Protein Data Bank ID Research Articles

Contemporary advances of cyclic molecules proposed for inflammation.

This review stretches insight about the advancement (2011-2021) of synthesized non-heterocyclic, heterocyclic and natural occurring cyclic molecules for inflammation. While inflammation is very significant in the abolition of pathogens and other causes of soreness, a protracted inflammatory procedure takes to outcomes in chronic disease that might finally affect in organ failure or damage. Thus, restraining the provocative process by the use of anti-inflammatory agents is chief in controlling this damage. It also reveals other pursuit along with their anti-inflammatory activity. Molecular docking studies represent most suitable PDB (Protein Data Bank) ID for the synthesized heterocyclic molecules with their selective inhibitor. It discusses the findings presented in recent research papers and provides understanding to researchers intended for the growth of newer combinations/molecules having littler side things.

Antigenic Peptide Loading into Major Histocompatibility Complex Class I Is Driven by the Substrate N-Terminus

Major histocompatibility complex class I (MHC-I), a key element of the acquired immune system, plays essential roles in activating CD8+ T cells by recognizing intracellular antigens derived from pa...

Testing for Lipase Activity in Enzymes of Unknown Function

There are over 3800 structures in the Protein Data Bank (PDB) that have unknown function. The Biochemistry Authentic Scientific Inquiry Lab (BASIL) curriculum uses authentic inquiry to teach students to use structural bioinformatics tools to compare these structures to known enzymes and predict a function. We have predicted lipase function for several structures after performing both global and local structure alignments using Dali and ProMOL. This function was supported by sequence alignment data from BLAST and PFam. Autodock Vina and PyRx were then used for ligand docking to determine possible lipid substrates to test activity. Students next used standard wet-lab biochemistry techniques to express and purify the target enzymes and performed kinetic assays first using p-nitrophenyl acetate to test for esterase activity. After completing the BASIL curriculum, students continued with independent research projects to develop assays to test for lipase function. We have focused our efforts on the protein structures with PDB IDs 2O14 and 4Q7Q, as they showed the most promise through initial enzymatic testing. Both proteins show significant esterase activity with the p-nitrophenyl acetate substrate. Additionally, both proteins show significant hydrolysis of p-nitrophenyl dodecanoate when sodium deoxycholate is present in the buffer solution for solubility of the substrate. We have also incorporated the p-nitrophenyl dodecanoate in DMPC vesicles, and both proteins can hydrolyze the substrate from the vesicle. We have tested pancreatic lipase under all these conditions as a positive control for the experiments. Students will eventually be able to update the PDB with the demonstrated function for these proteins, and they will also create a Proteopedia page for each protein. This project is supported in part by NSF IUSE 1709355.

In silico and In vitro Perspective to Elucidate the Anticancer Effect of Natural Compound Hesperetin in Inhibiting Mammalian Target of Rapamycin Pathway

In this study we intended to perform in silico and in vitro analysis of naturally derived flavonoid, hesperetin as a promising mammalian target of rapamycin inhibitor. This study features in silico screening of natural compound hesperetin against mammalian target of rapamycin FK506 binding proteins 12 domain by using Schrodinger glide based virtual screening and further molecular dynamics simulation was done to infer the stability of complex formation. Mammalian target of rapamycin co-crystallized with P2X (a known inhibitor of mTOR) (Protein Data Bank ID: 4JT5) was used for reference guided docking protocol. Then in vitro analysis applying hesperetin for cell viability followed by protein expressions in ovarian PA-1 and MCF-7 breast cancer cell lines were performed dose dependently. in silico molecular docking and dynamic studies with mammalian target of rapamycin protein revealed that hesperetin was found to be a potent compound that could inhibit the FK506 binding proteins 12 domain of mammalian target of rapamycin. The in vitro studies with hesperetin on PA-1 and MCF-7 breast cancer cell lines, found that hesperetin in a dose dependent manner significantly reduced the phosphorylation of mammalian target of rapamycin on Serine 2448 a marker for mammalian target of rapamycin complex 1 activity, as well as phosphorylation of eukaryotic translation initiation factor 4E binding protein 1 and Ribosomal protein S6 kinase beta-1 which are downstream molecules of mammalian target of rapamycin was also significantly inhibited. To the best of our knowledge this is the first study that brings up the scientific evidence for the efficacy of hesperetin in inhibiting mammalian target of rapamycin with a similar docking score to the native ligand and also in a dose dependent manner in PA-1 human ovarian cancer cells and MCF-7 breast cancer cells, as an anticancer agent with further studies in near future.

