Alpha Helix

12 Key excerpts on "Alpha Helix"

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  Biochemistry, International Adaptation

  • Donald Voet, Judith G. Voet(Authors)
  • 2023(Publication Date)
  • Wiley

    (Publisher)

  The α Helix Only one helical polypeptide conformation has simultane- ously allowed conformation angles and a favorable hydro- gen bonding pattern: the α helix (Fig. 7-11), a particularly rigid arrangement of the polypeptide chain. Its discovery through model building, by Pauling in 1951, ranks as one of the landmarks of structural biochemistry. For a polypeptide made from l-α-amino acid residues, the α helix is right handed with torsion angles ϕ = –57° and ψ = –47°, n = 3.6 residues per turn, and a pitch of 5.4 Å. (An α helix of d-α-amino acid residues is the mirror image of that made from l-amino acid residues: It is left handed with conformation angles ϕ = +57°, ψ = +47°, and n = –3.6 but with the same value of p.) Figure 7-11 indicates that the hydrogen bonds of an α helix are arranged such that the peptide N—H bond of the nth residue points along the helix toward the peptide C O group of the (n – 4)th residue. This results in a strong hydro- gen bond that has the nearly optimum N · · · O distance of 2.8 Å. In addition, the core of the α helix is tightly packed; that is, its atoms are in van der Waals contact across the helix, thereby maximizing their association energies (Sec- tion 7-4Ab). The R groups, whose positions, as we saw, are not fully dealt with by the Ramachandran diagram, all pro- ject backward (downward in Fig. 7-11) and outward from the helix so as to avoid steric interference with the poly- peptide backbone and with each other. Such an arrange- ment can also be seen in Fig. 7-12. Indeed, a major reason why the left-handed α helix has never been observed (its helical parameters are but mildly forbidden; Fig. 7-7) is that its side chains contact its polypeptide backbone too closely. Note, however, that 1 to 2% of the individual non-Gly resi- dues in proteins assume this conformation (Fig. 7-8). The α helix is a common secondary structural element of both fibrous and globular proteins.

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  Molecular Biology

  • David P. Clark(Author)
  • 2009(Publication Date)
  • Academic Cell

    (Publisher)

  Fig. 7.06 ), a single polypeptide chain is coiled into a right-handed helix and the hydrogen bonds run vertically up and down, parallel to the helix axis. In fact, the hydrogen bonds in an α-helix are not quite parallel to the axis. They are slightly tilted relative to the helix axis because there are 3.6 amino acids per turn rather than a whole number. The pitch (repeat length) is 0.54 nm and the rise per residue is about 0.15 nm.

  Figure 7.06 The Alpha Helix A) The general shape of an α-helix. B) The carbon backbone of the polypeptide chain. C) The hydrogen bonds between peptide groups.

  Hydrogen bonding is responsible for the formation of alpha-helix and beta-sheet structures in proteins.

  The hydrogen bonds hold successive twists of the helix together and run from the C˭O group of one amino acid to the NH group of the fourth amino acid residue down the chain. The α-helix is very stable because all of the peptide groups (—CO—NH—) take part in two hydrogen bonds, one up and one down the helix axis. A right-handed helix is most stable for L - amino acids.(A stable helix cannot be formed with a mixture of D - and L - amino acids, although a stable left-handed helix could theoretically be formed from D - amino acids).

  The R-groups extend outwards from the tightly packed helical polypeptide backbone. Of the 20 amino acids, Ala, Glu, Leu and Met are good α-helix formers but Tyr, Ser, Gly and Pro are not. Proline is totally incompatible with the α-helix, due to its rigid ring structure. Furthermore, when proline resides are incorporated, no hydrogen atoms remain on the nitrogen atom that takes part in peptide bonding. Consequently, proline residues interrupt hydrogen-bonding patterns. In addition, two bulky residues or two residues with the same charge that lie next to each other in the polypeptide chain will not fit properly into an α-helix. Overall, the α-helix forms a solid cylindrical rod.

