Computational study of the furin cleavage domain of SARS-CoV-2: delta binds strongest of extant variants

We demonstrate that AlphaFold and AlphaFold Multimer, implemented within the ColabFold suite, can accurately predict the structures of the furin enzyme with known six residue inhibitory peptides. Noting the similarity of the peptide inhibitors to polybasic furin cleavage domain insertion region of the SARS-CoV-2, which begins at P681, we implement this approach to study the wild type furin cleavage domain for the virus and several mutants. We introduce mutations in silico for alpha, omicron, and delta variants, for several sequences which have been rarely observed, for sequences which have not yet been observed, for other coronaviruses (NL63, OC43, HUK1a, HUK1b, MERS, and 229E), and for the H5N1 flu. We show that interfacial hydrogen bonds between the furin cleavage domain and furin are a good measure of binding strength that correlate well with endpoint binding free energy estimates, and conclude that among all candidate viral sequences studied, delta is near the very top binding strength within statistical accuracy. However, the binding strength of several rare sequences match delta within statistical accuracy. We find that the furin S1 pocket is optimized for binding arginine as opposed to lysine. This residue, typically at sequence position five, contains the most hydrogen bonds to the furin, and hydrogen bond count for just this residue shows a strong positive correlation with the overall hydrogen bond count . We demonstrate that the root mean square backbone C-alpha fluctuation of the first residue in the furin cleavage domain has a strong negative correlation with the interfacial hydrogen bond count. We show by considering the variation with the number of basic residues that the maximum mean number of interfacial hydrogen bonds expected is 15.7 at 4 basic residues.

Simulation of the omicron variant of SARS-CoV-2 shows broad antibody escape, weakened ACE2 binding, and modest increase in furin binding

The recent emergence of the omicron variant of the SARS-CoV-2 virus with large numbers of mutations has raised concern about a potential new surge in infections. Here we use molecular dynamics to study the biophysics of the interface of the omicron spike protein binding to (i) the ACE2 receptor protein, (ii) antibodies from all known binding regions, and (iii) the furin binding domain. Our simulations suggest that while there is significant reduction of antibody binding strength corresponding to escape, the omicron spike pays a cost in terms of weaker receptor binding. The furin cleavage domain is the same or weaker binding than the alpha variant, suggesting less viral load and disease intensity than the extant delta variant.

Defluorination and adsorption of tetrafluoroethylene (TFE) on TiO2(110) and Cr2O3(0001)

Here, we show that metal oxide surfaces catalyze the formation of intermediate defluorinated tetrafluoroethylene (TFE) radicals, resulting in enhanced binding on the corresponding metal oxide surfaces. We attribute the preferential adsorption and radical formation of TFE on Cr2O3(0001) relative to TiO2(110) to the low oxygen coordination of Cr surface atoms. This hints at a possible dependence of the TFE binding strength to the surface stoichiometry of metal-oxide surfaces.

Bright, fluorogenic and photostable avidity probes for RNA imaging

Fluorescent light-up aptamers (FLAPs) emerged as valuable tools to visualize RNA, but are mostly limited by poor brightness, low photostability and high fluorescence background. In this study, we combine bivalent (silicon) rhodamine fluorophores with dimeric FLAPs to yield bright and photostable complexes with low picomolar dissociation constants. Our avidity-based approach resulted in extreme binding strength and high fluorogenicity, enabling single mRNA tracking in living cells.

Hak Subrogasi Penanggung dalam Borgtocht

The guarantee agreement (borgtocht) creates legal consequences such as subrogation rights for the guarantor who has borne debtor's debt to creditor. The provisions of Article 1820 of Civil Code and other articles related to borgtocht in other laws and regulations relating to guarantees show that there are no regulations for the protection of subrogation rights that the guarantor obtained in the guarantee agreement, resulting in a vacuum of norm against this matter. Determining the guarantor’s legal standing in guarantee agreement according to the Indonesian guarantee legal system and the binding strength of the authentic deed in protecting the subrogation rights of guarantor in the guarantee agreement are the goals from this research. The normative juridical research method is used in this paper by carrying out legal construction through the argumentum per analogiam method to solve the vacuum of norms, implemented by expanding the meaning of statutory provisions on similar issues and the existence of community interests that demand the same assessment. This research shows that the legal standing of guarantor are implicitly regulated in Articles 1831-1843 Civil Code and based on the argumentum per analogiam method the provisions of the authentic deed formulation in subrogation that occur because the meaning of the agreement is expanded to be applied to this issue, therefore the third parties obtain legal protection for the rights of subrogation that arise, after bearing repayment of debtor's debt. Perjanjian penanggungan (borgtocht) menimbulkan akibat hukum berupa hak subrogasi bagi penanggung yang telah melakukan penanggungan utang debitur terhadap kreditur. Ketentuan Pasal 1820 KUH Perdata dan pasal-pasal lainnya terkait dengan penanggungan serta pasal-pasal dalam peraturan perundang-undangan lainnya terkait dengan jaminan tidak terdapat pengaturan perumusan hak subrogasi yang diperoleh penanggung dalam perjanjian penanggungan, sehingga terjadi suatu kekosongan norma (vacuum of norm) terhadap persoalan ini. Mengetahui kedudukan hukum penanggung dalam perjanjian penanggungan menurut sistem hukum jaminan Indonesia dan kekuatan mengikat akta otentik dalam melindungi hak subrogasi penanggung dalam perjanjian penanggungan menjadi tujuan dalam penelitian ini. Metode penelitian yuridis normatif digunakan dalam penulisan karya tulis ini dengan melakukan konstruksi hukum melalui metode argumentum per analogiam untuk mengatasi kekosongan norma, yaitu perluasan makna ketentuan perundang-undangan terhadap persoalan yang mirip serta adanya kepentingan masyarakat yang menuntut penilaian sama. Hasil penelitian menunjukan kedudukan hukum bagi penanggung diatur secara implisit pada Pasal 1831-1843 KUH Perdara serta berdasarkan metode argumentum per analogiam ketentuan perumusan akta otentik pada peristiwa subrogasi yang terjadi karena persetujuan diperluas maknanya untuk diterapkan pada persoalan ini, sehingga pihak ketiga memperoleh perlindungan hukum atas hak subrogasinya yang timbul setelah dilakukannya penanggungan utang.

Tuning epithelial cell-cell adhesion and collective dynamics with functional DNA-E-cadherin hybrid linkers

The binding strength between epithelial cells is crucial for tissue integrity, signal transduction and collective cell dynamics. However, there is no experimental approach to precisely modulate cell-cell adhesion strength at the cellular and molecular level. Here, we establish DNA nanotechnology as tool to control cell-cell adhesion of epithelial cells. We designed a DNA-E-cadherin hybrid system consisting of complementary DNA strands covalently bound to a truncated E-cadherin with a modified extracellular domain. DNA sequence design allows to tune the DNA-E-cadherin hybrid molecular binding strength, while retaining its cytosolic interactions and downstream signaling capabilities. The DNA-E-cadherin hybrid facilitates strong and reversible cell-cell adhesion in E-cadherin deficient cells by forming mechanotransducive adherens junctions. We assess the direct influence of cell-cell adhesion strength on intracellular signaling and collective cell dynamics. This highlights the scope of DNA nanotechnology as a precision technology to study and engineer cell collectives.