NationMaster - Encyclopedia: Beta sheet

The β sheet (also β-pleated sheet) is the second form of regular secondary structure in proteins — the first is the alpha helix — consisting of beta strands connected laterally by three or more hydrogen bonds, forming a generally twisted, pleated sheet. A beta strand (also β-strand) is a stretch of amino acids typically 5-10 amino acids long whose peptide backbones are almost fully extended. The association of beta sheets has been implicated in the formation of protein aggregates and fibrils observed in many human diseases, including Alzheimer's disease and mad cow disease. Image File history File links Diagram of beta-Pleated sheet structure of protein User talk:G3pro#Image source File history Legend: (cur) = this is the current file, (del) = delete this old version, (rev) = revert to this old version. ... Image File history File links Diagram of beta-Pleated sheet structure of protein User talk:G3pro#Image source File history Legend: (cur) = this is the current file, (del) = delete this old version, (rev) = revert to this old version. ... A representation of the 3D structure of the Myoglobin protein. ... A representation of the 3D structure of myoglobin, showing coloured alpha helices. ... A diagram of the alpha helix structure of amino acids In proteins, the Î± helix is a major structural motif in secondary structure. ... Snapshot from a simulation of liquid water. ... The general structure of an Î±-amino acid molecule, with the amine group on the left and the carboxyl group on the right. ... Bovine spongiform encephalopathy (BSE or commonly mad cow disease) is a fatal, neurodegenerative disease of cattle, which infects by a mechanism that shocked biologists on its discovery in late 20th century and appears transmissible to humans. ...

Nomenclature

In the most common usage, β strand refers to a single continuous stretch of amino acids adopting an extended conformation and involved in hydrogen bonds; by contrast, a β sheet refers to an assembly of such strands that are hydrogen-bonded to each other. However, the term "β sheet" is also sometimes used as a synonym of "β strand", i.e., for a single segment of extended, hydrogen-bonded amino acids. Snapshot from a simulation of liquid water. ... Snapshot from a simulation of liquid water. ...

History

The first β sheet structure was proposed by William Astbury in the 1930's. He proposed the idea of hydrogen bonding between the peptide bonds of parallel or antiparallel extended β strands. However, Astbury did not have the necessary data on the bond geometry of the amino acids in order to build accurate models, especially since he did not then know that the peptide bond was planar. A refined version was proposed by Linus Pauling and Robert Corey in 1951. William Astbury (1898-1961) was an English biochemist who made X-ray diffraction studies of nucleic acid in 1937. ... A peptide bond is a chemical bond formed between two molecules when the carboxyl group of one molecule reacts with the amino group of the other molecule, releasing a molecule of water (H2O). ... A peptide bond is a chemical bond formed between two molecules when the carboxyl group of one molecule reacts with the amino group of the other molecule, releasing a molecule of water (H2O). ... Linus Carl Pauling (February 28, 1901 â€“ August 19, 1994) was an American quantum chemist and biochemist. ...

Structure and Orientation

Geometry

The majority of β strands are arranged adjacent to other strands and form an extensive hydrogen bond network with their neighbors in which the N-H groups in the backbone of one strand establish hydrogen bonds with the C=O groups in the backbone of the adjacent strands. In the fully extended β strand, successive side chains point straight up, then straight down, then straight up, etc.. What's more, adjacent β strands in a β sheet are aligned so that their

C α

atoms are adjacent and their side chains point in the same direction. The "pleated" appearance of β strands arises from tetrahedral chemical bonding at the

C α

atom; for example, if a side chain points straight up, then the bond to the $mathrm{C^{prime}}$ must point slightly downwards, since its bond angle is approximately 109.5°. The pleating causes the distance between $mathrm{C^{alpha}}_{i}$ and $mathrm{C^{alpha}_{i+2}}$ to be approximately 6 Å, rather than the 7.6 Å (2 x 3.8 Å) expected from two fully extended trans peptide virtual bonds. The "sideways" distance between adjacent

C α

atoms in hydrogen-bonded β strands is roughly 5 Å. Snapshot from a simulation of liquid water. ... The general structure of an amine Amines are organic compounds and a type of functional group that contain nitrogen as the key atom. ... Snapshot from a simulation of liquid water. ... Carbonyl group In organic chemistry, a carbonyl group is a functional group composed of a carbon atom double-bonded to an oxygen atom. ... Trans is a Latin word meaning across, beyond or on the opposite side and is the opposite of cis, which means on the same side. In chemistry, a bond not subject to free rotation in which the greater radical on both ends is on the opposite side of the bond... A peptide bond is a chemical bond formed between two molecules when the carboxyl group of one molecule reacts with the amino group of the other molecule, releasing a molecule of water (H2O). ... Snapshot from a simulation of liquid water. ...

