Beta-sheet/turns

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. 

Resilin-like polypeptide and sequence motif Technique Helices (%) Strands (%) Turns (%) Unordered (%) (or random coil) Beta sheet (%) PPII (%)... 

Asparagine (Asn or N) ((2S )-2-amino-3-carbamoyl-propanoic acid) is a polar, uncharged amino acid with the formula HOOCCH(NH2)CH2CONH2. It has a carboxamide as the side chain s functional group. Asx or B represent either Asn or Asp. Asn are often found near the beginning and end of alpha-helices, and in turn motifs in beta sheets. ... 

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. 

Manning, M.C., Illangasekare, M., and Woody, R.W. "Circular-dichroism studies of distorted alpha-helices, twisted beta-sheets, and beta-turns". Biophys. Chem. 31(1-2), 77-86 (1988). 

Secondary Structure Polypeptide Chains Can Fold Into Regular Structures Such as the Alpha Helix, the Beta Sheet, and Turns and Loops... 

Amino Acids Have Different Propensities for Forming Alpha Helices, Beta Sheets, and Beta Turns... 

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". ... 

SECONDARY STRUCTURE POLYPEPTIDE CHAINS CAN FOLD INTO REGULAR STRUCTURES SUCH AS THE ALPHA HELIX, THE BETA SHEET, AND TURNS AND LOOPS... 

Milner-White, E.J, (1990) Situations of gamma-turns in proteins. Their relation to alpha-helices, beta-sheets and ligand binding sites. J. Mol. Biol. 216 386-397. 

Different amino acids favor the formation of alpha helices, beta pleated sheets, or loops. The primary sequences and secondary structures are known for over 1,000 different proteins. Correlation of these sequences and structures revealed that some amino acids are found more often in alpha helices, beta sheets, or neither. Helix formers include alanine, cysteine, leucine, methionine, glutamic acid, glutamine, histidine, and lysine. Beta formers include valine, isoleucine, phenylalanine, tyrosine, tryptophan, and threonine. Serine, glycine, aspartic acid, asparagine, and proline are found most often in turns. 

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