Beta-strand

Beta strands can also combine into mixed P sheets with some P strand pairs parallel and some antiparallel. There is a strong bias against mixed P sheets only about 20% of the strands inside the p sheets of known protein structures have parallel bonding on one side and antiparallel bonding on the other. Figure 2.7 illustrates how the hydrogen bonds between the p strands are arranged in a mixed P sheet. 

Figure 2.16 Suggested folding pathway from a hairpinlike structure to the Greek key motif. Beta strands 2 and 3 fold over such that strand 2 is aligned adjacent and antiparallel to strand 1. The topology diagram of the Greek key shown here is the same as in Figure 2.15a but rotated 180° in the plane of the page.

Figure 2.17 Two adjacent parallel p strands are usually connected by an a helix from the C-termlnus of strand 1 to the N-termlnus of strand 2. Most protein structures that contain parallel p sheets are built up from combinations of such p-a-P motifs. Beta strands are red, and a helices are yellow. Arrows represent P strands, and cylinders represent helices, (a) Schematic diagram of the path of the main chain, (b) Topological diagrams of the P-a-P motif.

Figure S.2 Schematic and topological diagrams of an up-and-down fi barrel. The eight p strands are all antiparallel to each other and are connected by hairpin loops. Beta strands that are adjacent in the amino acid sequence are also adjacent in the three-dimensional structure of up-and-down barrels.

Figure 16.14 Schematic diagrams of three different viral coat proteins, viewed in approximately the same direction. Beta strands I through 8 form the common jelly roll barrel core, (a) Satellite tobacco necrosis virus coat protein, (b) Subunit VPl from poliovirus.

A beta barrel is a three-dimensional protein fold motif in which beta strands connected by loops form a barrellike structure. For example, this fold motif is found in many proteins of the immunoglobulin family and of the chymotrypsin family of serine proteases. 

Starting from the protein sequence (primary structure) several algorithms can be used to analyze the primary structure and to predict secondary structural elements like beta-strands, turns, and helices. The first algorithms from Chou and Fasman occurred already in 1978. The latest algorithms find e.g., that predictions of transmembrane... 

If the sequence of a protein has more than 90% identity to a protein with known experimental 3D-stmcture, then it is an optimal case to build a homologous structural model based on that structural template. The margins of error for the model and for the experimental method are in similar ranges. The different amino acids have to be mutated virtually. The conformations of the new side chains can be derived either from residues of structurally characterized amino acids in a similar spatial environment or from side chain rotamer libraries for each amino acid type which are stored for different structural environments like beta-strands or alpha-helices. 

Hamley IW, Ansari A, Castelletto V et al (2005) Solution self-assembly of hybrid block copolymers containing poly(ethylene glycol) and amphiphilic beta-strand peptide sequences. 

Amara A, Lorthioir O, Valenzuela A, et al. Stromal cell-derived factor-lalpha associates with heparan sulfates through the first beta-strand of the chemokine. J Biol Chem 1999 274 23916-25. 

Soto C, Castano EM, Frangione B, Inestrosa NC. The alpha-helica to beta-strand transition in the amino-terminal fragment of the amyloid beta-peptide modulates amyloid formation. J Biol Chem 1995 270 3063-3067. 

Fig. 1. Schematic diagram of nuclease A131A in the folded conformation. The alpha helices and beta strands are labeled. NMR analysis suggests the two turns and one helix in black are modestly populated in the denatured state, whereas the shaded helix is slightly populated. Strands / l-/ 2-/ 3 form an extended structure about which littie is known. Reproduced from Barron, L. D., Hecht, L., Blanch, E. W., and Bell, A. F. (2000). Prog. Biophys. Mol Chem. 73, 1-49. 2000, with permission from Elsevier Science.

TyndaU, J.D.A., TessaNaU, T. andFairUe, D.P., Proteases universally recognize beta strands in their active sites. Chem. Rev., 2005,105, 973-1000. 

The secondary structure of the proteins are shown as dark gray helices and the beta strands and coil regions are in light gray. The zinc ions are shown as spheres, (b) The NAD molecule bound to the enzyme and the acetylated peptide of p53 are shown as ball and sticks. The acetylated lysine is labeled. 

Griffiths-Jones SR, Searle MS. Stmcture, folding, and energetics of cooperative interactions between the beta-strands of a de novo designed three-stranded antiparallel beta-sheet peptide. J Am Chem Soc 2000 122 8350-8356. 

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