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Secondary structure of proteins : sheets supersecondary structure. Levels of protein structure organization. Peptide bond geometry. Hybrid of two canonical structures. 60% 40%. Dihedrals with which to describe polypeptide geometry. side chain. main chain.

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secondary structure of proteins sheets supersecondary structure
Secondarystructure of proteins: sheetssupersecondarystructure
peptide bond geometry
Peptide bond geometry

Hybrid of two canonical structures

60% 40%

slide5

Because of peptide group planarity, main chain conformation is effectively defined by the f and y angles.

conformations of a terminally blocked amino acid residue
Conformations of a terminally-blocked amino-acid residue

E

Zimmerman, Pottle, Nemethy, Scheraga, Macromolecules, 10, 1-9 (1977)

C7eq

C7ax

types of b turns in proteins
Types of b-turns in proteins

Hutchinson and Thornton, Protein Sci., 3, 2207-2216 (1994)

older classification
Older classification

Lewis, Momany, Scheraga, Biochim. Biophys. Acta, 303, 211-229 (1973)

slide14

fi+1=-60o, yi+1=-30o, fi+2=-90o, yi+2=0o

fi+1=60o, yi+1=30o, fi+2=90o, yi+2=0o

fi+1=-60o, yi+1=-30o, fi+2=-60o, yi+2=-30o

fi+1=60o, yi+1=30o, fi+2=60o, yi+2=30o

slide15

fi+1=-60o, yi+1=120o, fi+2=80o, yi+1=0o

fi+1=60o, yi+1=-120o, fi+2=-80o, yi+1=0o

slide17

cis-proline

|yi+1|»80o, |fi+2|<60o

|yi+1|»60o, |fi+2|»180o

slide18

Hydrogen bond geometry in b-turns

Type of structure

Average for b-turns

g-turn

Asx-type b-turns

slide19

Helical structures

a-helical structure predicted by L. Pauling; the name was given after classification of X-ray diagrams.

Helices do have handedness.

slide20

Geometrical parameters of helices

Average parameters of helical structures

Turns closed by H-bond

H-bond

radius

Type

slide21

Idealized hydrogen-bonded helical structures:

310-helix (left), a-helix (middle), p-helix (right)

slide22

Schematic representation a-helices: helical wheel

3.6 residues per turn = a residue every 100o.

slide24

Amphipatic (or amphiphilic) helices

One side contains hydrophobic amino-acids, the other one hydrophilic ones.

In globular proteins, the hydrophilic side is exposed to the solvent and the hydrophobic

side is packed against the inside of the globule

Hydrophobic

Hydrophilic

Amphipatic helices often interact with lipid membranes

hydrophilic head group

aliphatic carbon chain

lipid

bilayer

slide26

Length of a-helices in proteins

10-17 amino acids on average (3-5 turns); however much longer helices occur in muscle proteins (myosin, actin)

proline helices without h bonds
Proline helices (without H-bonds)

Polyproline helices I, II, and III (PI, PII, and PIII): contain proline and glycine residues and are left-handed.

PII is the building block of collagen; has also been postulated as the conformation of polypeptide chains at initial folding stages.

slide28

Structure

F

Y

w

turns/residue

residues/turn

a-helix

-57

-47

180

+3.6

1.5

310-helix

-49

-26

180

+3.0

2.0

p-helix

-57

-70

180

+4.4

1.15

Polyproline I

-83

+158

0

+3.33

1.9

Polyproline II

-78

+149

180

-3.0

3.12

Polyproline III

-80

+150

180

+3.0

3.1

f and y angles of regular and polyproline helices

slide29

Deca-glycine in PPII and PPI without hydrogen atoms, spacefill modells, CPK colouring

Poly-L-proline in PPII conformation, viewed parallel to the helix axis, presented as sticks, without H-atoms. (PDB)It can be seen, that the PPII helix has a 3-fold symmetry, and every 4th residue is in the same position (at a distance of 9.3 Å from each other).

PPI-PRO.PDB

PPII-PRO.PDB

b sheet s tructures
b-sheet structures

Pauling and Corey continued thinking about periodic structures that could satisfy the hydrogen bonding potential of the peptide backbone. They proposed that two extended peptide chains could bond together through alternating hydrogen bonds.

