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Encyclopedia > Secondary structure
A representation of the 3D structure of the myoglobin protein. Alpha helices are shown in colour, and random coil in white, there are no beta sheets shown. This protein was the first to have its structure resolved by X-ray crystallography by Max Perutz and Sir John Cowdery Kendrew in 1958, which led to them receiving a Nobel Prize in Chemistry in 1962.

In biochemistry and structural biology, secondary structure is the general three-dimensional form of local segments of biopolymers such as proteins and nucleic acids (DNA/RNA). It does not, however, describe specific atomic positions in three-dimensional space, which are considered to be tertiary structure. Download high resolution version (695x702, 67 KB)Image created by uploader from PDB file: Source: Sperm whale (Physeter catodon) Authors: S.E.V. Phillips Reference: Structure and refinement of oxymyoglobin at 1. ... Download high resolution version (695x702, 67 KB)Image created by uploader from PDB file: Source: Sperm whale (Physeter catodon) Authors: S.E.V. Phillips Reference: Structure and refinement of oxymyoglobin at 1. ... An X-ray diffraction image for the protein myoglobin. ... Side view of an Î±-helix of alanine residues in atomic detail. ... Illustration of a 3-dimensional polypeptide A random coil is a polymer conformation where the monomer subunits are oriented randomly while still being bonded to adjacent units. ... Diagram of Î²-pleated sheet with H-bonding between protein strands The Î² sheet (also Î²-pleated sheet) is the second form of regular secondary structure in proteins â€” the first is the alpha helix â€” consisting of beta strands connected laterally by three or more hydrogen bonds, forming a generally twisted, pleated sheet. ... X-ray crystallography, also known as single-crystal X-ray diffraction, is the oldest and most common crystallographic method for determining the structure of molecules. ... Max Ferdinand Perutz, OM (May 19, 1914 â€“ February 6, 2002) was an Austrian-British molecular biologist. ... This article or section does not cite its references or sources. ... This is a list of Nobel Prize laureates in Chemistry from 1901 to 2006. ... Biochemistry is the study of the chemical processes in living organisms. ... Structural biology is a branch of molecular biology concerned with the study of the architecture and shape of biological macromolecules--proteins and nucleic acids in particularâ€”and what causes them to have the structures they have. ... Biopolymers are a class of polymers produced by living organisms. ... A representation of the 3D structure of myoglobin, showing coloured alpha helices. ... Look up nucleic acid in Wiktionary, the free dictionary. ... In biochemistry, the tertiary structure of a protein is its overall shape. ...

Secondary structure is formally defined by the hydrogen bonds of the biopolymer, as observed in an atomic-resolution structure. In proteins, the secondary structure is defined by patterns of hydrogen bonds between backbone amide groups (sidechain-mainchain and sidechain-sidechain hydrogen bonds are irrelevant), where the DSSP definition of a hydrogen bond is used. In nucleic acids, the secondary structure is defined by the hydrogen bonding between the nitrogenous bases. An example of a quadruple hydrogen bond between a self-assembled dimer complex reported by Meijer and coworkers. ... In protein structure, the DSSP algorithm is the standard method for assigning secondary structure to the amino acids of a protein, given the atomic-resolution coordinates of the protein. ...

The hydrogen bonding is correlated with other structural features, however, which has given rise to less formal definitions of secondary structure. For example, residues in protein helices generally adopt backbone dihedral angles in a particular region of the Ramachandran plot; thus, a segment of residues with such dihedral angles is often called a "helix", regardless of whether it has the correct hydrogen bonds. Many other less formal definitions have been proposed, often applying concepts from the differential geometry of curves, such as curvature and torsion. Least formally, structural biologists solving a new atomic-resolution structure will sometimes assign its secondary structure "by eye" and record their assignments in the corresponding PDB file. In Aerospace engineering, the dihedral is the angle that the two wings make with each other. ... A Ramachandran plot generated from the protein PCNA, a human DNA clamp protein that is composed of both beta sheets and alpha helices (PDB ID 1AXC). ... In mathematics, differential topology is the field dealing with differentiable functions on differentiable manifolds. ... In mathematics, curvature refers to a number of loosely related concepts in different areas of geometry. ... // Mathmatics In mathematics, the term torsion has several meanings, mostly unrelated to each other. ... Through the years the Protein Data Bank has undergone many, many changes and revisions. ...