FDA-Approved Drugs with Potent In Vitro Antiviral Activity against Severe Acute Respiratory Syndrome Coronavirus 2.

(1) Background: Drug repositioning is an unconventional drug discovery approach to explore new therapeutic benefits of existing drugs. Currently, it emerges as a rapid avenue to alleviate the COVID-19 pandemic disease. (2) Methods: Herein, we tested the antiviral activity of anti-microbial and anti-inflammatory Food and Drug Administration (FDA)-approved drugs, commonly prescribed to relieve respiratory symptoms, against Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), the viral causative agent of the COVID-19 pandemic. (3) Results: Of these FDA-approved antimicrobial drugs, Azithromycin, Niclosamide, and Nitazoxanide showed a promising ability to hinder the replication of a SARS-CoV-2 isolate, with IC50 of 0.32, 0.16, and 1.29 µM, respectively. We provided evidence that several antihistamine and anti-inflammatory drugs could partially reduce SARS-CoV-2 replication in vitro. Furthermore, this study showed that Azithromycin can selectively impair SARS-CoV-2 replication, but not the Middle East Respiratory Syndrome Coronavirus (MERS-CoV). A virtual screening study illustrated that Azithromycin, Niclosamide, and Nitazoxanide bind to the main protease of SARS-CoV-2 (Protein data bank (PDB) ID: 6lu7) in binding mode similar to the reported co-crystalized ligand. Also, Niclosamide displayed hydrogen bond (HB) interaction with the key peptide moiety GLN: 493A of the spike glycoprotein active site. (4) Conclusions: The results suggest that Piroxicam should be prescribed in combination with Azithromycin for COVID-19 patients.

New Putative Antimicrobial Candidates: In silico Design of Fish-Derived Antibacterial Peptide-Motifs.

Antimicrobial resistance remains a great threat to global health. In response to the World Health Organizations’ global call for action, nature has been explored for novel and safe antimicrobial candidates. To date, fish have gained recognition as potential source of safe, broad spectrum and effective antimicrobial therapeutics. The use of computational methods to design antimicrobial candidates of industrial application has however, been lagging behind. To fill the gap and contribute to the current fish-derived antimicrobial peptide repertoire, this study used Support Vector Machines algorithm to fish out fish-antimicrobial peptide-motif candidates encrypted in 127 peptides submitted at the Antimicrobial Peptide Database (APD3), steered by their physico-chemical characteristics (i.e., positive net charge, hydrophobicity, stability, molecular weight and sequence length). The best two novel antimicrobial peptide-motifs (A15_B, A15_E) with the lowest instability index (−28.25, −22.49, respectively) and highest isoelectric point (pI) index (10.48 for each) were selected for further analysis. Their 3D structures were predicted using I-TASSER and PEP-FOLD servers while ProSA, PROCHECK, and ANOLEA were used to validate them. The models predicted by I-TASSER were found to be better than those predicted by PEP-FOLD upon validation. Two I-TASSER models with the lowest c-score of −0.10 and −0.30 for A15_B and A15_E peptide-motifs, respectively, were selected for docking against known bacterial-antimicrobial target-proteins retrieved from protein databank (PDB). Carbapenam-3-carboxylate synthase (PDB ID; 4oj8) yielded the lowest docking energy (−8.80 and −7.80 Kcal/mol) against motif A15_B and A15_E, respectively, using AutoDock VINA. Further, in addition to Carbapenam-3-carboxylate synthase, these peptides (A15_B and A15_E) were found to as well bind to membrane protein (PDB ID: 1by3) and Carbapenem synthetase (PDB: 1q15) when ClusPro and HPEPDOCK tools were used. The membrane protein yielded docking energy scores (DES): −290.094, −270.751; coefficient weight (CW): −763.6, 763.3 for A15_B and A15_E) whereas, Carbapenem synthetase (PDB: 1q15) had a DES of −236.802, −262.75 and a CW of −819.7, −829.7 for peptides A15_B and A15_E, respectively. Motif A15_B of amino acid positions 2–19 in Pleurocidin exhibited the strongest in silico antimicrobial potentials. This segment could be a good biological candidate of great application in pharmaceutical industries as an antimicrobial drug candidate.

