Ramachandran Plot

Proteins – Secondary Structures

 Ramachandran Plot
unfolded polymer - folded form

The rigidity of the peptide unit and the restricted set of

allowed phi and psi angles limits the number of structures
accessible to the unfolded form sufficiently to allow protein
folding to occur
 Unlike the simple and beautiful double stranded DNA
Ramachandran Plot
structure, protein conformations are complex in nature and
lack any kind of symmetry

 Such structural irregularity is required for the proteins to

fulfill their diverse function as they have to recognize many
thousands of different molecules in the cell by detailed
three dimensional interactions, which require diverse and
irregular structures of protein molecules

 But within the protein structure, there are also certain

regular features which is their secondary structure
 The interior of the protein is Hydrophobic

Ramachandran Plot
 The globular proteins fold into 3 dimensional / 4 D str
 While folding, the hydrophobic side chains are packed into
the interior of the molecule – driving force, thus creating a
hydrophobic core and a hydrophilic surface
 In the folded protein, the main chain peptide backbone
polar groups C=O and N-H group must be neutralized by
the formation of H bonds
 This leads to the formation of regular secondary structures
within the interior of the protein molecule – Secondary
structures
 Secondary Structure

 The chemical nature of the carboxyl and amino groups of all

amino acids permit hydrogen bond formation (stability) and
hence defines secondary structures within the protein.
 The R group has an impact on the likelihood of secondary
structure formation (proline is an extreme case)
 This leads to a propensity for amino acids to exist in a
particular secondary structure conformation
 Helices and sheets are the regular secondary structures, but
irregular secondary structures exist and can be critical for
biological function
 Overview on Secondary Structures

 Secondary structure is the initial folding pattern (periodic

repeats) of the linear polypeptide
 3 main types of secondary structure: α- helix, β-sheet and
turns
 Approximately 31% of the residues in known globular
proteins are located in alpha helices and 28% in beta
strands
 Structures that cannot be classified as one the standard
three classes is usually grouped into a category called
other or random coils – unfolded conformations
 Secondary structures are stabilized by hydrogen bonds
 The segments of alpha helix and beta sheets in globular
proteins are generally short, being limited to the diameter
of the protein globule. The length of an alpha helix is
usually 10 – 12 residues and that of a beta strand is 3 – 10
residues.
 Alpha Helix – coiled structure stabilized by intrachain
Hydrogen bonding

 First described by Linus Pauling (1951)

 Built from one continuous polypeptide chain
 Classical element, size varies from 4 or 5 to over 40
residues
 Represented by cylinders or coiled ribbons
 In a helical conformation, the relationship of one peptide unit
to the next is the same for all alpha carbons. This means that
the dihedral angle pair phi and psi are the same for each
residue in the helical conformation. The phi and psi pair is
approximately -60° and -50° for a consecutive stretch of
residues.
 Two parameters describe the helix about the axis – n is the
number of residues per helical turn and r is the rise per helical
residue
 A positive value of n denotes a right handed helix. Only right-
handed are observed in nature as this produces less clashes
 The side chain project outward into solution from the alpha
helix – Tilted towards the amino end of the helix
 The helix is stabilized by H-bonds between –N-H and –C=O
groups of every 4th amino acid
 All hydrogen bonds are satisfied except at the ends = stable
 There are 3.6 residues per turn which corresponds to 5.4A
per residue.
 Average length – 10 residues i.e three turns
 α-helices can wind around each other to form ‘coiled coils’
that are extremely stable and found in fibrous structural
proteins such as keratin, myosin (muscle fibers) etc
The alpha helix has a dipole moment (0.5 – 0.7 unit charge)
 The alpha helix has a dipole moment (0.5 – 0.7 unit charge).
All the NH and CO groups are joined with H bonds except
the first NH group and last CO group at the end of the alpha
helix. As a consequence, the ends are always polar and are
almost at the surface of the proteins

 Negatively charged groups such as phosphate ions

frequently bind to the amino ends of alpha helices – Ligand
interactions. The dipole moment of an alpha helix as well as
the possibility of hydrogen bonding to free NH groups at the
end of the helix favors such binding
 Some amino acids are preferred in alpha helices

 Eight most common residues as helix formers – Glu, Met,

Ala, Leu, Lys, Phe, Gln, Trp
 Eight least common residues as Helix formers – Gly, Pro,
Asn, Thy, Cys, Ser, Thr, Arg
Many alpha helices are amphipathic. They have
predominantly non polar side chains along one side of the
helical cylinder and polar residues along the remainder of its
surfaces.

