Helical conformation side-chain packing

Protein structures are so diverse that it is sometimes difficult to assign them unambiguously to particular structural classes. Such borderline cases are, in fact, useful in that they mandate precise definition of the structural classes. In the present context, several proteins have been called //-helical although, in a strict sense, they do not fit the definitions of //-helices or //-solenoids. For example, Perutz et al. (2002) proposed a water-filled nanotube model for amyloid fibrils formed as polymers of the Asp2Glni5Lys2 peptide. This model has been called //-helical (Kishimoto et al., 2004 Merlino et al., 2006), but it differs from known //-helices in that (i) it has circular coils formed by uniform deformation of the peptide //-conformation with no turns or linear //-strands, as are usually observed in //-solenoids and (ii) it envisages a tubular structure with a water-filled axial lumen instead of the water-excluding core with tightly packed side chains that is characteristic of //-solenoids. 

The linker between helix and strand (H-L3-E) has one major sub-cluster. The first residue is mostly Gly and the second is hydrophobic with significant population of Ala residues, liie side chain of the centi linker residue points outwards but the carbonyl oxygen of L2 points inside the space between the packed helices (Figure 7), nu g this different from those observed in H-L3-H or E-L3-E linkers. The linker E-L3-H that links strands and helices has two major clusters and descriptions of backbone conformations are listed in Table n. The third linker residue L3 of the first sub-cluster has x, of g conformation. For the second sub-cluster, L2 has main chain conformation and g side chain conformationand L3 has extended backbone conformation and g side chain conformation. 

Hydrophobic homopolypeptides are stable in their a-helical conformation at the air/water surface. a-Helices are adsorbed with their long axis parallel to the water surface, the long axis being predominantly perpendicular to the direction of compression. Poly-L-alanine and poly-L-leucine pack together in the form of a-helices on the water surfaces. Inflection points appeared at 12.8 A and 17.0 A per residue. The a-helices are organized in such a way that their side-chains are interdigitated (Figure 6.16) . ... 

X-Ray crystallographic analysis of two crystalline forms of tetrameric melittin showed that the conformation of the peptide is essentially the same in each form. " Melittin was found to adopt a helical conformation in the crystalline state. The presence of Pro-14 also caused the helix to bend with an angle of about 120° between residues 1-10 and 16-26. The large helix bend allows for the optimal packing of hydrophobic side-chains vnthin the tetramer. Melittin provides a rare example of a membrane-bound peptide whose structure has been determined in low dielectric solvents, micelles and in the crystalline state and found to be quite similar. The similarities of these structures lends confidence to the idea that they represent good models for the membrane-bound conformation. ... 

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