In silico investigation on alkaloids of Rauwolfia serpentina as potential inhibitors of 3-hydroxy-3-methyl-glutaryl-CoA reductase.

Present work aimed to investigate the in silico activity of the alkaloids of roots of Rauwolfia serpentina as inhibitors of 3-hydroxy-3-methyl-glutaryl-CoA reductase (HMGCR). For this purpose, the three-dimensional (3D) structure of the protein HMGCR (PDB ID: 1HW9) was downloaded from Protein Data Bank (PDB) database, as a target enzyme. The structures of twelve alkaloids from the roots of R. serpentina were selected as ligands and docked with the selected HMGCR enzyme using Molegro Virtual Docker (MVD) software. The software ‘MVD’ computes the binding (atom) energies of selected protein (enzyme) and each ligand at minimum energetic conformation state by using the PLP (Piecewise Linear Potential) scoring mechanism. Docking results of twelve tested alkaloids showed that five alkaloids including compound 1 (ajmalicine), 2 (reserpine), 3 (indobinine), 4 (yohimbine), and 5 (indobine) have displayed the highest MolDock scores and best fit within the prominent active site residues (positioned between 684 and 692 of cis-loop) of HMGCR. According to the lowest MolDock energies obtained through non-covalent interactions of alkaloids with HMGCR, these are characterized to be the potential inhibitors of HMGCR. Therefore, the alkaloids from R. serpentina can effectively suppress the cholesterol biosynthesis pathway through inhibition of HMGCR and can serve as potential lead compounds for the development of new drugs for the treatment of hyperlipidaemia.

The cyanidin-3-O-glucoside of Black Rice inhibits the interaction of HMG-CoA and HMG-CoA Reductase: three-and two-dimension structure

The hypercholesterolemia condition is one metabolic disorder has affected to onset and prevalence of the dyslipidemia and cardiovascular disease. The cholesterol synthesized from HMG-CoA by co-enzyme HMG-CoA reductase. The research focus was to determine the effect of Cyanidin-O-glucose of black rice to prevent the HMG-CoA and HMG-CoA reductase interaction. The anthocyanins retrieved from the database of PubChem, is cyanidin-3-O-glucoside (CID: 12303221). We obtained HMG-CoA canonical SMILES (CID: 445127) from PubChem and reconstructed it using VEGAZZ software. RCSB Protein Data Bank (PDB) was used as a database to get the 3D structures of HMGR (PDB ID: 1DQ9). The water molecules and or previously existing ligands incorporated in their 3D structures were removed using Discovery Studio 2019. The docking results were visualized and analyzed by Discovery Studio, and Hex 8.0.0 software. This result determined that cyaniding-O-glucose of black rice prevented the interaction between HMG-CoA into HMG-CoA reductase respectively. This result indicates that the cyaniding-O-glucose of black rice has potential function as lowering cholesterol biosynthesis.

