Encode-Guess-Educated

 view release on metacpan or  search on metacpan

t/data/good/10398587.utf8  view on Meta::CPAN

   Met159Thr mutation. The Ala124Val mutation in InhA is not located in
   the putative triclosan-binding site and its structural effect can not
   be explained with our current model.
     __________________________________________________________________

   [123]Full-size image (32K) - Opens new window [124]Full-size image
   (32K)

   Figure 4. Location of residues conferring resistance against triclosan.
   Stereo view of the cofactor/inhibitor binding pocket with the molecular
   surface of EnvM rendered transparent. Residues leading to triclosan
   resistance in E. coli are shown in all-bonds representation and are
   mapped in red onto the molecular surface. Phe203 forms part of the
   binding pocket near the 2-hydroxyl containing ring of triclosan, which
   can not be seen in this orientation. [125]Figure 4 has been generated
   with the program SPOCK [[126]Christopher 1998].
   [127]View Within Article
   The high-resolution structure of EnvM in complex with triclosan and
   NADH provides a framework for understanding the inhibitory mechanisms
   of triclosan in bacterial fatty acid biosynthesis. This structure
   suggests explanations for the decreased effectiveness of triclosan in

t/data/good/11278591.utf8  view on Meta::CPAN

   Structure of GNA1 and AcCoA, GlcNAc6P binding sites. A, ribbon
   representations of the GNA1 fold (left) and the intertwined GNA1 dimer
   (right). In subunit 1, the GNA1 secondary structure elements forming
   the structurally conserved GNAT core are shown ingreen, the exchanged
   β-strand in yellow, and the remaining structural elements in cyan.
   Subunit 2 is shown in magenta with its exchanged strand β6 inred. The
   molecular surface of AcCoA-(B) and CoA-GlcNAc6P-(C) complexed GNA1,
   oriented as in Fig.[82]1 B (left view) and color-coded (B) as in Fig.
   [83]1 B, with the regions undergoing small structural rearrangements
   upon AcCoA binding displayed under a transparent surface (the cyan and
   yellow bonds refer to the apo and AcCoA-complexed GNA1 models,
   respectively). AcCoA is shown with carbon (white), nitrogen (blue),
   sulfur (green), oxygen (red), and phosphorous (purple) atoms. C, the
   color code is according to the electrostatic potential with positive
   and negative charges shown inblue and red, respectively. The essential
   catalytic Tyr-143 is displayed through a transparent surface. CoA and
   GlcNAc6P are shown with yellow carbon atoms. D, stereoview of the
   GlcNAc6P binding site with residues from subunit 1 and 2 shown in cyan
   and magenta, respectively. The dotted lines indicate hydrogen bonds.
   Residues within the GNAT conserved β-bulge are displayed in green.

   The GNA1 structure is dimeric in the crystal as well as in solution, as
   attested from gel filtration data (not shown). The crystalline dimer is
   made of two intertwined GNA1 monomers in which strand β6 of one subunit
   exchanges with the identical strand from the other subunit (Fig. [84]2
   A). A β-strand exchange between subunits in a dimer is an unusual

t/data/macroman/10542098.macroman  view on Meta::CPAN

   structure (crystallographic R factor 22.1% and R[free] 27.0%; see
   Methods and [68]Table 1). The overall structure of the TRAIL−DR5
   complex, including representative electron density, is shown in
   [69]Fig. 1.
   [70]Figure 1. The structure of TRAIL, DR5 and the TRAIL−DR5 complex.
   [71]Figure 1 thumbnail

   a, Stereo view of the complex. The three crystallographically
   equivalent copies of the TRAIL subunit (yellow, cyan, pink) and DR5
   (blue, green, red) are depicted schematically and the TRAIL trimer is
   enclosed in a transparent molecular envelope. This orientation defines
   a standard view. b, The complex as depicted in (a) but viewed down the
   three-fold axis. The orientation is such that the cell surface
   presenting DR5 is above the page and that for TRAIL is below the page.
   c, Superposition of TRAIL (pink) with TNF beta (blue). The secondary
   structure elements for TRAIL are also marked on the sequence alignment
   in [72]Fig. 2a. The r.m.s. deviation is 0.9  for 120 structurally
   equivalent C alpha atoms. The major extension of the AA" loop in TRAIL
   is highlighted by yellow stripes. The cell surface position is not to
   scale. d, Comparison of DR5 and TNF-R1. DR5 and TNF-R1 (from the TNF
   beta −TNF-R1 complex) are depicted schematically in the left and right

t/data/macroman/10542098.macroman  view on Meta::CPAN

   completely between the two complexes ([112]Fig. 3b).
   [113]Figure 3. Elements of conservation and specificity in
   ligand−receptor binding.
   [114]Figure 3 thumbnail

   a, Conservation in ligand-receptor interactions. Close up of the
   interaction involving the B1 (cyan) surfaces in the TRAIL−DR5 and TNF
   beta −TNF-R1 complexes centered on the key tyrosine residue (Tyr 216 in
   TRAIL). In this and in (c), the polypeptide chains are represented
   schematically as in [115]Fig. 1a and the solvent-accessible surfaces of
   the receptors (calculated in isolation) are shown as semi-transparent
   envelopes. b, Comparison of surface charge between TRAIL, TNF alpha ,
   TNF beta and their receptors. Blue denotes positive, and red negative;
   electrostatic potential is contoured at plusminus 8.0 kT in program
   GRASP^[116]31. The views of ligand and receptor are as in [117]Fig. 2b.
   c, Interaction of Arg 149 in the AA" loop of TRAIL with Glu 147 in DR5.
   d, BIAcore analysis showing binding of DR5 to wild type TRAIL or the
   mutant lacking the AA" loop. e, Immunoprecipitation with DR5-Fc in the
   presence of wild type (W) or the slightly smaller AA" TRAIL mutant (M).
   Lanes 1 and 2 immunoprecipitated material (IP), lanes 3 and 4 material
   left in supernatant (SN) following immunoprecipitation.