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  Essential Microbiology

  • Stuart Hogg(Author)
  • 2013(Publication Date)
  • Wiley-Blackwell

    (Publisher)

  A stable helix is formed by the –NH group of an amino acid bonding to the –CO group of the amino acid four residues further along the chain (Fig- ure 2.16a). This causes the chain to twist into the characteristic helical shape. One turn of the helix occurs every 3.6 amino acid residues, and results in a rise of 5.4 ˚ A; this is called the pitch height of the helix. The ability to form a helix like this is dependent on the component amino acids; if there are too many with large R-groups, or R-groups carrying the same charge, a stable helix will not be formed. Because of its rigid structure, proline (see Figure 2.13) cannot be accommodated in an α-helix. Naturally occurring α-helices are always right- handed, that is, the chain of amino acids coils round the central axis in a clock- wise direction. This is a much more stable configuration than a left-handed helix, due to the fact that there is less steric hindrance (overlapping of elec- tron clouds) between the R-groups and the C=O group on the peptide back- bone. (Note that if proteins were made up of the D-form of amino acids, we would have the reverse situation, with a left-handed form favoured). In the β-pleated sheet, the hydrogen bonding occurs between amino acids either on 2.3 BIOMACROMOLECULES 39 =5.4Å ´ Hydrogen bonding (a) (b) Pitch height Figure 2.16 Secondary structure in proteins: the α-helix and β-pleated sheet. (a) Hydrogen bonding between amino acids four residues apart in the primary sequence results in the formation of an α-helix. (b) In the β-pleated sheet hydrogen bonding joins adjacent chains. Note how each chain is more fully extended than in the α-helix. In the example shown, the chains run in the same direction (parallel). separate polypeptide chains or on residues on the same chain but far apart in the primary structure (Figure 2.16b). The chains in a β-pleated sheet are fully extended, with 3.5 ˚ A between adjacent amino acid residues (cf. α-helix, 1.5 ˚ A).

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  Proteins

  Concepts in Biochemistry

  • Paulo Almeida(Author)
  • 2016(Publication Date)
  • Garland Science

    (Publisher)

  “And then I looked to see if I could form hydrogen bonds from one part of the chain to the next.” Folding the strip of paper to a helix, Pauling realized that hydrogen bonds could be established between the amide C == O group of a residue ( i ) and the amide N −− H of another ( i + 4), four residues away along the polypeptide chain (see Figure 2.42). Pauling had discovered the α -helix. The simplicity of his paper model, however, hides Pauling’s deep knowledge of chemistry, and the importance of structure, of which he was well aware. Later, he told Judson, “We got the Alpha Helix, you know, and Bragg and Perutz and Kendrew were trying to do the same thing, and they—ah, failed— because of, really, a lack of knowledge of the principles of chemistry, of structural chemistry.” The α -helix, shown in several representations in Figure 2.43 , is one of the most common types of secondary structure found in pro-teins. On average there are 3.6 residues per turn of the helix and the rise per residue is 1.5 Å, which means that the rise per turn, or the pitch of the helix, is 5.4 Å. The α -helix is stabilized by hydro-gen bonds between the amide C == O group of residue i and the amide N −− H group of residue i + 4. The hydrogen bond length in the helix is about 2.8 Å (distance between the heavy atoms, N and O). The common L amino acids preferentially form a right-handed α -helix. Its mirror 58 Chapter 2 PROTEIN STRUCTURE Figure 2.43 The right-handed α -helix, in three different representations. The N-terminus is at the bottom and the C-terminus on top. (A) Stick model; (B) sticks and cartoon (ribbon); (C) ribbon structure only. The carbonyl groups of the peptide groups are pointing up, whereas the amide protons (NH) are pointing down. Model: glycophorin A (PDB 1MSR), a membrane protein of the red blood cell. (A) (B) (C) image, the left-handed α -helix, would be preferred by D amino acids.

