Journal: Biochimie Open

Article Title: Identification of a nicotinamide/nicotinate mononucleotide adenylyltransferase in Giardia lamblia (GlNMNAT)

doi: 10.1016/j.biopen.2015.11.001

Figure Lengend Snippet: Multiple sequence alignment of 16 homologous NMNAT proteins from phylogenetically divergent organisms with GlNMNAT isoenzymes . The percentage of conservation is displayed throughout the sequence in bars. Alignment was done with the ClustalO algorithm in the CLC Sequence Viewer v7.0.2 program (CLCBio A/S, Additional Alignments plugin v.1.5.1).

Article Snippet: The multiple alignment was done with ClustalO (CLC Sequence Viewer v7.0.2 program, CLCBio A/S, Additional Alignments plugin v.1.5.1).

Techniques: Sequencing

Journal: Biochimie Open

Article Title: Identification of a nicotinamide/nicotinate mononucleotide adenylyltransferase in Giardia lamblia (GlNMNAT)

doi: 10.1016/j.biopen.2015.11.001

Figure Lengend Snippet: Alignment between the three NMNAT human isoenzymes and the two NMNAT isoenzymes from Giardia lamblia . Conservation percentage per residue position is observed in pink bars. The multiple alignment was done with ClustalO (CLC Sequence Viewer v7.0.2 program, CLCBio A/S, Additional Alignments plugin v.1.5.1). Identity percentages calculated with BLASTP algorithm (NCBI) and shown in the adjacent table. ATP active site motif for recognition and binding in N-terminus and C-terminus regions depicted in red (GxFxPx[H/T]xxH) and violet respectively (ISSTxxR) . (For interpretation of the references to colour in this figure legend, the reader is referred to the web version of this article.)

Article Snippet: The multiple alignment was done with ClustalO (CLC Sequence Viewer v7.0.2 program, CLCBio A/S, Additional Alignments plugin v.1.5.1).

Techniques: Residue, Sequencing, Binding Assay

Journal: Biochemistry

Article Title: Biochemical and spectroscopic characterization of a radical SAM enzyme involved in the formation of a peptide thioether crosslink

doi: 10.1021/acs.biochem.6b00145

Figure Lengend Snippet: (A) The mature nisin peptide has thioether crosslinks between Cys and dehydroalanine (Dha) and dehydrobutyrine (Dhb) residues. (B) The sactipeptide subtilosin A is shown, highlighting the three thioether crosslinks. In its fully mature form, subtilosin A is circularized. The stereochemistry at the three attachment sites is shown in red. The sactipeptides are distinct from the lanthipeptides in that the thioether crosslinks are formed to the Cα of the peptide. (C) Sequence logo for the SCIFF peptides showing the conserved C-terminal sequence. The figure was generated by aligning 100 SCIFF sequences selected from Interpro family IPR023975 using the Clustal Omega61 multiple sequence alignment and visualized by Weblogo.62,63

Article Snippet: The figure was generated by aligning 100 SCIFF sequences selected from Interpro family IPR023975 using the Clustal Omega61 multiple sequence alignment and visualized by Weblogo.62,63.

Techniques: Sequencing, Generated

Journal: The Journal of Biological Chemistry

Article Title: Cardiac Troponin T, a Sarcomeric AKAP, Tethers Protein Kinase A at the Myofilaments *

doi: 10.1074/jbc.M110.148684

Figure Lengend Snippet: Cardiac TnT contains a highly conserved PKA docking site. A, schematic illustration shows the location of the PKA binding site and cardiac-specific cTnI-Ser23-Ser24 phosphorylation sites (star). Drawing of the troponin complex is based on the crystal structure of the troponin core domain (50). N-terminal region of cTnT (residues 1–204) was not solved in the crystal structure. Rectangles represent helical structures. cTnC is colored red, cTnI is green, and cTnT is blue. B, ClustalW multiple sequence alignment of cTnT with nine other AKAPs. Conserved residues responsible for tethering PKA are shown in white. The high homology between cTnT and Ht31 is also shown (boxed). C, surface representation of cTnT (PDB 1J1D) helix 203–224 shows the position of hydrophobic residues (red) involved in PKA docking.

Article Snippet: In silico analysis of the cTnT amino acid sequence using the ClustalW multiple alignment algorithm (part of the MacVector 11 sequence analysis suite) identified a fragment of an amphipathic α-helix (spanning residues 212–224) as a putative PKA-R binding site ( ). fig ft0 fig mode=article f1 fig/graphic|fig/alternatives/graphic mode="anchored" m1 Open in a separate window FIGURE 2. caption a7 Cardiac TnT contains a highly conserved PKA docking site.

Techniques: Binding Assay, Phospho-proteomics, Sequencing