Efficient Synthesis, In-Vitro Antioxidant, Anticancer and Molecular Docking Studies of Bidentate Schiff Base Complexes of Vo(Ii) and Zn(Ii) by Green Route Method

Vanadium(II) and Zn(II) chelates with Schiff base derived from the condensation of orthophenylenediamine and cinnamaldehyde. Schiff base are multilateral ligand and offer resistant series of ligand to coordinate with metals. The Schiff base and its metal complexes were synthesized and characterized by elemental analysis, metal estimation, molar conductance, magnetic moment, UV-Visible, IR, Far-IR and NMR spectral studies. The elemental analysis suggest the stoichiometry to be 1:1 (M:L).The complexes are non-electrolyte in acetonitrile solution. The molar conductance and spectral properties indicate the complexes don’t dissociate in acetonitrile solution and retain their coordination. Melting points support the thermal stability of the complex. Coordination of ligand was confirmed by constant change of FT-IR. The electronic spectral data support octahedral geometry of VO(II) and square planar geometry of Zn(II) complexes. IR spectral data suggest that the ligand coordinated to the metal ion by imino nitrogen and amine nitrogen as bidentate manner. The NMR (1H & 13C) spectrum of schiff base and its diamagnetic Zn(II) complex was carried out and confirmed by the geometry and magnetic property of them. The antibacterial activity of the schiff base and VO(II) and Zn(II) complexes was assessed against Staphylococcus aureus, Enterococcus as Gram-positive bacteria and further against Escherichia coli, Vibrio parahaemolyticus and Pseudomonas as Gram–negative bacteria and one pathogenic yeast C.albicans by agar well diffusion method. The results of anticancer activity of schiff base and VO(II) and Zn(II) complexes indicated that the metal complex have moderately active than the corresponding ligand. The cell cycle proteins, CDK4 (PDB ID: 3G33), P-53 (PDB ID: 1YCS) were downloaded from the RCSB PDB (protein data bank) database and the auto Dock (V. 4.0) in the PyRx GUI has been used to confirm the binding abilities of the selected ligand and VO(II) complex.

Molecular docking, validation, dynamics simulations, and pharmacokinetic prediction of natural compounds against the SARS-CoV-2 main-protease

The study aims to evaluate the potency of two hundred natural antiviral phytocompounds against the active site of the Severe Acquired Respiratory Syndrome - Coronavirus − 2 (SARS-CoV-2) Main-Protease (Mpro) using AutoDock 4.2.6. The three- dimensional crystal structure of the Mpro (PDB Id: 6LU7) was retrieved from the Protein Data Bank (PDB), the active site was predicted using MetaPocket 2.0. Food and Drug Administration (FDA) approved viral protease inhibitors were used as standards for comparison of results. The compounds theaflavin-3-3’-digallate, rutin, hypericin, robustaflavone, and (-)-solenolide A with respective binding energy of −12.41 (Ki = 794.96 pM); −11.33 (Ki = 4.98 nM); −11.17 (Ki = 6.54 nM); −10.92 (Ki = 9.85 nM); and −10.82 kcal/mol (Ki = 11.88 nM) were ranked top as Coronavirus Disease − 2019 (COVID-19) Mpro inhibitors. The interacting amino acid residues were visualized using Discovery Studio 3.5 to elucidate the 2-dimensional and 3-dimensional interactions. The study was validated by i) re-docking the N3-peptide inhibitor-Mpro and superimposing them onto co-crystallized complex and ii) docking decoy ligands to Mpro. The ligands that showed low binding energy were further predicted for and pharmacokinetic properties and Lipinski’s rule of 5 and the results are tabulated and discussed. Molecular dynamics simulations were performed for 50 ns for those compounds using the Desmond package, Schrödinger to assess the conformational stability and fluctuations of protein-ligand complexes during the simulation. Thus, the natural compounds could act as a lead for the COVID-19 regimen after in-vitro and in- vivo clinical trials. Communicated by Ramaswamy H. Sarma

In Silico Analyses and Cytotoxicity Study of Asiaticoside and Asiatic Acid from Malaysian Plant as Potential mTOR Inhibitors.

