• β turns (also β-bends, tight turns, reverse turns, Venkatachalam 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.
  • Venkatachalam, CM (1968). “Stereochemical criteria for polypeptides and proteins. V. Conformation of a system of three linked peptide units” (PDF). Biopolymers. 6 (10): 1425–1436. doi:10.1002/bip.1968.360061006. hdl:2027.42/37819. PMID 5685102.
  • Lewis, PN; Momany FA (1973). “Chain reversal in proteins”. Biochim Biophys Acta. 303 (2): 211–29. doi:10.1016/0005-2795(73)90350-4. PMID 4351002.
  • Toniolo, C; Benedetti E (1980). “Intramolecularly hydrogen-bonded peptide conformations”. CRC Crit Rev Biochem. 9 (1): 1–44. doi:10.3109/10409238009105471. PMID 6254725.
  • Richardson, JS (1981). “The anatomy and taxonomy of protein structure”. Adv Prot Chem. 34: 167–339. doi:10.1016/S0065-3233(08)60520-3. PMID 7020376.
  • Rose, GD; Gierasch LM (1985). “Turns in peptides and proteins”. Adv Prot Chem. 37: 1–109. doi:10.1016/S0065-3233(08)60063-7. PMID 2865874.
  • Milner-White, EJ; Poet R (1987). “Loops, bulges, turns and hairpins in proteins”. Trends Biochem Sci. 12: 189–192. doi:10.1016/0968-0004(87)90091-0.
  • Wilmot, CM; Thornton JM (1988). “Analysis and prediction of the different types of beta-turn in proteins”. J Mol Biol. 203: 221–232. doi:10.1016/0022-2836(88)90103-9. PMID 3184187.
  • Sibanda, BL; Blundell TL (1989). “Conformation of β-hairpins in protein structures: A systematic classification with applications to modelling by homology, electron density fitting and protein engineering”. J Mol Biol. 206 (4): 759–777. doi:10.1016/0022-2836(89)90583-4. PMID 2500530.
  • Hutchinson, EG; Thornton JM (1994). “A revised set of potentials for β-turn formation in proteins”. J Mol Biol. 3 (12): 2207–2216. doi:10.1002/pro.5560031206. PMC 2142776. PMID 7756980.

Each consists of four amino acid residues (labelled i, i+1, i+2 and i+3). 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;
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.

• A hydrogen bond (or H-bond) is a primarily electrostatic force of attraction between a hydrogen (H) atom which is covalently bound to a more electronegative “donor” atom or group (Dn), and another electronegative atom bearing a lone pair of electrons—the hydrogen bond acceptor (Ac). Such an interacting system is generally denoted Dn–H···Ac, where the solid line denotes a polar covalent bond, and the dotted or dashed line indicates the hydrogen bond.
  • ^{Arunan, Elangannan; Desiraju, Gautam R.; Klein, Roger A.; Sadlej, Joanna; Scheiner, Steve; Alkorta, Ibon; Clary, David C.; Crabtree, Robert H.; Dannenberg, Joseph J. (2011-07-08). “Definition of the hydrogen bond (IUPAC Recommendations 2011)”. Pure and Applied Chemistry. 83 (8): 1637–1641. doi:10.1351/PAC-REC-10-01-02. ISSN 1365-3075. S2CID 97688573.} 
• The most frequent donor and acceptor atoms are the second-row elements nitrogen (N), oxygen (O), and fluorine (F).

• Hydrogen bonds can be intermolecular (occurring between separate molecules) or intramolecular (occurring among parts of the same molecule).
  • ^{Pimentel, G. The Hydrogen Bond Franklin Classics, 2018), ISBN 0343171600}
  • ^{Jeffrey, G. A.; An introduction to hydrogen bonding; Oxford university press New York, 1997. ISBN 0195095499}
  • ^{Jeffrey, G. A.; Saenger, W. Hydrogen bonding in biological structures; Springer: Berlin, 1994, 2012 Springer; ISBN 3540579036}
  • ^{IUPAC, Compendium of Chemical Terminology, 2nd ed. (the “Gold Book”) (1997). Online corrected version: (2006–) “hydrogen bond“. doi:10.1351/goldbook.H02899} 
• The energy of a hydrogen bond depends on the geometry, the environment, and the nature of the specific donor and acceptor atoms, and can vary between 1 and 40 kcal/mol.
  • ^{Steiner, Thomas (2002). “The Hydrogen Bond in the Solid State”. Angew. Chem. Int. Ed. 41 (1): 48–76. doi:10.1002/1521-3773(20020104)41:1<48::AID-ANIE48>3.0.CO;2-U. PMID 12491444.} 
• This makes them somewhat stronger than a van der Waals interaction, and weaker than fully covalent or ionic bonds. This type of bond can occur in inorganic molecules such as water and in organic molecules like DNA and proteins. Hydrogen bonds are responsible for holding materials such as paper and felted wool together, and for causing separate sheets of paper to stick together after becoming wet and subsequently drying.

