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Folds and motifs

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Folds and motifs Using SCOP, CATH, CE to find structural homologs. What class/architecture, etc does your molecule fall in? Use CE to identify structural homologs for ... – PowerPoint PPT presentation

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Title: Folds and motifs


1
Folds and motifs
  • Using SCOP, CATH, CE to find structural homologs.
  • What class/architecture, etc does your molecule
    fall in?
  • Use CE to identify structural homologs for your
    protein of interest.
  • Motifs classic turn types. Extended turn types.
  • Use Rasmol to find the glycines in your
    structure. That are the phi angles? What type of
    turn is it?

2
The SCOP database
  • Contains information about classification of
    protein structures and within that
    classification, their sequences
  • http//scop.berkeley.edu

3
SCOP classification heirarchy
global characteristics (no evolutionary relation)
(1) class (2) fold (3) superfamily (4) family (5)
protein (6) species
Similar topology . Distant evolutionary cousins?
Clear structural homology
Clear sequence homology
functionally identical
unique sequences
4
protein classes
  • 1. all ???????
  • 2. all ??????
  • ???????????
  • ?????????????
  • 5. multidomain (21)
  • 6. membrane (21)
  • 7. small (10)
  • 8. coiled coil (4)
  • 9. low-resolution (4)
  • 10. peptides (61)
  • 11. designed proteins (17)

number of sub-categories
possibly not complete, or erroneous
5
class ????proteins
Mainly parallel beta sheets (beta-alpha-beta
units)
Folds TIM-barrel (22) swivelling beta/beta/alpha
domain (5) spoIIaa-like (2) flavodoxin-like
(10) restriction endonuclease-like
(2) ribokinase-like (2) chelatase-like (2)
Many folds have historical names. TIM barrel
was first seen in TIM. These classifications are
done by eye, mostly.
6
fold flavodoxin-like
3 layers, ????? parallel beta-sheet of 5
strand, order 21345
Superfamilies 1.Catalase, C-terminal domain
(1) 2.CheY-like (1) 3.Succinyl-CoA
synthetase domains (1) 4.Flavoproteins (3)
5.Cobalamin (vitamin B12)-binding domain (1)
6.Ornithine decarboxylase N-terminal "wing"
domain (1) 7.Cutinase-like (1)
8.Esterase/acetylhydrolase (2)
9.Formate/glycerate dehydrogenase catalytic
domain-like (3) 10.Type II 3-dehydroquinate
dehydratase (1)
Note the term layers These are not domains. No
implication of structural independence. Note how
beta sheets are described number of strands,
order (N-gtC)
7
fold-level similarity
common topological features
catalase
flavodoxin
At the fold level, a common core of secondary
structure is conserved. Outer secondary structure
units may not be conserved.
8
SuperfamilyFlavoproteins
Flavodoxin-related (7)
NADPH-cytochrome p450 reductase, N-terminal domain
Quinone reductase
These molecules do not superimpose well, but
side-by-side you can easily see the similar
topology. Sec structs align 1-to-1, mostly.
9
Family quinone reductases
binds FAD
Proteins
NADPH quinone reductase
quinone reductase type 2
Different members of the same family superimpose
well. At this level, a structure may be used as a
molecular replacement model.
10
CATH
  • Class
  • Architecture
  • Topology
  • Homology

