Beta ribbons

Beta ribbons. An antiparallel double-stranded (3 ribbon can fit into the major groove of DNA and form... 

Beta propeller 67,560, 764 Beta ribbons 241 Beta sheet 64 Beta spiral 74 Bicarbonate ion... 

ColUnson SK, Emody L, Muller KH, Trust TJ, Kay WW (1991) Purification and characterization of thin, aggregative fimbriae from Salmonella enteritidis. J Bacteriol 173 4773 781 Cordes MH, Walsh NP, McKnight CJ, Sauer RT (2003) Solution structure of switch Arc, a mutant with 3(10) helices replacing a wild-type beta-ribbon. J Mol Biol 326 899-909 Cottingham MG, Hollinshead MS, Vaux DJ (2002) Amyloid fibril formation by a synthetic peptide from a region of human acetylcholinesterase that is homologous to the Alzheimer s amyloid-beta peptide. Biochemistry 41 13539-13547... 

Fig. 4.1.13 A ribbon representation of the crystal structure of recombinant acquorin molecule showing the secondary structure elements in the protein. Alpha-helices are denoted in cyan, beta-sheet in yellow, loops in magenta coelenterazine (yellow) and the side chain of tyrosine 184 are shown as stick representations. From Head et al., 2000, with permission from Macmillan Publishers.

Fig. 3. (A) Ribbon diagram of ribosomal L9 protein from B. stearothermophilus. The N- and C-terminal domains are labelled. The C-terminal construct consisting of residues 58-149 is shaded. (B) Ribbon diagram of the C-terminal domain showing the location of the three histidine residues. Reprinted from J. Mol. Biol., Vol. 318, S. Sato and D. P. Raleigh, pH-dependent stability and folding kinetics of a protein with an unusual alpha-beta topology The C-terminal domain of the ribosomal protein L9 , pp. 571-582, Copyright 2002, with permission from Elsevier Science.

Figure 3. Model of (p a)s TIM barrel from triose phosphate isomerase. Numbered arrow and twisted ribbon structures are beta sheets and alpha helicies, respectively. (Adapted and reproduced from Ref. 66 with permission. Cop3night 1984 American Association for the Advancement of Science.)...

Figure 4.2 This three-dimensional image of a protein shows the many twists and folds in its structure. The coils, called alpha helices, and the ribbons, called beta pleated sheets, are generally determined by the amino acid sequence of the protein and how the amino acids in different parts form weak bonds with each other. The shape of a protein is often critical for its function.

FIGURE 2.3 The antiparallel and the parallel beta (P) sheet or ribbon, showing the pattern of interchain hydrogen bonds and the protrusion out of the ribbon s plane of the amino acid side chains (denoted by R). The arrows indicate the relative directions of the peptide chains. 

Aggeli, A., Nyrkova, I. A., Bell, M., etal., Hierarchical self-assembly of chiral rod-like molecules as amodel for peptide beta-sheet tapes, ribbons, fibrils, and fibers. Proc. Natl. Acad. Sci. U. S. A. 2001,98, 11857-11862. 

Fig. 9 The hydrophobic binding pocket for T -Taxol on beta tubulin. Color on the surface model ranges from most lipophilic (brown) to most hydrophilic (blue). The ribbon view of beta tubulin is colored by secondary structure with red - alpha helices and blue - beta sheets...

Marini, D.M., Hwang, W., Lauffenburger, D.A., Zhang, S.G., and Kamm, R.D. "Left-handed helical ribbon intermediates in the self-assembly of a beta-sheet peptide". Nano Lett. 2(4), 295-299 (2002). 

Fig. 3. Architecture of the kelch domain, (a) Stereoview of Domain II with the active site metal ion and protein ligands superimposed on a ribbon diagram of the polypeptide chain, (b) The modular organization of the sevenfold propeller domain is based on four-stranded antiparallel beta sheet subdomains.

