Peptide plane flipping
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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[edit]
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 between beta sheet and the so-called alpha sheet conformation is suggested to 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[edit]
In protein structures determined by X-ray crystallography, poor peptide-plane geometry has been described as a common problem; many structures need correction by peptide-plane flips or peptide bond flips.[6]
References[edit]
- ^ a b Hayward, S. (2001). "Peptide-plane flipping in proteins". Protein Sci. 10 (11): 2219–27. doi:10.1110/ps.23101. PMC 2374056. PMID 11604529.
- ^ 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. doi:10.1021/bi962180o. PMID 9063874.
- ^ 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. 14 (9): 1369–76. doi:10.1016/j.str.2006.06.016. PMID 16962968.
- ^ Daggett, V. (2006). "Alpha-sheet: The toxic conformer in amyloid diseases?". Acc Chem Res. 39 (9): 594–602. doi:10.1021/ar0500719. PMID 16981675.
- ^ 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. Bibcode:2004PNAS..10111622A. doi:10.1073/pnas.0401781101. PMC 511030. PMID 15280548.
- ^ Touw, WG; Joosten, RP; Vriend, G (August 2015). "Detection of trans-cis flips and peptide-plane flips in protein structures". Acta Crystallographica Section D. 71 (Pt 8): 1604–14. doi:10.1107/S1399004715008263. PMC 4528797. PMID 26249342.
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