Proteins ribbon model

Fig. 3. Structural features of heterotrimeric G proteins. Ribbon model of Gat/i(GDP)/f1y1 heterotrimer (1GOT), where a is blue, [I is green, and y is gold. The three Switch regions in Ga are highlighted in yellow, and GDP (red) is buried between the GTPase and helical domains of Ga. The subunits have been rotated outward to show the intersubunit interface, which is primarily composed of the aN helix (truncated in this view) and Switch II on Ga and blades 1-3 on GjS.

Left side of Fig. 4 shows a ribbon model of the catalytic (C-) subunit of the mammalian cAMP-dependent protein kinase. This was the first protein kinase whose structure was determined [35]. Figure 4 includes also a ribbon model of the peptide substrate, and ATP (stick representation) with two manganese ions (CPK representation). All kinetic evidence is consistent with a preferred ordered mechanism of catalysis with ATP binding proceeding substrate binding. 

Fig. 4. Ribbon model of protein kinase with peptide substrate and Mn2ATP (left) and protein phosphatase (right)...

Figure 26.9 X-ray crystal structure of citrate synthase. Part (a) is a space-filling model and part (b) is a ribbon model, which emphasizes the a-helical segments of the protein chain and indicates that the enzyme is dimeric that is, it consists of two identical chains held together by hydrogen bonds and other intermolecular attractions. Part (cl is a close-up of the active site in which oxaloacetate and an unreactive acetyl CoA mimic are bound.

Fig. 6.1 Schematic representation of the cysteinyl leukotriene 2 (CysLT ) receptor. Ribbon model of this family A G protein-coupled receptor (GPCR) is pictured in its heptahelical configuration. The extracellular amino terminus of the receptor, the transmembrane domains, and the intracellular carboxyl tail extend behind the intracellular palmitoylation site. The putative binding pocket for cysteinyl leukotriene ligands is derived from a rhodopsin model...

FIGURE 12-21 Calmodulin. This is the protein mediator of many Ca2+-stimu-lated enzymatic reactions. Calmodulin has four high-affinity Ca2+-binding sites (Kd 0.1 to 1 /cm), (a) A ribbon model of the crystal structure of calmodulin (PDB ID 1CLL). The four Ca2+-binding sites are occupied by Ca2+ (purple). 

Fig. 21. Changes in distance between R1 residues in TM3 and TM6. (A) Ribbon model of rhodopsin in the dark state showing the location of R1 side chains. For each distance measurement, only two R1 side chains were in the protein, one fixed at the reference site 139 in TM3, and the other at a site in the sequence 248-252. (B) After photoactivation, showing the movement of TM6 and the new positions of the pairs. (C) The corresponding EPR spectra of the double mutants in the dark (solid traces) and after photoactivation (light traces). A decrease in spectral amplitude represents a decrease in interspin distance.

Fig. 4. (A) Schematic representation of the occurrence of CxxC motifs in various proteins. The polypeptide chains are drawn to scale as boxes. Transmembrane helices are indicated by empty rectangles and CxxC motifs by filled rectangles. (B) Ribbon model of the structure of CopZ. The position of the copper ion is inferred. Other metallochaperones and the CopZ-like building blocks shown in (A) probably all have a very similar structure.

Fig. 3.3 The structure of the N-terminal SH3 domain of Grb2 bound to a proline-rich Sos peptide has been determined by NMR.29.30 The structure of the Gbr2 N-terminal SH3 domain, compiexed with a 10-residue peptide, comprising residues 1134-1144 (VPPPVPPRRR-NHz) of Sos, is shown. The prolyl residues, P2, P3, P6, and P7, which interact with the SH3 domain of Grb2 are marked. (The ribbon model was reproduced with permission of the authors and J. Mol. Biol, from data in ref. 30, available In databanks.) A variation of this scheme is the recognition of a proline-rich sequence (APTMPPPLPP) in the GAP protein for Rho by the SH3-domain of the cytosolic c-Abi tyrosine kinase. i This interaction couples the Rho/GAP tightly to this cytosolic tyrosine kinase and brings the momomeric G protein, Rho, under the control of phosphorylation by the kinase.

Fig. 5.4 A ribbon model of the G p-subunit, which has WD (Tip-Asp) repeats and forms p-propellers. This structure is like a scaffold, presenting a surface to which other proteins can bind. (The structure was solved in Paul Sigler s laboratory s and is reproduced with permission of the authors and Nature.)...

