Secondary Structures, Protein Beta-Strand

Figure 1.1 The amino acid sequence of a protein s polypeptide chain is called Its primary structure. Different regions of the sequence form local regular secondary structures, such as alpha (a) helices or beta (P) strands. The tertiary structure is formed by packing such structural elements into one or several compact globular units called domains. The final protein may contain several polypeptide chains arranged in a quaternary structure. By formation of such tertiary and quaternary structure amino acids far apart In the sequence are brought close together in three dimensions to form a functional region, an active site.

Figure 2.5 Schematic illustrations of antiparallel (3 sheets. Beta sheets are the second major element of secondary structure in proteins. The (3 strands are either all antiparallel as in this figure or all parallel or mixed as illustrated in following figures, (a) The extended conformation of a (3 strand. Side chains are shown as purple circles. The orientation of the (3 strand is at right angles to those of (b) and (c). A p strand is schematically illustrated as an arrow, from N to C terminus, (bj Schematic illustration of the hydrogen bond pattern in an antiparallel p sheet. Main-chain NH and O atoms within a p sheet are hydrogen bonded to each other.

The interiors of protein molecules contain mainly hydrophobic side chains. The main chain in the interior is arranged in secondary structures to neutralize its polar atoms through hydrogen bonds. There are two main types of secondary structure, a helices and p sheets. Beta sheets can have their strands parallel, antiparallel, or mixed. 

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... 

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. 

Secondary structure refers to regularities or repeating features in the conformation of the protein chain s backbone. Four major types of secondary structure in proteins are (1) the alpha (a) helix, formed from a single strand of amino acids (2) the beta (P) sheet, formed from two or more amino acid strands (from either the same chain or from different chains) (3) the beta (P) bend or reverse turn, in a single strand and (4) the collagen helix, composed of three strands of amino acids. 

The P structure is one of the most important secondary structures in proteins. It occurs in about 80% of the soluble globular proteins whose structures have been determined. In many cases almost the entire protein is made up of P structure. Single strands of extended polypeptide chain are sometimes present within globular proteins but more often a chain folds back on itself to form a hairpin loop. A second fold may be added to form an antiparallel "P meander"102 and additional folds to form P sheets. Beta structures are found in silk fibers (Box 2-B) as well as in soluble 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... 

The linear peptide as observed in its primary structure starts folding on itself because of the interactions among the side chains of the adjacent amino acids. This leads to the formation of different structures, which include (a) helical structure called an alpha helix, (b) stranded folds called beta sheets or beta strands, and (c) random coils. Now, certain criteria can be used to predict the occurrence of these structures in the secondary structure of the protein. This was first established by Chow and Fasman (1978) based on the propensity of certain amino acids associated with these structures, i.e., helix and beta sheet. For example, the amino acids glu, met, ala, and lys are predominantly associated with the helix structure whereas the amino acids val, ile, and tyr are strongly associated with the beta sheet structure. The amino acid leucine is associated with both the helix and the beta sheet. The amino acids glycine and proline occur as breakers of the helix proline usually occurs as the first residue in the helix. Also, asp and glu occurs at the N-terminus, whereas arg and lys occur at the C-terminus. 

Normal mode analysis of the mechanical properties of a triosephosphate isomerase-barrel protein suggests that the region between the secondary structures plays an important role in the dynamics of the protein. The beta-barrel region at the core of the protein is found to be soft in contrast to the helical, strand and loop regions [62]. A detailed discussion of other properties of proteins is mechanically highly non-linear systems is given by Kharakoz [63]. 

The other common secondary structure of proteins is the beta (/3) sheet. Beta sheets are made of two or more strands of peptides that hydrogen-bond from an amide FI in one strand to a carbonyl O in the other strand (Figure 24.20). 

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