Motifs and folds, contd'

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Motifs and folds, contd.
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Proline helix C-cap
note hydrophobic cluster
structural variability
Sequence pattern...nppnnppHNYFPDEn
Pro blocks helix
D or E stabilizes tight turn
Locations of non-polar (magenta) and polar
(green) sidechains
nnon-polarppolar...alternative aas
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Two Helix motifs
a-a corner(helix-turn-helix)
EF-hand (binds Ca2)
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beta-strand
middle strand
edge strand
Antiparallel
Parallel
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Sequence motifs for beta strands
Hydrophobic
Amphipathic
Note preference for beta-branched aas I,V,T
Found at the edges of a sheet, or when one side
of the sheet is exposed to solvent (i.e. 2-layer
proteins).
Found in the buried middle strands of sheets in
3-layer proteins.
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beta hairpins
Two adjacent antiparallel beta strands a beta
hairpin Shown are tight turns, 2 residues in
the loop region (shaded). Hairpins can have as
many as 20 residues in the loop region.
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hairpin motifs
Serine beta-hairpin (my naming). A specific
pattern (DPESG) forms an incomplete alpha-helical
turn 4-residues long.
Extended Type-1 hairpin. A type-1 tight turn
has only 2 residues in the turn. This motif, more
common than the tight turn, has an additional Pro
or polar sidechain. Pattern PDG.
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diverging turn
Exercise Find the diverging turn in 1CSK.
Diverging turns have a Type-2 beta turn and two
strands that do not pair. The consensus sequence
pattern is PDG. The residue before G can be
anything polar, but not a D or an N.
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Greek key motif
One of the most common arrangements of four
strands. Two permutations. 2341 and 3214
beta meander
Exercise Download 2PLT. Find the Greek key
motifs.
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bab motif
When a helix occurs between two strands, they are
often paired in a parallel sheet.
The cross-over from one strand to the next is
almost always right-handed. It is not known why
this is true. (NOTE the cross-over is always
right-handed even when the two strands are not
paired!!)
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TOPS diagrams
beta strand pointing up
beta strand pointing down
alpha helix
bab motif
C
N
Note R-handed crossover!
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babab motif
1
2
3
Only 3 are possible. (with R-handed crossovers)
1
2
3
3
1
2
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Efimovs theory
A. Efimov showed that almost all protein
structures can be classified as being one of 7
trees, each starting with a motif and growing
by one secondary structure unit at time. Does
this recapitulate evolution? the folding pathway?
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Domains
Proteins fold heirarchically. secondary structure
--gt motifs --gt subdomains--gtdomains --gt
multidomain proteins --gt complexes
Most domains fold independently of the rest of
the chain.
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All alpha folds
3-helix bundle 1CUK 156-203 4-helix
bundle 1NFN Globin 1DWT ...many many other
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alpha/beta folds
TIM barrel 8TIM Rossman fold 1HET
176-318 many others...
Exercise in 1HET, find the crevice between two
babab motifs where NAD binding commonly occurs.
Exercise Draw TOPS diagram for 1HET 176-318.
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all beta folds
Jelly roll 1JMU 371-500D,
2PLT barrels 1EMC propellers beta-helix
Exercise Draw TOPS diagrams for the two domains
above.