However, β strands are rarely perfectly extended; rather, they exhibit a slight twist due to the chirality of their component amino acids. The energetically preferred dihedral angles (φ, ψ) = $(-135^{circ}, 135^{circ})$ (broadly, the upper left region of the Ramachandran plot) diverge somewhat from the fully extended conformation (φ, ψ) = $(-180^{circ}, 180^{circ})$ .^[1] The twist is often associated with alternating fluctuations in the dihedral angles to prevent the individual β strands in a larger sheet from splaying apart. A good example of such a twisted β-hairpin can be seen in the protein BPTI. The term chiral (pronounced ) is used to describe an object which is non-superimposable on its mirror image. ... In Aerospace engineering, the dihedral is the angle that the two wings make with each other. ... Ã Ã¹Ã†[][[]]A Ramachandran plot (also known as a Ramachandran Map or a Ramachandran diagram), developed by Gopalasamudram Narayana Ramachandran, is a way to visualize dihedral angles Ï† against Ïˆ of amino acid residues in protein structure. ... In Aerospace engineering, the dihedral is the angle that the two wings make with each other. ... The Bovine Pancreatic Trypsin Inhibitor (BPTI) is a monomeric globular polypeptide containing 58 amino acid residues and three disulfide bonds (Cys5-Cys55, Cys14-Cys38 and Cys30-Cys51). ...

The sidechains point outwards from the folds of the pleats, roughly perpendicularly to the plane of the sheet; successive residues point outwards on alternating faces of the sheet.

Hydrogen bonding patterns

Because peptide chains have a directionality conferred by their N-terminus and C-terminus, β strands too can be said to be directional. They are usually represented in protein topology diagrams by an arrow pointing toward the C-terminus. Adjacent β strands can form hydrogen bonds in antiparallel, parallel, or mixed arrangements. Image File history File links Download high-resolution version (669x834, 180 KB) File links The following pages on the English Wikipedia link to this file (pages on other projects are not listed): Beta sheet ... Image File history File links Download high-resolution version (669x834, 180 KB) File links The following pages on the English Wikipedia link to this file (pages on other projects are not listed): Beta sheet ... Cartoon representation of a Î²-hairpin The beta hairpin (or beta-beta unit) structural motif is the simplest protein motif involving two beta strands. ... The N-terminal end refers to the extremity of a protein or polypeptide terminated by an amino acid with a free amine group (NH2). ... The C-terminal end refers to the extremity of a protein or polypeptide terminated by an amino acid with a free carboxyl group (COOH). ... Snapshot from a simulation of liquid water. ...

In an antiparallel arrangement, the successive β strands alternate directions so that the N-terminus of one strand is adjacent to the C-terminus of the next. This is the arrangement that produces the strongest inter-strand stability because it allows the inter-strand hydrogen bonds between carbonyls and amines to be planar, which is their preferred orientation. The peptide backbone dihedral angles (φ, ψ) are about $(-140^{circ}, 135^{circ})$ in antiparallel sheets. In this case, if two atoms $mathrm{C^{alpha}_{i}}$ and $mathrm{C^{alpha}_{j}}$ are adjacent in two hydrogen-bonded β strands, then they form two mutual backbone hydrogen bonds to each other's flanking peptide groups; this is known as a close pair of hydrogen bonds. Image File history File links Beta-anti-parallel. ... Image File history File links Beta-anti-parallel. ... Snapshot from a simulation of liquid water. ... A peptide bond is a chemical bond formed between two molecules when the carboxyl group of one molecule reacts with the amino group of the other molecule, releasing a molecule of water (H2O). ...

In a parallel arrangement, all of the N-termini of successive strands are oriented in the same direction; this orientation is slightly less stable because it introduces nonplanarity in the inter-strand hydrogen bonding pattern. The dihedral angles (φ, ψ) are about $(-120^{circ}, 115^{circ})$ in parallel sheets. It is rare to find less than five interacting parallel strands in a motif, suggesting that a smaller number of strands may be unstable. In this case, if two atoms $mathrm{C^{alpha}_{i}}$ and $mathrm{C^{alpha}_{j}}$ are adjacent in two hydrogen-bonded β strands, then they do not hydrogen bond to each other; rather one residue forms hydrogen bonds to the residues that flank the other (but not vice versa). For example, residue

i

may form hydrogen bonds to residues

j - 1

and

j + 1

; this is known as a wide pair of hydrogen bonds. By contrast, residue

j

may hydrogen-bond to different residues altogether, or to none at all. Snapshot from a simulation of liquid water. ...

