Secondary structure of proteins sheets supersecondary structure
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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%



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


The ramachandran map
The Ramachandran map is effectively defined by the


Conformations of a terminally blocked amino acid residue
Conformations of a terminally-blocked amino-acid residue is effectively defined by the

E

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

C7eq

C7ax


A ramachandran plot for bpti m6 10
A is effectively defined by the Ramachandran plot for BPTI(M6.10)




Dominant fieldb-turns


Types of b turns in proteins
Types of fieldb-turns in proteins

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


Older classification
Older classification field

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


f fieldi+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


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

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


f fieldi+1=-80o, yi+1=80o, fi+2=80o, yi+2=-80o


cis-proline field

|yi+1|»80o, |fi+2|<60o

|yi+1|»60o, |fi+2|»180o


Hydrogen bond geometry in fieldb-turns

Type of structure

Average for b-turns

g-turn

Asx-type b-turns


Helical structures field

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

Helices do have handedness.


Geometrical parameters of helices field

Average parameters of helical structures

Turns closed by H-bond

H-bond

radius

Type


Idealized hydrogen-bonded helical structures: field

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


Schematic representation fielda-helices: helical wheel

3.6 residues per turn = a residue every 100o.



Amphipatic (or amphiphilic) helices field

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



Length of fielda-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) field

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.


Structure field

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


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


The spacefill modells, CPK colouring b-helix


Comparison of a helical and b sheet structure
Comparison of spacefill modells, CPK colouring a-helical and b-sheet structure


B sheet s tructures
b spacefill modells, CPK colouring -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!


A single b strand
A single spacefill modells, CPK colouring b-strand


An example of b sheet
An example of spacefill modells, CPK colouring b-sheet


Antiparallel sheet l6 7
Antiparallel sheet (L6-7) spacefill modells, CPK colouring

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) spacefill modells, CPK colouring

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

2TRX.PDB


Residues/turn spacefill modells, CPK colouring

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.


Schemes for antiparallel (a) and parallel (b) spacefill modells, CPK colouring b-sheets


Dipole moment of b sheets
Dipole moment of spacefill modells, CPK colouring 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


The b sheets are stabilized by long range hydrogen bonds and side chain contacts
The spacefill modells, CPK colouring b-sheets are stabilized by long-range hydrogen bonds and side chain contacts


b spacefill modells, CPK colouring -sheets are pleated


And the ruffles add flavor! spacefill modells, CPK colouring

  • 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)


b spacefill modells, CPK colouring -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


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 the intrachain hydrogen bonds in the presence of side-chain crowdingb-sheets

parallel

‘twisted’

anti-parallel


The the intrachain hydrogen bonds in the presence of side-chain crowding geometry of parallel­­ twistedb -sheets

thioredoxin

trioseposphate isomerase


Parallel the intrachain hydrogen bonds in the presence of side-chain crowdingb-structures occur mostly in a/b proteins where the b-sheet is covered by a-helical helices


Geometry of antiparallel the intrachain hydrogen bonds in the presence of side-chain crowding­¯b-sheets (mostly outside proteins and between domains)

twisted (coiled)

Multistrand twisted

Cyllinders

Threestrand with a b-bulge

Three strand helicoidal

Cupola (dome)


Example of a coiled two-strand antiparallel the intrachain hydrogen bonds in the presence of side-chain crowdingb-sheet

TERMOLIZYNA-RASMOL


Example of a three-strand antiparallel the intrachain hydrogen bonds in the presence of side-chain crowdingb-structure

RYBONUKLEAZA-RASMOL

Ribonuclease A

  • The central strand is least deformed


Geometria skręconych (ang. the intrachain hydrogen bonds in the presence of side-chain crowdingtwisted) 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


Example of a cyllindrical ( the intrachain hydrogen bonds in the presence of side-chain crowdingb-barrel) structure


Large antiparallel the intrachain hydrogen bonds in the presence of side-chain crowdingb-sheets: twisted planes not barrels

2CNA (3CNA) i 3BCL

Concavalin


b the intrachain hydrogen bonds in the presence of side-chain crowding-bulges


Local the intrachain hydrogen bonds in the presence of side-chain crowdinga-state at the bulging residue

1

X

2


Four types of the intrachain hydrogen bonds in the presence of side-chain crowdingb-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 the intrachain hydrogen bonds in the presence of side-chain crowding-sheet amphipacity

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

1B9C - RASMOL


Length of the intrachain hydrogen bonds in the presence of side-chain crowdingb-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


Covalent the intrachain hydrogen bonds in the presence of side-chain crowdinginterstrandconnectionsinb-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


b the intrachain hydrogen bonds in the presence of side-chain crowding-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


Topologia the intrachain hydrogen bonds in the presence of side-chain crowdingb struktur białkowych


Typical connections in b structures
Typical connections in the intrachain hydrogen bonds in the presence of side-chain crowdingb-structures


An example of complex beta-sheets: the intrachain hydrogen bonds in the presence of side-chain crowding

Silk Fibroin

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


a-b the intrachain hydrogen bonds in the presence of side-chain crowding and b-a connections

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

1CTF 100-120 - RASMOL


„Paperclips” the intrachain hydrogen bonds in the presence of side-chain crowding

  • Turn structures at the ends of a-helices


Green key and the intrachain hydrogen bonds in the presence of side-chain crowdingb-arch

PCY 74-80 - RASMOL


Secondary structure preference
Secondary Structure Preference the intrachain hydrogen bonds in the presence of side-chain crowding

  • 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 the intrachain hydrogen bonds in the presence of side-chain crowding

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 the intrachain hydrogen bonds in the presence of side-chain crowding

  • 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 the intrachain hydrogen bonds in the presence of side-chain crowding

  • 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 the intrachain hydrogen bonds in the presence of side-chain crowding

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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