http//www.biochem.ucl.ac.uk/bsm/cath_new/index.ht
ml
11
Remote homologs are more likely than close ones
likelihood
percent identity for structural homologs
12
Structural conservation is stronger than sequence
conservation
The existence of large numbers of remote homologs
shows us that true structural similarity is hard
to see in the amino acid sequence.
13
Structural homology is sometimes difficult to see
beta-catenin versus clathrin (from FSSP database)
14
Rasmol practice
Using your protein of interest Find all
glycines. select gly Label each alpha-carbon by
number label r Measure the phi-angle by eye
(align N and CA. R-handed is positive) Write down
the residue number and phi angle.
15
Rasmol exercises
(1) Color the ribbon drawing of 1qajA.pdb (its
in your home directory) from the N-terminus
(blue) to C-terminus (red) (2) Divide 1qajA.pdb
into domains of different color. (3) In
1qajA.pdb, display only residues 66-87. What are
the first and last residues with helical backbone
angles? (4) Find all of the atoms that H-bond to
the sidechain of Ser92.
16
Secondary structure
Alpha helix
Right-handed Overall dipole N-gtC- 3.6
residues/turn i-gti4 H-bonds
17
3 types of Alpha helix
non-polar
amphipathic
polar
a
Two ways to display position of sidechain on a
helix.
d
e
For amphipathic and non-polar, sidechains line up
in a favorable way.
b
g
f
c
18
Helix caps
Capping motifs stabilize helices.
Please go to http//isites.bio.rpi.edu/
Click on Glycine alpha (Schellman) C-cap Type 1
Glycine alpha (Schellman) C-cap Type 2 Proline
alpha C-cap Frayed alpha helix Serine alpha
N-cap (capping box)
Exercise Find a helix cap in 1QAJ. What type is
it?
19
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
20
Two Helix motifs
a-a corner(helix-turn-helix)
EF-hand (binds Ca2)
21
a-a corner motif
backbone anglesgreenpsiredphi
redfavorable blue unfavorablegreenneutral
I-sites motif (Also described by A. Efimov)
nnon-polarppolar...alternative aas
motif pattern (summary)nnppnHGnPDSPxpn
Exercise Find a a-a corner motif in myoglobin.
22
Find a a-a corner in 1DWT
Download 1dwt from www.rcsb.orgOpen using
Rasmol Rasmol commands Display-gtCartoons Color-
gtstructure select alpha label m color labels
yellow
Find the a-a corner pattern (sequence and
structure).
23
Can you see the a-a motif in the sequence?
1 GLSDGEWQQV LNVWGKVEAD IAGHGQEVLI RLFTGHPETL
EKFDKFKHLK HHHHHHH HHHHHHHHHT HHHHHHHHHH
HHHHHTHHHH HTTTTTTT 51 TEAEMKASED
LKKHGTVVLT ALGGILKKKG HHEAELKPLA QSHATKHKIP
SHHHHHTTHH HHHHHHHHHH HHHHHHHTTT HHHHHHHH
HHHHHTS 101 IKYLEFISDA IIHVLHSKHP
GDFGADAQGA MTKALELFRN DIAAKYKELG HHHHHHHHHH
HHHHHHHHST TSS HHHHHH HHHHHHHHHH HHHHHHHHHT
151 FQG
24
EF-hand
Exercise Rasmol 1CLL. Follow instructions on
next page
25
1CLL exercise. How does the EF-hand bind calcium?
restrict hetero and CA (comments in
blue...) spacefill (this
displays only calciums)click to get residue
(x residue number)restrict within (10.,
x)center selected (so you can rotate it
easily)Display-gtball-and-stick (from menu item.
you see atoms and bonds)select protein and
within (10., x)Display-gtsticks (now protein
part has think bonds)select hoh and within (10.,
x) ( selects nearby waters)spacefillcolor
cyan (or your favorite water color...)select
within (3., x) ( atoms within bonding
distance)label ( these are the
atoms bonded to calcium x)color labels yellow
(..so you can see them)
26
Calcium causes a conformational change in the EF
hand.
red1CLL
green1cfd
27
Create a Rasmol script
Write a file using jot or vi (for example vi
script.ras)Put keyboard commands in the
script.Start RasmolInvoke the script using the
script command(for example script
script.ras) Useful keyboard commands for
scripts load xxx.pdb (loads a new PDB
file)zap (closes PDB file, blanks the
display)pause (stops the script until you hit a
key)
28
Create a Rasmol script to survey many structures
List the pdb files in the xtal directory (ls
xtal/.pdb) Create a script file (myscript.ras)
as follows load xtal/file1.pdb (use one of
the PDB files listed)backbone 0.6color
blueselect hohspacefill 1.0color redset
unitcell onpausezapload xtal/file2.pdb (repeat
as before for each file listed)
Run the script script myscript.ras Next, change
the script and run it again (i.e. change the
colors to green and magenta)
29
Nested scripts
Tired of having to edit the script 10 times
over??Write a nested script. Create a file
called mynestedscript.rasPut in all the
commands except the load line. Just one
copy.The last line is zap. Create a file
called mymainscript.ras containing load
file1.pdbscript mynestedscript.rasload
file2.pdbscript mynestedscript.rasetc. etc. etc
30
Further exercises just a few examples!
Select atoms by temperature factor select
temperature gt 5000 (Rasmol uses B100, so this
selects all atoms with B gt 50.00) Find crystal
contacts select B within (8., A)(This gets
all atoms of chain B that are close to chain A.
Your chain IDs may vary.) Can you determine the
crystal form (triclinic, orthorhombic, etc) just
by looking at the unit cell? (set unitcell
on) Survey the B-factors of waters in several
structures using a nested script. (Use color
temperature) Use logic operators! Find alpha
carbons within 10.A or residue x but not within
6.A. (select within (10.,x) and not within (6.,
x) ) Practice stereo viewing. (stereo -7 for
walleyed viewing)
31
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
32
Two Helix motifs
a-a corner(helix-turn-helix)
EF-hand (binds Ca2)
33
beta-strand
middle strand
edge strand
Antiparallel
Parallel
34
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.
35
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.
36
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.
37
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.
38
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.
39
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!!)
40
TOPS diagrams
beta strand pointing up
beta strand pointing down
alpha helix
bab motif
C
N
Note R-handed crossover!
41
babab motif
1
2
3
Only 3 are possible. (with R-handed crossovers)
1
2
3
3
1
2
42
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?
43
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.
44
All alpha folds
3-helix bundle 1CUK 156-203 4-helix
bundle 1NFN Globin 1DWT ...many many other
45
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.
46
all beta folds
Jelly roll 1JMU 371-500D,
2PLT barrels 1EMC propellers beta-helix
Exercise Draw TOPS diagrams for the two domains
above.
47
Term projects
Look at the description online. Choose a molecule
to study. Check with me before you start. Look at
Molecule of the Month at RCSB.org for
inspiration. But dont pick one of these
molecules.
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