Secondary Structure Regular Structural Elements

Recently, a / -dodecapeptide was found to display a CD spectrum in water which was very similar to that assigned to the 12/10-helix, with a single maximum near 200 nm. Careful NMR analysis however, revealed a predominantely extended conformation without regular secondary structure elements [174]. This result stresses that the CD signature assigned to the 12/10-structure might not be unique and again (see Section 2.2.3.1) that CD spectra must be interpreted with caution. 

There are different classes of protein sequence databases. Primary and secondary databases are used to address different aspects of sequence analysis. Composite databases amalgamate a variety of different primary sources to facilitate sequence searching efficiently. The primary structure (amino acid sequence) of a protein is stored in primary databases as linear alphabets that represent the constituent residues. The secondary structure of a protein corresponding to region of local regularity (e.g., a-helices, /1-strands, and turns), which in sequence alignments are often apparent as conserved motifs, is stored in secondary databases as patterns. The tertiary structure of a protein derived from the packing of its secondary structural elements which may form folds and domains is stored in structure databases as sets of atomic coordinates. Some of the most important protein sequence databases are PIR (Protein Information Resource), SWISS-PROT (at EBI and ExPASy), MIPS (Munich Information Center for Protein Sequences), JIPID (Japanese International Protein Sequence Database), and TrEMBL (at EBI). ... 

The steric relations of residues nearby in the primary structure which give rise to local regularities of conformation. These structures are maintained by hydrogen bonds between peptide bond carbonyl oxygens and amide hydrogens. The major secondary structural elements are the helix and the beta strand. (Characteristic bond type hydrogen.)... 

Secondary structures [39, 40] are regular local structure elements identified in the 1950s [41, 42] which are characteristic abstractions for proteins and believed to be of great importance for the 3D folding. Secondary structure elements are defined via characteristic main chain torsion angles. Usually, three discrete states, a-helix (H), /i-strand (E, extended), or other (L, loop) are distinguished [1] (see Chapter 5 for details). 

The deviations between a model built by homology and the real x-ray structure vary throughout the molecule, the largest deviations occurring in loops at the protein surface. In regular secondary structure elements (helix, strand) and in the hydrophobic core, models normally are more accurate. 

The globular domain structure, which has the same architecture as mPrP, was independently determined from data collected with hPrP(23-230), hPrP(90-230), and hPrP(121-230) (Zahn et al., 2000). In the intact protein, the regular secondary structure elements coincide identically with those in hPrP(90-230) and hPrP(121-230), with the residues 128-131 forming the p strand 1, 144-154 the a helix 1, 161-164 the p strand 2, 173-194 the a helix 2, and 200-228 the a helix... 

In practical terms, transition (a) is observed as a 190 nm absorption band with a shoulder at 208 nm. Transition (b) is observed only at lower wavelengths with good optical equipment. UV-visible tt tt transitions involving either /i-sheets or less regular structures (known broadly as random coil) are not subject to extensive chromophore perturbation effects and hence UV-visible spectroscopy is unable to identify the presence of either secondary structural elements directly. 

Repetition of the same angles from one amino acid to the next gives rise to a regular secondary structure element, of which a-helix and P-sheet are the most common examples. In these structures the angles... 

One of the general principles of protein structure is that hydrophobic residues prefer to be inside the protein contributing to form a hydrophobic core and a hydrophilic surface. To maintain a high residue density in the hydrophobic core, proteins adopt regular secondary structures that allow non covalent hydrogen-bond and hold a rigid and stable framework. There are two main classes of secondary structure elements (SSE), a-helices and P-sheets (see Fig 1). 

Monge et al. [188] also assumed exact knowledge of the geometry of the regular secondary structure elements (helices in this case). Tertiary interactions have been modeled via a pairwise, knowledge-based potential for the CP-CP interactions. Then, the Monte Carlo method employed rotations within the loop regions to search conformational space. Their search process assembled only compact conformations. Moderate resolution (4-5 A of RMSD from native) structures of four highly helical proteins have been obtained as the... 

Many proteins contain secondary structure that cannot be described as either helix or turn. This is typically classified as turn, loop, or random coil. These sections of the polypeptide chain are characterized by nonrepetitive conformational angles however, this does not necessarily imply that these residues are less stable or less well ordered than the regular secondary structural elements. Many active site residues and components critical for ligand recognition reside in loops or random coil and adopt an exquisitely well-defined conformation. 

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.

---