- Sailee Gurav
It‟s completely defined & predictable.
Each amino acid in one of these giant
macromolecules is located at a specific site
within the structure , giving the protein the
It can be described at several levels of
organization , each emphasizing a different
aspect & each dependent on different types
It‟s simply the sequence of the amino acid
By convention, written from amino end to
It is important as it is the foundation in which
ultimately the higher structures of the protein
are determined, and thus the function of the
It is a local, regularly occurring structure in
proteins and is mainly formed through hydrogen
bonds between backbone atoms.
Pauling & Corey studied the secondary
structures and proposed 2 conformations.
The α helix and β sheets.
Right-handed coiled or spiral
3.6 residues per turn stabilized by
Hydrogen bonding between
C' = O of residue n and NH of
residue n + 4
All C'O and NH groups are joined
Except: Terminal NH and C'O
α-helix is tightly packed
Almost no free space within the
Amino acid side chains are on the
outside of the helix
Roughly point “downwards”
Resembles branches of a
Most common location of α helices
is along the protein periphery
One side facing the solution
One side facing hydrophobic
Also called the 4₁₃
Very loosely coiled Hbonding pattern n + 5
Raerly found in nature.
Very tightley coiled Hbonding pattern n+3 rarely
found in nature
Beta sheets are another major structural element in globular proteins
containing 20–28 % of all residues
The basic unit of a beta sheet is a beta strand with approximate
backbone dihedral angles phi = -120 and psi = +120
Two types: anti-parallel and parallel strand.
Due to the extended nature of the chain, no significant intra-segment
hydrogen bonds and van der Waals interactions between atoms of
Sometimes called the beta "pleated" sheet since sequentially
neighboring Ca atoms are alternately above and below the plane of
Main-chain NH and O atoms within a b
sheet are hydrogen bonded to each other.
The amino acids in successive strands have
alternating directions (anti-parallel).
Antiparallel beta sheets are considered
intrinsically more stable than parallel
sheets due to the more optimal
orientation of the interstrand hydrogen
Hairpin loops – often between anti-parallel beta strands
Omega loops – beginning and end close (6-16 residues)
Extended loops – more than 16 residues
Secondary structures are joined together by additional
structures called loops.
These patterns are called motifs
Defining motifs-small, specific combinations of secondary
A supersecondary structure is a compact
three-dimensional protein structure of
several adjacent elements of secondary
structure that is smaller than a protein
domain or a subunit
Tertiary structures is defined as the overall arrangement of polypeptide
chains in three-dimensional space, describing how secondary structures
arrange into supersecondary structures that in turn arrange into domains
and domains into tertiary structures.
Motif : a recognizable subcomponent of the fold – several motifs
usually comprise a domain
Fold: used differently in different contexts – most broadly a
reproducible and recognizable 3 dimensional arrangement
Domain: a compact and self folding component of the protein that
usually represents a discreet structural and functional unit
Tertiary structures can be divided into three main
The domain is the unit of tertiary structure
In globular proteins
Tertiary interactions are frequently stabilized by sequestration
of hydrophobic amino acid residues in the protein core
Consequent enrichment of charged or hydrophilic residues
on the protein's water-exposed surface.
In secreted proteins
disulfide bonds between cysteine residue helps to maintain
the protein's tertiary structure
They describes the arrangement of sub-units in a
protein consisting of more than one polypeptide
chain, where the sub-units may be identical or
The sub-units in a quaternary structure are held
together by non-covalent interactions where the
„contact regions‟ between the sub-units resemble the
interior of tertiary structure proteins as being
These structures cannot have mirror image superpositioning resulting in symmetrical distribution of
the sub-units in the quaternary structure.
Poly proline -II helix in proteins:
Structure & Function.
The polyproline type II (PPII) helix in recent years has
emerged clearly as a structural class not only of fibrillar
proteins but also of the folded and unfolded proteins.
The left-handed, extended PPII helix represents the only
frequently occurring regular structure .
Natively unfolded proteins have a high content of the
PPII helices identified by spectroscopic methods.
PPII is favorable for protein-protein and protein-nucleic
acid interactions and plays a major role in signal
transduction and protein complex assembly.
PPII helices do not necessarily contain proline,
but proline has high PPII propensity.
PPII helices are involved in transcription, cell
motility, self-assembly, elasticity, and bacterial
and viral pathogenesis, & has an important
structural role in amyloidogenic proteins.
PPII helices are not always assigned in
experimentally solved structures, & they are
rarely used in protein structure modeling.