SECONDARY STRUCTURE OF
PROTEINS: HELICES, 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
Because of peptide group planarity, main chain conformation is
effectively defined by the f and y angles.
The Ramachandran map
Conformations of a terminally-blocked amino-acid residue
E
Zimmerman, Pottle, Nemethy, Scheraga,
Macromolecules, 10, 1-9 (1977)
C7eq
C7ax
A
Ramachandran
plot for BPTI
(M6.10)
Energy maps of Ac-Ala-NHMe and Ac-Gly-AHMe
obtained with the ECEPP/2 force field
Energy curve of Ac-Pro-NHMe obtained with the
ECEPP/2 force field
fL-Pro-68o
Dominant b-turns
Types of b-turns in proteins
Hutchinson and Thornton, Protein Sci., 3, 2207-2216 (1994)
Older classification
Lewis, Momany, Scheraga, Biochim. Biophys. Acta, 303, 211-229 (1973)
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=90o, yi+2=0o
fi+1=60o, yi+1=30o, fi+2=60o, yi+2=30o
fi+1=-60o, yi+1=120o, fi+2=80o, yi+1=0o
fi+1=60o, yi+1=-120o, fi+2=-80o, yi+1=0o
fi+1=-80o, yi+1=80o, fi+2=80o, yi+2=-80o
cis-proline
|yi+1|80o, |fi+2|<60o
|yi+1|60o, |fi+2|180o
Hydrogen bond geometry in b-turns
Type of structure
Average for bturns
g-turn
Asx-type b-turns
Helical structures
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
Average parameters of helical structures
Type
H-bond
Size of the
ring closed by
the H-bond
radius
Idealized hydrogen-bonded helical structures:
310-helix (left), a-helix (middle), p-helix (right)
Criterion for hydrogen bonding:
the DSSP formula
Define Secondary Structure of Proteins
qN=qO=-0.42 e ; qH=qC=+0.20 e
Kabsch W, Sander C (1983). "Dictionary of protein secondary structure: pattern
recognition of hydrogen-bonded and geometrical features". Biopolymers 22 (12):
2577–637
Schematic representation a-helices: helical wheel
3.6 residues per turn = a residue every 100o.
Examples of helical
wheels
Amphipatic (or amphiphilic) helices
One side contains hydrophobic aminoacids, 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
download cytochrome B562
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)
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.
The f, y, and w angles of regular and polyproline helices
Structure
f
y
w
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
residues/turn
translation/residue
Deca-glycine in PPII and PPI without hydrogen atoms,
spacefill modells, CPK colouring
PPI-PRO.PDB
PPII-PRO.PDB
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).
The b-helix
Comparison of ahelical and bsheet structure
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!
A single b-strand
An example of b-sheet
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)
The amino acid R groups face up & down from a beta sheet
2TRX.PDB
Structure
f
Antiparallel b
y
w
Residues/turn
Translation/residue
-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) 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
The b-sheets are stabilized by long-range
hydrogen bonds and side chain contacts
b-sheets are pleated
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) than the helical structures (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-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
parallel
‘twisted’
anti-parallel
The geometry of parallel twisted b -sheets
thioredoxin
trioseposphate isomerase
Parallel bstructures occur
mostly in a/b
proteins where the
b-sheet is covered
by a-helical helices
twisted (coiled)
Geometry of
antiparallel  bsheets (mostly
outside proteins and
between domains)
Multistrand
twisted
Cyllinders
Threestrand
with a b-bulge
Three strand
helicoidal
Cupola (dome)
Example of a coiled two-strand antiparallel b-sheet
Stereoscopic views of some examples of two-strand,
coiled antiparallel b-structures: a) pancreatic trypsin
inhibitor, b) lactate dehydrogenase, TERMOLIZYNA-RASMOL
c) thermolysin.
Example of a three-strand antiparallel b-structure
Ribonuclease A
•The central strand is least deformed
The geometry of twisted) b structures

A fragment of the antiparallel b-cyllinder in chymotrypsin, with local
deviations from the ideal b-structure. Note that the divergence of the
strands near cyllinder edge which occurrs to relieve local strains
results in twisting the strands.
