A polyproline helix is a type of protein secondary structure which occurs in proteins comprising repeating proline residues.A left-handed polyproline II helix (PPII, poly-Pro II) is formed when sequential residues all adopt (φ,ψ) backbone dihedral angles of roughly (-75°, 150°) 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 (PPI, poly-Pro I) is formed when sequential residues all adopt (φ,ψ) backbone dihedral angles of roughly (-75°, 160°) 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 (such as sarcosine) are also likely to adopt the cis isomer.
The PPII helix is defined by (φ,ψ) backbone dihedral angles of roughly (-75°, 150°) and trans isomers of the peptide bonds. The rotation angle Ω per residue of any polypeptide helix with trans isomers is given by the equation
Substitution of the poly-Pro II (φ,ψ) dihedral angles into this equation yields almost exactly Ω = -120°, i.e., the PPII helix is a left-handed helix (since Ω is negative) with three residues per turn (360°/120° = 3). The rise per residue is approximately 3.1 Å. This structure is somewhat similar to that adopted in the fibrous protein collagen, which is composed mainly of proline, hydroxyproline, and glycine. PPII helices are specifically bound by SH3 domains; this binding is important for many protein-protein interactions and even for interactions between the domains of a single protein.
The PPII helix is relatively open and has no internal hydrogen bonding, as opposed to the more common helical secondary structures, the alpha helix and its relatives the 310 helix and the pi helix, as well as the β-helix. The amide nitrogen and oxygen atoms are too far apart (approximately 3.8 Å) and oriented incorrectly for hydrogen bonding. Moreover, these atoms are both H-bond acceptors in proline; there is no H-bond donor due to the cyclic side chain.
The PPII backbone dihedral angles (-75°, 150°) are observed frequently in proteins, even for amino acids other than proline.The Ramachandran plot is highly populated in the PPII region, comparably to the beta sheet region around (-135°, 135°). For example, the PPII backbone dihedral angles are often observed in turns, most commonly in the first residue of a type II β-turn. The "mirror image" PPII backbone dihedral angles (75°, -150°) are rarely seen, except in polymers of the achiral amino acid glycine. The analog of the poly-Pro II helix in poly-glycine is called the poly-Gly II helix. Some proteins, such as the antifreeze protein of Hypogastrura harveyi consist of bundles of glycine-rich polyglycine II helices. This remarkable protein, whose 3D structure is known, has unique NMR spectra and is stabilized by dimerization and 28 Cα-H··O=C hydrogen bonds. The PPII helix is not common in transmembrane proteins, and this secondary structure does not traverse lipid membranes in natural conditions. In 2018, a group of researcher from Germany constructed and experimentally observed the first transmembrane PPII helix formed by specifically designed artificial peptides.
The poly-Pro I helix is much denser than the PPII helix due to the cis isomers of its peptide bonds. It is also rarer than the PPII conformation because the cis isomer is higher in energy than the trans. Its typical dihedral angles (-75°, 160°) are close, but not identical to, those of the PPII helix. However, the PPI helix is a right-handed helix and more tightly wound, with roughly 3.3 residues per turn (rather than 3). The rise per residue in the PPI helix is also much smaller, roughly 1.9 Å. Again, there is no internal hydrogen bonding in the poly-Pro I helix, both because an H-bond donor atom is lacking and because the amide nitrogen and oxygen atoms are too distant (roughly 3.8 Å again) and oriented incorrectly.
Traditionally, PPII has been considered to be relatively rigid and used as a "molecular ruler" in structural biology, e.g., to calibrate FRET efficiency measurements. However, subsequent experimental and theoretical studies have called into question this picture of a polyproline peptide as a "rigid rod".Further studies using terahertz spectroscopy and density functional theory calculations highlighted that polyproline is in fact much less rigid than originally thought. Interconversions between the PPII and PPI helix forms of poly-proline are slow, due to the high activation energy of X-Pro cis-trans isomerization (Ea ≈ 20 kcal/mol); however, this interconversion may be catalyzed by specific isomerases known as prolyl isomerases or PPIases. The interconversion between the PPII and PPI helices involve the cis-trans peptide bond isomerization along the whole peptide chain. Studies based on ion-mobility spectrometry revealed existence of a defined set of intermediates along this process.