Alpha, Beta, … I got ALL the letters up here, baby!

antiparallel sheet l6 7
Antiparallel sheet (L6-7)

The side chains have alternating arrangement; usually hydrophobic on one and hydrophilic on the opposite site

resulting in a bilayer

2TRX.PDB

parallel sheet l6 7
Parallel sheet (L6-7)

The amino acid R groups face up & down from a beta sheet

2TRX.PDB

slide38

Residues/turn

Structure

F

Y

w

Distance along axis/turn

Antiparallel b

-139

+135

-178

2.0

3.4

Parallel b

-119

+113

180

2.0

3.2

a-helix

-57

-47

180

3.6

1.5

310-helix

-49

-26

180

3.0

2.0

p-helix

-57

-70

180

4.4

1.15

Polyproline I

-83

+158

0

3.33

1.9

Polyproline II

-78

+149

180

3.0

3.12

Polyproline III

-80

+150

180

3.0

3.1

A diagram showing the dihedral bond angles for regular polypeptide conformations.Note: omega = 0º is a cis peptide bond and omega = 180º is a trans peptide bond.

dipole moment of b sheets
Dipole moment of b-sheets
  • 1/3 peptide-bond dipole is parallel to strand direction for parallel b-sheets
  • 1/15 peptide-bond dipole is parallel to strand direction for antiparallel b-sheets
slide43

And the ruffles add flavor!

  • Backbone hydrogen bonds in b-sheets are by about 0.1 Å shorter from those in a-helices and more linear (160o) od helikalnych (157o)
  • b-sheets are not initiated by any specific residue types
  • Pro residues are rare inside b-strands; one exception is dendrotoxin K (1DTK)
slide44

b-sheet chirality

Because of interactions between the side chains of the neighboring strands, the b-strands have left-handed chirality which results in the right twist of the b-sheets

N-end

C-end

slide45

The degree of twist is determined by the tendency to save the intrachain hydrogen bonds in the presence of side-chain crowding

the geometry of twisted b sheets
The geometry of twisted b-sheets

parallel

‘twisted’

anti-parallel

slide47

The geometry of parallel­­ twistedb -sheets

thioredoxin

trioseposphate isomerase

slide48

Parallel b-structures occur mostly in a/b proteins where the b-sheet is covered by a-helical helices

slide49

Geometry of antiparallel­¯b-sheets (mostly outside proteins and between domains)

twisted (coiled)

Multistrand twisted

Cyllinders

Threestrand with a b-bulge

Three strand helicoidal

Cupola (dome)

slide51

Example of a three-strand antiparallel b-structure

RYBONUKLEAZA-RASMOL

Ribonuclease A

  • The central strand is least deformed
slide52

Geometria skręconych (ang. twisted) struktur b­¯

CHYMOTRYPSYNA-RASMOL

W powierzchniach cylindrycznych b­¯(podobnie jak w b­­) konformacja nici na końcach cylindra jest często nieregularna

Kąt pod jakim układają się nici na powierzchni cylindra, mierzony między dwiema przeciwległymi nićmi, przybiera różne wartości w zależności od liczby nici

slide57

Four types of b-bulges

Classical

F, Y angles of residue 1 as for a structures; those for residue 2 and X for b-structures

G1

Link of a b- and turn structure

Gly almost exclusively at position 1

Broad

LargerH-bonddistancesbetweentheconsecutiveb-strands

GX

Strong preference for Gly at position X

b sheet amphipacity
b-sheet amphipacity

The hydrophobic and hydrophilic side chains are arranged on alternative sides of a b-sheet.

1B9C - RASMOL

slide59

Length of b-sheets in proteins

20 Å (6 aa residues)/strand on average, corresponding to single domain length

Usually up to do 6 b-strands (about 25 Å)

Usually and odd number of b-strands because of better accommodation of hydrogen bonds in a b-sheet

slide60

Covalentinterstrandconnectionsinb-sheets

There are two basic categories of connections between the individual strands of a beta sheet (Richardson, 1981). When the backbone enters the same end of the sheet that it left it is called a hairpin connection and when the backbone enters the opposite end it is called a crossover connection.

