Proteins space-filling model

All pictorial representations of molecules are simplified versions of our current model of real molecules, which are quantum mechanical, probabilistic collections of atoms as both particles and waves. These are difficult to illustrate. Therefore we use different types of simplified representations, including space-filling models ball-and-stick models, where atoms are spheres and bonds are sticks and models that illustrate surface properties. The most detailed representation is the ball-and-stick model. However, a model of a protein structure where all atoms are displayed is confusing because of the sheer amount of information present (Figure 2.9a). 

The binding model, suggested by Brian Matthews, is shown schematically in (a) with connected circles for the Ca positions, (b) A schematic diagram of the Cro dimer with different colors for the two subunits, (c) A schematic space-filling model of the dimer of Cro bound to a bent B-DNA molecule. The sugar-phosphate backbone of DNA is orange, and the bases ate yellow. Protein atoms are colored red, blue, green, and white, [(a) Adapted from D. Ohlendorf et al., /. Mol. Evol. 19 109-114, 1983. (c) Courtesy of Brian Matthews.]... 

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. 2. The structure of the Fe protein (Av2) from Azotobacter vinelandii, after Geor-giadis et al. (1). The dimeric polypeptide is depicted by a ribbon diagram and the Fe4S4 cluster and ADP by space-filling models (MOLSCRIPT (196)). The Fe4S4 cluster is at the top of the molecule, bound equally to the two identical subunits, Emd the ADP molecule spans the interface between the subunits with MoO apparently binding in place of the terminal phosphate of ATP.

Fig. 3. The tetrameric structure of the MoFe protein (Kpl) from Klebsiella pneumoniae (7). The two FeMoco clusters and the P clusters are depicted by space-filling models and the polypeptides by ribbons diagrams (MOLSCRIPT (196)). The FeMoco clusters are bound only to the a subunits, whereas the P clusters span the interface of the a and j8 subunits.

Fig. 10. The putative transition-state complex formed between the Fe protein MgADP AlFj and the MoFe protein. For simplicity only one a/3 pair of subunits of the MoFe protein is shown. The polypeptides are indicated by ribbon diagrams and the metal-sulfur clusters and MgADP AlFi" by space-filling models (MOLSCRIPT (196)). The figure indicates the spatial relationship between the metal-sulfur clusters of the two proteins in the complex.

FIGURE 2.1 A side view of the structure of the prototype G-protein-coupled, 7TM receptor rhodopsin. The x-ray structure of bovine rhodopsin is shown with horizontal gray lines, indicating the limits of the cellular lipid membrane. The retinal ligand is shown in a space-filling model as the cloud in the middle of the structure. The seven transmembrane (7TM) helices are shown in solid ribbon form. Note that TM-III is rather tilted (see TM-III at the extracellular and intracellular end of the helix) and that kinks are present in several of the other helices, such as TM-V (to the left), TM-VI (in front of the retinal), and TM-VII. In all of these cases, these kinks are due to the presence of a well-conserved proline residue, which creates a weak point in the helical structure. These kinks are believed to be of functional importance in the activation mechanism for 7TM receptors in general. Also note the amphipathic helix-VIII which is located parallel to the membrane at the membrane interface. 

Figure 4.32 A space-filling model of the 70S ribosome the three RNA molecules—5S, 16S and 23 S—are in white, yellow and purple, respectively ribosomal proteins of the large and small subunit are in blue and green, respectively the tRNA in the A-site, with its 3 -end extending into the peptidyl-transferase cavity is in red and the P-site tRNA is in yellow. (From Moore and Steitz, 2005. Copyright (2005) with permission from Elsevier.)...

Figure 17.8 Ribbon diagrams of the heterodimeric MoFe-protein (left) and homodimeric Fe-proteins of nitrogenase (right). The a- and P-subunits to the left of the MoFe-protein are shown in light and dark shading, respectively, while the metalloclusters are shown as dark space-filling models on the right side. The two subunits of the Fe-protein are shown in light and dark shading, with the 4Fe-4S cluster at the dimer interface as a space-filling model. (From Rees et al., 2005. Reproduced with permission of the Royal Society.)...

