Secondary structure, of a protein

R I he secondary structure of a protein describes how segments of the peptide backbone orient into a regular pattern. 

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. 

Second law of thermodynamics in any spontaneous process, there is always an increase in the entropy of the universe. (10.5) Secondary structure (of a protein) the three-dimensional structure of the protein chain (for example, a-helix, random coil, or pleated sheet). (22.6)... 

P-Pleated sheet (Section 28.8B) A secondary structure of a protein formed when two or more peptide chains line up side by side. 

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 folding of polypeptide chain regions into regular structures defines die secondary structure of a protein. The tertiary folding between these regions involves both covalent disulfide bonds and non-covalent bonds. The quaternary structure exists in proteins that contain... 

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