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  The Molecular Fabric of Cells

  • BIOTOL, B C Currell, R C E Dam-Mieras(Authors)
  • 2013(Publication Date)
  • Butterworth-Heinemann

    (Publisher)

  This is why the a-helix occurs frequently, whilst other configurations do not. The a-helix is a right-handed helix in which there are 3.6 amino acid residues per turn of the helix (Figure 3.13). This gives a pitch of 0.54nm for one complete turn of the helix. The -carbon atom to -carbon atom distance along the helix axis is 0.15nm. These dimensions are consistent with the repeat distances found for -keratin. These particular dimensions mean that both the carbonyl and amide groups of the peptide bond point along the helix axis and are almost perfectly positioned to form hydrogen bonds. 56 Chapter 3 Figure 3.13 The a- helix, found in many proteins. Only the carbon and nitrogen atoms of the peptide core are shown. See text for detailed description. The repeating structure of the a-helix means that bond angles adopted by those bonds which can rotate are reasonably uniform. Thus the angle of the carbonyl carbon to -carbon atom bond (known as ) is the same for each residue in an a-helix. Similarly, the angle of the amide nitrogen to -carbon atom bond (identified as ) is also constant from residue to residue, although it differs from that of . influence of Sidechain groups stick out from the helix. Since hydrogen bonding is maximised, sidechains on polypeptides would be expected to form -helices, providing other factors do not S ^ucture interfere. These include possible interactions between sidechains or difficulty in adopting the required bond angles on either side of the -carbon atom. The first point is illustrated by studies on the conformation of synthetic polypeptides composed of a single amino acid such as L-glutamic acid or L-lysine. Conformation changes can be studied by techniques based on optical rotation of plane polarised light. Since polypeptides are composed of L-amino acid residues, each amino acid residue contains an asymmetric centre (except glycine) and, as a consequence, will rotate plane polarised light.

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  Introduction to Protein Structure

  • Carl Ivar Branden, John Tooze(Authors)
  • 2012(Publication Date)
  • Garland Science

    (Publisher)

  Within each class the structures are arranged in superfamilies according to their tertiary structure and, within the superfamilies, in families according to function and sequence homology. This database is freely available on the World Wide Web. Conclusion The interiors of protein molecules contain mainly hydrophobic side chains. The main chain in the interior is arranged in secondary structures to neu-tralize its polar atoms through hydrogen bonds. There are two main types of secondary structure, a helices and b sheets. Beta sheets can have their strands parallel, antiparallel, or mixed. Protein structures are built up by combinations of secondary structural elements, a helices, and b strands. These form the core regions—the interior of the molecule—and they are connected by loop regions at the surface. Schematic and simple topological diagrams where these secondary structure elements are highlighted are very useful and are frequently used. Alpha helices or b strands that are adjacent in the amino acid sequence are also usually adjacent in the three-dimensional structure. Certain combinations, called motifs, occur very frequently, including the helix-loop-helix motif and the hairpin motif. A DNA-binding helix-loop-helix motif and a calcium-bind-ing helix-loop-helix motif, each with its own specific geometry and amino acid sequence requirements, are used in many different proteins. The b -a -b motif, which consists of two parallel b strands joined by an a helix, occurs in almost all structures that have a parallel b sheet. Four anti-parallel b strands that are arranged in a specific way comprise the Greek key motif, which is frequently found in structures with antiparallel b sheets. Polypeptide chains are folded into one or several discrete units, domains, which are the fundamental functional and three-dimensional structural units.

