Secondary structure

In biochemistry and structural biology, the secondary structure of a protein includes alpha helices, beta sheets, turns, and random coil, among other less common structure. Such structures often can be detected by circular dichroism spectroscopy. Nucleic acids also have secondary structure, most notably single-stranded RNA molecules.

At a higher level, secondary structure generally reflects how individual molecules in a biopolymer are connected to each other, e.g. whether or not individual nucleotides in an RNA molecule are connected. It does not, however, refer to their actual position in three-dimensional space; the actual positions are considered to be tertiary structure.

Table of contents

1 Proteins 1.1 The DSSP Code 2 RNA 3 Alignment 4 Prediction 5 References

Proteins

The DSSP Code

The DSSP code is frequently used to describe the most frequent secondary structures as a single letter. DSSP is an acronym for "Dictionary of Protein Secondary Structure".

• B = residue in isolated beta-bridge
• I = 5 helix (pi helix)
• G = 3-helix (3/10 helix)
• S = bend
• E = beta sheet (extended strand, participates in beta ladder)
• T = hydrogen bonded turn
• H = alpha helix

Other types of structure are sometimes designated with C or L.

RNA

RNA secondary structure is generally divided into helices (contiguous base pairs), and various kinds of loops (unpaired nucleotides surrounded by helices). Another reasonable definition of secondary structure of RNA is that it defines which nucleotides bind each other, and, for example, nucleotide pairs that are bound form helices. RNA secondary structure can also include pseudoknots and base triples.

For many RNA molecules, the secondary structure is highly important to the correct function of the RNA -- often more so than the actual sequence. This fact aids in the analysis of non-coding RNA sometimes termed "RNA genes". RNA secondary structure can be predicted with some accuracy by computer, and many bioinformatics applications use some notion of secondary structure in analysis of RNA.

See also : primary structure -- tertiary structure -- quaternary structure -- translation -- structural motif

Alignment

Both protein and RNA secondary structures can be used to analyze sequences by alignment. These alignments can be made more accurate by the inclusion of secondary structure information, in addition to the usual use of sequence.

Distant relationships amound proteins whose primary structures are unalignable can sometimes be found by secondary structure.

Prediction

Algorithms to predict RNA secondary structure typically use dynamic programming, and many algorithms are based on Stochastic context-free grammars.

References

W. Kabsch and C. Sander. Dictionary of Protein Secondary Structure: Pattern Recognition of Hydrogen Bonded and Geometrical Features. Biopolymers 22: 2577-2637 (1983).

M. Zuker "Computer prediction of RNA structure", Methods in Enzymology, 180:262-88 (1989). (The classic paper on dynamic programming algorithms to predict RNA secondary structure.)