Protein Secondary Structure 1

1958: Kendrew Solves the Structure of Myoglobin “Perhaps the most remarkable features of the molecule are its complexity and its lack of symmetry. The arrangement seems to be almost totally lacking in the kind of regularities which one instinctively anticipates, and is more complicated than has been predicted by any theory of protein structure” 2

Protein Secondary Structure Protein interior: Hydrophobic core Main chain folds also into interior, but it is highly polar → Problem: Polar atoms must be neutralized through hydrogen bonds → Solution: Regular secondary structure 3

 Helix Discovered 1951 by Pauling 5-40 aa long Average: 10aa Right handed O i -NH i+4 : bb atoms satisfied  helix: i - i helix: i - i+3 1.5Ǻ/res 4

 Helix is a Dipole … and binds negative charges at N-term 5

Side Chains project out from the Helix View down one helical turn 6

Proline Disrupts Helix No donor! N CO CH CH 2 H2CH2C 7

Frequent Amino Acids at the N-terminus of  helices Pro Blocks the continuation of the helix by its side chain Asn, Ser Block the continuation of the helix by hydrogen bonding with the donor (NH) of N 3 N cap, N 1, N 2, N 3 …….C cap 8

Helices of Different Character Buried, partially exposed, and exposed 9

Representation: Helical Wheel Buried, partially exposed, and exposed 10

 Dihedral Angles  and  define Backbone Geometry   The peptide bond  is planar and polar 11

Ramachandran Plots Glycine: flexible backbone All except Glycine   12

Ramachandran Plots  helix:  around -60,-50, respectively Other defined regions:  strand and loops   13

 Sheet Involves several regions in sequence O i -NH j Parallel and anti-parallel sheets 14

Antiparallel  Sheet Parallel Hbonds Residue side chains point up/down/up.. Pleated 15

Parallel  Sheet Less stable than antiparallel sheet Angled hbonds 16

Combined  Sheet Rare: strains in middle strand 17

Examples of  Sheet Topologies Topology diagram Closed barrel 18

Connecting Elements of Secondary Structure defines Tertiary Structure 19

Loops Connect helices and strands At surface of molecule More flexible Contain functional sites 20

Hairpin Loops (  turns) Connect strands in antiparallel sheet G,N,DGGS,T 21

Super Secondary Structures: (1) Greek Key Motif 24 possible topologies for 2 hairpins 8 found Most common: Greek key motif 22

Super Secondary Structures: (2)  Motif Connect strands in parallel sheet 23

Repeated  Motif Creates  -meander: TIM Barrel 24

Large Polypeptide Chains Fold into Several Domains 25

Protein Classification 26

Protein Classification Alphacontain only  helices Betacontain only  sheets Alpha/Betacontain combination of both Alpha + Betacontain domains of  and  27

ALPHA Occur in Transmembrane proteins Structural and motile proteins Fibrous proteins (Keratin) Fibrinogen, myosin Coiled-coils (Leucine Zippers) 4-helix-bundles  -helical domains Globins 28

ALPHA: Coiled-Coils Francis Crick, 1953: maximal sc interactions if two helices are wound around each other Left-handed supercoil: 3.5 residues/turn: Heptad repeat “knobs-into-holes” Leucine zipper motif in Transcription Factors (more about this later..) 29

ALPHA: 4-Helix Bundle “ridges-into-grooves” ROP protein 30

Ridges-into-Grooves 2 possible arrangements: i-i+4 ridge: Globins i-i+3 ridge: ROP 31

ALPHA:  -Helical Domains >20  helices form globular domain Example: muramidase 27 helices right-handed superhelical twist Hole in center

ALPHA/BETA Most frequent 3 classes: Barrel Twisted sheet Horseshoe fold Functional sites in loop regions 33

ALPHA/BETA: Barrels Consecutive  units in same orientation Usually 8;  8 -hb-  1 → closed core of  strands TIM barrel Triose Phosphate Isomerase Usually enzymes 34

TIM Barrels aa 2,4 point out to helices branched aas V,I,L aa 1, 3, 5 point into barrel Bulky hydrophobic aas form tightly packed hydrophobic core Polar aas (KRE) at tip of barrel: participate in formation of hydrophobic core 35

TIM Barrels Active site formed by loops at one end of the barrel Distinct from structural region 36

ALPHA/BETA: Open Sheet Consecutive  units in opposite orientation: helices on both sides Rossman Fold (discovered in 1970 in lactate dehydrogenase) Many different arrangements 37

Open Sheet: Functional Sites at Topological Switch Points 38

ALPHA/BETA: Horseshoe Fold Consecutive  units in same orientation Not closed: horseshoe Ribonuclease Inhibitor One side points to helix, The other is exposed 39

Horseshoe Fold Leucine-rich repeats each ~30aa L responsible for packing 40

BETA Antiparallel  structures Usually two sheets packed against each other Barrel: composed of anti-parallel strands with hairpin connections Propeller: multi-domain protein 41

BETA Barrels Retinol-binding protein 8 strands Center: hydrophobic pocket binds lipids 42

BETA Propellors (I) Neuraminidase 6  -sheets (each 4 strands) organized as propellor blades Active site formed by loops from each blade Others: G-proteins, etc 43

BETA Propellors (II) Neuraminidase 6  -sheets (each 4 strands) organized as propellor blades Active site formed by loops from each blade 44

BETA Propellors (III) Neuraminidase 6  -sheets (each 4 strands) organized as propellor blades Active site formed by loops from each blade 45

BETA: Jelly-Roll Motif Wrapped around a Barrel Composed of repeats of greek keys Concavalin, Hemagglutinin 46

BETA:  -helix Structures Right-handed coiled structure 18aa: 6 in loop + 3 in  GGXGXDXUX (U=hydrophobic) Loop stabilized by Ca ion Pectate lyase

Additional Useful Material 48