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Terminology

• Secondary structure • Defined by torsional angles at the alpha carbon and hydrogen bonding of the backbone. Alpha, Beta , Turns.

• Supersecondary structure or motifs •  Recurring combinations of secondary structure

elements close in sequence

• Domains • Stable 3D structure formed by a continous peptide chain. Folding units.

• Mostly motifs or secondary structure.

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Illustrations of protein structure -1

Line, wireframe (Dreiding) CPK (spacefilling)

(Ribonukleas A, Weblab Viewer)

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Illustrations of protein structure- 2 -stylized representations

Lines between alfa carbons Ribbon

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Illustrations of protein structure - 3

Ribbon for beta strands och cylinders of for alfa helices

Accessible surface (colored according to charge)

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Connection of antiparallel β-strands

β-meander Greek key β-hairpin (hårnål)

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Greek key from extended harpin

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α-hairpin

short loops with 2-4 residues connection two nearly antiparallel alpha helices

1

2

Figurer efter Jon Cooper, PPS

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Helix-turn-helix motif Approx. perpendicular alpha helixes connected by short loop. Common in DNA binding

Petsko& Ringe Fig 150

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EF-hand

se även Bränden &Tooze 2.13

Calcium binding loop with carboxylate side chains

Ca Asp Asp

Asp

Calcium binding proteins, e.g. calmodulin

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Crossover in parallel β-structures

All observed crossovers are right-handed; probably related to twist

β-x-β-unit (chiral)

Petsko&Ringe fig. 1.60

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β-α-β motif

α-helix as crossover, parallel with the strands

α

β β

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Zinc fingers Domain structure containing alpha helix+beta hairpin, coordination of zinc by his and cys residues contribute to stability

DNA-binding proteins often contain several Zn-finger domains

Petsko&Ringe fig 1.49

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Domains/Folds Domains

• Smallest unit of tertiary structure

• Building elements are secondary structures and/or supersecondary structures

• Continuous peptide chain, independent folding unit • Proteins contain one or several domains

• Domains are sometimes functional units

• Tertiary structure includes structures of domains and domain interfaces.

• Quarternary structure includes subunit interfaces; similar to domain interfaces

14 A limited number of folds?

Statistik från PDB (2010)

0

200

400

600

800

1000

1200

1400

1600

Un

ika

fold

s

0

2

4

6

8

10

12

An

del

nya

fol

ds

un

der

åre

t, %

Unique folds

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Domain structure

•  Architecture

Secondary structure and motifs, their orientation and packing

•  Topology

The ordering of secondary structure elements in the amino acid sequence A given architecture can be realized with different topologies

Example: antiparallellt 4-stranded β-sheet is an architecture that can be a beta meander or a Greek key

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Topology diagrams Beta structure

One domain of aspartate transcarbamylas Flavodoxin plastocyanin

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TOPS topology diagrams

Cu/Zn superoxide dismutase

Topologidiagram i TOPS

helix (alfa eller 3.10)

betasträng

Topology databaseTOPS

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The major domain types

•  Alpha helix domains Mainly alpha helix (CATH:>60% alpha and <5% beta . >50% alpha-alpha and <5% beta-beta contacts )

•  Beta-sheet domains antiparallella beta sheetl (CATH:<5% alpha and >50% beta . <10% alpha-alpha and >50% beta-beta contacts

•  Alpha beta domains • Alpha /beta domains

Beta-alpha-beta motifs ; parallel beta structure • Alpha+beta domains

Some alfahelix, some beta sheet (antiparallel) with helix-sheet packing

•  Small irregular domains Disulphides, metal ions with structural function

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19 A universe of proteins

Alpha- ness

Alpha/ Beta- ness

Beta- ness

Factor analysis of structural differences:

•  Most of the variability described by 3 factors

•  Can be transformed into variables alpha, beta and alpha/beta.

