Beta bend ribbon

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The beta bend ribbon, or beta-bend ribbon, is a structural feature in polypeptides [1] [2] [3] [4] [5] [6] [7] and proteins. [8] The shortest possible has six amino acid residues (numbered i to i+5) arranged as two overlapping hydrogen bonded beta turns in which the carbonyl group of residue i is hydrogen-bonded to the NH of residue i+3 while the carbonyl group of residue i+2 is hydrogen-bonded to the NH of residue i+5. In longer ribbons, this bonding is continued in peptides of 8, 10, etc., amino acid residues. A beta bend ribbon can be regarded as an aberrant 310 helix (3/10-helix) that has lost some of its hydrogen bonds. [9] Two websites are available to facilitate finding and examining these features in proteins: Motivated Proteins; [10] and PDBeMotif. [11]

Protein biological molecule consisting of chains of amino acid residues

Proteins are large biomolecules, or macromolecules, consisting of one or more long chains of amino acid residues. Proteins perform a vast array of functions within organisms, including catalysing metabolic reactions, DNA replication, responding to stimuli, providing structure to cells and organisms, and transporting molecules from one location to another. Proteins differ from one another primarily in their sequence of amino acids, which is dictated by the nucleotide sequence of their genes, and which usually results in protein folding into a specific three-dimensional structure that determines its activity.

Amino acid Organic compounds containing amine and carboxylic groups

Amino acids are organic compounds containing amine (-NH2) and carboxyl (-COOH) functional groups, along with a side chain (R group) specific to each amino acid. The key elements of an amino acid are carbon (C), hydrogen (H), oxygen (O), and nitrogen (N), although other elements are found in the side chains of certain amino acids. About 500 naturally occurring amino acids are known (though only 20 appear in the genetic code) and can be classified in many ways. They can be classified according to the core structural functional groups' locations as alpha- (α-), beta- (β-), gamma- (γ-) or delta- (δ-) amino acids; other categories relate to polarity, pH level, and side chain group type (aliphatic, acyclic, aromatic, containing hydroxyl or sulfur, etc.). In the form of proteins, amino acid residues form the second-largest component (water is the largest) of human muscles and other tissues. Beyond their role as residues in proteins, amino acids participate in a number of processes such as neurotransmitter transport and biosynthesis.

Residue (chemistry) in chemistry, whatever remains or acts as a contaminant after a given class of events

In chemistry residue is whatever remains or acts as a contaminant after a given class of events.

A beta bend ribbon with 12 alanine residues. Colors of atoms: carbon, green; oxygen red; nitrogen blue. The four dashed lines are hydrogen bonds, each of which defines a beta turn. BetaBendRibbon.png
A beta bend ribbon with 12 alanine residues. Colors of atoms: carbon, green; oxygen red; nitrogen blue. The four dashed lines are hydrogen bonds, each of which defines a beta turn.

The four main types of hydrogen-bonded beta turns are types I, I’, II and II’. [12] Beta bend ribbons may be formed from any of these types but type I is the commonest in proteins, as it is for single beta turns. Beta bend ribbons made from type I or I’ turns are somewhat twisted, while beta bend ribbons made from type II or II’ beta turns are flat. Beta bend ribbons with mixtures of different beta turn types also occur.

β turns are a type of non-regular secondary structure in proteins that cause a change in direction of the polypeptide chain. They are very common motifs in proteins and polypeptides. Each consists of four amino acid residues. They can be defined in two ways: 1. By the possession of an intra-main-chain hydrogen bond between the CO of residue i and the NH of residue i+3; Alternatively, 2. By having a distance of less than 7Å between the Cα atoms of residues i and i+3. The hydrogen bond criterion is the one most appropriate for everyday use, partly because it gives rise to four distinct categories; the distance criterion gives rise to the same four categories but yields additional turn types.

Type I beta-bend ribbons regularly occur in leucine-rich repeats, in the environments sometimes occupied by helices. A protein with a stack of these features is the extracellular ligand-binding domain of the Nogo receptor. [13] Another beta bend ribbon occurs in the GTPase-activating protein for Rho in the active, but not the inactive, form of the enzyme. The beta bend ribbon, which incorporates the catalytic arginine, allows its side-chain guanidino group to approach the active site and enhance enzyme activity. [14]

Leucine-rich repeat protein structural motif that forms an α/β horseshoe fold

A leucine-rich repeat (LRR) is a protein structural motif that forms an α/β horseshoe fold. It is composed of repeating 20–30 amino acid stretches that are unusually rich in the hydrophobic amino acid leucine. These tandem repeats commonly fold together to form a solenoid protein domain, termed leucine-rich repeat domain. Typically, each repeat unit has beta strand-turn-alpha helix structure, and the assembled domain, composed of many such repeats, has a horseshoe shape with an interior parallel beta sheet and an exterior array of helices. One face of the beta sheet and one side of the helix array are exposed to solvent and are therefore dominated by hydrophilic residues. The region between the helices and sheets is the protein's hydrophobic core and is tightly sterically packed with leucine residues.

