Proteins 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 2.17 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 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. 

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. 

A Channel Protein Can Be Formed from Beta Strands. 

Figure 12.20. Structure of Bacterial Poriu (from Rhodopseudomonas blastica). Porin is a membrane protein built entirely of beta strands. (A) Side view. (B) View from the periplasmic space. Only one monomer of the trimeric protein is shown.

Coronin-1 possesses 5 WD repeats and based on the homology with the G protein beta subunits it has been proposed that the WD repeat folds into a 5-bladed beta propeller. However, an extensive sequence analysis of coronin 1 revealed the presence of two additional sequence stretches of 46 and 44 residues, respectively, that flank the WD repeat-containing core sequence and are predicted to form four short P-strands and align with the corresponding P-strands of the five WD repeats. Since WD repeats are not strictly necessary to assert a propeller fold, the prediction suggests that the coronin 1 propeller domain is, in fact, made up of at least seven blades instead of the previously proposed five blades. Consistent with this analysis, the crystal structure of coronin 1 indeed revealed the presence of a 7-bladed propeller (see Fig. 1B,C). Furthermore, the presence of a 7-bladed propeller in coronin 1 is consistent with the predicted similarity between the coronin 1 N-terminal domain and the yeast transcriptional repressor Tupl as well as the G protein p-subunit, both WD repeat containing seven-bladed P-propeller proteins. 

Ubiquitin is a small (76 amino acids) extremely stable protein containing a broad collection of secondary structure elements including parallel and antiparallel beta strands assembled into a mixed beta sheet, alpha and 3io helices and a variety of turns (Vijay-Kumar et al., 1987 Di Stefano Wand, 1987). In previous work, we have examined the fast main chain dynamics of ubiquitin by use of 15n NMR relaxation methods (Schneider et al., 1992). These data were analyzed in terms of the so-called model free treatment of Lipari and Szabo (1982a,b). The amplitudes of motion of the backbone amide N-H vectors of the packed regions of the protein are generally highly restricted and show no apparent correlation with secondary stmcture context but do show a strong... 

Thioredoxin from E. coli has been studied extensively using biochemical, spectroscopic and X-ray diffraction techniques. The protein consists of a single polypeptide chain of 108 amino acid residues of known sequence. The protein has been cloned and expressed. Thioredoxin of E. coli is a compact molecule with 90% of its residues in hehces, beta-strands or reverse turns. This protein transports electrons via an oxidation-reduction active disulfide". The oxidized form thioredoxin-(S2) is reduced to thioredoxin-(SH)2. In particular, this protein was found to participate in the reduction of ribonucleotides to deoxyribonucleotides. In Fig. 1, the optimized stracture is shown with a carbon backbone for clarity only. The molecule consists of two conformational domains, connected by two helices. The beta-sheet forms the core of the molecule packed on either side by clusters of hydrophobic residues. Helices form the external surface. We used a crystal stracture of the oxidized form of thioredoxin from Escherichia coli that has been refined by the stereochemically restrained least-squares procedure at 1.68 A resolution". ... 

A Channel Protein Can Be Formed from Beta Strands. Porin, a protein... 

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