Conformational and Sequence Signatures in β Helix Proteins

Abstract

beta helix proteins are characterized by a repetitive fold, in which the repeating unit is a beta-helical coil formed by three strand segments linked by three loop segments. Using a data set of left- and right-handed beta helix proteins, we have examined conformational features at equivalent positions in successive coils. This has provided insights into the conformational rules that the proteins employ to fold into beta helices. Left-handed beta helices attain their equilateral prism fold by incorporating "corners" with the conformational sequence P(II)-P(II)-alpha(L)-P(II), which imposes sequence restrictions, resulting in the first and third P(II) residues often being G and a small, uncharged residue (V, A, S, T, C), respectively. Right-handed beta helices feature mid-sized loops (4, 5, or 6 residues) of conserved conformation, but not of conserved sequence; they also display an alpha-helical residue at the C-terminal end of L2 loops. Backbone conformational parameters (phi,psi) that permit the formation of continuous, loopless beta helices (Perutz nanotubes) have also been investigated.

Simulation of the β‐ to α‐sheet transition results in a twisted sheet for antiparallel and an α‐nanotube for parallel strands: Implications for amyloid formation

“…It has a diameter of 25 Å. The angles are different to the angles given by Iengar et al ,36 (160°, −170°) i , (−161°, 168°) i +1 in that the ϕ and ψ angles are swapped around.…”

Heterologous Stacking of Prion Protein Peptides Reveals Structural Details of Fibrils and Facilitates Complete Inhibition of Fibril Growth

“…Because the rungs are taken out of the structural context and to satisfy the ideal left-handed ␤-helix motif, mutations were introduced in rung 6. The Met on position 6 was replaced by a Gly, being the most prevalent residue at that position in ideal left-handed ␤-helices (30). The Asn at position 3 of rung 6 forms a hydrogen bond with a residue from rung 5, which is not a part of the structure anymore; therefore, it was replaced by Thr an ideal alternative at this position.…”

β arcades: recurring motifs in naturally occurring and disease‐related amyloid fibrils

“…Less is known about the interactions of ␤ arcs, as structural data on fibrils are not yet sufficiently detailed to define the arc conformations. The most reliable source of information on these conformations comes from crystal structures of ␤-solenoids (16,42,48,49). Analysis of these structures has revealed that ␤ arcs assume a limited number of preferred conformations, which are coded by different sequence motifs (42).…”