The rough secondary-structure content of a biopolymer (e.g., "this protein is 40% α-helix and 20% β-sheet.") can often be estimated spectroscopically. For proteins, a common method is far-ultraviolet (far-UV, 170-250 nm) circular dichroism. A pronounced double minimum at 208 and 222 nm indicate α-helical structure, whereas a single minimum at 204 nm or 217 nm reflects random-coil or β-sheet structure, respectively. A less common method is infrared spectroscopy, which detects differences in the bond oscillations of amide groups due to hydrogen-bonding. Finally, secondary-structure contents may be estimated accurately using the chemical shifts of an unassigned NMR spectrum. Extremely high resolution spectrogram of the Sun showing thousands of elemental absorption lines (fraunhofer lines) Spectroscopy is the study of the interaction between radiation (electromagnetic radiation, or light, as well as particle radiation) and matter. ... Circular dichroism (CD) is a form of spectroscopy based on the differential absorption of left- and right-handed circularly polarized light. ... For other uses, see Infrared (disambiguation). ... In nuclear magnetic resonance (NMR), the chemical shift describes the dependence of nuclear magnetic energy levels on the electronic environment in a molecule. ... NMR redirects here. ...

Secondary structure was introduced by Kaj Ulrik Linderstrom-Lang in the 1952 Lane medical lectures at Stanford. Kaj Ulrik LinderstrÃ¸m-Lang (Nov. ... Stanford may refer: Stanford University Places: Stanford, Kentucky Stanford, California, home of Stanford University Stanford Shopping Center Stanford, New York, town in Dutchess County. ...

Secondary structure in proteins consists of local inter-residue interactions mediated by hydrogen bonds. The most common secondary structures are alpha helices and beta sheets. Other helices, such as the 310 helix and π helix, are calculated to have energetically favorable hydrogen-bonding patterns but are rarely if ever observed in natural proteins except at the ends of α helices due to unfavorable backbone packing in the center of the helix. Other extended structures such as the polyproline helix and alpha sheet are rare in native state proteins but are often hypothesized as important protein folding intermediates. Tight turns and loose, flexible loops link the more "regular" secondary structure elements. The random coil is not a true secondary structure, but is the class of conformations that indicate an absence of regular secondary structure. Side view of an Î±-helix of alanine residues in atomic detail. ... Diagram of Î²-pleated sheet with H-bonding between protein strands The Î² sheet (also Î²-pleated sheet) is the second form of regular secondary structure in proteins â€” the first is the alpha helix â€” consisting of beta strands connected laterally by three or more hydrogen bonds, forming a generally twisted, pleated sheet. ... Side view of an 310-helix of alanine residues in atomic detail. ... Side view of an Ï€-helix of alanine residues in atomic detail. ... In proteins, a left-handed polyproline II helix (PPII, poly-Pro II) is formed when sequential residues all adopt (Ï†,Ïˆ) backbone dihedral angles of roughly (-75Â°, 150Â°) and have trans isomers of their peptide bonds. ... The alpha sheet (also known as an alpha pleated sheet or a polar pleated sheet) is a hypothetical secondary structure in proteins, first proposed by Linus Pauling and Robert Corey in 1951. ... In biochemistry, the native state of a protein is its operative or functional form. ... Protein before and after folding. ... A turn is an element of secondary structure in proteins. ... Illustration of a 3-dimensional polypeptide A random coil is a polymer conformation where the monomer subunits are oriented randomly while still being bonded to adjacent units. ...

