• Conformation – spatial arrangement
of atoms in a protein
• Native conformation – conformation
of functional protein
One polypeptide chain - monomeric protein
More than one - multimeric protein
Homomultimer - one kind of chain
Heteromultimer - two or more different
(e.g. Hemoglobin is a heterotetramer. It has
two alpha chains and two beta chains.)
Protein Classification(chemical nature and
• Simple – composed only of amino acid residues
• Conjugated – contain prosthetic groups
(metal ions, co-factors, lipids, carbohydrates)
Example: Hemoglobin – Heme
Protein Classification – simple proteins
polypeptides arranged in long strands or sheets
water insoluble (lots of hydrophobic AA’s)
strong but flexible
Structural (keratin, collagen, elastins)
polypeptide chains folded into spherical or
contain several types of secondary structure
diverse functions (enzymes, regulatory proteins)
ORGANISATION OF PROTEINS
a) Primary Structure of a protein is the linear sequence
of amino acids & location of disulphide bonds of its
polypeptide chain or chains (if it comprises more than one
polypeptide). Only covalent peptide bond
b) Secondary Structure is the local spatial relationship of
neighboring amino acid in the polypeptide backbone atoms
without regard to the conformations of its side chains.
c) Tertiary Structure- the 3 D structure of an entire
polypeptide. Describes the folding of the secondary
structural elements and specifies the position of each atom
including those of the side chains.
d) Quaternary Structure refers to the spatial
arrangement of the polypeptides (subunits) if present in a
Organization of Proteins
a) Primary Structure (10) of a protein refers to the
linear number and order of the amino acids
present and location of disulphide bonds of its
polypeptide chain or chains (if it comprises more than
one polypeptide) Primary structure determines Biological
Designation= N-terminal end on the left as No 1 with free αamino gp), C-terminal end a free a-carboxyl group) is to the
Sequence predetermined by the nucleotide sequence of the
Covalent peptide bond is the only type of bond linking amino
• The peptide bond has a partial double-bond character it is
shorter than a single bond and is therefore RIGID and
PLANAR [This prevents free rotation around the bond between the
carbonyl carbon and the nitrogen of the peptide bond]
• The peptide bond is generally a trans bond. [There will be
steric interference of R-Group if it is in Cis position.]
• The – C =O and –NH groups of the peptide bond are polar
and are involved in hydrogen bonds but they are uncharged
[they neither accept nor give off protons]
1o Structure Determines 2o, 3o, 4o
• Sickle Cell Anemia – single amino acid
change in hemoglobin related to disease
• Osteoarthritis – single amino acid change in
collagen protein causes joint damage
2O Structure is the local spatial relationship of
neighboring amino acids in a polypeptide.
An important characteristic of 2o structure is the
formation of hydrogen bonds between –CO group of one
peptide and the –NH group of another nearby peptide
1. α helix
β- pleated sheet
3. β bend
2o Structure Related to Peptide Backbone
•Double bond nature of peptide
bond cause planar geometry
•Free rotation at N - αC and αCcarbonyl C bonds
•Angle about the C(alpha)-N bond
is denoted phi (φ)
•Angle about the C(alpha)-C bond is
denoted psi (ψ)
•The entire path of the peptide
backbone is known if all phi and psi
angles are specified
•Describes acceptable φ/ψ angles for individual
AA’s in a polypeptide chain.
•Helps determine what types of 2o structure
• First proposed by Linus Pauling and Robert
Corey in 1951
• Identified in keratin by Max Perutz
• A ubiquitous component of proteins
• Stabilized by H-bonds
Right handed turn: 3.6
•Rise per residue:
•Rise per turn
(pitch): 3.6 x 1.5A
= 5.4 Angstroms
located 4 AA’s
away forms 13
All H-bonds in the
oriented in the
giving the helix a
dipole with the Nterminus being
positive and the
•Side chain groups
point outwards from
•AA’s with bulky side
chains less common in
•Glycine and proline
One side of the helix (dark) has mostly hydrophobic
Two amphipathic helices can associate through
Beta-Strands and Beta-Sheets
• Also first postulated by Pauling and Corey, 1951
• Strands may be parallel or antiparallel
• Rise per residue:
– 3.47 Angstroms for antiparallel strands
– 3.25 Angstroms for parallel strands
– Each strand of a beta sheet may be pictured as
a helix with two residues per turn
• Beta-sheets formed
from multiple side-byside beta-strands.
• Can be in parallel or
• Anti-parallel betasheets more stable
• Side chains point alternately above and below the
plane of the beta-sheet
• 2- to 15 beta-strands/beta-sheet
• Each strand made of ~ 6 amino acids
Loops and turns
• Loops usually contain hydrophillic residues.
• Found on surfaces of proteins
• Connect alpha-helices and beta-sheets
• Loops with < 5 AA’s are called turns
• Beta-turns are common
• allows the peptide chain to reverse direction
• carbonyl C of one residue is H-bonded to the amide
proton of a residue three residues away
• proline and glycine are prevalent in beta turns
Supersecondary Structures (Motifs)
• Certain combinations of secondary structures (α-helix & β-pleated
sheet) can be observed in different folded protein structures called
• They are also called structural motifs. Eg. helix-turn-helix
• α-Helix and β-pleated sheet are combined in many ways as the
polypeptide chain folds back on itself in a protein.
• Glycine & proline are frequently encountered in reverse turns, at
which polypeptide chain changes direction.
• Eg. βαβ unit - 2 parallel strands of β-sheet is connected by a
stretch of α-helix.