Natural products remain a popular alternative treatment for many ailments in various countries. This study aimed to screen for potential mammalian target of rapamycin (mTOR) inhibitors from Malaysian natural substance, using the Natural Product Discovery database, and to determine the IC50 of the selected mTOR inhibitors against UMB1949 cell line. The crystallographic structure of the molecular target (mTOR) was obtained from Protein Data Bank, with Protein Data Bank (PDB) ID: 4DRI. Everolimus, an mTOR inhibitor, was used as a standard compound for the comparative analysis. Computational docking approach was performed, using AutoDock Vina (screening) and AutoDock 4.2.6 (analysis). Based on our analysis, asiaticoside and its derivative, asiatic acid, both from Centella asiatica, revealed optimum-binding affinities with mTOR that were comparable to our standard compound. The effect of asiaticoside and asiatic acid on mTOR inhibition was validated with UMB1949 cell line, and their IC50 values were 300 and 60 µM, respectively, compared to everolimus (29.5 µM). Interestingly, this is the first study of asiaticoside and asiatic acid against tuberous sclerosis complex (TSC) disease model by targeting mTOR. These results, coupled with our in silico findings, should prompt further studies, to clarify the mode of action, safety, and efficacy of these compounds as mTOR inhibitors.

Prediction of Mycobacterium tuberculosis pyrazinamidase function based on structural stability, physicochemical and geometrical descriptors.

BackgroundPyrazinamide is an important drug against the latent stage of tuberculosis and is used in both first- and second-line treatment regimens. Pyrazinamide-susceptibility test usually takes a week to have a diagnosis to guide initial therapy, implying a delay in receiving appropriate therapy. The continued increase in multi-drug resistant tuberculosis and the prevalence of pyrazinamide resistance in several countries makes the development of assays for prompt identification of resistance necessary. The main cause of pyrazinamide resistance is the impairment of pyrazinamidase function attributed to mutations in the promoter and/or pncA coding gene. However, not all pncA mutations necessarily affect the pyrazinamidase function.ObjectiveTo develop a methodology to predict pyrazinamidase function from detected mutations in the pncA gene.MethodsWe measured the catalytic constant (kcat), KM, enzymatic efficiency, and enzymatic activity of 35 recombinant mutated pyrazinamidase and the wild type (Protein Data Bank ID = 3pl1). From all the 3D modeled structures, we extracted several predictors based on three categories: structural stability (estimated by normal mode analysis and molecular dynamics), physicochemical, and geometrical characteristics. We used a stepwise Akaike’s information criterion forward multiple log-linear regression to model each kinetic parameter with each category of predictors. We also developed weighted models combining the three categories of predictive models for each kinetic parameter. We tested the robustness of the predictive ability of each model by 6-fold cross-validation against random models.ResultsThe stability, physicochemical, and geometrical descriptors explained most of the variability (R2) of the kinetic parameters. Our models are best suited to predict kcat, efficiency, and activity based on the root-mean-square error of prediction of the 6-fold cross-validation.ConclusionsThis study shows a quick approach to predict the pyrazinamidase function only from the pncA sequence when point mutations are present. This can be an important tool to detect pyrazinamide resistance.

Activation mechanism of plasmepsins, pepsin-like aspartic proteases from Plasmodium, follows a unique trans-activation pathway.