GTPase-activating proteins or GTPase-accelerating proteins (GAPs) are a family of regulatory proteins whose members can bind to activated G proteins and stimulate their GTPase activity, with the result of terminating the signaling event. GAPs are also known as RGS protein, or RGS proteins, and these proteins are crucial in controlling the activity of G proteins. Regulation of G proteins is important because these proteins are involved in a variety of important cellular processes. The large G proteins, for example, are involved in transduction of signaling from the G protein-coupled receptor for a variety of signaling processes like hormonal signaling, and small G proteins are involved in processes like cellular trafficking and cell cycling. GAP’s role in this function is to turn the G protein’s activity off. In this sense, GAPs function is opposite to that of guanine nucleotide exchange factors (GEFs), which serve to enhance G protein signaling.

Arginine chemical compound

Arginine, also known as L-arginine (symbol Arg or R), is an α-amino acid that is used in the biosynthesis of proteins. It contains an α-amino group, an α-carboxylic acid group, and a side chain consisting of a 3-carbon aliphatic straight chain ending in a guanidino group. At physiological pH, the carboxylic acid is deprotonated (−COO−), the amino group is protonated (−NH3+), and the guanidino group is also protonated to give the guanidinium form (-C-(NH2)2+), making arginine a charged, aliphatic amino acid. It is the precursor for the biosynthesis of nitric oxide. It is encoded by the codons CGU, CGC, CGA, CGG, AGA, and AGG.

Polypeptides consisting of repeats of the dipeptide (α-amino-γ-lactam plus a conventional amino acid) have been shown to adopt a beta bend ribbon conformation. [15]

Related Research Articles

Alpha helix type of secondary structure

The alpha helix (α-helix) is a common motif in the secondary structure of proteins and is a right hand-helix conformation in which every backbone N−H group donates a hydrogen bond to the backbone C=O group of the amino acid located three or four residues earlier along the protein sequence.

Beta sheet common motif of regular secondary structure in proteinst; stretch of polypeptide chain typically 3 to 10 amino acids long with backbone in an extended conformation

The β-sheet is a common motif of regular secondary structure in proteins. Beta sheets consist of beta strands connected laterally by at least two or three backbone hydrogen bonds, forming a generally twisted, pleated sheet. A β-strand is a stretch of polypeptide chain typically 3 to 10 amino acids long with backbone in an extended conformation. The supramolecular association of β-sheets has been implicated in formation of the protein aggregates and fibrils observed in many human diseases, notably the amyloidoses such as Alzheimer's disease.

Protein secondary structure general three-dimensional form of local segments of proteins

Protein secondary structure is the three dimensional form of local segments of proteins. The two most common secondary structural elements are alpha helices and beta sheets, though beta turns and omega loops occur as well. Secondary structure elements typically spontaneously form as an intermediate before the protein folds into its three dimensional tertiary structure.

In polymer science, the backbone chain of a polymer is the longest series of covalently bonded atoms that together create the continuous chain of the molecule. This science is subdivided into the study of organic polymers, which consist of a carbon backbone, and inorganic polymers which have backbones containing only main group elements.

Beta-peptide

β-peptides consist of β amino acids, which have their amino group bonded to the β carbon rather than the α carbon as in the 20 standard biological amino acids. The only common naturally occurring β amino acid is β-alanine; although it is used as a component of larger bioactive molecules, β-peptides in general do not appear in nature. For this reason β-peptide-based antibiotics are being explored as ways of evading antibiotic resistance. Early studies in this field were published in 1996 by the group of Dieter Seebach and that of Samuel Gellman.

A turn is an element of secondary structure in proteins where the polypeptide chain reverses its overall direction.

A polyproline helix is a type of protein secondary structure which occurs in proteins comprising repeating proline residues. A left-handed polyproline II helix is formed when sequential residues all adopt (φ,ψ) backbone dihedral angles of roughly and have trans isomers of their peptide bonds. This PPII conformation is also common in proteins and polypeptides with other amino acids apart from proline. Similarly, a more compact right-handed polyproline I helix is formed when sequential residues all adopt (φ,ψ) backbone dihedral angles of roughly and have cis isomers of their peptide bonds. Of the twenty common naturally occurring amino acids, only proline is likely to adopt the cis isomer of the peptide bond, specifically the X-Pro peptide bond; steric and electronic factors heavily favor the trans isomer in most other peptide bonds. However, peptide bonds that replace proline with another N-substituted amino acid are also likely to adopt the cis isomer.

