MOESM1 of Scoria: a Python module for manipulating 3D molecular data

Additional file 1: Table S1. Main Scoria functions, with associated dependencies (if any)

MOESM2 of Scoria: a Python module for manipulating 3D molecular data

Additional file 2. An archived version of Scoria, without MDAnalysis support

MOESM3 of Scoria: a Python module for manipulating 3D molecular data

Additional file 3. An archived version of Scoria, derived from the main Scoria branch, that includes MDAnalysis support

Toward Understanding the Conformational Dynamics of RNA Ligation

Members of the genus <i>Trypanosoma</i>, which include the pathogenic species <i>Trypanosoma brucei</i> and <i>Trypanosoma cruzi</i>, edit their post-transcriptional mitochondrial RNA via a multiprotein complex called the editosome. In <i>T. brucei</i>, the RNA is nicked prior to uridylate insertion and deletion. Following editing, nicked RNA is religated by one of two RNA-editing ligases (<i>Tb</i>REL). This study describes a recent 70 ns molecular dynamics simulation of <i>Tb</i>REL1, an ATP-dependent RNA-editing ligase of the nucleotidyltransferase superfamily that is required for the survival of <i>T. brucei</i> insect and bloodstream forms. In this work, a model of <i>Tb</i>REL1 in complex with its full double-stranded RNA (dsRNA) substrate is created on the basis of the homologous relation between <i>Tb</i>REL1 and T4 Rnl2. The simulation captures <i>Tb</i>REL1 dynamics in the state immediately preceding RNA ligation, providing insights into the functional dynamics and catalytic mechanism of the kinetoplastid ligation reaction. Important features of RNA binding and specificity are revealed for kinetoplastid ligases and the broader nucleotidyltransferase superfamily

Toward Understanding the Conformational Dynamics of RNA Ligation

Members of the genus <i>Trypanosoma</i>, which include the pathogenic species <i>Trypanosoma brucei</i> and <i>Trypanosoma cruzi</i>, edit their post-transcriptional mitochondrial RNA via a multiprotein complex called the editosome. In <i>T. brucei</i>, the RNA is nicked prior to uridylate insertion and deletion. Following editing, nicked RNA is religated by one of two RNA-editing ligases (<i>Tb</i>REL). This study describes a recent 70 ns molecular dynamics simulation of <i>Tb</i>REL1, an ATP-dependent RNA-editing ligase of the nucleotidyltransferase superfamily that is required for the survival of <i>T. brucei</i> insect and bloodstream forms. In this work, a model of <i>Tb</i>REL1 in complex with its full double-stranded RNA (dsRNA) substrate is created on the basis of the homologous relation between <i>Tb</i>REL1 and T4 Rnl2. The simulation captures <i>Tb</i>REL1 dynamics in the state immediately preceding RNA ligation, providing insights into the functional dynamics and catalytic mechanism of the kinetoplastid ligation reaction. Important features of RNA binding and specificity are revealed for kinetoplastid ligases and the broader nucleotidyltransferase superfamily

MOESM1 of Two inhibitors of yeast plasma membrane ATPase 1 (ScPma1p): toward the development of novel antifungal therapies

Additional file 1: Table S1. A list of additional antifungal compounds found in our whole-cell screen. Figure S1. IC50 curves for the cell-free, vesicle-based ScPma1p assays. Figure S2. IC50 curves for the whole-cell assays. Figure S3. Compound IC50 values against whole-cell ABC16-Monster yeast, with and without two distinct spiroindolone-binding-pocket ScPMA1 mutations (L290S and P399T)