The secondary structure of a protein

The origin of the secondary structure of a protein is found in the rules formulated by Linus Pauling and Robert Corey in 1951. The essential feature is the stabilization of structures by hydrogen bonds involving the peptide link. The latter can act both as a donor of the H atom (the NH part of the link) and as an acceptor (the CO part). The Corey-Pauling rules are as follows (Fig. 11.39)  

The four atoms of the peptide link lie in a relatively rigid plane. The planarity of the hnk is due to delocalization of n electrons over the O, C, and N atoms and the maintenance of maximum overlap of their p orbitals (see 

and O atoms of a hydrogen bond lie in a straight line (with displacements of H tolerated up to not more than 30° from the N-O vector). 

The rules are satisfied by two structures. One, in which hydrogen bonding between peptide links leads to a helical structure, is the a helix. The other, in which hydrogen bonding between peptide links leads to a planar structure, is the p sheet this form is the secondary structure of the protein fibroin, the constituent of silk. 

The a-helixis illustrated in Fig. 11.40. Each turn of the helix contains 3.6 amino acid residues, so the period of the helix corresponds to five turns (18 residues). The pitch of a single turn (the distance between points separated by 360°) is 544 pm. The N-H—O bonds lie parallel to the axis and link every fourth group (so residue i is linked to residues i - 4 and i+4). All the R groups point away from the major axis of the helix. 

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The secondary structure of a protein is the shape adopted by the polypeptide chain—in particular, how it coils or forms sheets. The order of the amino acids in the chain controls the secondary structure, because their intermolecular forces hold the chains together. The most common secondary structure in animal proteins is the a helix, a helical conformation of a polypeptide chain held in place by hydrogen bonds between residues (Fig. 19.19). One alternative secondary structure is the P sheet, which is characteristic of the protein that we know as silk. In silk, protein... 

The secondary structure of a protein is determined by hydrogen bonding between CDO and N—H groups of the peptide linkages that make up the backbone of the protein. Hydrogen bonds can exist within the same protein... 

The secondary structure of a protein is the three-dimensional shape of a polypeptide chain. 

The secondary structure of a protein is generally defined as regular arrangements of amino acids that are located near to each other in the linear sequence. Examples of such elements are the a-helix, p-sheet, and P-bend. Some secondary structure is not regular, but rather is considered non-repetitive (loop and coil). 

Secondary Structure of Proteins The secondary structure of a protein is how the polypeptide chain is twisted. There are two common types of secondary structure the alpha helix and the beta pleated sheet. 

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). ... 

NH and carbonyl groups in a tram orientation, it is possible to extend a P sheet into a multistranded structure by adding successive chains to the sheet, p sheets can occur in two different arrangements with the same N-to-C polypeptide sense to produce parallel p sheets. Alternatively, the chains can be ahgned with opposite N-to-C senses to produce an antiparallel p sheet. The a helix and p sheet represent the secondary structure of a protein. 

Far UV circular dichroism spectra contain information about secondary structure content in proteins and peptides. Small peptides are almost invariably unstructured in aqueous solution, but can adopt regular secondary structure upon binding to a protein. In general, the secondary structure of a protein is unlikely to change dramatically upon binding to a peptide. However, as shown in this work, the binding of a target peptide to a mutated protein with an altered structure (compared with the wildtype) may partially restore the "native" structure of the protein. 

The relationship between NMR chemical shifts and the secondary structure of a protein has been well established (19,20,21). The C and carbonyl carbons experience an upfield shift in extended structures, such as a P-strand, and a downfield shift in helical structures. Both the Cp and the Ha proton chemical shifts exhibit the opposite correlation. These shifts have proven to be sufficiently consistent to permit the prediction of secondary structural elements for a number of proteins (1,19,20). Knowledge of the secondary structure of a protein can be useful in identifying spin-diffusion effects during the analysis of 4D N/ N-separated NOES Y data collected with long mixing times as described below. The secondary structure can also be used as a constraint in the calculation of protein global folds. 

O Which of these bond types is primarily responsible for defining the secondary structure of a protein ... 

RNA is chemically very similar to DNA but differs in important ways. The sugar miit is ribose with an added hydroxyl group at the 2 position, and the methylated pyrim-idine uracil (U) replaces thymine. RNA exists in various functional forms but typically as a single-stranded polymer that is much shorter than DNA and that has an irregular three-dimensional structure. Research from recent years has revealed that RNA conformations are not random structures and the folding mechanism of RNA molecules is complex. The secondary structure adopted by an RNA molecule is to a large extent related to its nucleotide sequence. The secondary structure for particular RNA sequences can be as regular as the secondary structure of a protein. It is now known that RNA molecules can further interact to form complex tertiary structures, which are intimately related to novel functions of RNA, such as the catalytic activity of ribozymes, ... 

The secondary and tertiary structure of a peptide is a function of the primary structure or the amino acid sequence of the peptide. This fact was established by Christian Anfinsen based on the denaturation or unfolding of an enzyme ribonuclease in the presence of urea and the renaturation or folding of the same enzyme after removal of the denaturing substance, i.e., urea. It is important to understand the secondary structure of a protein as a prelude to understanding of the tertiary structure and the function of proteins. It is important to know the rules that proteins follow to assume a 3D structure because of their roles in cellular function and their manipulation in biotechnology and drug design. 

The molecular mechanics model is extremely popular among chemists and there is an overwhelming number of articles reporting the application of this method. Their broad application also is considered to raise our understanding and our capability to explain the structural features of the treated molecules.5 But still, as the last example shows, there exist upper limits concerning the size of the molecules for which a proper prediction of structure can be made. Especially in the case of proteins, such predictions can have tremendous practical importance. The last model, I discuss is a method used to predict the secondary structure of a protein, i.e., its folding mode, starting with only information on its primary structure, i.e., its amino acid sequence. 

We have seen that the forces that maintain the secondary structure of a protein are hydrogen bonds between the amide hydrogen and the carbonyl oxygen of the peptide bond. What are the forces that maintain the tertiary structure of a protein The globular tertiary structure forms spontaneously and is maintained as a result of interactions among the side chains, the R groups, of the amino acids. The structure is maintained by the following molecular interactions ... 

A glycoprotein is a protein with covalently attached sugars. Hydrogen bonding maintains the secondary structure of a protein and contributes to the stability of the tertiary and quaternary levels of structure. 

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