A helical wheel will outline the surface properties of the

helix
 A helical wheel is a type of plot or visual representation used to
illustrate the properties of alpha helices in proteins.
 The sequence of amino acids that make up a helical region of the
protein's secondary structure are plotted in a rotating manner
where the angle of rotation between consecutive amino acids is
100° (360 / 3.6), so that the final representation looks down the
helical axis.
 The plot reveals whether hydrophobic amino acids are
concentrated on one side of the helix, usually
with polar or hydrophilic amino acids on the other.
 This arrangement is common in alpha helices within globular
proteins, where one face of the helix is oriented toward
the hydrophobic core and one face is oriented toward
the solvent-exposed surface.
 Other (Rarer) Helix Types

 Variations on the alpha helix in which the chain is either

more loosely or more tightly coiled with hydrogen bonds
to residues n+5 or n+3 instead of n+4 are called the Pi
helix or 310 helix
 Rare occurrence
 Occur at the ends of the alpha helices or as single turn
helices
 Not energetically favorable
 310 Helix

 The amino acids in a 310 Helix are arranged in a right-

handed helical structure.
 Each amino acid corresponds to a 120° turn in the helix (i.e.,
the helix has three residues per turn) and a larger radius of
2.0 Å (= 0.2 nm) along the helical axis and has 10 atoms in
the ring formed by making the hydrogen bond (3.2 residues
per turn).
 Residues in 310-helices typically adopt (φ, ψ) dihedral
angles near (−49°, −26°). More generally, they adopt
dihedral angles such that the ψ dihedral angle of one residue
and the φ dihedral angle of the next residue sum to roughly
−75°. Hence narrower and more elongated. Usually seen at
the end of an alpha helix
 Π helix

 Less favorable geometry

 4 residues per turn
 The amino acids in a standard π-helix are arranged in a right
handed helical structure
 Each amino acid corresponds to a 87° turn in the helix (i.e.,
the helix has 4.1 residues per turn), and a translation of
1.15 Å (=0.115 nm) along the helical axis.
 The N-H group of an amino acid forms a hydrogen bond with
the C=O group of the amino acid five residues ahead
 The majority of π-helices are only 7 residues in length and
do not adopt regularly repeating (φ, ψ) dihedral angles
throughout the entire structure like that of α-helices or ß-
sheets.
 Dihedral angles exist such that the ψ dihedral angle of one
residue and the φ dihedral angle of the next residue sum to
roughly -125°.
 The first and last residue pairs sum to -95° and -105°,
respectively
 Proline is often seen immediately following the end of π-
helices
 Beta Sheets – Stabilized by H bonding between
polypeptide strands
 Beta sheets are another major structural element in globular
proteins containing 20 – 28% of all residues
 Built up from a combination of several regions of the
polypeptide chain
 Fully extended stretches of 5 or more amino acids are called
β- strands.
 β-strands organized next to each other make β-sheets
 The beta sheet is sometimes called the beta pleated sheet
since sequentially neighboring Cα atoms are alternately
above and below the plane of the sheet
 Represented by broad arrows
 Due to the extended nature of the chain there are no
significant intra segment hydrogen bonds and van der
waals interactions between atoms of neighboring residues.
 In the beta sheets, the hydrogen bonding occurs between
the C=O of one beta strand and the N-H of another beta
strand and vice versa
 If adjacent strands are oriented in the same direction (N-
end to C-end), it is a parallel β-sheet, if adjacent strands
run opposite to each other, it is an antiparallel β-sheet.
There can also be mixed β-sheets
 Fatty acid binding proteins are made almost entirely of β-
sheets
 Phi and psi are rotated approximately 180 degrees from each
other.
 The backbone dihedral angles phi = -120 and psi = +120
producing a translation of 3.2 to 3.4A / residue in anti-
parallel and anti parallel strands respectively
Fatty acid binding protein
 Twist of beta sheet

