Structural Cartoons

Fig. 3. Structure and sequence of repeats present in the fibrous proteins discussed in this chapter. (A) The adenovirus triple -spiral. A single repeat of one of the chains is shown as a stick model colored by atom, the other two as a secondary structure cartoon in yellow and orange. Amino acids contributing to the hydrophobic core are labeled, as is the glycine in the turn. (B) Triple -spiral sequence repeats. Conserved hydrophobic residues are indicated by a hash sign, the conserved glycine or proline by an asterisk. (C) The T4-hber fold. A single repeat of one of the chains is shown as a stick model colored by atom, the other two as a secondary structure cartoon in yellow and orange. Several of the conserved amino acids are labeled. (D) Repeating sequences present in bacteriophage T4 fiber proteins (Cerritelli et al., 1996). Conserved amino acids are indicated by a small letter conserved hydrophobic residues by a hash sign, and conserved small amino acids by a dot.

Fig. 2. The histone octamer. The 3.1 A X-ray diffraction data model of Arents et al. [20] is shown in secondary structure cartoon format. The core of the histone octamer is well defined, but more than 30% of the histone sequence is in regions without secondary structure. These are unfortunately the most interesting regions in terms of epigenetic signaling. 25% of the molecule located in the N-terminal tails (and the C-termini of H2A) in the 3.1 A octamer structure has no interpretable electron density. Despite these limitations, this structure is sufficient to use as a starting model for molecular replacement phasing of the NCP. (Image courtesy of E. Moudrianakis.)...

The standard presentation of NCP molecular models uses skeleton building blocks ball and stick representations of atoms and bonds, or secondary structural cartoon features that emphasize the a-helical nature of the histone core. While these simplifications are necessary to convey some of the character of the salient... 

Structure cartoons constructed with ACD/Chemsketch Freeware 10.02 bond-lengths adjusted for easy viewing Inferred hydrogen atoms not shown Some inferred hydrogen atoms not shown... 

In our low-resolution picture, the proteinase domains differ most obviously from the pancreatic proteinases in that they contain inserted sequences. These insertions are found primarily on the surfaces of the proteinase domains and are responsible for the high specificity that the coagulation proteinases have for their protein substrates, all of which are cleaved at Arg (or Lys) residues. Conventional secondary structure cartoons that illustrate the differences between trypsin and thrombin are shown in Figure 36-4. 

Fig. 2. N-Terminal domain of yeast Hsp90. (a) Secondary structure cartoon of the crystal structure of the yeast Hsp90 N-terminal domain color ramped from the protein N terminus (blue) to the C terminus of the domain at residue 215 (red). The strands of the twisted /3-sheet are labeled as in Prodromou et al. (1997b). (b) As in (a) but rotated 90° around the vertical (c) as in (a) but rotated 180° around the vertical.

Fig. 3. Adenine-nucleotide bindingto the N-terminal domain, (a) Secondary structure cartoon (as in Fig. lc),with ADP (stickmodel) boundin the pocket formed by the helical face of the domain, (b) Detail of the ATP/ADP-binding site. The bound nucleotide is shown as a CPK-colored ball-and-stick model, and the many water molecules bound in the site are shown as red spheres. Hydrogen bonds are indicated by broken yellow rods, and the ligand interactions of the magnesium ion by broken blue rods.

Figure 7.5 (a] Myoglobin structure (cartoon representation], its heme and two neighboring side chains (licorice], iron and the CO molecule (bulky], (b] Free energy profile of CO migration along two reaction coordinates linking different pockets DP — Xe4 and Xe4 -> Xe2. The two curves represent PC (red] and MTP (blue] electrostatics. See Ref [150] for more details. 

Matrix Metalloproteinases. Figure 2 ProMMP-2-TIMP-2 structure (adopted from [4]). TIMP-2 cartoon and transparent surface structure is shown in blue, MMP-2 in red. The C-terminal ends of both molecules are marked as spheres. 

Fig. 1. Subunit structure of dihydropyridine-sensitive channels from skeletal muscle. Cartoon...

Fig. 2.5. Interactions of chemokines with heparin disaccharides. (A to C) Monomeric forms of chemokines are displayed as cartoons with residues found to interact with heparin colored red. (A) Monomer of crystal structure of CCL5 (RANTES) with heparin disaccharide I-S bound (red). (B) CXCL4 (PF4) with low-molecular-weight heparin (MW <9000d). (C) CXCL8 with heparin disaccharide I-S. (D) CXCL12 (SDF-la) with heparin disaccharide I-S. (E) CCL2, human IP-10, with conserved residues from murine IP-10 highlighted.

The generalization to the case of a thermally averaged parent state describes an interesting modulation curve that reflects in position and width the rotational eigenvalue spectrum of the resonant intermediate [31]. This structure has been observed in studies of HI ionization in Ref. 33. A schematic cartoon depicting the excitation scheme and the form of the channel phase for the case of a thermally averaged initial state is shown in Fig. 5g. 

Figure 14-7. Snapshots of the active site structures near the transition state of (top) the nucleophilic attack and (bottom) the exocyclic cleavage for the in-line monoanionic O2p mechanism of cleavage transesterification in the hairpin ribozyme. The yellow and red colored cartoon is for the substrate and ribozyme strands, respectively, and water molecules interacting with non-bridging oxygens and O5/ are shown...

Scheme 9. Cartoons of some dream structures of dendronized polymers and cylindrical objects...

