Peptide plane flipping is a type of

conformational change In biochemistry, a conformational change is a change in the shape of a macromolecule, often induced by environmental factors. A macromolecule is usually flexible and dynamic. Its shape can change in response to changes in its environment or oth ...

that can occur in

protein Proteins are large biomolecules and macromolecules that comprise one or more long chains of amino acid residues. Proteins perform a vast array of functions within organisms, including catalysing metabolic reactions, DNA replication, respo ...

s by which the

dihedral angle A dihedral angle is the angle between two intersecting planes or half-planes. In chemistry, it is the clockwise angle between half-planes through two sets of three atoms, having two atoms in common. In solid geometry, it is defined as the u ...

s of adjacent

amino acid Amino acids are organic compounds that contain both amino and carboxylic acid functional groups. Although hundreds of amino acids exist in nature, by far the most important are the alpha-amino acids, which comprise proteins. Only 22 alpha a ...

s undergo large-scale rotations with little displacement of the

side chain In organic chemistry and biochemistry, a side chain is a chemical group that is attached to a core part of the molecule called the "main chain" or backbone. The side chain is a hydrocarbon branching element of a molecule that is attached to a ...

s. 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 ψ_''i'' angle of residue ''i'' and the φ_''i+1'' angle of residue ''i+1'' remain roughly constant; in effect, the flip is a

crankshaft A crankshaft is a mechanical component used in a piston engine to convert the reciprocating motion into rotational motion. The crankshaft is a rotating shaft containing one or more crankpins, that are driven by the pistons via the connecting r ...

move about the axis defined by the C^α-C¹ and N-C^α 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. For example, peptide flips have been described as significant in the catalytic cycle of

flavodoxin Flavodoxins (Fld) are small, soluble electron-transfer proteins. Flavodoxins contains flavin mononucleotide as prosthetic group. The structure of flavodoxin is characterized by a five-stranded parallel beta sheet, surrounded by five alpha helices. T ...

and in the formation of

amyloid Amyloids are aggregates of proteins characterised by a fibrillar morphology of 7–13 nm in diameter, a beta sheet (β-sheet) secondary structure (known as cross-β) and ability to be stained by particular dyes, such as Congo red. In the hum ...

structures, where their ability to provide a low-energy pathway between

beta sheet The beta sheet, (β-sheet) (also β-pleated sheet) is a common motif of the regular protein secondary structure. Beta sheets consist of beta strands (β-strands) connected laterally by at least two or three backbone hydrogen bonds, forming a ge ...

and the so-called alpha sheet conformation is suggested to facilitate the early stages of amyloidogenesis. Peptide plane flipping may also be significant in the early stages of

protein folding Protein folding is the physical process by which a protein chain is translated to its native three-dimensional structure, typically a "folded" conformation by which the protein becomes biologically functional. Via an expeditious and reproduc ...

In crystallography

In protein structures determined by

X-ray crystallography X-ray crystallography is the experimental science determining the atomic and molecular structure of a crystal, in which the crystalline structure causes a beam of incident X-rays to diffract into many specific directions. By measuring the angles ...

, poor peptide-plane geometry has been described as a common problem; many structures need correction by peptide-plane flips or peptide bond flips.

References

Protein structure {{biochem-stub