Plasmodium parasites that cause malaria produce plasmepsins (PMs), pepsin-like aspartic proteases that are important antimalarial drug targets due to their role in host hemoglobin degradation. The enzymes are synthesized as inactive zymogens (pro-PMs), and the mechanism of their conversion to the active, mature forms has not been clearly elucidated. Our structural investigations of vacuolar pro-PMs with truncated prosegment (pro-tPMs) reveal that the formation of the S-shaped dimer is their innate property. Further structural studies, biochemical analysis, and molecular dynamics simulations indicate that disruption of the Tyr-Asp loop (121p-4), coordinated with the movement of the loop L1 (237-247) and helix H2 (101p-113p), is responsible for the extension of the pro-mature region (harboring the cleavage site). Consequently, under acidic pH conditions, these structural changes result in the dissociation of the dimers to monomers and the protonation of the residues in the prosegment prompts its unfolding. Subsequently, we demonstrated that the active site of the monomeric pro-tPMs with the unfolded prosegment is accessible for peptide substrate binding; in contrast, the active site is blocked in folded prosegment form of pro-tPMs. Thus, we propose a novel mechanism of auto-activation of vacuolar pro-tPMs that under acidic conditions can form a catalytically competent active site. One monomer cleaves the prosegment of the other one through a trans-activation process, resulting in formation of mature enzyme. As a result, once a mature enzyme is generated, it leads to the complete conversion of all the inactive pro-tPMs to their mature form. DATABASE: Atomic coordinates and structure factors have been submitted in the Protein Data Bank (PDB) under the PDB IDs 6KUB, 6KUC, and 6KUD.

Synthesis, crystal structure, Hirshfeld surface analysis, spectral characterization, and quantum computational evaluation of (E)-2-(((4-bromophenyl)imino)methyl)-6-methylphenol

A newly synthesized compound, (E)-2-(((4-bromophenyl)imino)methyl)-6-methylphenol (C14H12BrNO), is analyzed in detail for structural clarification by experimental X-ray, Fourier transform IR, 1H and 13C NMR, and UV–vis spectral data along with theoretical quantum chemical computations. For the theoretical computations, the density functional theory B3LYP functional and 6–311++G (d,p) basis set were used in the gas phase, and the harmonic vibrational wavenumbers were assigned with the help of the potential energy distribution. The theoretical NMR spectra were obtained with the gauge-including atomic orbital (GIAO) method and for the UV–vis spectrum time-dependent density functional theory based on the integral equation formalism polarizable continuum model (IEFPCM) was used. By Hirshfeld surface analysis, the most important contributions were obtained for the crystal packing, and the possible contact points were determined. In addition, frontier molecular orbital (highest occupied molecular orbital–lowest unoccupied molecular orbital), molecular electrostatic potential, and nonlinear optical analyses were performed for the calculated optimized structure. Finally, molecular docking between (E)-2-(((4-bromophenyl)imino)methyl)-6-methylphenol and two different receptors (ubiquinol-cytochrome c reductase [Protein Data Bank ID 1BE3] and glucan endo-1,6-β-glucosidase [Protein Data Bank ID 5NGL]) was studied. From the results, (E)-2-(((4-bromophenyl)imino)methyl)-6-methylphenol was determined to be a good ubiquinol-cytochrome c reductase inhibitor because of its binding energy and affinity for protein active sites.

Screening of preferential binding affinity of selected natural compounds to SARS-CoV-2 proteins using in silico methods

Objectives: The global burden of the current severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causing the corona virus disease-19 (COVID-19) is enormous. No definitive treatment and prophylactic guidelines for COVID-19 currently exist except for physical distancing and aerial barriers between individuals. This work explored the natural compound-binding efficiency of SARS-CoV-2 proteins essential for host cell interaction and infection. Methods: The binding activity of artemisinin to SARS-CoV-2 spike glycoprotein (Protein Data Bank (PDB) ID: 6VYB), SARS-CoV-2 main protease (3C-like main protease (3CLpro); PDB ID: 6Y84) and SARS-CoV-2 papain-like protease (PLpro; PDB ID: 6W9C), were tested using in silico methods. Moreover, chloroquine and hesperidin were used as the positive control of binding affinity and proven therapeutic effect, respectively. Results: The highest affinities for binding to all tested SARS-CoV-2 proteins are observed for hesperidin (?5.8,?10.0, and ?8.1 kcal/mol), then for artemisinin (?4.8,?8.3, and ?6.0 kcal/mol), and the lowest for chloroquine (?4.1,?8.2, and ?4.8 kcal/mol). Artemisinin, hesperidin, and chloroquine had similar positioning toward targeted proteins at specific sites when these interactions were visualized. Conclusion: This study shows that artemisinin has the potential to bind and inhibit the SARS-CoV-2 spike protein, the 3CLpro main protease, and PLpro proteinase similar to hesperidin and chloroquine that have been proven as antivirals in previous preclinical and clinical studies. Keywords: Artemisinin, molecular docking study, SARS-CoV-2 proteins