Tetriary structure of a protein is the 3-D structure of a
protein. The 3-D structure depends on;
Folding of the secondary structural elements
Geometric relationship between distant segments of
Relationship of the side chains with one another in
• Major cohesive forces in tertiary structures are
noncovalent forces such as hydrophobic interactions
between amino acid side chains.
• Other forces – electrostatic, H-bonding, S-S
• In water-soluble globular proteins, surface is occupied by
hydrophilic side chains, while the nonpolar residues form
the hydrophobic core.
Three-dimensional folding of the protein myoglobin
Hydrogen bonds : (a) are formed by sharing of a hydrogen
between 2 electron donors.
(b) Hydrogen releasing groups are –NH [of imidazole, indole and
peptide] -OH [serine and threonine] –NH2 [lysine and Arginine]
(c) Hydrogen accepting groups are COO- [aspartic, Glutamic C=O
[peptide and S-S [disulphide]
Electrostatic bonds: [ Ionic bonds]: (a) are the βattractive forces
between 2 opposite charges or repulsion between 2 similar charges
(b) Positive charges are produced by lysine, arginine and histidine
(c) Negative charges are provided by βand ץcarboxyl groups of aspartic
acid and glutamic acid
• Hydrophobic bonds: are formed by interactions between
nonpolar hydrophobic side chains by eliminating water
• Van der Waals forces: (a) are attractive forces operating
between all atoms due to oscillating dipoles.
(b) Although very weak, vander waals forces collectively
contribute maximum towards the stability of protein
Quaternary Structure ( 40 )
• Formed by interaction between different polypeptides
• Quaternary structure found in proteins with more
than one polypeptide
• Subunits held together by non-covalent interactions
inter chain disulphide bonds.
Eg. Hemoglobin consists of 2 α and 2 β subunits
Protein Folding Pathways
Random or Directed?
Evidence indicates that proteins fold to their native
conformations via directed pathways rather than via
random manner. Not well understood.
Directed Pathway for Protein Folding
• Protein folding begins with formation of local segments of secondary
structure (α helices and β sheets). Very rapid process.
• These segments condense to resemble the secondary structure of native
• Secondary structures become stabilized and 3o structures begin to
• Protein undergoes complex motions to form the hydrophobic core
• In multi-subunit protein, the subunits associate through slight
conformational adjustments to form the quaternary structure..
Protein Folding Pathways cont…….
• Folded protein usually are quite compact but bonds may be
available to bind metal ions, cofactors, substrates etc which can
increase stability of protein.
• If sulphydryl groups are located on the surface or near the
points of contact between the associating species, the formation
S-S linkages can serve to stabilize the structures.
Protein disulphide isomerases catalyse the breakage and
formation of disulphide bonds so that incorrect linkages are
not stabilised and allowing stable ones to be formed.
Chaperone proteins or Chaperonins bind to unfolded or partiallyfolded polypeptide chains.
Prevents improper association of exposed segments which can
lead to non-native folding, polypeptide aggregation or precipitation.
ERROR IN PROTEIN FOLDING AND DISEASES
• Misfolded versions of proteins normally present in the same tissues
can aggregate among themselves and form fibrous deposits. In the
brain, this gives rise to a number of neurological diseases.
Fibrous proteins or plaques are deposited in brain of patients and is
due to alteration of a normal protein.
The neurofibrillary tangles are paired helical filaments made up of
Error in Protein Folding and Diseases
2. Bovine spongiform encephalopathy (“mad cow disease”)
( Creutzfeldt-Jacob Disease)
Proteins normally found in brain and nervous system [PrP] change into
some abnormal protein [PrPsc] known as Prions. They have normal
primary structure but abnormal tertiary structure.
The abnormal proteins convert normal proteins into abnormal varieties,
producing a chain reaction that generates new infectious materials.
The normal protein PrP is 253 aminoacids, is soluble and can be digested
by lysosomal enzymes but abnormal PrPsc is insoluble and cannot
be digested and is accumulated inside nerve cells which damage brain
• The phenomenon of disorganization of native
protein structure is known as
denaturation.Denaturation results in the loss of
secondary,tertiary and quaternary structure of
proteins .This involves a change in physical
,chemical and biological properties of protein
Agents of denaturation
• Physical agents-Heat,voilent shaking,xrays,UV radiation.
• Chemical agents-Acids,alkalies,organic
Characteristics of denaturation
Native helical structure of protein is lost.
Primary structure of a protein with peptide linkage remains intact
Protein loses it’s biological activities.
Denatured protein becomes insoluble in solvent in which it was
• Viscosity of denatured protein increases while it’s surface tension
• Denaturation is associated with increase in ionizable and
sulfahydryl group of protein.this is due to loss of hydrogen and
Characteristics of denaturation
• Denatured protein is more easily digested. this is due to increase
exposure of peptide bonds to enzymes.Ex-cooking causes
• Denaturation is usually irreversible.Ex-omelet can be prepared from
egg but the reversal is not possible.
• Careful denaturation is sometimes reversible
(Renaturation).Hemoglobin undergoes denaturation in the presence of
salicylate.By removal of salicylate ,hemoglobin is renatured.
• Denatured protein can’t be crystallized.
• Term ‘coagulum’ refers to semi-solid viscous precipitate
of protein.irreversible denaturation results in
coagulation.coagulation is optimum and requires lowest
temperature at isoelectric Ph.Albumins and globulins are
coagulable proteins.HEAT COAGULATION TEST IS
COMMONLY USED TO DETECT THE PRESENCE OF
ALBUMIN IN URINE.