Fig. 6.1 Ribbon model of bone morphogenetic protein-7. From the cystine knot emerge four antiparallel p-sheets, which form the finger 1 and 2 projections. An a-helix on the left-hand side of the knot lies perpendicular to the axis of the two fingers and forms the heel of the hand. (The cystine knot forming the core of the monomer consists of three disulphide bonds. Two disulphides form a ring through which the third disulphide passes.) (Reproduced with permission of the authors of ref. 2, and the Proc. Natl. Acad. Sci USA, from data filed with the Brookhaven protein databanks.)...

Fig. 7.2 Tlie crystal structure of mammalian Ser/Thr protein phosphatase-1, complexed with the toxin mycrocystin was determined at 2.1 A resolution. PPl has a single domain with a fold, distinct from that of the protein tyrosine phosphatases. The Ser/Thr protein phosphatase-1, is a metalloenzyme with two metal ions positioned at the active site with the help of a p-a-p-o-p scaffold. A dinuclear ion centre consisting of Mn2+ And Fe2+ g situated at the catalytic site that binds the phosphate moiety of the substrate. Ser/Thr phosphatases, PPl and PP2A, are inhibited by the membrane-permeable ocadaic acid and by cyclic hexapeptides, known as microcystins. The toxin molecule is depicted as a ball-and-stick structure. On the left and on the ri t, two different views of the same molecule are shown. Microcystin binds to three distinct regions of the phosphatase to the metaLbinding site, to a hydrophobic groove, and to the edge of a C-terminal groove in the vicinity of the active site. At the surface are binding sites for substrates and inhibitors. These ribbon models are reproduced vnth permission of the authors and Nature from ref. 9.

Phospholipids, such as phosphatidyl inositol-4,5-bisphosphate and IP3, have been shown to associate with PH domains, (ref. 49 of Chapter 3). The aminoacids in the PH domain which are responsible for this interaction are Y (tyrosine), W (tryptophan), K (lysine), R (arginine), and S (serine). In many PH-domains there is a group of lysines and arginines. (This ribbon model was reproduced with permission of the authors and Nature from data in ref. 48 of Chapter 3, available in protein data banks.)... 

Figures 4.4 and 4.5 show examples of two common types of representations of protein structures. In Figure 4.4 some of the global structural features of the myoglobin molecule are shown from the most commonly used perspective [341]. In this view the helical segments as well as the heme group are clearly recognizable. In Figure 4.5 a ribbon model of the same molecule is shown.

A simple 3D representation of the large scale features of a protein is obtained from the ribbon model of Richardson if one considers only the central line of the ribbon. This line is a space curve, usually oriented, from the N-terminal toward the C-terminal of the protein chain. The ribbon model shows the internal turns within a helical segment, consequently, the central line of the ribbon, as a space curve, also shows these details. 

An alternative technique is used for general chain molecules [197,198]. Most biologically important chain molecules do not form knots or links, yet knot theoretical methods are applicable for their shape characterization. One can take a projection of the molecular backbone and characterize the projection (where for simplicity, we shall assume that all crossings of the projection are nondegenerate). For example, the space curve of the median line of a ribbon model of a protein is not in general a knot, since the two endpoints of the median line are usually not joined. Nevertheless, for the given projection we may convert the space curve of the median into a knot by the following steps ... 

A ribbon model of the protein calmodulin. In this type of model, the ribbon represents the polypeptide chain. This protein coordinates with Ca + ions (white spheres) and aids in transporting them in living systems. 

Fig. 5. Crystal structure ofthe A. carterae PCP monomer. (A) stereogram ofthe ribbon model ofthe PCP monomer. The scaffold formed by the helices is likened to a boat the various parts of a boat (bow, stern, deck and keel) are marked. The chromophores in the hydro-phobic cavity ofthe monomer complex are likened to "cargos. (B) stereogram ofthe arrangement of peridinins and chlorophyll in the N-terminal domain [oniy two peridinins ofthe C-terminai domain are shown by thinner iines]. Figure source Hofmann, Wrench, Sharpies, Hiller, Werte and Diederichs (1996) Structural basis of light harvesting by carotenoids Peridinin-chlorophyll-protein from Amphidinlum carterae. Science 272 1789,1790. A color stereogram of (A) kindiy provided by Dr. Eckhard Hofmann and Dr. Wolfram Weite is shown in Color Plate 7.

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