Motif and Folds of Protein Structure in Biology

Protein motifs are tiny areas of three-dimensional structure or amino acid sequence that are common by several proteins. They are recognised areas of protein structure that are characterised (or not) by a specific chemical or biological activity. A protein fold, such as helix bundle, beta-barrel, Rossman fold, or other “folds” included in the Structural Classification of Proteins database, refers to a generic characteristic of protein architecture.

The Motif of Protein structure

A structural motif is a typical three-dimensional structure that arises in a range of diverse, evolutionarily unrelated biological entities, such as proteins or nucleic acids.  A structural motif does not have to be coupled with a sequence motif; it might be represented by multiple sequences in different proteins or RNA.

Nucleic acids can generate a number of structural motifs that are hypothesised to have biological importance depending on the sequence and other facts.

Step-loop

Intramolecular stem-loop base pairing is a pattern found in single-stranded DNA and, more typically, RNA.  A hairpin or hairpin loop is another name for the construction. When two portions of the same strand, which are generally complementary in nucleotide sequence when read in opposing directions, base-pair to form a double helix that terminates in an unpaired loop, this is known as a double helix. Many RNA secondary structures use this structure as a building block.

Cruciform DNA

Cruciform DNA is a type of non-B DNA that requires at least a six-nucleotide sequence of inverted repetitions to form a cruciform structure with a stem, branch point, and loop supported by negative DNA supercoiling. The folded and unfolded classes of cruciform DNA have been identified.

G-quadruplex

In nucleic acids, G-quadruplex secondary structures (G4) are produced by guanine-rich sequences. They have a helical shape and contain guanine tetrads with one, two, or four strands. [

D-loop

A displacement loop, also known as a D-loop, is a DNA structure in which the two strands of a double-stranded DNA molecule are stretched apart and held apart by a third DNA strand.  An R-loop is identical to a D-loop, except that instead of DNA, the third strand is RNA.  The third strand has a complementary base sequence that couples with one of the main strands, displacing the other complementary major strand in the region. The structure is thus a triple-stranded DNA within that area. The D-loop was depicted in a graphic in the publication that introduced the name as a capital “D” with the displaced strand forming the loop of the “D.”

Folds of Protein Structure

• Proteins fold into three-dimensional conformations that are defined by their amino acid sequence. A protein’s entire structure can be defined on four different degrees of complexity: Structures are classified as primary, secondary, tertiary, and quaternary.

• Protein folding is the physical process of translating a protein chain to its native three-dimensional structure, which is often a “folded” conformation that allows the protein to operate biologically. A polypeptide folds into its characteristic three-dimensional structure from a random coil in a quick and repeatable process. After being translated from mRNA to a linear chain of amino acids, each protein exists as an unfolded polypeptide or random coil. The polypeptide has no stable (long-lasting) three-dimensional structure at this point (the left hand side of the first figure). The linear polypeptide chain begins to fold into its three-dimensional form as it is generated by a ribosome

• Many proteins begin folding even before the polypeptide chain is translated. Amino acids interact with one another to form a well-defined three-dimensional structure called the native state (the right hand side of the picture). The amino acid sequence or primary structure determines the three-dimensional structure (Anfinsen’s dogma)

Conclusion

Protein domains are areas of a protein that can fold stably and serve a specific purpose. One or more domains can be found in proteins. Each protein domain has a fold, which describes how the secondary structure elements in that domain are organised. Because there are so few individual folds compared to the amount of protein sequences, one fold can be used by many different proteins to fulfil a variety of activities. Proteins fold into three-dimensional conformations that are defined by their amino acid sequence. A structural motif is a typical three-dimensional structure that arises in a range of diverse, evolutionarily unrelated biological entities, such as proteins or nucleic acids.