• The hydrogen bond is responsible for many of the abnormal physical and chemical properties of compounds of N, O, and F. In particular, intermolecular hydrogen bonding is responsible for the high boiling point of water (100 °C) compared to the other group-16 hydrides that have much weaker hydrogen bonds.
  • ^{Sabin, John R. (1971). “Hydrogen bonds involving sulfur. I. Hydrogen sulfide dimer”. J. Am. Chem. Soc. 93 (15): 3613–3620. doi:10.1021/ja00744a012.} 
• Intramolecular hydrogen bonding is partly responsible for the secondary and tertiary structures of proteins and nucleic acids. It also plays an important role in the structure of polymers, both synthetic and natural.
  • An intramolecular force (or primary forces) is any force that binds together the atoms making up a molecule or compound, not to be confused with intermolecular forces, which are the forces present between molecules.
    • ^{Zumdahl, Steven S.; Zumdahl, Susan A. (2007). Chemistry (7th ed.). Boston: Houghton Mifflin. ISBN 978-0618713707. OCLC 85824942} 
  • The subtle difference in the name comes from the Latin roots of English with inter meaning between or among and intra meaning inside.
    • ^{“Inter vs. Intra”. www.grammar.com. Retrieved 2018-04-26.} 
  • Chemical bonds are considered to be intramolecular forces, for example. These forces are often stronger than intermolecular forces, which are present between atoms or molecules that are not bonded.
    • The classical model identifies three main types of chemical bonds — ionic, covalent, and metallic — distinguished by the degree of charge separation between participating atoms.
      • ^{Oxtoby, David W.; Gills, H. P.; Campion, Alan (2012). Principles of modern chemistry (7th ed.). Belmont, Calif.: Brooks/Cole Cengage Learning. ISBN 978-0-8400-4931-5.} 
    • The characteristics of the bond formed can be predicted by the properties of constituent atoms, namely electronegativity. They differ in the magnitude of their bond enthalpies, a measure of bond strength, and thus affect the physical and chemical properties of compounds in different ways. % of ionic character is directly proportional difference in electronegitivity of bonded atom.^{[clarification needed]}
      • Ionic bond – An ionic bond can be approximated as complete transfer of one or more valence electrons of atoms participating in bond formation, resulting in a positive ion and a negative ion bound together by electrostatic forces.
        • ^{Bader, R. F. W.; Henneker, W. H. (1965). “The Ionic Bond”. Journal of the American Chemical Society. 87 (14): 3063–3068. doi:10.1021/ja01092a008} 
      • Electrons in an ionic bond tend to be mostly found around one of the two constituent atoms due to the large electronegativity difference between the two atoms (greater difference in electronegativity results in a stronger bond); this is often described as one atom giving electrons to the other. This type of bond is generally formed between a metal and nonmetal, such as sodium and chlorine in NaCl. Sodium would give an electron to chlorine, forming a positively charged sodium ion and a negatively charged chloride ion.
      • Covalent bond – In a true covalent bond, the electrons are shared evenly between the two atoms of the bond; there is little or no charge separation. Covalent bonds are generally formed between two nonmetals. There are several types of covalent bonds: in polar covalent bonds, electrons are more likely to be found around one of the two atoms, whereas in nonpolar covalent bonds, electrons are evenly shared. Homonuclear diatomic molecules are purely covalent. The polarity of a covalent bond is determined by the electronegativities of each atom and thus a polar covalent bond has a dipole moment pointing from the partial positive end to the partial negative end.
        • ^{Helmenstine, Anne Marie. “Understand What a Covalent Bond Is in Chemistry”. ThoughtCo.} 
      • Polar covalent bonds represent an intermediate type in which the electrons are neither completely transferred from one atom to another nor evenly shared.
      • Metallic bond – Metallic bonds generally form within a pure metal or metal alloy. Metallic electrons are generally delocalized; the result is a large number of free electrons around positive nuclei, sometimes called an electron sea.
    • Bonds are formed by atoms so that they are able to achieve a lower energy state. Free atoms will have more energy than a bonded atom. This is because some energy is released during bond formation, allowing the entire system to achieve a lower energy state. The bond length, or the minimum separating distance between two atoms participating in bond formation, is determined by their repulsive and attractive forces along the internuclear direction.
      • ^{Oxtoby, David W.; Gills, H. P.; Campion, Alan (2012). Principles of modern chemistry (7th ed.). Belmont, Calif.: Brooks/Cole Cengage Learning. ISBN 978-0-8400-4931-5.} 
    • As the two atoms get closer and closer, the positively charged nuclei repel, creating a force that attempts to push the atoms apart. As the two atoms get further apart, attractive forces work to pull them back together. Thus an equilibrium bond length is achieved and is a good measure of bond stability.
    • Biochemistry – Intramolecular forces are extremely important in the field of biochemistry, where it comes into play at the most basic levels of biological structures. Intramolecular forces such as disulfide bonds give proteins and DNA their structure. Proteins derive their structure from the intramolecular forces that shape them and hold them together. The main source of structure in these molecules is the interaction between the amino acid residues that form the foundation of proteins.
      •  ^{Nelson, David L.; Cox, Michael M.; Lehninger, Albert L. (2013). Lehninger principles of biochemistry (6th ed.). New York: W.H. Freeman and Company. ISBN9781429234146. OCLC824794893}
    • The interactions between residues of the same proteins forms the secondary structure of the protein, allowing for the formation of beta sheets and alpha helices, which are important structures for proteins and in the case of alpha helices, for DNA.