In silico Molecular docking of Luteolin from Momordica charantia for dementia in Alzheimer's disease

Objective: In the present study, luteolin was isolated from Momordica charantia and characterized by IR and NMR spectroscopy, undergone in silico docking to study its anti-Alzheimer's role. In silico molecular docking is a computational system employed to predict the interaction vitality between two particles and the best introduction of ligand that shapes a complex with general least vitality. Methods: In this Protein Ligand Docking, we have used HEX 8.0.0 as a Docking Software. The receptors (PDB ID: 4PQE, 1P0I, 5O3L, 1J1C, 3NYJ, 2FJZ) were retrieved from the RCSB Protein Data Bank (PDB) Database while the ligand structure was retrieved as mol format from ChEBI database and it was converted as.pdb format using Chimera 1.12 and docking was done according to the specified parameters. Results: The molecular docking process for the luteolin was performed with the receptors and the E-value was determined. Further, the result of the binding site of ligand with the target proteins was interpreted by using Chimera 1.12 software. Conclusion: Luteolin was proved to have good affinity for target protein and it is having multitarget activity that is responsible for AD.

Structural and biochemical analysis of Bacillusanthracis prephenate dehydrogenase reveals an unusual mode of inhibition by tyrosine via the ACT domain.

Tyrosine biosynthesis via the shikimate pathway is absent in humans and other animals, making it an attractive target for next-generation antibiotics, which is increasingly important due to the looming proliferation of multidrug-resistant pathogens. Tyrosine biosynthesis is also of commercial importance for the environmentally friendly production of numerous compounds, such as pharmaceuticals, opioids, aromatic polymers, and petrochemical aromatics. Prephenate dehydrogenase (PDH) catalyzes the penultimate step of tyrosine biosynthesis in bacteria: the oxidative decarboxylation of prephenate to 4-hydroxyphenylpyruvate. The majority of PDHs are competitively inhibited by tyrosine and consist of a nucleotide-binding domain and a dimerization domain. Certain PDHs, including several from pathogens on the World Health Organization priority list of antibiotic-resistant bacteria, possess an additional ACT domain. However, biochemical and structural knowledge was lacking for these enzymes. In this study, we successfully established a recombinant protein expression system for PDH from Bacillusanthracis (BaPDH), the causative agent of anthrax, and determined the structure of a BaPDH ternary complex with NAD+ and tyrosine, a binary complex with tyrosine, and a structure of an isolated ACT domain dimer. We also conducted detailed kinetic and biophysical analyses of the enzyme. We show that BaPDH is allosterically regulated by tyrosine binding to the ACT domains, resulting in an asymmetric conformation of the BaDPH dimer that sterically prevents prephenate binding to either active site. The presented mode of allosteric inhibition is unique compared to both the competitive inhibition established for other PDHs and to the allosteric mechanisms for other ACT-containing enzymes. This study provides new structural and mechanistic insights that advance our understanding of tyrosine biosynthesis in bacteria. ENZYMES: Prephenate dehydrogenase from Bacillusanthracis (PDH): EC database ID: 1.3.1.12. DATABASES: Coordinates and structure factors have been deposited in the Protein Data Bank (PDB) with accession numbers PDB ID: 6U60 (BaPDH complex with NAD+ and tyrosine), PDB ID: 5UYY (BaPDH complex with tyrosine), and PDB ID: 5V0S (BaPDH isolated ACT domain dimer). The diffraction images are available at http://proteindiffraction.org with DOIs: https://doi.org/10.18430/M35USC, https://doi.org/10.18430/M35UYY, and https://doi.org/10.18430/M35V0S.

