Beta-turn conformation

J. H. Baik, S. K. Lim, Type I beta-turn conformation is important for biological activity of the melanocyte-stimulating hormone analogues, Eur. J. Biochem. 

Alzheimer s Disease. Figure 1 A(3 monomers can self-associate to form dimers, trimers and higher oligomers. Globular structures of synthetic A(342 are known as A(3-derived diffusible ligands (ADDLs) (3-12-mers of A(3). These structures are similar to the smallest protofibrils and represent the earliest macromolecular assembly of synthetic A(3. The characteristic amyloid fiber exhibits a high beta-sheet content and is derived in vitro by a nucleation-dependent self-association and an associated conformational transition from random to beta-sheet conformation of the A(3 molecule. Intermediate protofibrils in turn self-associate to form mature fibers. 

Lazo, N. D., and Downing, D. T. (1999). Crystalline regions of Bombyx mori silk fibroin may exhibit beta-turn and beta-helix conformations. Macromolecules 32, 4700-4705. Lee, K. H. (2004). Silk sericin retards the crystallization of silk fibroin. Macromol. Rapid Commun. 25, 1792-1796. 

Bond, J. P., Deverin, S. P., Inouye, H., el-Agnaf, O. M., Teeter, M. M., and Kirschner, D. A. (2003). Assemblies of Alzheimer s peptides A beta 25—35 and A beta 31-35 Reverse-turn conformation and side-chain interactions revealed by X-ray diffraction./. Struct. Biol. 141, 156-170. 

Ma, K., and Wang, K. (2003). Malleable conformation of the elastic PEVK segment of titin Non-cooperative interconversion of polyproline II helix, beta-turn and unordered structures. Biochem.J. 374, 687-695. 

For polypeptide, the B program provides options for building various protein conformations including 3-10 helix, alpha helix, alpha helix (L-H), beta sheet (anti-prl), beta sheet (parallel), various beta turns, extended, gamma turns, omega helix, pi helix, polyglycine, and polyproline. Choose the desired conformation and isomer (l or d) and then add amino acids from N-terminus to construct polypeptide chain. 

Blomberg, D., Hedenstrom, M., Kreye, P., Sethson, I., Brickmann, K., and Kihlberg, J. (2004) Synthesis and conformational studies of a beta-turn mimetic incorporated in Leu-enkephalin./. Org. Chem. 69, 3500-3508. 

Since this domain is conserved in several enterotoxins, one expects this 13 residue domain to be the primary reason for the toxicity of the 19-residue long protein. lETN has a simple secondary structure it has got 3 beta (/ ) turns. The /9i spans from Cys to Cys , (32 from Asn to Cys, and 02 from Cys to Cys . In addition, the crystal structure contains 5 intramolecular (i.e., within the protein) hydrogen bonds that also add to the stability of the conformation. The lETN structure is reasonably rigid (because of 3 disulfide bridges, and 5 intramolecular hydrogen bonds), making it an ideal candidate for studies by computer simulations using empirical intermolecular potentials. 

Several studies have confirmed that beta-amyloid peptides undergo structural transitions to form mobile oligomers that are composed of a particular aggregation-prone conformation of the peptide. Once the oligomers exceed critical size, they nucleate to form protofilaments which finally transform to crossbeta sheets or fibrils that are responsible for the formation of extracellular amyloid plaques. The tendency to form beta-strands is due to its ability to stabilize the beta-turn by a salt bridge between residues aspartic acid-23 and lysine-28 and the hydrophobic region. 

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.

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. 

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". ... 

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