Super secondary structure of protein
- 1. Super Secondary Structure of protein
- 2. Introduction to motif and domain in protein structure MOTIF: A simple combination of few secondary structures elements with a specific geometrical arrangement (E.G. HELIX-LOOP-HELIX). DOMAIN: The fundamental unit of structure folding and evolution.It combines several secondary structures and motifs . A domain can fold independently in a 3D structure and it has a specific function.
- 3. Super secondary structure of protein is simply a combination of secondary structures They are intermediate between secondary & teritary structures Typically composed of two secondary structures or a turn or loop.
- 5. 1.) HELIX Helix turn helix Helix loop helix Helix-hairpin helix α- α corner
- 6. (a) Helix - turn-helix It is a major structural motif capable of binding to the DNA . It is composed of two antiparallel alpha helices joined by a short strand of amino acids. It is found in many proteins that regulates the gene expression. One of the helix contributes to the DNA recognition & other help in stabilizing the interaction between protein and DNA. Involved in cell proliferation, establishment of DNA structure ,maintenance of circadian rhythm.
- 7. (b) Helix-loop-Helix It is a protein structural motif. Characterize a family of transcription factors. It is composed of two alpha helices joined by a loop . In this , one helix is smaller & flexible allowing dimerization by folding and packing against another helix. The larger helix contains the DNA binding region.
- 8. (c) Helix-hairpin-helix It is a stretch of approximately 20 amino acids that is present in prokaryotic and eukaryotic non specific sequence DNA binding proteins . Non sequence DNA binding occurs via the formation of hydrogen bonds between protein backbone nitrogen and DNA phosphate groups.
- 9. (d) α- α corner Short region loops connecting helices. Perpendicular to one another
- 10. 2. Sheets β hairpins β - β - corner Greek key motif
- 11. (a) β- hairpins Most simplest super secondary structure. Mostly found in globular proteins. They occur as the short loop regions between antiparallel hydrogen bonded beta strands. However, it is said that beta hairpin motif has no specific function .But certain evidences shows that beta hairpin do have function and structural role..
- 12. (b) β - β – corner Consists of two anti parallel beta strands . Its like a long beta hairpin like structure ,folded orthogonally. Can change the direction abruptly, at about 90°. The abrupt angle change is achieved by one strand having a glycine residue and the other having a beta bulge. No known function is known for this.
- 13. (c) Greek key motif Four adjacent beta stands are joined together by short loops. It consists of three antiparallel strands and their linking loops. It is a very common structural motif in proteins. The motif is not associated with any specific function but is commonly found in protein structures.
- 14. 3. Mix super secondary structures β - α – β motif Rossmann fold Zinc finger motif
- 15. (a) β - α – β motif Two adjacent beta sheets are connected by an alpha helix Connection is at C-terminus from one strand and at N- terminus on other strand Most proteins that contains parallel beta sheets are built up from, such combinations of β - α – β motif The loop that connects both the strands is frequently involved in ligand binding functions, & the motif is found in ion channels.
- 16. (b) Rossmann fold It is a structural motif found in proteins that binds nucleotides, cofactors such as FAD+, NAD+ ,NADP+ , etc. This fold is composed of alternating beta strands & alpha helical segments where the beta strands are hydrogen bonded to each other. It is frequently occurring motif in nucleotide binding proteins. The function of Rossmann fold in enzymes is to bind nucleotide cofactors, & also it often contributes to substrate binding.
- 17. (c) Zinc finger motif It is a small protein structural motif. It is coordinated by one or more zinc ion in order to stabilize the fold. The zinc ion is held in place by two cysteine and two histidine R groups. Most of the time this motif is found in the proteins that interact with DNA, RNA.