Definition

Hydrogen bond criterion

The hydrogen bond criterion for beta turns, applied to polypeptides whose amino acids are linked by trans peptide bonds, gives rise to just four categories, as shown by Venkatachalam in 1968. They are called types I, II, I’ and II’. All occur regularly in proteins and polypeptides but type I is most common, because it most resembles an alpha helix, occurring within 3₁₀ helices and at the ends of some classic alpha helices. Type II beta turns, on the other hand, often occur in association with beta-sheet as part of beta-links.

The four types of beta turn are distinguished by the φ, ψ angles of residues i+1 and i+2 as shown in the table below giving the typical average values. Glycines are especially common as amino acids with positive φ angles; for prolines such a conformation is sterically impossible but they occur frequently at amino acid positions where φ is negative.

	φi+1	ψi+1	φi+2	ψi+2
type I	-60	-30	-90	0
type II	-60	120	80	0
type I’	60	30	90	0
type II’	60	-120	-80	0

The main chain atoms of type I and I’ β turns are enantiomers (mirror images) of one another. So are the main chain atoms of type II and II’ β turns.

• Type I and II β turns exhibit a relationship to one another because they potentially interconvert by the process of peptide plane flipping (180° rotation of the CONH peptide plane with little positional alteration to side chains and surrounding peptides). The same relationship exists between type I’ and II’ β turns. Some evidence has indicated that these interconversions occur in beta turns in proteins such that crystal or NMR structures merely provide a snapshot of β turns that are, in reality, interchanging.
  • ^{Hayward, S (2001). “Peptide plane flipping in proteins”. Protein Science. 10 (11): 2219–2227. doi:10.1110/ps.23101. PMC 2374056. PMID 11604529.} 
• In proteins in general all four beta turn types occur frequently but I is most common, followed by II, I’ and II’ in that order. Beta turns are especially common at the loop ends of beta hairpins; they have a different distribution of types from the others; type I’ is the most common, followed by types II’, I and II.

• Asx turns and ST turns resemble beta turns except that residue i is replaced by the side chain of an aspartate, asparagine, serine or threonine. The main chain–main chain hydrogen bond is replaced by a side chain–main chain hydrogen bond. 3D computer superimposition shows that, in proteins, they occur
  • ^{Duddy, WM; Nissink JWM (2004). “Mimicry by asx- and ST-turns of the four main types of β turn in proteins”. Protein Science. 13 (11): 3051–3055. doi:10.1110/ps.04920904. PMC 2286581. PMID 15459339.} 
• as one of the same four types that beta turns do, except that their relative frequency of occurrence differs: type II’ is the most common, followed by types I, II and I’.

Distance criterion

Apart from the type I, I’,II and II’ beta turns as identified via the hydrogen bond criterion, non-hydrogen-bonded beta-turns named type VIII often occur. Three other, fairly rare, types of beta turn have been identified in which the peptide bond between residues i+1 and i+2 is cis rather than trans; these are named types VIa1, VIa2 and VIb. Another category, type IV, was used for turns not belonging to any of the above. Further details of these turns are given in turn (biochemistry).

External links

Two websites are available for finding and examining hydrogen-bonded beta turns in proteins:

• Motivated Proteins 
  • ^{Leader, DP; Milner-White EJ (2009). “Motivated Proteins: A web application for studying small three-dimensional protein motifs”. BMC Bioinformatics. 10 (1): 60. doi:10.1186/1471-2105-10-60. PMC 2651126. PMID 19210785.}
• PDBeMotif 
  • ^{Golovin, A; Henrick K (2008). “MSDmotif: exploring protein sites and motifs”. BMC Bioinformatics. 9 (1): 312. doi:10.1186/1471-2105-9-312. PMC 2491636. PMID 18637174}

Categories: 

• Protein structural motifs

From Wikipedia where the main page was last updated June 6, 2022