In cyllindrical antiparallel b-sheets  (as in parallel b-sheets ) strand conformation at
cyllinder ends is often irregular.
The interstrand angle depends on the number of strands in a cyllinder.
Example of a cyllindrical (b-barrel) structure
Large antiparallel b-sheets: twisted planes not barrels
2CNA (3CNA) and 3BCL
Concavalin
b-bulges
1
X
2
Local a-state at the
bulging residue
Four types of b-bulges
Classical
G1
Broad
GX
F, Y angles of
residue 1 as for a
structures; those for
residue 2 and X for
b-structures
Link of a b- and
turn structure
Larger H-bond
distances between
the consecutive
b-strands
Strong
preference
for Gly at
position X
Gly almost
exclusively at
position 1
b-sheet amphipacity
The hydrophobic and hydrophilic side chains are arranged on alternative sides of a bsheet.
1B9C - RASMOL
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
Covalent interstrand connections in b-sheets
antiparallel
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 lefthanded crossovers are available (e.g.,
subtilisin and glucose phosphate
isomerase).
parallel
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”.
antiparallel
The cross-over connection denoted as +1x
if the connected strands are neioghbors in
sequence or +2x if they are second
neighbors
parallel
Topologia b struktur białkowych
Typical connections in b-structures
An example of
complex beta-sheets:
Silk Fibroin
- multiple pleated
sheets provide
toughness & rigidity
to many structural
proteins.
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
„Paperclips”
• Turn structures at the ends of a-helices
Green key and b-arch
PCY 74-80 - RASMOL
Secondary Structure Preference
• Amino acids form chains, the sequence or primary structure.
• These chains fold in a-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 tertiary
structure.
• There are relations between the physico-chemical characteristics of the
amino acids and their secondary structure preference. I.e., the bbranched 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
•Alanine
•Arginine
•Aspartic Acid
•Asparagine
•Cysteine
•Glutamic Acid
•Glutamine
•Glycine
•Histidine
•Isoleucine
•Leucine
•Lysine
•Methionine
•Phenylalanine
•Proline
•Serine
•Threonine
•Tryptophan
•Tyrosine
•Valine
helix
1.42
0.98
1.01
0.67
0.70
1.39
1.11
0.57
1.00
1.08
1.41
1.14
1.45
1.13
0.57
0.77
0.83
1.08
0.69
1.06
strand
0.83
0.93
0.54
0.89
1.19
1.17
1.10
0.75
0.87
1.60
1.30
0.74
1.05
1.38
0.55
0.75
1.19
1.37
1.47
1.70
turn
0.66
0.95
1.46
1.56
1.19
0.74
0.98
1.56
0.95
0.47
0.59
1.01
0.60
0.60
1.52
1.43
0.96
0.96
1.14
0.50
Secondary Structure Preferences
•
•
•
•
•
•
•
•
•
Alanine
Glutamic Acid
Glutamine
Leucine
Lysine
Methionine
Phenylalanine
helix
1.42
1.39
1.11
1.41
1.14
1.45
1.13
strand
0.83
1.17
1.10
1.30
0.74
1.05
1.38
turn
0.66
0.74
0.98
0.59
1.01
0.60
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, Cg 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 Preferences
•
•
•
•
•
•
•
•
Isoleucine
Leucine
Phenylalanine
Threonine
Tryptophan
Tyrosine
Valine
helix
1.08
1.41
1.13
0.83
1.08
0.69
1.06
strand
1.60
1.30
1.38
1.19
1.37
1.47
1.70
turn
0.47
0.59
0.60
0.96
0.96
1.14
0.50
• Subset of strand-lovers. These residues either have in common their bbranched nature (Ile, Thr, Val) or their large and hydrophobic
character (rest).
Secondary Structure Preferences
•
•
•
•
•
•
•
helix
Aspartic Acid 1.01
Asparagine
0.67
Glycine
0.57
Proline
0.57
Serine
0.77
strand
0.54
0.89
0.75
0.55
0.75
turn
1.46
1.56
1.56
1.52
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.