Pi helix

A pi helix is a type of secondary structure found in proteins. Although once thought to be rare, short π-helices are found in 15% of known protein structures and are believed to be an evolutionary adaptation derived by the insertion of a single amino acid into an α-helix. Because such insertions are highly destabilizing, the formation of π-helices would tend to be selected against unless it provided some functional advantage to the protein. π-helices therefore are typically found near functional sites of proteins.

3<sub>10</sub> helix

A 310 helix is a type of secondary structure found in proteins and polypeptides. Of the numerous protein secondary structures present, the 310-helix is the fourth most common type observed; following α-helices, β-sheets and reverse turns. 310-helices constitute nearly 10–15% of all helices in protein secondary structures, and are typically observed as extensions of α-helices found at either their N- or C- termini. Because of the α-helices tendency to consistently fold and unfold, it has been proposed that the 310-helix serves as an intermediary conformation of sorts, and provides insight into the initiation of α-helix folding.

Beta hairpin

The beta hairpin is a simple protein structural motif involving two beta strands that look like a hairpin. The motif consists of two strands that are adjacent in primary structure, oriented in an antiparallel direction, and linked by a short loop of two to five amino acids. Beta hairpins can occur in isolation or as part of a series of hydrogen bonded strands that collectively comprise a beta sheet.

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 abbreviation is only mentioned once in the 1983 paper describing this algorithm, where it is the name of the Pascal program that implements the algorithm Define Secondary Structure of Proteins.

In polymer science, the Lifson–Roig model is a helix-coil transition model applied to the alpha helix-random coil transition of polypeptides; it is a refinement of the Zimm-Bragg model that recognizes that a polypeptide alpha helix is only stabilized by a hydrogen bond only once three consecutive residues have adopted the helical conformation. To consider three consecutive residues each with two states, the Lifson–Roig model uses a 4x4 transfer matrix instead of the 2x2 transfer matrix of the Zimm-Bragg model, which considers only two consecutive residues. However, the simple nature of the coil state allows this to be reduced to a 3x3 matrix for most applications.

Alpha sheet

Alpha sheet is an atypical secondary structure in proteins, first proposed by Linus Pauling and Robert Corey in 1951. The hydrogen bonding pattern in an alpha sheet is similar to that of a beta sheet, but the orientation of the carbonyl and amino groups in the peptide bond units is distinctive; in a single strand, all the carbonyl groups are oriented in the same direction on one side of the pleat, and all the amino groups are oriented in the same direction on the opposite side of the sheet. Thus the alpha sheet accumulates an inherent separation of electrostatic charge, with one edge of the sheet exposing negatively charged carbonyl groups and the opposite edge exposing positively charged amino groups. Unlike the alpha helix and beta sheet, the alpha sheet configuration does not require all component amino acid residues to lie within a single region of dihedral angles; instead, the alpha sheet contains residues of alternating dihedrals in the traditional right-handed (αR) and left-handed (αL) helical regions of Ramachandran space. Although the alpha sheet is only rarely observed in natural protein structures, it has been speculated to play a role in amyloid disease and it was found to be a stable form for amyloidogenic proteins in molecular dynamics simulations. Alpha sheets have also been observed in X-ray crystallography structures of designed peptides.

Nest (protein structural motif) Protein structural motif

The Nest is a type of protein structural motif. It is a small recurring anion-binding feature of both proteins and peptides. Each consists of the main chain atoms of three consecutive amino acid residues. The main chain NH groups bind the anions while the side chain atoms are often not involved. Proline residues lack NH groups so are rare in nests. About one in 12 of amino acid residues in proteins, on average, belongs to a nest.

Schellman loop

Schellman loops are commonly occurring structural features of proteins and polypeptides. Each has six amino acid residues with two specific inter-mainchain hydrogen bonds and a characteristic main chain dihedral angle conformation. The CO group of residue i is hydrogen-bonded to the NH of residue i+5, and the CO group of residue i+1 is hydrogen-bonded to the NH of residue i+4. Residues i+1, i+2, and i+3 have negative φ (phi) angle values and the phi value of residue i+4 is positive. Schellman loops incorporate a three amino acid residue RL nest, in which three mainchain NH groups form a concavity for hydrogen bonding to carbonyl oxygens. About 2.5% of amino acids in proteins belong to Schellman loops. Two websites are available for examining small motifs in proteins, Motivated Proteins: ; or PDBeMotif:.

