Super secondary structures of proteins or Motif

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Super secondary structures of proteins

Proteins

The basic amino acid sequence which makes a polypeptide chain and folding into different confirmations leads to proteins. Proteins are composed of Motifs (when secondary structures combine, they make a motif that does not function independently) and Domains (when specific motifs and secondary structures combine, they form a domain that has a particular function and may exist independently).

Super secondary structures / Motif

Super secondary motifs are the structures that are formed by the combination of secondary structures containing alpha-helices and beta-pleated sheets. These structures are found in the globular proteins and are joined by loop, turn, or hairpin (short amino acids sequences which are required to join the alpha helixes and beta-pleated sheets) they are found in globular proteins where the bend is required.

Super secondary structures are in between secondary structures and tertiary structures of proteins.

The best example of the super secondary motif is the β-α-β super secondary motif.

Classification of Super secondary structures

Super secondary structures
Alpha Helix

Beta sheets

 Mix
    Helix -turn -helix Β-hairpins β-α-β corner
     Helix-loop-helix β-βcorner Rossmann
Helix-hairpin-helix

α-α corner

 Greek key motif Zinc-finger motif

Super secondary structures / Motif

Alpha Helix

The structures are formed when alpha helixes are connected via a loop, turn, or hairpin.

Helix turn helix

  • Helix-turn-helix is a motif that could also be called an α-α type.
  • It is composed of two anti-parallel α helices which are connected by a turn.
  • It is a functional motif that is found in proteins that bind to DNA major and minor grooves, along with in calcium binding proteins.

Function:

  • Its major function is in DNA recognition, as one helix is involved in the recognition and is known as “recognization helix” while another one stabilizes the interaction between DNA and Protein.
  • Also involved in the establishment of the structure of DNA.
  • Promotes cell proliferation.
  • Maintenance of the biological clock, circadian rhythms.
  • It can initiate the transcription of DNA itself.
  • It can regulate bacterial operons like lac operon, trp operon, etc.

Helix-loop-helix

  • It is involved in the characterization of transcription factors.
  • One of the 2 helices is small and involved in the dimerization by packing and folding against another helix.
  • The larger one contains a DNA binding region.

Function

  • This type of motif typically binds to a consensus sequence called E-box (CACGTG).
  • Helix loop helix motifs are dimeric each with one helix containing a basic amino acid that facilitates the DNA binding.

For example

  • C-Myc
  • N-Myc
  • BMAL-1- CLOCK

Helix-hairpin-Helix

  • This type of motif is similar but also distinct in many ways from helix-loop-helix and helix-turn-helix.
  • These types of motifs are involved in non-sequence specific DNA binding that occurs via the formation of hydrogen bonds between the protein backbone nitrogen and phosphate groups.

For example

  • 5’-exonuclease domains of prokaryotic DNA polymerases.
  • RAD2 family 5’-3’ exonucleases (such as T4 and T5 RNase).
  • Viral exonucleases.

α-α corner

  • These motifs are short loops regions that connect the helices.
  • The helices are perpendicular to each other.

Function

  • This type of motif is also involved in DNA binding.

β Sheets

This type of motif contains beta-sheets which are connected via hairpins hydrogen bonds.

  • Beta hairpins are the post simplest super secondary structure.
  • They are abundantly presenting the globular proteins.
  • They are also known as β-β unit or β-ribbon.
  • Beta sheets are arranged in reverse sheets and look like a hairpin.
  • They occur in the short loop regions between antiparallel hydrogen-bonded beta-sheets.
  • 2 antiparallel beta sheets and 1 beta-turn makes a beta-hairpin.

Function

  • No specific function is associated with it.

β-β corner

  • It consists of 2 anti-parallel beta strands.
  • It can change its direction abruptly at an angle of 90 degrees mean they are perpendicular.
  • The abrupt change in angle is only achieved when one strand has a glycine residue while the other one has a beta bulge.

Greek key motif

  • This motif formed by four sequentially connected beta strands which are adjacent to each (geometrically aligned to each other).
  • The strands are alternate to each other.
  • The first strand of beta-sheet has (N- terminus) which connects the last strand of beta-sheet having (C-terminus) and hydrogen bond exists between them.
  • Connecting loops between beta-sheets maybe longer and they may include secondary structures.

For example

  • Pear albumin
  • PaP-D (chaperon)
  • Nitrite reductase
  • Bacterial cellulase
  • Spherical virus capsid proteins

Mix- super secondary structures

β-α-β motif

  • These motifs contain 2 beta-sheets which are connected by an alpha helix.
  • Connection between this type of motif is from C terminus to N terminus.
  • Proteins containing beta-sheets are made up of these types of motifs.

Function

The loops that connect both strands are involved in ligand binding and motif is found in ion channels.

Rossmann fold

  • It is a structural motif that is found in proteins that binds to the nucleotides, co-factors such as FAD+, NAD+, and NADP+.
  • This motif consists of 2 alternate beta strands and alpha-helical segments which are bound to each other via hydrogen bonds.
  • Occurs in nucleotide-binding proteins.

Function

It binds enzymes to nucleotides cofactor and also contributes to substrate binding.

Zinc finger motif

  • This motif is a small structural motif.
  • It is coordinated by 1 or more than 1 zinc ion so that it can stabilize the fold.
  • Zinc ion is held in place by cysteine and 2 histidine R groups.

Function

  • This motif is found in proteins that interact with DNA, RNA.

Reference and Sources

  • https://www.slideshare.net/RajeshG5/bt631-6-structuralmotifs
  • https://www.slideshare.net/MaryTheresa4/supersecondary-structure-ppt
  • https://www.sciencedirect.com/topics/biochemistry-genetics-and-molecular-biology/supersecondary-structure
  • https://www.thoughtco.com/protein-structure-373563
  • https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3315372/

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