

The geometries, stabilities and electronic properties of vanadium-doped germanium clusters GenV0/+ (n=2-8) were systematically investigated by using density functional theory (DFT) at the PBE level and the 6-311+G(d) basis set. The results show that the geometries of lowest-energy structures of the cationic clusters are only significant different from those of the neutral at n = 6 or 7. The ground state of neutral clusters is a doublet, except Ge2V which is a quartet while that of cationic clusters is a triplet, except Ge8V+, which is a singlet. The average binding energy values generally increase with increasing cluster size. The results from average binding energies showed that it is more stable for the cationic than neutral clusters at the same size. Furthermore, the calculated values of fragmentation energy, second-order energy difference, HOMO-LUMO gap and adiabatic ionization potential suggest that the neutral clusters possess higher stability when n = 2, 5, 8 and the cations are more stable when n = 2, 3, 5 and 6.


F1000Research ◽  
2022 ◽  
Vol 11 ◽  
pp. 9
Author(s):  
Boon Zhan Sia ◽  
Wan Xin Boon ◽  
Yoke Yee Yap ◽  
Shalini Kumar ◽  
Chong Han Ng

Background: SARS-CoV-2 virus is a highly transmissible pathogen that causes COVID-19. The outbreak originated in Wuhan, China in December 2019. A number of nonsynonymous mutations located at different SARS-CoV-2 proteins have been reported by multiple studies. However, there are limited computational studies on the biological impacts of these mutations on the structure and function of the proteins.   Methods: In our study nonsynonymous mutations of the SARS-CoV-2 genome and their frequencies were identified from 30,229 sequences. Subsequently, the effects of the top 10 nonsynonymous mutations of different SARS-CoV-2 proteins were analyzed using bioinformatics tools including co-mutation analysis, prediction of the protein structure stability and flexibility analysis, and prediction of the protein functions.   Results: A total of 231 nonsynonymous mutations were identified from 30,229 SARS-CoV-2 genome sequences. The top 10 nonsynonymous mutations affecting nine amino acid residues were ORF1a nsp5 P108S, ORF1b nsp12 P323L and A423V, S protein N501Y and D614G, ORF3a Q57H, N protein P151L, R203K and G204R. Many nonsynonymous mutations showed a high concurrence ratio, suggesting these mutations may evolve together and interact functionally. Our result showed that ORF1a nsp5 P108S, ORF3a Q57H and N protein P151L mutations may be deleterious to the function of SARS-CoV-2 proteins. In addition, ORF1a nsp5 P108S and S protein D614G may destabilize the protein structures while S protein D614G may have a more open conformation compared to the wild type.   Conclusion: The biological consequences of these nonsynonymous mutations of SARS-CoV-2 proteins should be further validated by in vivo and in vitro experimental studies in the future.


2022 ◽  
Vol 955 (1) ◽  
pp. 012005
Author(s):  
H P Adi ◽  
S I Wahyudi ◽  
A Soebagyo

Abstract Panjang Island is a small island in Jepara, Indonesia which is very vulnerable to coastal damage due to crashing waves. Therefore, presence of coastal protection structure is essentially important. Gabion structure was constructed to protect this coastal area. Considering the age, the existing gabion structure needed assessment and analysis to ensure its performance in term of protecting the coastal area. This study aimed at assessing and analyzing the performance of the existing gabion structure. Data of the study were collected through observing the condition of the structure. Assessment was carried out by scaling 1 (minor) to 5 (severe damage). Results of the analysis showed that the value of stability to overturning was 3.96, while the stability to shearing was 2.07, the structure stability was in safe category. Soil pressure under the structure in σ max. was 0.39 kg/cm2, while σ min was 0.16 kg/cm2, which means safe. The condition of gabion as a coastal protection structure in section 1 was partially damaged with a moderate level of damage, in section 2, the damage was revealed to be a minor level of damage, while in section 3, the damage was in a minor level of damage.


2022 ◽  
Vol 1247 ◽  
pp. 131372
Author(s):  
Sima Moradi ◽  
Behzad Shareghi ◽  
Ali Akbar Saboury ◽  
Sadegh Farhadian

2021 ◽  
Vol 23 (1) ◽  
pp. 116
Author(s):  
Olamide Jeje ◽  
Reabetswe Maake ◽  
Ruan van Deventer ◽  
Veruschka Esau ◽  
Emmanuel Amarachi Iwuchukwu ◽  
...  

The continuous threat of drug-resistant Klebsiella pneumoniae justifies identifying novel targets and developing effective antibacterial agents. A potential target is nicotinate nucleotide adenylyltransferase (NNAT), an indispensable enzyme in the biosynthesis of the cell-dependent metabolite, NAD+. NNAT catalyses the adenylation of nicotinamide/nicotinate mononucleotide (NMN/NaMN), using ATP to form nicotinamide/nicotinate adenine dinucleotide (NAD+/NaAD). In addition, it employs divalent cations for co-substrate binding and catalysis and has a preference for different divalent cations. Here, the biophysical structure of NNAT from K. pneumoniae (KpNNAT) and the impact of divalent cations on its activity, conformational stability and substrate-binding are described using experimental and computational approaches. The experimental study was executed using an enzyme-coupled assay, far-UV circular dichroism, extrinsic fluorescence spectroscopy, and thermal shift assays, alongside homology modelling, molecular docking, and molecular dynamic simulation. The structure of KpNNAT revealed a predominately α-helical secondary structure content and a binding site that is partially hydrophobic. Its substrates ATP and NMN share the same binding pocket with similar affinity and exhibit an energetically favourable binding. KpNNAT showed maximum activity and minimal conformational changes with Mg2+ as a cofactor compared to Zn2+, Cu2+ and Ni2+. Overall, ATP binding affects KpNNAT dynamics, and the dynamics of ATP binding depend on the presence and type of divalent cation. The data obtained from this study would serve as a basis for further evaluation towards designing structure-based inhibitors with therapeutic potential.


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