A-Helix stability

Fig. 2. Protein secondary stmcture (a) the right-handed a-helix, stabilized by intrasegmental hydrogen-bonding between the backbone CO of residue i and the NH of residue t + 4 along the polypeptide chain. Each turn of the helix requires 3.6 residues. Translation along the hehcal axis is 0.15 nm per residue, or 0.54 nm per turn and (b) the -pleated sheet where the polypeptide is in an extended conformation and backbone hydrogen-bonding occurs between residues on adjacent strands. Here, the backbone CO and NH atoms are in the plane of the page and the amino acid side chains extend from C ...

Fig. 1. The two principal elements of secondary stmcture in proteins, (a) The a-helix stabilized by hydrogen bonds between the backbone of residue i and i + 4. There are 3.6 residues per turn of helix and an axial translation of 150 pm per residue. represents the carbon connected to the amino acid side chain, R. (b) The P sheet showing the hydrogen bonding pattern between neighboring extended -strands. Successive residues along the chain point...

Vila, J. A., Ripoll, D. R., and Scheraga, H. A. (2000). Physical reasons for the unusual a helix stabilization afforded by charged or neutral polar residues in alanine-rich peptides. Proc. Natl. Acad. Sd. USA 97, 13075-13079. 

Amino Acid Sequence Affects a Helix Stability... 

Table 2. Formation of the a-helix Stabilizing, destabilizing and breaking off amino acids...

Yun, R.H., Anderson, A. Hermans, J. (1991) Proline in a-helix stability and conformation studied by dynamics simulation. Proteins Struct. Funct. Genet. 10, 219-228. 

Liu J, Wang D, Zheng Q et al (2008) Atomic structure of a short a-helix stabilized by a main chain hdrogen surrogate. J Am Chem Soc 130 4334 -337... 

Domain 3 stretches from amino acids 463 (432) to 645 (589) and corresponds to exons 5, 6, and 7. The core of domain 3 is again a single a-helix stabilized by intrahelix salt bridges. The sequence from 565 (509) to 621 (565) is 43% identical to the amino acids 90-146 of rabbit skeletal muscle troponin T, which is a TM binding site in troponin T. Domain 4 stretches from 646 (590) to the C terminus and corresponds to exons 8-13. This is an extended and stably folded region that contains little regular secondary structure (Levine et al.,... 

The molecule is amphipathic with one flexible loop between residues 4 and 12, a helix from residues 15 to 23, and an antiparallel sheet (residues 24-31 and 34-40). The insect defensins are structurally similar to peptides such as charybdotoxin that contain an a-helix stabilized by cysteine bridges... 

Finally, loop VII links His-118 of strand 7 with Ala-143 of strand 8. Loop VII (GIu-119-Leu-142) is made of two antiparallel stretches joined by a wide turn. This loop forms a lid for the active site with its two antiparallel sides. Loop VII contains the only portion of a-helix present in SOD (residues 131-136) (see Fig. 2). It is a six-residue-long a-helix stabilized by only two main-chain H bonds, whereas the six side-chain to main-chain H bonds distort it fi om the ideal conformation. Alternatively, this short helical region can be described as formed by a series of five interpenetrating tight turns 41a). 

R. H. Yun, A. G. Anderson, and J. Hermans, Proteins Struct. Funct. Genet., 10,219 (1991). Proline in a-Helix Stability and Conformation Studied by Dynamics Simulation. 

Poly(a-amino acids) serve as model substances for proteins. In the solid state, they occur in two forms. The a-form is a helix stabilized by intramolecular hydrogen bonding (see also Section 4.2.1). The )8-form has the pleated sheet structure (see also Figure 5.10). Because of intermolecular hydrogen bonding, this form is infusible and insoluble. The a form yields wool-like, the j3-form silklike fibers. 

Figure 10.4 Cartoon presentation of four different a-helix stabilization strategies.

In 1998, Grubbs and coworkers published an a-helix stabilization attempt through 0-allyl serine residues located on adjacent helical turns, via ruthenium-catalyzed ring closing metathesis (RCM) [56] unfortunately, this study did not result in enhanced a-helical structure stabilization. Subsequently, Verdine and coworkers advanced this idea by introducing two alpha-olefin substituted... 

It is well known that molecules of PBG in a numbo of solvents (called coiling solvents) exist in the form of a-helixes stabilized by intramolecular hydrogen bonds. Separation of the solution into isotropic and anisotropic phases is observed in these solvents (such as dioxane, chloroform, methylene chloride, etc.) for a certain critical concentration of the polypeptide (c ) in accordance with the theoretical concepts of Flory [3] (see also Chapter 1). The anisotropic phase in a solution of PBG is separated as liquid spherulites which become larger and form a continuous anisotropic phase of the cholesteric type in cooling or concentration of the solution. 

---