Slide 1 : • Secondary structure is the initial folding
pattern (periodic repeats) of the linear
polypeptide
• 3 main types of secondary structure: a-
helix, ß-sheet and bend/loop
• Secondary structures are stabilized by
hydrogen bonds Secondary Structure
Slide 2 :
Slide 3 : • The a-helix is right-handed or clock-wise
• Each turn has 3.6 aa residues and is 5.4 Ao high
• The helix is stabilized by H-bonds between –N-H
and –C=O groups of every 4th amino acid
• a-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 a-helix
Slide 4 :
Slide 5 : • Extended stretches of 5 or more aa are called ß-
strands
• ß-strands organized next to each other make ß-sheets
• If adjacent strands are oriented in the same direction
(N-end to C-end), it is a parallel ß-sheet, if adjacent
strands run opposite to each other, it is an antiparallel
ß-sheet. There can also be mixed ß-sheets
• H-bonding pattern varies depending on type of sheet
• ß-sheets are usually twisted rather than flat
• Fatty acid binding proteins are made almost entirely
of ß-sheets ß-Pleated Sheet
Slide 6 :
Slide 7 : • Polypeptide chains can fold upon themselves
forming a bend or a loop.
• Usually 4 aa are required to form the turn
• H-bond between the 1st and 4th aa in the turn
• Bends are usually on the surface of globular
proteins
• Proline residues frequently found in bends / loops Bend / Loop
Slide 8 :
Slide 9 : • 3D folding or ‘bundling up’ of the protein
• Non-polar residues are buried inside, polar residues are
exposed outwards to aqueous environment
• Many proteins are organized into multiple ‘domains’
• Domains are compact globular units that are connected
by a flexible segment of the polypeptide
• Each domain is contributes a specific function to the
overall protein
• Different proteins may share similar domain structures,
eg: kinase-, cysteine-rich-, globin-domains Tertiary Structure
Slide 10 :
Slide 11 : • 5 kinds of bonds stabilize tertiary structure: H-bonds,
van der waals interactions, hydrophobic interactions,
ionic interactions and disulphide linkages
• In disulphide linkages, the SH groups of two
neighboring cysteines form a –S-S- bond called as a
disulphide linkage. It is a covalent bond, but readily
cleaved by reducing agents that supply the protons to
form the SH groups again
• Reducing agents include ß-mercaptoethanol Tertiary Structure
Slide 12 : • association of more than one polypeptides
• Each unit of this protein is called as a subunit and
the protein is an oligomeric protein
• Subunits (monomers) can be identical or different
• The protein is homopolymeric or heteropolymeric
• Disulfide bonds usually stabilize the oligomer Quaternary Structure
Slide 13 :
Slide 14 : • Each protein has a unique and specific 3D structure
that depends on the aa sequence. This is their native
conformation.
• Denaturing agents such as urea or guanidinium
chloride disrupt the 3D structure. This is called
denaturation
• Denaturation is reversible. Removal of denaturants
agents and sometimes, presence of a chaperones, is
required for refolding
• Protein folding is a cooperative ‘all or none’ process AA sequence dictates protein structure
Slide 15 : • Individual aa have a preference for specific 2o
structure
• a-helix (default): A, E, L, M, C
• ß-sheets (steric clash): V, T, I, F, W, Y
• Bends: P, G, N
• No definite rules for 3o structure. Determined by
overall sequence and tertiary interactions between
remote residues; decrease in free energy.
• Prediction based on computer calculations and
comparison to similar domains of known structure Prediction of Protein Structure
Slide 16 : THANK YOU