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 hydrogen bonds to the backbone C=O group of the amino acid located three or four residues earlier along the protein sequence.
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.
In collagen, the collagen helix, or type-2 helix, is a major shape in secondary structure. It consists of a triple helix made of the repetitious amino acid sequence glycine - X - Y, where X and Y are frequently proline or hydroxyproline. Glycine, proline, and hydroxyproline must be in their designated positions with the correct configuration. For example, hydroxyproline in the Y position increases the thermal stability of the triple helix, but not when it is located in the X position. The thermal stabilization is also hindered when the hydroxyl group has the wrong configuration. Due to the high abundance of glycine and proline contents, collagen fails to form a regular α-helix and β-sheet structure. Three left-handed helical strands twist to form a right-handed triple helix. A collagen triple helix has 3.3 residues per turn. Each of the three chains is stabilized by the steric repulsion due to the pyrrolidine rings of proline and hydroxyproline residues. The pyrrolidine rings keep out of each other's way when the polypeptide chain assumes this extended helical form, which is much more open than the tightly coiled form of the alpha helix. The three chains are hydrogen bonded to each other. The hydrogen bond donors are the peptide NH groups of glycine residues. The hydrogen bond acceptors are the CO groups of residues on the other chains. The OH group of hydroxyproline does not participate in hydrogen bonding but stabilises the trans isomer of proline by stereoelectronic effects, therefore stabilizing the entire triple helix. The rise of the collagen helix (superhelix) is 2.9 Å (0.29 nm) per residue. The center of the collagen triple helix is very small and hydrophobic, and every third residue of the helix must have contact with the center. Due to the very tiny and tight space at the center, only the small hydrogen of the glycine side chain is capable of interacting with the center. This contact is impossible even when a slightly bigger amino acid residue is present other than glycine.
A peptide bond is an amide type of covalent chemical bond linking two consecutive alpha-amino acids from C1 of one alpha-amino acid and N2 of another along a peptide or protein chain.
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.
Proline (symbol Pro or P) is a proteinogenic amino acid that is used in the biosynthesis of proteins. It contains an α-amino group (which is in the protonated NH2+ form under biological conditions), an α-carboxylic acid group (which is in the deprotonated −COO− form under biological conditions), and a side chain pyrrolidine, classifying it as a nonpolar (at physiological pH), aliphatic amino acid. It is non-essential in humans, meaning the body can synthesize it from the non-essential amino acid L-glutamate. It is encoded by all the codons starting with CC (CCU, CCC, CCA, and CCG).
Protein structure prediction is the inference of the three-dimensional structure of a protein from its amino acid sequence—that is, the prediction of its folding and its secondary and tertiary structure from its primary structure. Structure prediction is fundamentally different from the inverse problem of protein design. Protein structure prediction is one of the most important goals pursued by bioinformatics and theoretical chemistry; it is highly important in medicine and biotechnology. Every two years, the performance of current methods is assessed in the CASP experiment. A continuous evaluation of protein structure prediction web servers is performed by the community project CAMEO3D.
A dihedral angle is the angle between two intersecting planes. In chemistry, it is the angle between planes through two sets of three atoms, having two atoms in common. In solid geometry, it is defined as the union of a line and two half-planes that have this line as a common edge. In higher dimensions, a dihedral angle represents the angle between two hyperplanes. The planes of a flying machine are said to be at positive dihedral angle when both starboard and port main planes are upwardly inclined to the lateral axis. When downwardly inclined they are said to be at a negative dihedral angle.
In biochemistry, a Ramachandran plot, originally developed in 1963 by G. N. Ramachandran, C. Ramakrishnan, and V. Sasisekharan, is a way to visualize energetically allowed regions for backbone dihedral angles ψ against φ of amino acid residues in protein structure. The figure on the left illustrates the definition of the φ and ψ backbone dihedral angles. The ω angle at the peptide bond is normally 180°, since the partial-double-bond character keeps the peptide planar. The figure in the top right shows the allowed φ,ψ backbone conformational regions from the Ramachandran et al. 1963 and 1968 hard-sphere calculations: full radius in solid outline, reduced radius in dashed, and relaxed tau (N-Cα-C) angle in dotted lines. Because dihedral angle values are circular and 0° is the same as 360°, the edges of the Ramachandran plot "wrap" right-to-left and bottom-to-top. For instance, the small strip of allowed values along the lower-left edge of the plot are a continuation of the large, extended-chain region at upper left.
