The document discusses various supersecondary structures of proteins, which are intermediate structures between secondary and tertiary protein structures. It describes several common motifs composed of two or more secondary structures, such as helix-turn-helix, helix-loop-helix, beta-hairpins, and the Rossmann fold. These motifs are building blocks that occur frequently in protein structures and are associated with specific functions like DNA binding. The document provides detailed examples and diagrams of different supersecondary structure motifs involving helices, strands, and their combinations.

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.

6. • 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..

8. • 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.

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

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

12. 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

14. • 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.

16. • 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.
•

18. 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.

20. 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.
βαβαβ

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

24. 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.

25. 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.

27. 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.

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

31. 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

32. • 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.