F . 2.1 Stereo ribbon diagram of human CDK2 with bound ATP (IHCK.PDB). Structural elements are colored as follows, glycine-rich loop in dark blue, N-terminal beta sheet... 

Fig. 1. Hierarchical protein structure Left Small part of the protein backbone. The peptide bond itself is marked by a shaded rectangle, R denotes one of the 20 amino acid side-chains. Middle Secondary structure in the form of an alpha-helix and beta-sheet. Only the backbone is shown and highlighted by a ribbon. The hydrogen bonds are indicated by dashed lines. Right Tertiary structure in the native state. The alpha-helices and beta-sheets are indicated by thick ribbons and arrows respectively...

Figure 4. Comparison of astacin and the catalytic domain of coUagenase. Stereo ribbon diagram [54] of the structure of astacin (green) and the catalytic domain of coUagenase (orange) superimposed using a rigid body fit of the catalytic hehces. The catalytic zinc atom (cyan) and the zinc ligands (blue) are marked. The overall similarity in the open beta sandwich region, N-terminal to the active site helix is apparent.

Globular proteins, such as most enzymes, usually consist of a combination of the two secondary structures—with important exceptions. For example, hemoglobin is almost entirely alpha-helical, and antibodies are composed almost entirely of beta structures. The secondary structures of proteins are often depicted in ribbon diagrams. 

Chain Conformation. From computer modeling studies of cellulose ( ), we know that the cellulose molecule has limited flexibility. Only a few regular (Internally symmetric) conformations are allowed for cellulose, a beta 1,4-llnked glucan, and structures similar to the traditional 2-fold helix are the only ones In accord with the observed z axis spacing. Such chains resemble flat ribbons. 

Fig. 1 The number of fold families identified from structural studies of proteins based on data obtained from SCOP. Representative structures are shown from each of the classes of protein fold, e.g., alpha or beta, that include enzymes. The proteins are represented as ribbons, colored from blue at the N-terminus through to red at the C-terminus. Cofactors and inhibitors are colored according to atom type and are represented in stick. For example, the alpha fold of Heme oxygenase is fold 143 out of 151 in the classification, a multihelical bundle containing two structural repeats of three-helical motif. The enzyme is an oxidoreductase EC 1.14.99.3 and is represented by the crystal structure of rat heme oxygenase-1 (HO-1) protein data bank acession code IDVG. (View this art in color at WWW. dekker. com.)...

Stigers DJ, Tew GN (2003) Poly(3-hydroxyalkanoate)s functionalized with carboxylic acid groups in the side chain. Biomacromolecules 4 193-195 Stockdale H, Ribbons DW, Dawes EA (1968) Occurrence of poly-beta-hydroxybutyrate in the Azotobacteriaceae. J Bacteriol 95 1798-1803... 

The ribbon model of a protein shows regions of alpha helices and beta-pleated sheets. 

Although carboxymethyl cellulase (CMCase) is a cellulose-degrading enzyme, it is involved in cellulose formation in acetic acid bacteria (Tonouchi et al. 1995). In plants, a membrane-bound endo-l,4-beta-glucanase called Korrigan (KOR) is involved in cellulose formation (Sato et al. 2001). In a previous report, the CMCase gene was also shown to be essential for cellulose production (Standal et al. 1994). Nevertheless, a recent study found that a very small amount of particulate material accumulated in the culture of the disrupted strain (Nakai et al. 2013). The particulate material was shown to contain highly twisted ribbons of cellulose. It was also reported that a portion of CMCase is localized to the cell surface (Yasutake... 

Figure 6 Simplified molecular representations (a) strands model of the backbone of enzyme trypsin color coded by secondary structure elements (yellow beta strands magenta alpha helices blue and white coils and turns) (b) ribbon model of the backbone of enzyme trypsin and (c) Richardson style representation of crambin (arrows beta strands cylinders alpha helices tubes coils and turns)...

New ribbon models of proteins for alpha helices, beta-pleated sheets, myoglobin, hemoglobin, denatured protein, prions in mad cow disease, and enzymes are added. 

---