Peptoids, or poly-N-substituted glycines, are a class of peptidomimetics whose side chains are appended to the nitrogen atom of the peptide backbone, rather than to the α-carbons.
Resilin is an elastomeric protein found in many insects and other arthropods. It provides soft rubber-elasticity to mechanically active organs and tissue; for example, it enables insects of many species to jump or pivot their wings efficiently. Resilin was first discovered by Torkel Weis-Fogh in locust wing-hinges.
A turn is an element of secondary structure in proteins where the polypeptide chain reverses its overall direction.
A pi helix is a type of secondary structure found in proteins. Discovered by crystallographer Barbara Low in 1952 and 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.
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.
Prolyl isomerase is an enzyme found in both prokaryotes and eukaryotes that interconverts the cis and trans isomers of peptide bonds with the imino acid proline. Proline has an unusually conformationally restrained peptide bond due to its cyclic structure with its side chain bonded to its secondary amine nitrogen. Most amino acids have a strong energetic preference for the trans peptide bond conformation due to steric hindrance, but proline's unusual structure stabilizes the cis form so that both isomers are populated under biologically relevant conditions. Proteins with prolyl isomerase activity include cyclophilin, FKBPs, and parvulin, although larger proteins can also contain prolyl isomerase domains.
Peptide plane flipping is a type of conformational change that can occur in proteins by which the dihedral angles of adjacent amino acids undergo large-scale rotations with little displacement of the side chains. The plane flip is defined as a rotation of the dihedral angles φ,ψ at amino acids i and i+1 such that the resulting angles remain in structurally stable regions of Ramachandran space. The key requirement is that the sum of the ψi angle of residue i and the φi+1 angle of residue i+1 remain roughly constant; in effect, the flip is a crankshaft move about the axis defined by the Cα-C¹ and N-Cα bond vectors of the peptide group, which are roughly parallel. As an example, the type I and type II beta turns differ by a simple flip of the central peptide group of the turn.
β turns are the most common form of turns—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.
In the fields of geometry and biochemistry, a triple helix is a set of three congruent geometrical helices with the same axis, differing by a translation along the axis. This means that each of the helices keeps the same distance from the central axis. As with a single helix, a triple helix may be characterized by its pitch, diameter, and handedness. Examples of triple helices include triplex DNA, triplex RNA, the collagen helix, and collagen-like proteins.
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:.
In epigenetics, proline isomerization is the effect that cis-trans isomerization of the amino acid proline has on the regulation of gene expression. Similar to aspartic acid, the amino acid proline has the rare property of being able to occupy both cis and trans isomers of its prolyl peptide bonds with ease. Peptidyl-prolyl isomerase, or PPIase, is an enzyme very commonly associated with proline isomerization due to their ability to catalyze the isomerization of prolines. PPIases are present in three types: cyclophilins, FK507-binding proteins, and the parvulins. PPIase enzymes catalyze the transition of proline between cis and trans isomers and are essential to the numerous biological functions controlled and affected by prolyl isomerization Without PPIases, prolyl peptide bonds will slowly switch between cis and trans isomers, a process that can lock proteins in a nonnative structure that can affect render the protein temporarily ineffective. Although this switch can occur on its own, PPIases are responsible for most isomerization of prolyl peptide bonds. The specific amino acid that precedes the prolyl peptide bond also can have an effect on which conformation the bond assumes. For instance, when an aromatic amino acid is bonded to a proline the bond is more favorable to the cis conformation. Cyclophilin A uses an "electrostatic handle" to pull proline into cis and trans formations. Most of these biological functions are affected by the isomerization of proline when one isomer interacts differently than the other, commonly causing an activation/deactivation relationship. As an amino acid, proline is present in many proteins. This aids in the multitude of effects that isomerization of proline can have in different biological mechanisms and functions.