Walker motifs

The Walker A and Walker B motifs are protein sequence motifs, now known to have highly conserved three-dimensional structures. These were first reported in ATP-binding proteins by Walker and co-workers in 1982.

Walker A motif

Walker A motif, also known as the Walker loop or P-loop (phosphate-binding loop) is a motif in proteins that is associated with phosphate binding. The motif has the pattern G-x(4)-GK-[TS], where G, K, T and S denote glycine, lysine, threonine and serine residues respectively, and x denotes any amino acid. It is present in many ATP or GTP utilizing proteins; it is the β phosphate of the nucleotide that is bound. The lysine (K) residue in the Walker A motif, together with the main chain NH atoms, are crucial for nucleotide-binding. It is a glycine-rich loop preceded by a beta strand and followed by an alpha helix; these features are typically part of an α/β domain with four strands sandwiched between two helices on each side. The phosphate groups of the nucleotide are also coordinated to a magnesium ion.

Quasigroup

In mathematics, especially in abstract algebra, a quasigroup is an algebraic structure resembling a group in the sense that "division" is always possible. Quasigroups differ from groups mainly in that they need not be associative.

A quasigroup with an identity element is called a loop.

Definitions

There are at least two equivalent formal definitions of quasigroup. One defines a quasigroup as a set with one binary operation, and the other, from universal algebra, defines a quasigroup as having three primitive operations. We begin with the first definition.

A quasigroup (Q, ∗) is a set, Q, with a binary operation, ∗, (that is, a magma), obeying the Latin square property. This states that, for each a and b in Q, there exist unique elements x and y in Q such that both

hold. (In other words: Each element of the set occurs exactly once in each row and exactly once in each column of the quasigroup's multiplication table, or Cayley table. This property ensures that the Cayley table of a finite quasigroup is a Latin square.)

Loop (knot)

In reference to knots, loop may refer to:

References

Turn (biochemistry)

A turn is an element of secondary structure in proteins where the polypeptide chain reverses its overall direction. For beta turns go to Beta turn.

Definition

According to one definition, a turn is a structural motif where the C^α atoms of two residues separated by few (usually 1 to 5) peptide bonds are close (< 7 Å), while the residues do not form a secondary structure element such as an alpha helix or beta sheet with regularly repeating backbone dihedral angles. Although the proximity of the terminal C^α atoms usually correlates with formation of a hydrogen bond between the corresponding residues, a hydrogen bond is not a requirement in this turn definition. That said, in many cases the H-bonding and C^α-distance definitions are equivalent.

Types of turns

Turns are classified according to the separation between the two end residues:

In an α-turn the end residues are separated by four peptide bonds ().

In a β-turn (the most common form), by three bonds ().

In a γ-turn, by two bonds ().