Crossover connections can be thought of as a type of helical connection of the strand ends. In globular proteins, right-handed crossovers are the rule, although a few examples of left-handed crossovers are available (e.g., subtilisin and glucose phosphate isomerase).

antiparallel

parallel

slide62

b-sheet topology in proteins

  • A b-hairpin connects the C-end of one strand with the N-end of another strand. If the strands are neighbors in sequence, this connection is denoted as „+1”; if they are separated by one strand it is denoted as „+2”.
  • The cross-over connection denoted as +1x if the connected strands are neioghbors in sequence or +2x if they are second neighbors

antyrównoległa

równoległa

slide66

An example of complex beta-sheets:

Silk Fibroin

- multiple pleated sheets provide toughness & rigidity to many structural proteins.

slide67

a-b and b-a connections

Conserved Gly residues and hydrophobic interactions between residues at positions Gly-4 and Gly+3

1CTF 100-120 - RASMOL

slide68

„Paperclips”

  • Turn structures at the ends of a-helices
slide69

Green key and b-arch

PCY 74-80 - RASMOL

secondary structure preference
Secondary Structure Preference
  • Amino acids form chains, the sequence or primary structure.
  • These chains fold in -helices, b-strands, b-turns, and loops (or for short, helix, strand, turn and loop), the secondary structure.
  • These secondary structure elements fold further to make whole proteins, but more about that later.
  • There are relations between the physico-chemical characteristics of the amino acids and their secondary structure preference. I.e., the b- branched residues (Ile, Thr, Val) like to sit in b-strands.
  • We will now discuss the 20 ‘natural’ amino acids, and we will later return to the problem of secondary structure preferences.
secondary structure preferences
Secondary Structure Preferences

helix strand turn

  • Alanine 1.42 0.83 0.66
  • Arginine 0.98 0.93 0.95
  • Aspartic Acid 1.01 0.54 1.46
  • Asparagine 0.67 0.89 1.56
  • Cysteine 0.70 1.19 1.19
  • Glutamic Acid 1.39 1.17 0.74
  • Glutamine 1.11 1.10 0.98
  • Glycine 0.57 0.75 1.56
  • Histidine 1.00 0.87 0.95
  • Isoleucine 1.08 1.60 0.47
  • Leucine 1.411.30 0.59
  • Lysine 1.14 0.74 1.01
  • Methionine 1.45 1.05 0.60
  • Phenylalanine 1.131.38 0.60
  • Proline 0.57 0.55 1.52
  • Serine 0.77 0.75 1.43
  • Threonine 0.83 1.19 0.96
  • Tryptophan 1.08 1.37 0.96
  • Tyrosine 0.69 1.47 1.14
  • Valine 1.06 1.70 0.50
secondary structure preferences1
Secondary Structure Preferences
  • helix strand turn
  • Alanine 1.42 0.83 0.66
  • Glutamic Acid 1.39 1.17 0.74
  • Glutamine 1.11 1.10 0.98
  • Leucine 1.411.30 0.59
  • Lysine 1.14 0.74 1.01
  • Methionine 1.45 1.05 0.60
  • Phenylalanine 1.131.38 0.60
  • Subset of helix-lovers. If we forget alanine (I don’t understand that things affair with the helix at all), they share the presence of a (hydrophobic) C-b, C-g and C-d (S-d in Met). These hydrophobic atoms pack on top of each other in the helix. That creates a hydrophobic effect.
secondary structure preferences2
Secondary Structure Preferences
  • helix strand turn
  • Isoleucine 1.08 1.60 0.47
  • Leucine 1.411.30 0.59
  • Phenylalanine 1.131.38 0.60
  • Threonine 0.83 1.19 0.96
  • Tryptophan 1.08 1.37 0.96
  • Tyrosine 0.69 1.47 1.14
  • Valine 1.06 1.70 0.50
  • Subset of strand-lovers. These residues either have in common their b-branched nature (Ile, Thr, Val) or their large and hydrophobic character (rest).
secondary structure preferences3
Secondary Structure Preferences

helix strand turn

  • Aspartic Acid 1.01 0.54 1.46
  • Asparagine 0.67 0.89 1.56
  • Glycine 0.57 0.75 1.56
  • Proline 0.57 0.55 1.52
  • Serine 0.77 0.75 1.43
  • Subset of turn-lovers. Glycine is special because it is so flexible, so it can easily make the sharp turns and bends needed in a b-turn. Proline is special because it is so rigid; you could say that it is pre-bend for the b-turn.
  • Aspartic acid, asparagine, and serine have in common that they have short side chains that can form hydrogen bonds with the own backbone. These hydrogen bonds compensate the energy loss caused by bending the chain into a b-turn.
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