### The DSSP code

Distribution obtained from nonredundant pdb_select dataset (March 2006); Secondary structure assigned by DSSP; 8 conformational states reduced to 3 states: H=HGI, E=EB, C=STC; Visible are mixtures of (gaussian) distributions, resulting also from the reduction of DSSP states

The DSSP code is frequently used to describe the protein secondary structures with a single letter code. DSSP is an acronym for "Dictionary of Protein Secondary Structure", which was the title of the original article actually listing the secondary structure of the proteins with known 3D structure (Kabsch and Sander 1983). The secondary structure is assigned based on hydrogen bonding patterns as those initially proposed by Pauling et al. in 1951 (before any protein structure had ever been experimentally determined). Image File history File links No higher resolution available. ... Image File history File links No higher resolution available. ... Proteins are an important class of biological macromolecules present in all biological organisms, made up of such elements as carbon, hydrogen, nitrogen, oxygen, and sulfur. ...

• G = 3-turn helix (310 helix). Min length 3 residues.
• H = 4-turn helix (alpha helix). Min length 4 residues.
• I = 5-turn helix (pi helix). Min length 5 residues.
• T = hydrogen bonded turn (3, 4 or 5 turn)
• E = beta sheet in parallel and/or anti-parallel sheet conformation (extended strand). Min length 2 residues.
• B = residue in isolated beta-bridge (single pair beta-sheet hydrogen bond formation)
• S = bend (the only non-hydrogen-bond based assignment)

In DSSP, residues which are not in any of the above conformations is designated as ' ' (space), which sometimes gets designated with C (coil) or L (loop). The helices (G,H and I) and sheet conformations are all required to have a reasonable length. This means that 2 adjacent residues in the primary structure must form the same hydrogen bonding pattern. If the helix or sheet hydrogen bonding pattern is too short they are designated as T or B, respectively. Other protein secondary structure assignment categories exist (sharp turns, Omega loops etc.), but they are less frequently used. Side view of an 310-helix of alanine residues in atomic detail. ... Side view of an Î±-helix of alanine residues in atomic detail. ... Side view of an Ï€-helix of alanine residues in atomic detail. ... Diagram of Î²-pleated sheet with H-bonding between protein strands The Î² sheet (also Î²-pleated sheet) is the second form of regular secondary structure in proteins â€” the first is the alpha helix â€” consisting of beta strands connected laterally by three or more hydrogen bonds, forming a generally twisted, pleated sheet. ...

### DSSP H-bond definition

Secondary structure is defined by hydrogen bonding, so the exact definition of a hydrogen bond is critical. The standard H-bond definition for secondary structure is that of DSSP, which is a purely electrostatic model. It assigns charges of $pm q_{1} equiv 0.42e$ to the carbonyl carbon and oxygen, respectively, and charges of $pm q_{2} equiv 0.20e$ to the amide nitrogen and hydrogen, respectively. The electrostatic energy is An example of a quadruple hydrogen bond between a self-assembled dimer complex reported by Meijer and coworkers. ... DSSP (Dialog System for Structured Programming) is a programming language. ...

$E = q_{1} q_{2} left[ frac{1}{r_{ON}} + frac{1}{r_{CH}} - frac{1}{r_{OH}} - frac{1}{r_{CN}} right] cdot 332 mathrm{kcal/mol}$

According to DSSP, an H-bond exists if and only if E is less than -0.5 kcal/mol. Although the DSSP formula is a relatively crude approximation of the physical H-bond energy, it is generally accepted as a tool for defining secondary structure. DSSP (Dialog System for Structured Programming) is a programming language. ...

### Protein secondary-structure prediction

Secondary-structure prediction methods are continuously benchmarked, e.g., in the EVA experiment. Based on ~270 weeks of testing, the most accurate methods at present are PsiPRED, SAM, PORTER, PROF and SABLE. Interestingly, it does not seem to be possible to improve upon these methods by taking a consensus of them [citation needed]. The chief area for improvement appears to be the prediction of β-strands; residues confidently predicted as β-strand are likely to be so, but the methods are apt to overlook some β-strand segments (false negatives). There is likely an upper limit of ~90% prediction accuracy overall, due to the idiosyncrasies of the standard method (DSSP) for assigning secondary-structure classes (helix/strand/coil) to PDB structures, against which the predictions are benchmarked. DSSP (Dialog System for Structured Programming) is a programming language. ...

