MOESM7 of Contribution of type W human endogenous retroviruses to the human genome: characterization of HERV-W proviral insertions and processed pseudogenes

Additional file 7: Fig. S6. MSRV Env puteins analysis with respect to the most similar HERV-W loci Env puteins and Syncytin-1 (locus 7q21.2). In Syncytin-1 ORF the domains mostly involved in the protein structure and function are annotated: Leader Peptide (LP), Binding Domain motif (BD), SU and TM disulphide bounds motifs (dS), Furin cleavage site (FCS), fusion core N- and C- terminal Heptad Repeats (NHR and CHR), Immunosuppressive domain (IM), Transmembrane unit (TM), Intracytoplasmic Tail (CYT) and the relative Syncytin-1 specific deletion (LQMV del). In Env puteins amino acid substitutions and internal stop codons with respect to Syncytin-1 are labeled with colored and black squares, respectively. The reading frames are reported below each sequence with a number and an arrow. The orange arrow indicates the Env portion frequently maintained in presence of flanking huge recurrent deletions

Office propre de saint Charles Borromee, latin-françois, dressé selon le bréviaire et le missel de Paris . Par un prêtre de la doctrine chrétienne

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MOESM6 of Classification and characterization of human endogenous retroviruses; mosaic forms are common

Additional file 6: Table S6. Translation table for HERV PBS sequences, taken from ReTe and hg19. The derivation and structure of this table is described in Methods

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<p>Reverse transcriptase (RT)-associated DNA polymerase (RDDP) and ribonucleaser H (RNase H) functions are both essential for HIV-1 genome replication, and the identification of new inhibitors to block both of them is a goal actively pursued by the scientific community. In this field, natural extracts have shown a great potential as source of new antivirals. In the present work, we investigated the effect of <i>Uvaria angolensis</i> extracts on the HIV-1 reverse transcriptase-associated DNA polymerase and ribonuclease H activities. The <i>U. angolensis</i> stem bark methanol extract inhibit both HIV-1 RNase H function and RDDP activity with IC₅₀ values of 1.0 ± 0.2 and 0.62 ± 0.15 μg/mL, respectively and, after been fractionated with different solvents, its solid residue showed an IC₅₀ of 0.10 ± 0.03 and of 0.23 ± 0.04 μg/mL against RNase H and RDDP, respectively, hence laying the bases for further studies for identification of single active components.</p

MOESM2 of Classification and characterization of human endogenous retroviruses; mosaic forms are common

Additional file 2. Supplementary figures, detailed discussions and detailed description of HERV groups

Chemical structure of the isatin derivative RMNC6.

<p>Chemical structure of the isatin derivative RMNC6.</p

Putative binding mode of RMC6 and critical residues individuated for RMNC6 binding in the pocket 1.

<p>(A) binding mode; (B) 2D depiction of RMNC6 and its respective interactions with RT residues: pale yellow sphere indicates hydrophobic interactions with lipophilic residues. Red arrow indicates an hydrogen bond (HB) acceptor interaction, green HB donor, while the violet sphere represents the aromatic π-π stacking interaction.</p

Yonetani-Theorell plot of the combination of RMNC6 and EFV on the HIV-1 RT RNA- dependent DNA polymerase activity.

<p>HIV-1 RT was incubated in the presence of RMNC6 alone (●) or in presence of different concentrations of EFV: 4 nM (Δ), 8 nM (■) and 16 nM (☐).</p

Effect of RT inhibitors on the thermal stability of p66/p51 HIV-1 RT.

<p>(A). The melting temperature of HIV-1 RT was measured by differential scanning fluorimetry in the presence of increasing concentrations of different inhibitors: (▼) Efavirenz (EFV), (○) β-thujaplicinol (BTP), (Δ) 2-(3, 4-dihydroxyphenyl)-5, 6-dimethylthieno[2, 3-d]pyrimidin-4(3H)-one (VU) and (●) RMNC6. (B). Maximum HIV-1 RT thermal shift (ΔTm) observed in the presence of 50 μM concentration of compounds. ΔTm values are the average of triplicate analysis, standard deviations are indicated as bars.</p

Binding sites of RMNC6 individuated after blind docking experiments on the whole wt HIV-1 RT structure.

<p>Binding sites of RMNC6 individuated after blind docking experiments on the whole wt HIV-1 RT structure.</p