Peptide schematic representation

Figure 2.2 Structures of CcnS histone acetyltransferase (HAT) bound to coenzymeA and various peptides. Schematic representation of Tetrahymena thermophiia CcnS HAT domain (ribbon representation) bound to coenzymeA and 19mers (both shown as ball and sticks) from (a) histone H3 (PDB code lpu9),...

Figure 5.27 Schematic representation of a model for the conformational change of hemagglutinin that at low pH brings the fusion peptide to the same end of the molecule as the receptor binding site. The fusion peptide (purple) is at the end of heUx A about 100 A away from the receptor binding site in the high pH form. In the low pH fragment this region of helix A has moved about 100 A towards the area where the receptor binding sites are expected to be in the intact hemagglutinin molecule. (Adapted from D. Stuart, Nature 371 19-20, 1994.)...

Figure 15.19 Schematic representation of the peptide-binding domain of a class I MHC protein. The al and a2 domains are viewed from the top of the molecule, showing the empty antigen-binding site as well as the surface that is contacted by a T-cell receptor. (Adapted from P.J. Bjdrkman et al.. Nature 329 506-512, 1987.)...

Fig. 2.14 Formulae of /5-peptides 81 and 82 forming stable 3,4-helical structures in aqueous solution and schematic representation of the position of the amino acid side-chains looking down the 3,4-helix axis [128, 165]...

Fig. 2.39 Schematic representation of the projection of idealized ji- and y-peptide helices in a plane perpendicular to the helix axis and comparison with the helical wheel of the natural a-helix...

Fig. 2.41 Schematic representation of type II peptides and unlike-y dipeptide illustrating...

Figure 3. Schematic representation of the PGII, PGI, PGC [13] and PGE proteins from A. niger, indicating the putative processing sites for the signal peptide ( ) and the mono- and dibasic processing site for the propeptide ( ). The position of introns (lA, IB and IC) are indicated ( [) and variation of amino acids number is shown in different parts of protein. The putative N-glycosylation sites are marked ( ).

Fig. 27. A schematic representation of the seven transmembrane helical peptide chains (A-G) viewed from inside the cell. The numbering denotes the first and last amino acid residues. The proton channel is believed to be the volume between helices C, D, F and G...

FIGURE 5.4 Schematic representation of a continous-flow system for the solid-phase synthesis of peptides. Solvent is forced through the system by a pump. The support is in the form of a column that is stationary. A reaction is monitored by measuring the change in absorbance of the solvent stream. 

Scheme 14 Schematic representations of the assay for nucleases and protease detection based on the complex of ACP, DNA-TR and peptide-H...

Fig. 8.24. Schematic representation of cyclic, double prodrugs of peptides and their mechanism of activation by enzymatic ester cleavage, followed by cyclization-elimination [168][169][238]...

Fig. 4. Schematic representation of template-assembled synthetic proteins. The conforma-tionally restricted template can be orthogonally protected and sequentially linked to helical segments to form a large variety of functionalized TASP proteins. Flexible spacers that connect the folded peptide segments and the template provide the necessary conformational freedom that will allow the hydrophobic residues to find their optimum orientations for packing the core...

Fig. 16. Schematic representation of the assembly of designed heme protein SAMs on silanized quartz substrates. Designed peptides are synthesized, homodimerized, and selfassociate to form four-helix bundles prior to heme incorporation, followed by chemisorption on prepared quartz surfaces. Reprinted with permission from Ref. (185) copyright 1998 American Chemical Society.

Fig. 4. A schematic representation of alternatively spliced Fas mRNA variants and the proteins they encode in normal PBMC. The upper three variants of FasA(4, 7), FasA(3, 4), and FasA(3, 4, 6) and the lower two variants of FasA(3, 4), and FasA(4, 6) were reported by Liu et al. (L6) and Papoff et al. (PI), respectively. The solid line indicates regions lacking in Fas mRNAs. The regions that are translated or not translated into proteins are indicated by boxes and broken lines, respectively. LR leader peptide CR, cysteine-rich subdomain TM, transmembrane domain ST, signal-transducing domain NR, negative regulation domain AL, altered amino acid region.

Figure 14.3 Helical wheel diagram of the YZl peptide and the schematic representation of the staggered dimer formation with an axial displacement of three heptad repeating units, which promote elongation into coiled coil fibrils. Reprinted from Zimenkov et al. (2004). Copyright 2004 Elsevier Science.

Figure 4.8. Schematic representation of amino acid 163-171 iL-1 peptide in reiationship to the whoie iL-1 p protein.