Accurate secondary-structure prediction is a key element in the prediction of tertiary structure, in all but the simplest (homology modeling) cases. For example, a confidently predicted pattern of six secondary structure elements βαββαβ is the signature of a ferredoxin fold. In biochemistry, the tertiary structure of a protein is its overall shape. ... Protein structure prediction is one of the most significant technologies pursued by computational structural biology and theoretical chemistry. ... Ferredoxin is an electron receptor used in both Cyclic and Non cyclic photophosphorylation. ...

## Nucleic acids

Nucleic acids also have secondary structure, most notably single-stranded RNA molecules. RNA secondary structure is generally divided into helices (contiguous base pairs), and various kinds of loops (unpaired nucleotides surrounded by helices). The stem-loop structure in which a base-paired helix ends in a short unpaired loop is extremely common and is a building block for larger structural motifs such as cloverleaf structures, which are four-helix junctions such as those found in transfer RNA. Internal loops (a short series of unpaired bases in a longer paired helix) and bulges (regions in which one strand of a helix has "extra" inserted bases with no counterparts in the opposite strand) are also frequent. Finally, both pseudoknots and base triples are present in RNA (though not DNA). Extremely complex DNA secondary structures have been designed and produced in DNA origami and other products of DNA nanotechnology. Look up nucleic acid in Wiktionary, the free dictionary. ... Left: An RNA strand, with its nitrogenous bases. ... An example of an RNA stem-loop Stem-loop intramolecular base pairing is a pattern that can occur in single-stranded DNA or, more commonly, in RNA. It occurs when two regions of the same molecule base-pair to form a double helix that ends in a short unpaired loop... Transfer RNA Transfer RNA (abbreviated tRNA), first hypothesized by Francis Crick, is a small RNA chain (73-93 nucleotides) that transfers a specific amino acid to a growing polypeptide chain at the ribosomal site of protein synthesis during translation. ... A pseudoknot is a RNA secondary structure that is minimally composed of two helical segments connected by single-stranded regions or loops. ... Nanoscale folding of DNA, also known as DNA origami, was pioneered by Paul Rothemund at California Institute of Technology. ...

Since it is almost entirely base pair-mediated, RNA secondary structure can be said to define which bases are paired in a molecule or complex. However, the traditional Watson-Crick base pair is not the only type of pairing that is permissible in RNA; Hoogsteen base pairing is also common. In genetics, two nucleotides on opposite complementary DNA or RNA strands that are connected via hydrogen bonds are called a base pair (often abbreviated bp). ... A Hoogsteen base pair is a minor variation of base-pairing in nucleic acids such as the Aâ€¢T pair shown in the figure. ...

### RNA secondary structure prediction

See also RNA structure The functional form of single stranded RNA molecules (like proteins) frequently requires a specific tertiary structure. ...

One application of bioinformatics uses predicted RNA secondary structures in searching a genome for noncoding but functional forms of RNA. For example, microRNAs have canonical long stem-loop structures interrupted by small internal loops. A general method of calculating probable RNA secondary structure is dynamic programming, although this has the disadvantage that it cannot detect pseudoknots or other cases in which base pairs are not fully nested. More general methods are based on stochastic context-free grammars. A web server that implements a type of dynamic programming is Mfold. Map of the human X chromosome (from the NCBI website). ... In biology the genome of an organism is the whole hereditary information of an organism that is encoded in the DNA (or, for some viruses, RNA). ... In genetics, a miRNA (micro-RNA) is a form of single-stranded RNA which is typically 20-25 nucleotides long, and is thought to regulate the expression of other genes. ... In mathematics and computer science, dynamic programming is a method of solving problems exhibiting the properties of overlapping subproblems and optimal substructure (described below) that takes much less time than naive methods. ... A pseudoknot is a RNA secondary structure that is minimally composed of two helical segments connected by single-stranded regions or loops. ... A stochastic context-free grammar (SCFG; also probabilistic context-free grammar, PCFG) is a context-free grammar in which each production is augmented with a probability. ...

