Supersecondary structure ppt

supersecondary structures
types of supersecondary structures

1. SUPERSECONDARY STRUCTURE OF PROTEIN Mary Theresa S1; MSc. Microbiology

2. Supersecondary structure of protein Intermediate between secondary and tertiary structures of protein. Also called motifs. Typically composed of two secondary structures and a turn or loop. Simple combinations of few secondary structure elements with a specific geometric arrangement – occur frequently in protein structures. Can be associated with particular function- DNA binding; others have no biological function alone but are part of larger structural and functional assemblies.

3. SUPERSECONDARY STURUCTURES Helix Sheet Mix helix-turn-helix β -hairpins β - α - β helix-loop-helix β - β corner Rossmann fold helix-hairpin-helix Greek key motif α - α corner

4. HELIX SUPERSECONDARY STRUCTURES HELIX-TURN-HELIX MOTIF Also called α- α type. Composed of two anti-parallel α helices connected by a turn. Functional motif- usually identified in proteins that bind to DNA minor and major grooves, and calcium-binding proteins. One of the helix contributes to the DNA recognition, “recognition helix” and the second helix stabilizes the interaction between protein and DNA. Involved in cell proliferation, establishment of DNA structure, developmental regulation, maintenance of circadian rhythms, movement of DNA, regulation of a myriad of bacterial operons and initiation of transcription itself.

5. HELIX-LOOP-HELIX Characterizes a family of transcription factors. One helix is smaller and flexible, allows dimerization by folding and packing against another helix. The larger helix typically contains the DNA- binding regions. HLH proteins typically bind to a consensus sequence called an E-box (CACGTG). In general, transcription factors having HLH motifs are dimeric , each with one helix containing basic amino acid residues that facilitate DNA binding. Eg ; BMAL-1-CLOCK, C- Myc , N- Myc , MyoD , Myf5, Pho4, HIF, ICE 1, NPAS1, NPAS3, MOP5, etc..

6. HELIX-HAIRPIN-HELIX HhH motif is similar to, but distinct from, HtH and HLH. DNA- binding proteins with a HhH structural motifs are involved in non-sequence specific DNA binding that occurs via the formation of hydrogen bonds between protein backbone nitrogens and DNA phosphate groups. Eg ; 5’-exonuclease domains of prokaryotic DNA polymerases, RAD2 family of 5’-3’exonucleases (such as T4 and T5 RNAase ), eukaryotic 5’ endonucleases (such as FEN-1) & some viral exonucleases .

7. HELIX CORNER ( α - α CORNER) Short loop regions connecting helices. Perpendicular to one another.

8. EF HAND Two helices connected by a loop that contains residues to coordinate calcium ion. Consists of E and F helices.

9. SHEET SUPERSECONDARY STRUCTURES β -HAIRPINS Most simplest supersecondary structure. Widespread in globular proteins. Also called β - β unit or β –ribbon. Reverse turns. Look like a hair pin. Occur as the short loop regions between antiparallel hydrogen bonded β –strands. No specific function associated with this motif. 2 anti-parallel beta-strands + beta-turn = beta- hairpin

10. β - β CORNER ( β CORNER) Consists of two anti-parallel beta strands. Can change the direction abruptly. The angle of change of direction is about 90°. The abrupt angle change is achieved by one strand having a glycine residue and the other hand having a beta bulge. No known function.

11. GREEK KEY MOTIF formed by four sequentially connected β -strands adjacent to each other (geometrically aligned to each other)- ββββ Alternate strands runs in the opposite direction. The first strand (N-terminal strand) and the last strand (C-terminal strand) are adjacent to each other and hydrogen bonds exist between them. Connecting loops can be long and include other secondary structures. Eg ; prealbumin , PapD (a chaperon), nitrite reductase , bacterial cellulase , spherical virus capsid proteins.

12. MIX SUPERSECONDARY STRUCTURES β - α - β MOTIF Parallel β - sheets are connected by longer segments of polypeptide chains. Frequently, the connections between parallel β - sheets contain helices forming the βαβ structural motif. Helix is parallel to the β - sheet and the connections are variable in length. Two types: helix above the plane- right-handed- >95% helix below the plane- left-handed First loop is evolutionarily conserved, whereas the second loop rarely has a known function. Found in most proteins that have a parallel β -sheet.

13. ROSSMANN FOLD Complex structure. It is α - helix and β -sheet connected with βαβ motif with the middle β shared between the two units and it binds to nucleotides. β αβαβ

14. OTHER MOTIFS β - MEANDER MOTIF Two or more consecutive anti-parallel β -strands linked together by hairpin loops. β ββ Common in β -sheets Found in several structural architectures including β - barrels and β - propellers.

15. ψ -LOOP MOTIF Consists of two anti-parallel strands with one strand in between that is connected to both by hydrogen bonds. Four possible strand topologies for single ψ –loops. Rare one – formation seems unlikely to occur during protein folding. First identified in the aspartic protease family.

16. ZINC FINGER MOTIF Consists of a segment of α -helix bound to a loop by a zinc ion. The zinc ion is held in place by two cysteine and two histidine R groups. Motifs are often repeated in clusters.

17. TRANS MEMBRANE MOTIFS HELIX BUNDLES It is long streches of a polar aminoacids , fold into trans membrane α -helices. Eg ; cell surface receptors, ion channels, active and passive transporters.

18. β - BARRELS Anti-parallel β -sheets rolled into a cylinder form. Eg ; outer membrane of Gram – ve bacteria, porins (passive, selective & diffusive).

19. REFERENCES Blanco F. J., G. Rivas, L. Serrano. A short linear polypeptide that folds into a native β - hairpin in aqueous solution. Natural Structural Biology, 1994; 1(9): 584-590. WWW.andrew.cmuedu/course/03-231/LecF05/Lec09/Lec09.pdf Swift.cmbi.ru.nl/ gv /students/ mtom /sup_2.html https://WWW.acsu.buffalo.edu/~sjpark6/pednotes/Motifs.pdf https://WWW.uibk.ac.at/organic/de/teaching/gruber_karp_2.pdf Faculty.ksu.edu.sa/77379/Documents/(14)_tertiary_prot.pdf

20. https://WWW.youtube.com/watch?v=9ypbWROaaLU Rao S. T, M. G. Rassmann . Comparison of supersecondary structure in protein. Journal of Molecular Biology, 1973; 76: 241-256. Janin J., C. Chothia . Packing of α -helices onto β -pleated sheets and the anatomy of α / β proteins,1980; 143: 95-128. Creighton E. Proteins- Structures and Molecular Proteins. 2 edition. W.H. Freeman and Company, New York,1993: 227-228.