 The classical beta sheets originally proposed are planar but

most sheets observed in globular proteins are twisted (0 to
30 degree / residue)
 Antiparallel beta sheets are more often twisted than
parallel sheets and exhibits more positive values of phi and
psi
 Beta bulge is a variant; two residues on one strand forms
hydrogen bonds with residue on other – causes one strand
to bulge – occurs most frequently in parallel sheets
 Bulges are most often found in antiparallel sheets with
approximately 5% of bulges occurring in parallel strands
Other Secondary Structures – Turns, Loops – change the direction
of polypeptide chain

 Turn is a general term that describes several types of

nonregular secondary structure in protein structures that
cause a change in the direction of the polypeptide chain
 Turns were first identified by Venkatachalam (1968) who
found three types each containing a hydrogen bond between
the carbonyl oxygen of residue i and the amide nitrogen of
i+3. These three types of turns are designated I, II, and III.
 Type III is simply a single turn of 3.10 helix
 Turns are also known as reverse turns (since they reverse
the chain direction). They include b-turns, g-turns,
hairpins, W-loops, and b-bulges (although for b-bulges,
the change in direction is much less than that of other
types of turn)

 Each of these three types of turns has a backbone mirror-

image conformation that is also found in some proteins
designated I', II', and III' even though these
conformations are disfavored due to steric hindrance.
 Contain between 6 and 16 residues

 Turns are distinguished from the regular types of secondary

structure (a-helix and b-sheet) in that they do not have
repetitive backbone conformations and hydrogen bonding
patterns

 Most residues in turns, however, adopt backbone

conformations close to the a-helical or b-strand
conformations.
 Glycine or proline residues are often found in turns,
especially where unusual backbone conformations are
required
 Contain predominantly polar residues
 Turns are usually found at the surface of proteins, where
the peptide bonds that do not interact with protein atoms
can form hydrogen bonds with the solvent.
 Compact and globular in structure
 Usually present as antigen binding sites or enzyme active
sites
 In an α-turn the end residues are separated by four peptide
bonds (i – i + 4).
 In a β-turn (the most common form), by three bonds (i – i +
3).
 In a γ-turn, by two bonds (i – i + 2).
 In a δ-turn, by one bond (i – i + 1).
 In a π-turn, by five bonds (i – i + 5).
Functions Type I Turn Type II Turn Type III Turn

Occurrence Type I turns occur most This is a single turn of

frequently (2-3 times right-handed (III) and
more frequently than type left-handed (III') 3.10
II). helix, respectively.

The mirror-image types I'

and II' are rare but type I'
appears to be preferred in
beta-hairpins
Hydrogen The hydrogen bond The hydrogen bond The hydrogen bond
Bond between CO of residue i between CO of between CO of residue
and NH of residue i + 3 residue i and NH of i and NH of residue i +
residue i + 3 3

Dihedral -60, -30 and -90, 0 of -60, -120 and 80, 0 The backbone dihedral
angles residues i + 1 and i + 2 of residues i + 1 and angles of residue are
respectively for type I i + 2 respectively (-60, -30) and (-60, -
Turns for type I Turns 30) of residues i+1
and i+2, respectively
of the classical type
III turn.
position Proline is often found in i + 1 Glycine is favoured in i
dependent in type 1 turn as its phi angle + 1 position as it
amino acid is restricted to -60 and its requires a positive
preferences imide nitrogen does not (left handed) phi
require a hydrogen bond. value.

Type I can tolerate all residues

in positions i to i+3 with the
exception of Pro at position
i+2. Proline is favored at
position i+1 and Gly is favored
at i+3 in type I and II turns.
The polar side chains of Asn,
Asp, Ser, and Cys often
populate position i where they
can hydrogen bond to the
backbone NH of residue i+2.
Loop regions are at the surface of protein molecules

Type I Type II