•  3-dimensional fold space

•  Size increases with distance from origo

Genomics&Proteomics vol 4,p. 22; Hou et al, PNAS vol 100 p. 2386

20 Statistics from CATH database for fold classification

1. Alpha

2. Beta 3. Alpha Beta

4. Few secondary structure

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Alpha helix proteins/domains

•  Lone helix Peptide hormones (glucagon); domains in larger proteins

•  Coiled coils, leucine zippers •  4-helix bundles

Several topologies •  Globin like

Heme binding Phycocyanins

•  Folds containing DNA-binding helix-turn-helix motifs

•  Long alfa hairpins (t superhelix) •  EF-hand •  Alfa horseshoe, alfa solenoid, alfa/alfa-barrel

CATH: five architectures, ortogonal bundle (bunt), up-down bundle och nonbundle , horseshoe alfa solenoid, alfa/alfa-barrel

SCOP: 144 different folds with alfa helix only Some interesting groups:

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Side chain packing: basics

Geometric packing density: Ratio between the volume included by the av van der Waals surfaceand the volumee occupied by the molecule or aggregate. Maximal packing of spheres 0.74 Organic crystals: 0.70-0.78 Oils, glasses < 0.70 Proteins: 0.68-0.82 compressibility: k(oil)/k(protein) ≈ 20 About 25% the volume unoccupied; mainly small cavities. Larger cavities can be filled with water av

Cut-away view of protein interior

Petsko&Ringe fig 1.27

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Coiled coil

•  Two amphiphilic α-helixes held together by hydrophobic interaction

•  Primary structure: Repeated sequence of 7 aa’s where residues 1 och 4 are hydrophic and residues 5 and 7 hydrophilic. ”Heptad repeat”

figur efter Antti Iivanainen, PPS

1 4

1 4

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The hydrophic surface is helical

Straightening the hydrophobic surface produces left-handed superhelixes

sidechains 1,4,8,11,15,18 green

Also complementary surfaces (“knobs into holes “)

See also figs 1.67, 1.68 in Petsko&Ringe

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Packing of α-helixes: the ridges and grooves model

±4n; 26o vinkel med axeln ±n; ca 80o

vinkel med axeln

±3n; ca 45o vinkel med axeln

1

2

4 5

8 9

12 11

7

1

2 4

5

8

9

12 11

7

1

2

4 5

8 9

12 11

7

Figurer efter Jon Cooper, PPS

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4n ridges and 4n grooves produces ca 50o angle 26 + 26 =52o

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4n ridges and 3n grooves produces ca 20o angle

4n; 26o 3n; 45o

ca 20o

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Observed helix-helix contact angles

Ω

Soluble proteins

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4-helix-bundle proteins: architecture

4 helices ; ca 20 degree angles

Petsko&Ringe fig 1.54

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Side chain distribution

•  Hydrophobic side chains (green) form a hydrophobic core, hydrophilic side chains om the outside (cytokrom b562 from top)

jfr Bränden & Tooze, fig 3.2

Binding site for prostethic groups (heme in this case) sandwiched between helixes

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4-helix-bundles: topologies

•  Up-and down (eg cyt b562, myohemyrytrin) •  Single cross-over (ferritin,

ribonukleotidreduktas; both with 2 Fe)

•  Two crossovers; cytokines (hormoner, e. g. interleukin)

Petsko&Ringe fig 1.28,1.51, 1.54

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Globin-like proteins

Architecture: 8 alpha helixes (A-H) with contact angle 20, 50 and 90 degrees . Contains heme or phtosynthetic pigment Supersecondary structure: helixes G och H in alpha hairpin

A

B

C

D

E F

G

H

heme

Myoglobin

• Heme-containing • Phycocyanins

Petsko&Ringe fig 1.55

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Helix-helix packing in globins

Helixes G och H constitute helix hairpin 20 deg. angle

Other helix-helixcontacts:

• ca 50 deg (B-G; F-H)

B G

F

H

G

H

• Ca 90 deg! (E-B, E-G) Glycine residues.

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Sequence-strucure correlation in globins? 12 different proteins with globin fold known (SCOP, 1998 [81 proteins 2010]),

•  Different sequences (only 16 % simlarity between the most distant) but same fold.

•  Common feature: hydrophobic interior (helix-helix and helix-heme contacts), hydrophilic exterior

Backbone grey Hydrophobic green Hydrphilic blue heme red

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Alpha horsehoe

PDB: 1lrv

Also Armadillo repeat (ARM) interaction domain ; see Petsko& Ringe fig 3.2

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Alpha solenoid

Containing lipids and pigments

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Alpha/alpha barrel

(barrel) Top view Side view

Pdb-file: 1cem. Cellulase from Clostridium thermocellum