Molecular dynamics study on DNA damage by tritium disintegration

Using molecular dynamics (MD) simulation, we simulate the structural change of a telomeric DNA by β-decay of substituted tritium to helium-3. The configuration of the telomeric DNA is obtained by removing TRF2 protein from the TRF2-Dbd-DNA complex (Protein Data Bank ID is 3SJM). We assume that hydrogens (H) of guanines in the telomeric DNA are replaced to helium-3. Since this replacement of the H atoms to the 3He atoms changes the charge distribution significantly, the charge distribution used in the MD simulation for the modified guanine is obtained by the density functional theory calculations. We adopt, as the MD simulation, nanoscale molecular dynamics code with CHARMM36 force field using Langevin thermostat and Nosé–Hoover Langevin piston to control the temperature and pressure of the system, respectively. Moreover, changing both the number of replaced guanine N and the temperature of the system T, we calculate the root mean square deviation RMSD to quantify the dependence of the durability of the telomeric DNA on the β-decays. From the MD simulation, it is found that as N or T becomes larger, the RMSD of the DNA becomes also larger. Namely, it denotes that as the intensity of the β-decays becomes larger or as the temperature is increased, the DNA structure becomes more fragile.

Crystallographic structure versus homology model: a case study of molecular dynamics simulation of human and zebrafish histone deacetylase 10

Histone deacetylase (HDAC) 10 has been implicated in the pathology of various cancers and neurodegenerative disorders, making the discovery of novel inhibitors of the isoform an important endeavor. However, the unavailability of crystallographic structure of human HDAC10 (hHDAC10) hinders structure-based drug design effort. Previously, we reported the homology modeled structure of human HDAC10 built using the crystallographic structure of Danio rerio (zebrafish) HDAC10 (zHDAC10) (Protein Data Bank (PDB) ID; 5TD7, released on 24 May 2017) as a template. Here, in continuation with our study, both hHDAC10 and zHDAC10, and their respective complexes with trichostatin A (TSA), quisinostat, and the native ligand (in 5TD7), 7-[(3-aminopropyl)amino]-1,1,1-trifluoroheptane-2,2-diol (PDB ID; FKS) were submitted to 100 ns-long unrestrained molecular dynamics (MD) simulations. Comparative analyses of the MD trajectories revealed that zHDAC10 and its complexes displayed higher stability than hHDAC10 and its corresponding complexes over time. Nonetheless, docking of active and inactive set molecules revealed that more reliable conformations of hHDAC10 could be obtained at an extended time period. This study may shed more light on the reliability of hHDAC10 modeled structure for use in selective inhibitor design.Communicated by Ramaswamy H. Sarma

The Sir4 H-BRCT domain interacts with phospho-proteins to sequester and repress yeast heterochromatin.

In Saccharomyces cerevisiae, the silent information regulator (SIR) proteins Sir2/3/4 form a complex that suppresses transcription in subtelomeric regions and at the homothallic mating-type (HM) loci. Here, we identify a non-canonical BRCA1 C-terminal domain (H-BRCT) in Sir4, which is responsible for tethering telomeres to the nuclear periphery. We show that Sir4 H-BRCT and the closely related Dbf4 H-BRCT serve as selective phospho-epitope recognition domains that bind to a variety of phosphorylated target peptides. We present detailed structural information about the binding mode of established Sir4 interactors (Esc1, Ty5, Ubp10) and identify several novel interactors of Sir4 H-BRCT, including the E3 ubiquitin ligase Tom1. Based on these findings, we propose a phospho-peptide consensus motif for interaction with Sir4 H-BRCT and Dbf4 H-BRCT. Ablation of the Sir4 H-BRCT phospho-peptide interaction disrupts SIR-mediated repression and perinuclear localization. In conclusion, the Sir4 H-BRCT domain serves as a hub for recruitment of phosphorylated target proteins to heterochromatin to properly regulate silencing and nuclear order.