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  The Language of Shape

  The Role of Curvature in Condensed Matter: Physics, Chemistry and Biology

  • S. Hyde, Z. Blum, T. Landh, S. Lidin, B.W. Ninham, S. Andersson, K. Larsson(Authors)
  • 1996(Publication Date)
  • Elsevier Science

    (Publisher)

  The other form is the planar peptide chain conformation, the β-sheet, where hydrogen bonds linking all carbonyl oxygens from one chain to all amide hydrogens of an adjacent chain, link neighbouring chains into a sheet. The peptide chains can either all have the same direction: a parallel β-sheet; or the directions can alternate, to give an antiparallel β-sheet (sometimes hybrids of these two types can occur). The amino acid residues from each β-strand point upwards and downwards in an alternating way in relation to the β-sheet. The β-sheet can thus be regarded as a surface separating one set of amino acid residues from another, and the curvature of this surface is a significant factor that determines protein molecular shape.

  All known protein structures contain domains consisting of a few types of folding patterns, which will be discussed in detail below. The relatively strong hydrogen-bond systems in α-helical and β-sheet regions, taken together with ionic bridges and disulphide bonds, can result in various deviations from the simple polar surface/non-polar core gross structure. We can regard these deviations as a “tuning” of the structure towards specific functions. Therefore hydrophobic regions exposed on the surface after a binding site for a non-polar molecule, and the changed energetic conditions after binding induce a conformational change of the peptide chain.

  An excellent review on protein structure containing clear diagrams of their topology is that of Brändén and Tooze [1 ]. Our introduction of curvature in the structural description given below is based on their classification of domains.

  6.2 α-helix domains

  This domain consists of a bundle of α-helices packed in pairs against each other. The most common arrangement is illustrated in Fig. 6.1 The space between the four helices is occupied by hydrophobic side chains, whereas polar side chains are directed towards the surrounding solution. The α-helices are twisted with respect to each other, and their arrangement is similar to that of a fragment of a blue phase (cf. Figure 5.5 ). In both cases, the chirality of the structural units leads to hyperbolic curvature within the aggregate.

  Figure 6.1 Four α-helices of an α-domain structure.

  (Adapted from [1 ].)

  The active site in this kind of structure is a pocket located on one side of the hydrophobic core at the end region of the helices.

  There is another group of important α-helix domains, which is the globin fold known from haem proteins. The haem group is located within a bundle of eight α-helices. It is interesting to note that the globin fold has been preserved during evolution. Comparative studies have shown that the mechanism behind the preservation of this fold during evolution is conservation of the hydrophobic character of the amino acid forming the core between helices [2

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  Introduction to Molecular Biology

  • S Bresler(Author)
  • 2012(Publication Date)
  • Academic Press

    (Publisher)

  In the first phase of the study of polypeptides it appeared that L -amino acids always form right helices. The investigation of proteins also indicated the presence of right-helical segments and attempts were made to generalize these findings. However, Blout and his co-workers succeeded in showing that a polypeptide composed of the benzyl ester of L -aspartic acid (poly-/?-benzyl -L -aspartate) forms a left helix although a less stable one than usual (33). We shall return to this problem in a future section (p. 58), but for the time being we shall assume that L -amino acids form a right Pauling-Corey helix, a notion consistent with the bulk of the experimental evidence. As an alternative to the α-helical structure with its characteristic intramolecular hydrogen bonds, Pauling and Corey considered the structure resulting from the forma-tion of intermolecular hydrogen bonds between different polypeptide chains (30, 34, 35). In this case, the polypeptide chains must be extended to their limit axially and laid either parallel or antiparallel with respect to one another (Fig. 1-13). This conformation is called the β-structure, or the β-pleated sheet. The side groups, R, project perpen-dicularly from the plane of the page in which the zigzag polypeptide backbones lie. Contrast this with the α-helix discussed above, where the side chains all fall on a cylindrical surface concentric with the helix axis (Fig. 1-10). A third type of ^-structure, called cross-β, can be formed intramolecularly if a single polypeptide molecule is folded back on itself so as to permit hydrogen bonding between separate segments of the chain. The task of differentiating the a- and ^-structures from one another experimentally is not an easy one. Optical criteria are in general ambiguous and they lead to a conclu-sion about the nature of polypeptide secondary structure only if they are used jointly. 36 I. Protein Structure Fig. l-13a 7. Secondary Structure of Polypeptides and Proteins 37 Fig.