The Asx turn is a structural feature in proteins and polypeptides. It consists of three amino acid residues in which residue i is an aspartate (Asp) or asparagine (Asn) that forms a hydrogen bond from its sidechain CO group to the mainchain NH group of residue i+2. About 14% of Asx residues present in proteins belong to Asx turns.

The term N cap describes an amino acid in a particular position within a protein or polypeptide. The N cap residue of an alpha helix is the first amino acid residue at the N terminus of the helix. More precisely, it is defined as the first residue (i) whose CO group is hydrogen-bonded to the NH group of residue i+4. Because of this it is sometimes also described as the residue prior to the helix.

The term C cap describes an amino acid in a particular position within a protein or polypeptide. The C cap residue of an alpha helix is the last amino acid residue at the C terminus of the helix. More precisely, it is defined as the last residue (i) whose NH group is hydrogen-bonded to the CO group of residue i-4. Because of this it is sometimes also described as the residue following the helix.

ST staple

The ST staple is a common four- or five-amino acid residue motif in proteins and polypeptides with serine or threonine as the C-terminal residue. It is characterized by a single hydrogen bond between the hydroxyl group of the serine or threonine and the main chain carbonyl group of residue i. Motifs are of two types, depending whether the motif has 4 or 5 residues. Most ST staples occur in conjunction with an alpha helix, and are usually associated with a slight bend in the helix. Two websites are available for finding and examining ST staples in proteins: Motivated Proteins and PDBeMotif.

References

  1. ↑ Karle IL, Flippen-Anderson J, Sukumar M, Balaram P. Conformation of a 16-residue zervamicin IIA analog peptide containing three different structural features: 3(10)-helix, alpha-helix, and beta-bend ribbon. Proc Natl Acad Sci USA 1987;84:5087–5091
  2. ↑ Crisma M, Formaggio F, Moretto A, Toniolo C. Peptide helices based on alpha-amino acids. Biopolymers 2006;84:3–12
  3. ↑ Gupta M, Chauhan VS. De novo design of alpha,beta-didehydrophenylalanine-containing peptides. From models to applications. Biopolymers 2011;95:161–173
  4. ↑ Di Blasio B, Pavone V, Saviano PM, Lombardi A, Nastri F, Pedone C, Benedetti E, Crisma M, Anzolin M, Toniolo C. Structural characterization of the beta-bend ribbon spiral: crystallographic analysis of two long (L-Pro-Aib), sequential peptides. J Am Chem Soc 1991;114:6278–6291
  5. ↑ Madalengoita JS. A novel peptide fold: a repeating betaII-turn secondary structure. J Am Chem Soc 2000;122:4986–4987
  6. ↑ Formaggio F, Toniolo C. Electronic and vibrational signatures of peptide helical structures. A tribute to Anton Mario Tamburro. Chirality 2010;22:E30–E39
  7. ↑ Kennedy DF, Crisma M, Toniolo C, Chapman D. Studies of peptides forming 3/10- and alpha-helices and beta-bend ribbon structures in organic solution and in model membranes by Fourier Transform Infrared spectroscopy. Biochemistry 1991;30:6541–6548
  8. ↑ Hayward, SJ, Leader, DP, Al-Shubailly, F, Milner-White, EJ. (2014) Rings and ribbons in protein structures: Characterization using helical parameters and Ramachandran plots for repeating dipeptides. Proteins 2014; 82:230–239
  9. ↑ Toniolo C, Benedetti E (1991) The polypeptide 3/10-helix. Trends Biochem Sci 16: 350-353
  10. ↑ Leader DP, Milner-White, EJ (2009) Motivated Proteins: A web application for studying small three-dimensional protein motifs. BMC Bioinformatics 10:60
  11. ↑ Golovin A; Henrick K (2008) MSDmotif: exploring protein sites and motifs. BMC Bioinformatics 9:312
  12. ↑ Venkatachalam CM (1968) Stereochemical criteria for polypeptides and proteins V. Conformation of a system of three-linked peptide units. Biopolymers 6:1425-1436
  13. ↑ He XL, Bazan JF, McDermott G, Park JB, Wang K, Tessier-Lavigne M, He Z, Garcia KC. Structure of the Nogo receptor ectodomain: a recognition module implicated in myelin inhibition. Neuron 2003; 38:177–185.
  14. ↑ Rittinger K, Walker PA, Eccleston JF, Smerdon SJ, Gamblin SJ. Structure at 1.65 Å of RhoA and its GTPase-activating protein in complex with a transition-state analogue. Nature 1997;389:758–762.
  15. ↑ Martin V, Legrand B, Vezenkov LL. Turning peptide sequences into ribbon foldamers by a straightforward multicyclization reaction. Angewandte Chemie 2015;54:1-6.
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