Atomic coordinates and structure factors for the DNA-binding domain of Cupriavidus necatorNH9 CbnR in complex with RBS are available in the Protein Data Bank under the accession code 5XXP.

LysR‐type transcription regulators (LTTRs) comprise one of the largest families of transcriptional regulators in bacteria. They are typically homo‐tetrameric proteins and interact with promoter DNA of ~ 50–60 bp. Earlier biochemical studies have suggested that LTTR binding to promoter DNA bends the DNA and, upon inducer binding, the bend angle of the DNA is reduced through a quaternary structure change of the tetrameric LTTR, leading to the activation of transcription. To date, crystal structures of full‐length LTTRs, DNA‐binding domains (DBD) with their target DNAs, and the regulatory domains with and without inducer molecules have been reported. However, these crystal structures have not provided direct evidence of the quaternary structure changes of LTTRs or of the molecular mechanism underlying these changes. Here, we report the first crystal structure of a full‐length LTTR, CbnR, in complex with its promoter DNA. The crystal structure showed that, in the absence of bound inducer molecules, the four DBDs of the tetrameric CbnR interact with the promoter DNA, bending the DNA by ~ 70°. Structural comparison between the DNA‐free and DNA‐bound forms demonstrates that the quaternary structure change of the tetrameric CbnR required for promoter region‐binding arises from relative orientation changes of the three domains in each subunit. The mechanism of the quaternary structure change caused by inducer binding is also discussed based on the present crystal structure, affinity analysis between CbnR and the promoter DNA, and earlier mutational studies on CbnR. Database Atomic coordinates and structure factors for the full‐length Cupriavidus necator NH9 CbnR in complex with promoter DNA are available in the Protein Data Bank under the accession code https://doi.org/10.2210/pdb7D98/pdb.

LysR-type transcriptional regulators (LTTRs) comprise one of the largest families of transcriptional regulators in bacteria andcontrol gene expression of various types of metabolic, virulence and physiological functions. LTTRs typically form homotetramers and require an inducer molecule(s) to activate the transcription of target genes. The N-terminal region of LTTRs contains a DNAbinding domain (DBD) with the winged helix-turn-helix motif that specifically binds the promoter region of target genes. The C-terminal region of LTTRs is connected to the DBD by a linker helix and forms the regulatory domain (RD) that contains a binding pocket for inducer molecules. Crystal structures of several LTTR family members together with their biochemical analyses have provided a potential mechanism for the initial process of transcriptional activation by LTTRs. First, helix 3 of the winged helix-turn-helix motif in DBD is supposed to distinguish the recognition binding site (RBS) in the promoter region, resulting in complex formation through interactions between two DBDs in the tetrameric LTTR and RBS. Formation of this complex seems to enable interactions between the other two DBDs in the LTTR tetramer and the activation binding site (ABS) in the promoter region.The binding of the tetrameric LTTR to both the RBS and ABS causes the promoter DNA to adopt a bent structure because the four DBDs in the tetrameric LTTR are arranged in a V-shaped manner at the bottom of the LTTR. Interaction of an inducer molecule(s) with the RD seems to cause a quaternary structural change of the LTTR that relaxes the bending angle of the promoter DNA with a concomitant shift of the bound DBDs at the ABS. These events facilitate recruitment of RNA polymerase to its binding site in the promoter region, which overlaps with the ABS for LTTR.

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The Potential of Moringa oleifera Bioactive Compounds for Inhibiting Angiotensin-Converting Enzyme 2 Interaction in SARS-Cov-2 Syndrome Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) disease (COVID-19) is a threat to human health. This infection is determined by the interaction of the spike S1 domain protein with angiotensin-converting enzyme 2 (ACE2) in the epithelial cells of the respiratory tract, especially the lungs. ACE2 inhibition is an important target in controlling COVID-19. Flavonoids of medicinal plants, are known to interfere with ACE (ACE2 homologous). Therefore, this study aims to explore the ability of apiin, epicatechin, and hesperetin from Moringa oleifera in interacting with the ACE2 using MOE 2008.10. The ligand molecules were prepared from PubChem database. The ACE2 protein was retrieved from Protein Data Bank (ID 1R4L) and analyzed for the active sites. Analysis of docking scores and hydrogen bonds of ACE2-ligand complex and active site showed that the affinity of flavonoids can be ranked as hesperetin > epicatechin > apiin > C19H23Cl2N3O4. The results provided computational information that apiin, epicatechin, and hesperetin have the potential to prevent COVID-19 infection. The prediction of activity spectra for substances (PASS) score showed the ligand displays antiviral activity. Infeksi severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) pada pandemi coronavirus disease 2019 (COVID-19) menjadi ancaman dunia kesehatan saat ini. Infeksi SARS-CoV-2 ditentukan oleh interaksi protein spike envelope S1 domain dengan reseptor angiotensin-converting enzyme 2 (ACE2) yang diekspresikan pada sel epitel saluran pernafasan terutama paru-paru. Mekanisme penghambatan ACE2 menjadi target penting dalam pengendalian COVID-19. Senyawa bioaktif tanaman obat, seperti flavonoid diketahui mampu mengganggu fungsi banyak makromolekul termasuk ACE (homolog dengan ACE2). Penelitian ini bertujuan mengeksplorasi kemampuan senyawa apiin, epicatechin, dan hesperetin dari Moringa oleifera dalam berinteraksi dengan sisi aktif ACE2 menggunakan metode penambatan molekul. Studi dilakukan dengan preparasi struktur molekul ligan dari PubChem database dan diolah dengan MOE 2008.10. Selanjutnya, data protein ACE2 (Protein Data Bank ID 1R4L) dianalisis sisi aktifnya untuk mengetahui lokasi penambatan ligan senyawa. Analisis skor docking dan ikatan hydrogen komplek ligan dan sisi aktif ACE2 menunjukkan bahwa afinitas flavonoid dapat diperingkatkan sebagai afinitas hesperetin > epicatechin > apiin > C19H23Cl2N3O4. Ketiga ligan senyawa yang terkandung dalam M. oleifera secara in silico mampu mengikat sisi aktif ACE2, sehingga berpotensi mencegah infeksi COVID-19. Skor PASS (prediction of activity spectra for substances) menunjukkan aktivitas biologis ligan yang menyerupai antiviral.

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Isolation of deoxyribonucleotide (DNA) is an important step in molecular analysis. In this process, DNA must be obtained in sufficient quantities and in good quality for any further analysis. The Cetyl Trimethylammonium Bromide (CTAB) method is commonly used in DNA isolation of plant or fungal. This method is an alternative in DNA isolation since it is easy and inexpensive. This study aims to modify the CTAB method for DNA isolation from human cheek epithelium for any molecular analysis. Epithelial cells were taken from the oral cavity of the researcher. The isolation protocol included cell lysis step with CTAB buffer and proteinase-K, purification step with the addition of chloroform:isoamylalcohol (24:1), precipitation step with isopropanol. The results of the ratio analysis of DNA spectrophotometer at wavelengths of 260 and 280 nm in the range of 1.73-1.85. The quality of DNA isolation was observed by agarose gel electrophoresis and a firm band was obtained after Ethidium Bromide staining. The DNA concentration in both methods ranged from 400-480 mg/mL. The time required for both methods ranges from 2.5-3 hours. The modified CTAB method DNA isolation protocol produces DNA that has good quality and quantity for molecular analysis processes, such as Polymerase Chain Reaction (PCR).