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  Molecular and Protein Engineering

  • (Author)
  • 2014(Publication Date)
  • Academic Studio

    (Publisher)

  The shape into which a protein naturally folds is known as its native conformation. Although many proteins can fold unassisted, simply through the chemical properties of their amino acids, others require the aid of molecular chaperones to fold into their native states. Biochemists often refer to four distinct aspects of a protein's structure: • Primary structure : the amino acid sequence. • Secondary structure : regularly repeating local structures stabilized by hydrogen bonds. The most common examples are the Alpha Helix, beta sheet and turns. ____________________ WORLD TECHNOLOGIES ____________________ Because secondary structures are local, many regions of different secondary structure can be present in the same protein molecule. • Tertiary structure : the overall shape of a single protein molecule; the spatial relationship of the secondary structures to one another. Tertiary structure is generally stabilized by nonlocal interactions, most commonly the formation of a hydrophobic core, but also through salt bridges, hydrogen bonds, disulfide bonds, and even post-translational modifications. The term tertiary structure is often used as synonymous with the term fold . The tertiary structure is what controls the basic function of the protein. • Quaternary structure : the structure formed by several protein molecules (polypeptide chains), usually called protein subunits in this context, which function as a single protein complex. Proteins are not entirely rigid molecules. In addition to these levels of structure, proteins may shift between several related structures while they perform their functions. In the context of these functional rearrangements, these tertiary or quaternary structures are usually referred to as conformations, and transitions between them are called conformational changes. Such changes are often induced by the binding of a substrate molecule to an enzyme's active site, or the physical region of the protein that participates in chemical catalysis.

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  Amino Acids, Peptides and Proteins

  Volume 37

  • Etelka Farkas, Maxim Ryadnov(Authors)
  • 2012(Publication Date)
  • Royal Society of Chemistry

    (Publisher)

  Helix bundles are rationalised by the number of helices and the number of sub-oligomers in a given bundle giving rise to different motifs with topologies similar to those observed for all b structures. The lowest oligo-mers, two-helix bundles, tend to be unstable and dimerise into four-helix bundles, whereas three-, four and five helix bundles are common and very stable (Fig. 14). 59–61 Fig. 13 aa -corner-derived motifs. Schematic representations of minimal motifs as one-helix extensions of a aa -corner. Both directions of the polypeptide chain are possible for each structure (only one direction is shown) (adapted from A. V. Efimov, A structural tree for a -helical proteins containing a -a -corners and its application to protein classification, FEBS Lett. , 391 , 167, Copyright (1996), with permission from Elsevier). 57 Amino Acids, Pept. Proteins , 2012, 37 , 190–237 | 205 Helix bundles share many similarities with other folding motifs – coiled coils. 62–64 In the oligomerisation context coiled coils can be defined as bundles of unconnected helices as opposed to helix bundles that are typically single-stranded structures. The independence of coiled coils on loops and turns renders them very diverse and readily amenable to design (Fig. 15). 65–69 However, such independence requires another means of constraining helices into specific bundle formations. A unifying determinant to ensure this for all coiled coils is the interdigitation of side chains of adjacent helices in the interface of a bundle. Thus, it is the hydrophobic residues along each polypeptide chain that predominantly determine a particular coiled-coil architecture. Usually referred to as ‘‘knobs-into-holes’’ packing such an arrangement can be supported by different patterns, canonical and non-canonical (Fig. 16).