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 (for example, the RNAsoft web server), and many bioinformatics applications use some notion of secondary structure in analysis of RNA. A non-coding RNA (ncRNA) is any RNA molecule that is not translated into a protein. ... Map of the human X chromosome (from the NCBI website). ...

## Alignment

Both protein and RNA secondary structures can be used to aid in multiple sequence alignment. These alignments can be made more accurate by the inclusion of secondary structure information in addition to simple sequence information. This is sometimes less useful in RNA because base pairing is much more highly conserved than sequence. Distant relationships between proteins whose primary structures are unalignable can sometimes be found by secondary structure. In bioinformatics, a sequence alignment is a way of arranging the primary sequences of DNA, RNA, or protein to identify regions of similarity that may be a consequence of functional, structural, or evolutionary relationships between the sequences. ...

Crystal structure of a foldamer reported by Lehn and coworkers in Helv. ... A protein primary structure is a chain of amino acids. ... In biochemistry, the tertiary structure of a protein is its overall shape. ... In biochemistry, many proteins are actually assemblies of more than one protein (polypeptide) molecule, which in the context of the larger assemblage are known as protein subunits. ... Translation is the second stage of protein biosynthesis (part of the overall process of gene expression). ... In an unbranched, chain-like biological molecule, such as a protein or a strand of RNA, a structural motif is a three-dimensional structural element or fold within the chain, which appears also in a variety of other molecules. ...

## References

• C Branden and J Tooze (1999). Introduction to Protein Structure 2nd ed. Garland Publishing: New York, NY.
• W. Kabsch and C. Sander. Dictionary of Protein Secondary Structure: Pattern Recognition of Hydrogen Bonded and Geometrical Features. Biopolymers 22: 2577-2637 (1983). [1]
• 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.)
• L. Pauling and R.B Corey. Configurations of polypeptide chains with favored orientations of the polypeptide around single bonds: Two pleated sheets. Proc. Natl. Acad. Sci. Wash., 37:729-740 (1951). (The original beta-sheet conformation article.)
• L. Pauling, R.B. Corey and H.R. Branson. Two hydrogen-bonded helical configurations of the polypeptide chain. Proc. Natl. Acad. Sci. Wash., 37:205-211 (1951). (alpha- and pi-helix conformations, since they predicted that 310 helices would not be possible.)
• (1983) "Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features". Biopolymers 22: 2577-2637. PMID 6667333.

Results from FactBites:

 SECONDARY STRUCTURE (904 words) Secondary Structure is the local structure which is typically recognized by specific backbone Torsion Angles and specific mainchain Hydrogen Bond pairings. The structure of plastocyanin is composed mostly of beta sheets and the Ramachandran plot shows a broad range of values in the -110,+130 region. Several definable turns and bends in protein structure have been recognized and classified either by the relationship between the phi,psi angles of the residues in the turn or the hydrogen bonding of their amide N-H and carbonyl-oxygen atoms.
 Proteins (11287 words) The primary structure of a segment of a polypeptide chain or of a protein is the amino-acid sequence of the polypeptide chain(s), without regard to spatial arrangement (apart from configuration at the alpha-carbon atom). The secondary structure of a segment of polypeptide chain is the local spatial arrangement of its main-chain atoms without regard to the conformation of its side chains or to its relationship with other segments (IUPAC-IUB, 1970). An intermediate compact structure known as the molten globule which is different from the native structure and whose formation is determined mainly by non-specific interactions of amino acid residues with their environment was presented.
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