Peptide plane flipping

Peptide plane flipping is a type of conformational change that can occur in proteins by which the dihedral angles of adjacent amino acids undergo large-scale rotations with little displacement of the side chains. The plane flip is defined as a rotation of the dihedral angles φ,ψ at amino acids i and i+1 such that the resulting angles remain in structurally stable regions of Ramachandran space. The key requirement is that the sum of the ψi angle of residue i and the φi+1 angle of residue i+1 remain roughly constant; in effect, the flip is a crankshaft move about the axis defined by the Cα-C¹ and N-Cα bond vectors of the peptide group, which are roughly parallel. As an example, the type I and type II beta turns differ by a simple flip of the central peptide group of the turn.

In protein dynamics

The significance of peptide plane flips in the dynamics of the native state has been inferred in some proteins by comparing crystal structures of the same protein in multiple conformations.[1] For example, peptide flips have been described as significant in the catalytic cycle of flavodoxin[2] and in the formation of amyloid structures, where their ability to provide a low-energy pathway from alpha sheet or left-handed alpha helix to beta strand conformations may facilitate the early stages of amyloidogenesis.[3][4][5] Peptide plane flipping may also be significant in the early stages of protein folding.[1]

In crystallography

In protein structures determined by X-ray crystallography, poor peptide-plane geometry has been described as a common problem; many structures in the Protein Data Bank can be identified as needing correction by peptide-plane flips or cis-trans peptide bond isomerization.[6] Conformational diversity in the form of plane flips can sometimes be detected in electron density maps.[7]

References

  1. 1 2 Hayward, S. (2001). "Peptide-plane flipping in proteins". Protein Sci 10 (11): 2219–27. doi:10.1110/ps.23101. PMC 2374056. PMID 11604529.
  2. ↑ Ludwig, ML; Pattridge, KA; Metzger, AL; Dixon, MM; Eren, M; Feng, Y; Swenson, RP (11 February 1997). "Control of oxidation-reduction potentials in flavodoxin from Clostridium beijerinckii: the role of conformation changes.". Biochemistry 36 (6): 1259–80. PMID 9063874.
  3. ↑ Milner-White, JE; Watson, JD; Qi, G; Hayward, S (September 2006). "Amyloid formation may involve alpha- to beta sheet interconversion via peptide plane flipping.". Structure (London, England : 1993) 14 (9): 1369–76. PMID 16962968.
  4. ↑ Daggett, V. (2006). "Alpha-sheet: The toxic conformer in amyloid diseases?". Acc Chem Res 39 (9): 594–602. doi:10.1021/ar0500719. PMID 16981675.
  5. ↑ Armen, RS; DeMarco, ML; Alonso, DO; Daggett, V. (2004). "Pauling and Corey's α-pleated sheet structure may define the prefibrillar amyloidogenic intermediate in amyloid disease". Proc Natl Acad Sci USA 101 (32): 11622–7. doi:10.1073/pnas.0401781101. PMC 511030. PMID 15280548.
  6. ↑ Touw, WG; Joosten, RP; Vriend, G (August 2015). "Detection of trans-cis flips and peptide-plane flips in protein structures.". Acta crystallographica. Section D, Biological crystallography 71 (Pt 8): 1604–14. PMID 26249342.
  7. ↑ Keedy, DA; Fraser, JS; van den Bedem, H (October 2015). "Exposing Hidden Alternative Backbone Conformations in X-ray Crystallography Using qFit.". PLoS computational biology 11 (10): e1004507. PMID 26506617.


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