Fig. 1. Space filling model of yeast iso-1-cytochrome c. The edge of the heme prosthetic group is visible as a black linear structure in the center of the protein. Phe-82 is shaded a dark gray at the left upper side of the heme group...

FIGURE 16.4 Space-filling models of deoxyhemoglobin (a) and oxyhemoglobin (b). Notice the small shifts in the overall geometry of the various protein chains and the decreased size of the inner core. 

Figure 29-6 Some protein-RNA interactions within the ribosome. (A) A space-filling model of the 23S and 5S RNA with associated proteins from the ribosome of Haloarcula marismortui. The CCA ends of bound tRNA molecules in the A, P, and E sites are also included. The view is looking into the active site cleft. The proteins with e after the number are related to eukaryotic ribosomal proteins more closely than to those of E. coli.17 Courtesy of T. A. Steitz. (B) Three-dimensional structure of a 70S ribosome from Thermus thermophilus. The 30S subunit is to the right of the 50S subunit. Courtesy of Yusupov et al.33a (C) Stereoscopic view of the helix 21 to helix 23b region of the 16S RNA with associated proteins S6 (upper left), S18 (upper center, front), and S15 (lower back) from T. thermophilus. Courtesy of Agalarov et at.31 (D) Simplified in vitro assembly map of the central domain of the 30S bacterial ribosome. Courtesy of Gloria Culver. (E) Contacts of proteins with the central (platform) domain of the 16S RNA component. The sequence shown is that of Thermus thermophilus. Courtesy of Agalarov et al. (F) Three drawings showing alternative location of the four copies of protein L7/L12. The N-terminal and C-terminal...

At the end of successful refinement, the 2F0 Fc map almost looks like a space-filling model of the protein. (Refer to Plate 2 b, which is the final model... 

Each representation of a protein or nucleic acid conveys to the viewer different aspects of its structure line drawings give the bones, space-filling models the flesh, and schematic diagrams the gestalt of the design. No single representation of a protein or nucleic acid is adequate for all purposes, but the combination of several is more powerful than the total of all taken independently. 

Fig. 1. Space-filling models illustrating the relative sizes of a G protein-coupled receptor and three chemoattractant ligands. Shown are (A) rhodopsin, with its G protein-coupling surface oriented downward (Palczewski et al, 2000), (B) the chemoattractant peptide formyl-Met-Leu-Phe, (C) the chemoattractant protein C5a (Zhang et al, 1997), and (D) the chemoattractant chemokine GGL8 (or interleukin 8) (Baldwin et al, 1991). (See Golor Insert.)...

Figure 7. Space filling model of yMIPS/NAD+ complex. NAD+ atoms are darkened relative to the protein atoms.

Figure 3.45. Distribution of Amino Acids in Myoglobin. (A) A space-filling model of myoglobin with hydrophobic amino acids shown in yellow, charged amino acids shown in blue, and others shown in white. The surface of the molecule has many charged amino acids, as well as some hydrophobic amino acids. (B) A cross-sectional view shows that mostly hydrophobic amino acids are found on the inside of the structure, whereas the charged amino acids are found on the protein surface.

Variations in the shape of the barrel, the number of residues involved, and the disposition of the a helices have been studied by superpositions of all such structures.A comparison of the shapes of Pfa barrels in nine proteins showed that the mean radius of the barrel is fairly constant but the axial ratio can vary from 1.0 to 1.5. There appear to be at least two classes of Pfa barrels, depending on the number of residues that the N-terminal strand and the other odd-numbered strands contribute. The interior of the barrel is filled mainly by amino acid side chains. By slicing through a space-filling model of the protein at 1 A intervals, it was possible to show that the total volume of amino acid residues in the interior of the barrel is that normally expected for the interior of proteins. The active site of the enzyme is generally found to lie at the C-terminal end of the P strands. ... 

The amphipathic a helix, defined as an a helix with opposing polar and nonpolar faces oriented along its long axis, is a common secondary structural motif in biologically active peptides and proteins. The discovery of this structural motif was made by studying space-filling models of... 

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