Finally, an individual strand may exhibit a mixed bonding pattern, with a parallel strand on one side and an antiparallel strand on the other. Such arrangements are less common than a random distribution of orientations would suggest, indicating that this pattern is less stable than the antiparallel arrangement. Image File history File links Beta-parallel. ... Image File history File links Beta-parallel. ...

The hydrogen bonding of β strands need not be perfect, but can exhibit localized disruptions known as beta bulges. Snapshot from a simulation of liquid water. ... A beta bulge is a localized disruption of the regular hydrogen bonding of a beta sheet, usually by inserting a residue with helical dihedral angles into one or both H-bonded Î²-strands. ...

The hydrogen bonds lie roughly in the plane of the sheet, with the peptide carbonyl groups pointing in alternating directions with successive residues; for comparison, successive carbonyls point in the same direction in the alpha helix. A peptide bond is a chemical bond formed between two molecules when the carboxyl group of one molecule reacts with the amino group of the other molecule, releasing a molecule of water (H2O). ... Carbonyl group In organic chemistry, a carbonyl group is a functional group composed of a carbon atom double-bonded to an oxygen atom. ... A diagram of the alpha helix structure of amino acids In proteins, the Î± helix is a major structural motif in secondary structure. ...

Amino acid propensities

Large aromatic residues (Tyr, Phe and Trp) and β-branched amino acids (Thr, Val, Ile) are favored to be found in β strands in the middle of β sheets. Interestingly, different types of residues (such as Pro) are likely to be found in the edge strands in β sheets, presumably to avoid the "edge-to-edge" association between proteins that might lead to aggregation and amyloid formation. Look up Aggregation in Wiktionary, the free dictionary The term aggregation may refer toâ€” in economics, combining entities into a single entity which represent them, like aggregation of individual demand to total, or market, demand. ... Amyloid describes various types of protein aggregations that share specific traits when examined microscopically. ...

Common Structural Motifs

A very simple structural motif involving β sheets is the β hairpin in which two antiparallel strands are linked by a short loop of two to five residues, of which one is frequently a glycine or a proline, both of which can assume the unusual dihedral-angle conformations required for a tight turn. However, individual strands can also be linked in more elaborate ways with long loops that may contain alpha helices or even entire protein domains. It has been suggested that Supersecondary structure be merged into this article or section. ... Cartoon representation of a Î²-hairpin The beta hairpin (or beta-beta unit) structural motif is the simplest protein motif involving two beta strands. ... Glycine (Gly, G) is a nonpolar amino acid. ... L-Proline is one of the twenty proteinogenic units which are used in living organisms as the building blocks of proteins. ... A turn is an element of secondary structure in proteins. ... A diagram of the alpha helix structure of amino acids In proteins, the Î± helix is a major structural motif in secondary structure. ...

Greek key motif

The Greek key motif consists of four adjacent antiparallel strands and their linking loops. It consists of three antiparallel strands connected by hairpins, while the fourth is adjacent to the first and linked to the third by a longer loop. This type of structure forms easily during the protein folding process. It was named after a pattern common to Greek ornamental artwork. A simple Greek key design A Greek Key is a repeating design element used in architecture, jewelry and fabrics. ...

The β-α-β motif

Due to the chirality of their component amino acids, all strands exhibit a "right-handed" twist evident in most higher-order β sheet structures. In particular, the linking loop between two parallel strands almost always has a right-handed crossover chirality, which is strongly favored by the inherent twist of the sheet. This linking loop frequently contains a helical region, in which case it is called a β-α-β motif. A closely related motif called a β-α-β-α motif forms the basic component of the most common protein tertiary structure, the TIM barrel. In biochemistry, the tertiary structure of a protein is its overall shape. ... Top view of a triosephosphateisomerase (TIM) barrel (PDB accession code 8TIM), colored from blue (N-terminus) to red (C-terminus). ...

Other structural motifs

A wide variety of topologies and connectivities between basic secondary structure elements leads to the formation of diverse protein folds. Prominent folds that feature β sheets include β barrels, β propellers, and "jelly roll fold" motifs. The Structural Classification of Proteins database includes a category specifically for all-β proteins. A beta barrel is a protein fold containing a series of beta sheets, typically arranged in an antiparallel fashion. ... Ribbon diagram of the C-terminal WD40 domain of Tup1 (a transcriptional co-repressor in yeast), which adopts a 7-bladed beta-propeller fold. ...