Figure 2.8 The structure of the dimeric cytochrome bcomplex of the respiratory chain, (a) The cave for chemistry constituted by the hollow between the two monomers (the essential dimer ) in a cartoon representation. Reprinted with permission from Smith, 1998. Copyright (1998), American Association for the Advancement of Science, (b) The structure viewed perpendicular to the twofold axis and parallel to the membrane. All of the eleven subunits are completely traced and their sequences assigned. The top of the molecule extends 3.8 nm into the intermembrane space, the middle spans the membrane (4.2 nm), and the bottom extends some 7.5 nm into the matrix. Reprinted with permission from Iwata et al., 1998. Copyright (1998) American Association for the Advancement of Science.

Fig. 13.1. Cartoon of the aspartyl-tRNA synthetase amino acid binding site. The aspartate ligand is shown, along with the most important recognition residues. Groups that have been mutated in free energy simulations are boxed or circled. Flexible loop and Motif 2 refer to conserved motifs in the enzyme structure...

Figure 6.1 Cartoon illustrating the structure of the enzyme nitrogenase.

Fig. 1. Cross-/] structure of amyloid fibrils. (A) Cartoon representation of a cross-/] X-ray diffraction pattern. The defining features are a meridional reflection at 4.7 A and an equatorial reflection on the order of 10 A. The 4.7-A reflection is generally much brighter and sharper than the reflection at 10 A. (B) The cross-/] core structure of amyloid fibrils. Parallel /(-sheets are depicted, but the structure could equivalendy be composed of antiparallel /(-sheets or a mix of parallel and antiparallel. The 4.7-A spacing of /(-strands within each /(-sheet is parallel to the long fibril axis. The depicted 10-A sheet-to-sheet spacing actually ranges from about 5 to 14 A (Fandrich and Dobson, 2002), depending on the size and packing of amino acid side chains. Amyloid fibrils have diameters on the order of 100 A.

Fig. 3. Refolding model of insulin protofilaments, from Jimenez et al. (2002). (A) Ribbon diagram of the crystal structure of porcine insulin (PDB ID code 3INS), generated with Pymol (DeLano, 2002). The two chains are shown as dark and light gray with N- and C-termini indicated. The dotted lines represent the three disulfide bonds 1 is the intrachain and 2 and 3 are the interchain bonds. (B) Cartoon representation of the structure of monomeric insulin in the fibril, as proposed by Jimenez et al. (2002). The thick, arrowed lines represent /1-strands, and thinner lines show the remaining sequence. The disulfide bonds are as represented in panel A, and N- and C-termini are indicated. (Components of this panel are not to scale.) (C) Cartoon representation of an insulin protofilament, showing a monomer inside. The monomers are proposed to stack with a slight twist to form two continuous /(-sheets. (Components of this panel, including the protofilament twist, are not to scale.) In the fibril cross sections presented byjimenez et al. (2002), two, four, or six protofilaments are proposed to associate to form the amyloid-like fibrils.

B) Cartoon representation of the parallel superpleated /J-structure proposed for the N-terminal 70 residues of Ure2p in the fibril. This view down the fibril axis shows the stacking of N-termini with a twist of 3°. For reference, the calculated twist based on fibril pitch ranges from 0.7° to 3.4° from one monomer to the next (Kajava et al., 2004). 

The cartoon-like drawing of the structure of the parent bicylobutonium ion C4H7+ 36 is adopted from an ingenious forward-looking paper of Olah and coworkers in 1972, 61) long before routine 13C-FT-NMR spectroscopy and routine ab initio quantum chemical calculations were available, which envisaged correctly the stabilization mode of the parent bicyclobutonium ion to arise from the interaction of the backside lobe of the Cy-Hendo sp3 orbital with the empty carbenium carbon p-orbital at Ca. 

Figure 16.8 Three different kinds of bolaamphiphiles containing different apo-lar spacers and/or polar head groups. The cartoons representthe orthogonal and nonorthogonal arrangements proposed to explain the fiber structures observed in solution...

Fig. 8.3 Cartoon illustrating the alignment of the particles of two different orienting media, a Disc particles represent lipid bicelles. b Rods represent viral particles. Bicelles orient with their normal orthogonal to the magnetic field and viruses with their long axis parallel to it. (Reproduced with permission from N. Tjandra, Structure 1999, 7, R205-R211.)...

Figure 1 Cartoon representation of the human cathelicidin hCAPI 8. The amino acid residues that define each of the three hCAP18 domains have been added. The sequence of LL-37, the host defense peptide derived from hCAP18, is found in the inset. Structure-activity relationship studies have identified regions within the peptide that are necessary for both antimicrobial and immunomodulatory activities.

Figure 13 X-ray structure of the four-domain termination moduie of surfactin synthetase (PDB code, 2VSQ). The coioring and representation of the domains is the same as in Figures 11 and 12. A cartoon diagram of the reiative domain structure is iiiustrated at the right of the two views. Ac and An signify the C-terminai and N-terminai subdomains of the A domain.

SAMs, in general, and thiol SAMs, in particular, are very often perceived as systems that easily form layers of high structural quality and this view is reflected in oversimplifying cartoons where a SAM is represented by a two-dimensional crystalline arrangement of molecules on a surface, similar to the one depicted in Figure 5.1b. For some systems one can get quite close to this ideal picture, as seen from Figure 5.2a, however, the more common case exemplified by Figure 5.2b is quite different. While... 

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