Figure 13.3. Schematic representation of the eye. (A) lacrimal drainage (B) cross section of the eye. Physiological factors diminishing the fraction of drug delivery across the corneal epithelium to the aqueous humor include tears that drain into the lacrimal duct and limited permeation of protein and peptide across the corneal epithelium.

Figure 13.6. Schematic representation of size-dependent protein disposition mechanisms. Depending on molecular weight, a protein or peptide predominantly undergoes selective Inactivation.

Fig. 7A-C. Schematic representations for guest-binding modes of hybrid assemblies formed with peptide lipid 9 and octopus (3 and 4) and steroid (5 and 6) cyclophanes a guest molecule is located in the hydrogen-belt domain (A for 11 and 12 each bound to 3 and 4 B for 11 and 12 bound to 6 and 5, respectively) a guest molecule is located in the hydrophobic domain (C for 11 and 12 bound to 5 and 6, respectively)...

Fig. 10. Schematic representation of guest-binding behavior of hybrid assemblies formed with peptide lipid 9 and cage-type cyclophanes 7 and 8, indicating conformational change of the host cavity...

Schematic representation of the specificity subsites of the PR active site with bound peptidic inhibitor JG-365. Amino acids forming the boundaries of the particular...

Schematic representation of the principal intermolecular interactions of a fibrinogen peptide A mimetic within the active site...

Figure 12-12 Formation of the oxyanion hole following cleavage of trypsinogen between Lys 15 and He 16. (A) Stereoscopic view. (B) Schematic representation. The newly created terminal -NH3+ of He 16 forms a hydrogen-bonded ion pair with the carboxylate of Asp 194. This breaks the hydrogen bond between Asp 194 and His 40 in trypsinogen, inducing the peptide segment 192-194 to shift from an extended conformation to a helical form in which the NH groups of Gly 193 and Ser 195 form the oxyanion hole. Notice that the positions and interactions of Asp 102, His 57, and Ser 195, the catalytic triad, are very little changed. From Birktoft et al.270...

Figure 25-11 Peptide chain of a protein coiled to form a right-handed alpha helix. Configuration of the helix is maintained by hydrogen bonds, shown as vertical dotted (or solid) lines. The helix on the left shows the detailed atom structure of the peptide chain. The helix on the right is a schematic representation without structural detail. 

Fig. 7. Schematic representations of the a-helix (axial view) and the /J-sheet (side view) conformations of peptides 8-10 (CE = crown-ether side chain). (Reproduced with the permission of Ref, 10a)...

Fig. 29. Schematic representation of a synthetic protease [73], Four a-helical peptides bearing a specific catalytic group are linked together. The correct folding of 80 brings the catalytic groups into a relationship that enables them to catalyze hydrolytic processes. (Reproduced with the permission of Ref. 73)...

Scheme 2 Left Schematic Representation of a Multiple Antigen Peptide (MAP), Consisting of Eight Peptide Monomers and a Di-K2K Dendron. Right Successive Generations of a Lys Branching Unit to Afford Various K2K Dendrons and Surface Amine Groups...

Inactive MoFe protein may also be isolated from the nitrogenase of nif B mutants of K. pneumoniae.14 4 Addition of FeMoco results in activation up to 40% of normal activity, apparently because only one mol of FeMoco could be added. The nif B preparation appeared to contain one atom of non-FeMoco Mo, and so formed the MoFe protein with two Mo but only one FeMoco. This suggests that the two FeMoco sites in wild-type MoFe protein operate independently.1485 The schematic representation of nitrogenase shown in Figure 72 thus contains two peptides, two P clusters and one FeMoco group. 

FIGURE 7.13. Schematic representation of the triple-helix formed by double tail amphiphiles that contain the peptide sequence of type IV collagen. The structure and sequence of peptides in the amphiphile is shown below the illustration. 

Figure 6 Schematic representation of the molecular packaging and sequential metabolism used for brain targeting of neuropeptides. TRH-CDS (8) is included to provide a concrete illustration for the targetor (T), spacer (S), peptide (P), adjuster (A), and lipophilic (L) moieties. 

Fig. 2. Schematic representation of NOESY cross peaks used in peptide assignments.

The basis of the sequential assignment approach is to use a combination of TOCSY/COSY spectra to assign peaks to residue type and then link those residue types sequentially together using NOESY spectra (53). A schematic representation of some of the key NOESY connectivities used in assigning the spectra of peptides is given in Fig. 2. 

Fig. 1. Schematic representation of peptidomimetics containing the amide surrogates that are isosteric with the natural peptidic amide bonds.

Representative results of HPLC chromatograms and mass spectra that we have obtained are shown in Fig. 1. Also shown are schematic representations of the peptide and lipopeptide structures. 

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