Structural topology

The topology of a β sheet describes the order of hydrogen-bonded β strands along the backbone. For example, the flavodoxin fold has a five-stranded, parallel β sheet with topology 21345; thus, the edge strands are β strand 2 and β strand 5 along the backbone. Spelled out explicitly, β strand 2 is H-bonded to β strand 1, which is H-bonded to β strand 3, which is H-bonded to β strand 4, which is H-bonded to β strand 5, the other edge strand. In the same system, the Greek key motif described above has a 4123 topology. The secondary structure of a β sheet can be described roughly by giving the number of strands, their topology, and whether their hydrogen bonds are parallel or antiparallel. Snapshot from a simulation of liquid water. ... Ribbon diagram of CheY (a regulator of the chemotactic response in bacteria, PDB accession code 3CHY), which adopts the flavodoxin fold. ... A representation of the 3D structure of the Myoglobin protein. ... Snapshot from a simulation of liquid water. ...

β sheets can be open, meaning that they have two edge strands (as in the flavodoxin fold or the immunoglobulin fold)) or they can be closed beta barrels (such as the TIM barrel). β-Barrels are often described by their stagger or shear. Some open β sheets are very curved and fold over on themselves (as in the SH3 domain) or form horseshoe shapes (as in the ribonuclease inhibitor). Open β sheets can assemble face-to-face (such as the beta-propeller domain or immunoglobulin fold) or edge-to-edge, forming one big β sheet. Ribbon diagram of CheY (a regulator of the chemotactic response in bacteria, PDB accession code 3CHY), which adopts the flavodoxin fold. ... Example of an immunoglobulin domain, the fibronectin type III domain from human tenascin (PDB accesion code 1TEN), colored from blue (N-terminus) to red (C-terminus). ... A beta barrel is a protein fold containing a series of beta sheets, typically arranged in an antiparallel fashion. ... Top view of a triosephosphateisomerase (TIM) barrel (PDB accession code 8TIM), colored from blue (N-terminus) to red (C-terminus). ... A beta barrel is a protein fold containing a series of beta sheets, typically arranged in an antiparallel fashion. ... An SH3 domain is a protein module, a characteristic peptide sequence. ... Top view of porcine ribonuclease inhibitor (PDB accesion code 2BNH), showing its horseshoe shape. ... Ribbon diagram of the C-terminal WD40 domain of Tup1 (a transcriptional co-repressor in yeast), which adopts a 7-bladed beta-propeller fold. ... Example of an immunoglobulin domain, the fibronectin type III domain from human tenascin (PDB accesion code 1TEN), colored from blue (N-terminus) to red (C-terminus). ...

Parallel β Helices

A β helix is formed from repeating structural units consisting of two or three short β strands linked by short loops. These units "stack" atop one another in a helical fashion so that successive repetitions of the same strand hydrogen-bond with each other in a parallel orientation. In β helices, the strands themselves are nearly planar, and the resulting helix surfaces are nearly flat, e.g., forming a triangular prism shape. Monomeric, left-handed Î²-helix antifreeze protein from the spruce budworm Choristoneura fumiferana (PDB accession code 1M8N). ... Monomeric, left-handed Î²-helix antifreeze protein from the spruce budworm Choristoneura fumiferana (PDB accession code 1M8N). ... In geometry, a triangular prism or three-sided prism is a polyhedron made of a triangular base, a translated copy, and 3 faces joining corresponding sides. ...

The two-strand helix is found in the enzyme pectate lyase. Its two loops are each six residues long and bind stabilizing calcium ions to maintain the integrity of the structure. The more complex three-strand helix contains three linking loops, of which one is consistently two residues long and the others are variable. This structure is found in bacteriophage P22 tailspike protein^[2].

β sheets in pathology

Some proteins that are disordered or helical as monomers, such as amyloid β (see amyloid plaque) can form β-sheet-rich oligomeric structures associated with pathological states. The amyloid β protein's oligomeric form is implicated as a cause of Alzheimer's. Its structure has yet to be determined in full, but recent data suggests that it may resemble an unusual two-strand β helix.^[3] Amyloid describes various types of protein aggregations that share specific traits when examined microscopically. ... Alzheimer redirects here. ...

The side chains from the amino acid residues found in a β sheet structure may also be arranged such that many of the adjacent sidechains on one side of the sheet are hydrophobic, while many of those adjacent to each other on the alternate side of the sheet are polar or charged (hydrophilic), which can be useful if the sheet is to form a boundary between polar/watery and nonpolar/greasy environments.

References

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