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  Conformation in Fibrous Proteins and Related Synthetic Polypeptides

  • R Fraser(Author)
  • 2012(Publication Date)
  • Academic Press

    (Publisher)

  The helix was assumed to be right-handed. Refinement of the model on the basis of the X-ray data was attempted and reasonable agreement between calculated and observed intensities was obtained for the equator. The agreement on other layer lines, however, was generally poor and the atomic coordinates cannot be regarded as being fully refined. 196 9. THE Alpha Helix (ii) ω-Helical Form. Takeda et aL (1970) further reported that when the α-helical form of [Asp(/>ClBzl)] n was heated to 190°C a different X-ray pattern was obtained which could be indexed on a tetragonal cell with side a = 23.3 A and an axial repeat of c = 5.20 A. It was concluded that the structure contained right-handed helices with exactly four residues per turn of pitch Ρ = 5.20 A and that the unit cell contained one up and one down chain. In view of the afore-mentioned change in helix sense in [Asp(Bzl)] n observed by Malcolm (1970), the assumption that the ω-helical form of [Asp(/>ClBzl)] n is right-handed is open to question. IV. OTHER POLYMERS a. Poly(S-benzylthio -L -cysteine) The polymer poly(S-benzylthio -L -cysteine), in which the side chain is —CH 2 —S—S—CH 2 —C 6 H 5 , was studied by Fraser et aL (1962a). No solvent could be found but oriented films were prepared by rolling and examined by X-ray diffraction. The pattern contained sharp reflec-tions which could be indexed on a tetragonal cell with edge a = 14.28 A and an axial repeat of c = 5.55 A. The tetragonal symmetry, together with the absence of meridional reflections except on the fourth layer line, indicated that the chains had a helical symmetry with u = 4 and ν = ±1. From density considerations only one chain could be accom-modated in the unit cell and the conformation of the main chain was presumed to be similar to that observed in the ω form of [Asp(Bzl)] n . The helix sense in this polymer is not known. b. Poly (L -tryptophan) Peggion et al.

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  Microcalorimetry of Macromolecules

  The Physical Basis of Biological Structures

  • Peter L. Privalov(Author)
  • 2012(Publication Date)
  • Wiley

    (Publisher)

  5 THE α-HELIX AND α-HELICAL COILED-COIL

  5.1. THE α-HELIX

  5.1.1. Calorimetric Studies of α-Helix Unfolding–Refolding

  The α-helix is the simplest regular structure formed by polypeptides without stresses and stabilized, as believed after Pauling et al. (1951), just by the hydrogen bonds between the –CO of the i th peptide unit and the –NH group of the (i  + 4)th peptide units (Fig. 4.8). Thus, it seemed that by analyzing the folding and unfolding of the α-helix one could determine the thermodynamic characteristics of hydrogen bonding in aqueous solution. However, the very first experiments showed that investigation of the folding–unfolding of the isolated α-helix is far from being so simple: the single α-helix is marginally stable and its folding–unfolding proceeds over a very broad temperature range: invariably it starts well below 0°C and ends well above 100°C. Therefore, unfolding of the α-helix does not appear to be a highly cooperative process, but is likely to propagate stepwise from both of its ends. Since it cannot be considered as a two-state transition, the temperature-induced unfolding of an α-helix cannot be analyzed using the van’t Hoff equation to determine the enthalpy of this process. Various theoretical models have been proposed to describe unfolding of an α-helix (Zimm and Bragg, 1959; Lifson and Roig, 1961), but these models are all based on assumptions that, in themselves, require justification by comparing the calculated thermodynamic characteristics, particularly the unfolding enthalpy, with the directly measured ones. Therefore, direct calorimetric measurement of the enthalpy of unfolding of the isolated α-helix has acquired a special importance.

  The first calorimetric estimates of the enthalpy of α-helix folding were done on ionizable polypeptides that form random coils when fully ionized, fold into an α-helix under pH conditions of partial ionization, and aggregate when fully uncharged. Using an isothermal reaction calorimeter, Rialdi and Hermans (1966) measured the heat effect upon acidification of the poly-L-glutamate solution (Fig. 5.1

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