PROTEINS

STRUCTURE

Dr. Mehtab Alam

Assistant Professor
Department of Biochemistry
Dow International Medical College
Dow University of Health Sciences
 Learning Objectives
• At the end of session the student should
be able to:
– Discuss structural level of proteins
– Define different bonding involve in maintaining
structures of protein
Proteins play key roles in a living
system….
system
If there is a job to be done in the molecular
world of our cells, usually that job is done
by a protein.

Examples of proteins include

• Hormones acting as messengers;
• Enzymes speeding up reactions;
• Cell receptors acting as ‘antennae’;
• Antibodies fighting foreign invaders;
• Membrane channels allowing specific molecules
to enter or leave a cell;
• They make up the muscles for moving;
• Let you grow hair, ligaments and fingernails;
• Let you see (the lens of your eye is pure
crystalized protein).
3
 Amino acid: Basic unit of
protein

R
Different side chains,
- R, determin the
NH3 +
C COO properties of 20
Amino group Carboxylic
acid group amino acids.
H
An amino acid
 Proteins
• Proteins are the polymer of amino acids
• The 20 amino acids commonly found in proteins
are joined together by peptide bonds
• Polypeptide backbone is the repeating sequence
of the N-C-C-N-C-C… in the peptide bond
 The Peptide Bond
• Is a covalent
bond
• are amide linkages
between the α-
carboxyl group of
one amino acid
and the α-amino
group of another
• Peptide bonds are
not broken by
conditions that
denature proteins
 Rotational Properties of Peptide Bonds

• Rotation around the peptide bond is not permitted. It

is rigid
• Rotation around bonds connected to the alpha carbon
is permitted
•  (phi): angle around the -carbon—amide nitrogen
bond
•  (psi): angle around the -carbon—carbonyl carbon
bond
• In a fully extended polypeptide, both  and  are 180°
• Allows the polypeptide chain to assume a variety of
possible configurations.
 Each Protein Has A Unique
Structure

Amino acid sequence

NLKTEWPELVGKSVEE
AKKVILQDKPEAQIIVL
PVGTIVTMEYRIDRVR
LFVDKLDNIAEVPRVG

Folding!
Why Investigate Protein Structure?

Proteins are complex molecules whose

structure can be discussed in terms
of:
primary structure
secondary structure
tertiary structure
quaternary structure

The structure of proteins is important as

the shape of a protein allows it to
perform its particular role or function
10
 Protein Primary Structure
The primary structure is the sequence of amino acids that are linked
together. The linear structure is called a polypeptide

11
 PROTEIN FOLDING
• The linear sequence of the linked amino
acids contains the information necessary to
generate a protein molecule with a unique
three-dimensional shape
• The peptide bond allows for rotation around it
and therefore the protein can fold and orient
the R groups in favorable positions
• Polar amino acids (acidic, basic and neutral)
are hydrophilic and tend to be placed on the
outside of the protein.
• Non-polar (hydrophobic) amino acids tend to
be placed on the inside of the protein
 Types Of Interactions In Protein
Folding
1. Hydrogen bond
2. Hydrophobic
3. Ionic
4. Disuphide linkage
5. VanderWaal’s
Protein Folding
• 2 regular folding patterns
have been identified –
formed between the
bonds of the peptide
backbone
 -helix – protein turns like
a spiral – fibrous proteins
(hair, nails, horns)
 -sheet – protein folds
back on itself as in a
ribbon –globular protein
 Secondary Structures
• The folding of short (3- to 30-residue), segments
of polypeptide into geometrically ordered units
• Secondary structure refers to a local spatial
arrangement of the polypeptide chain
• The  helix
– stabilized by hydrogen bonds between nearby
residues
• The  sheet
– stabilized by hydrogen bonds between adjacent
segments that may not be nearby
• Irregular arrangement of the polypeptide chain is
called the random coil
 The  Helix
• A complete turn of the helix contains an
average of 3.6 amino acyl residues (-C=O)
• The R group of each amino acyl residue in
an alpha helix face outwards
• Proteins contain only L-amino acids, for
which a right-handed α helix is by far
more stable, and only right-handed α
helices occur in nature
 The  helix (stability)
• The stability of an α helix arises primarily
from hydrogen bonds formed between the
 oxygen of the peptide bond carbonyl
group and the
 hydrogen atom of the peptide bond
nitrogen of the fourth residue down the
polypeptide chain
 Sequence Affects Helix
Stability
• Not all polypeptide
sequences adopt -helical
structures
• Small hydrophobic residues
such as Ala and Leu are
strong helix formers
• Pro acts as a helix breaker
because the rotation around
the N-Ca bond is impossible
• Gly acts as a helix breaker
because the tiny R-group
supports other
conformations
 The Amphipathic Helix
• Many α helices have
predominantly
hydrophobic R groups
on one side of the axis
of the helix and
hydrophilic ones on the
other.
• can create a channel,
or pore, that permits
specific polar
molecules to pass
through hydrophobic
cell membranes.
 β-Sheet
• The β-sheet is another form of secondary
structure in which all of the peptide bond
components are involved in hydrogen
bonding
• The surfaces of β-sheets appear “pleated,”
and these structures are, therefore, often
called “β-pleated sheets and visualized as
broad arrows
• Core of many proteins is the  sheet
• Form rigid structures with the H-bond
 Parallel And Antiparallel
Sheets
• A β-sheet can be formed from two or more
separate polypeptide chains (interchain H-
bond)or
• segments of same polypeptide chains that
are arranged either antiparallel to each other
(with the N-terminal and C-terminal ends of
the β-strands alternating) or parallel to each
other(with all the N-termini of the β-strands
together).
• A β-sheet can also be formed by a single
polypeptide chain folding back on itself
 2-9

Protein Structure: Sheets (Detail)

‘twisted’
Clusters of
twisted strands of
β sheet folding
upon itself
forming the core
of many globular
proteins
 Loops & Bends
• Turns and bends refer to short segments of
amino acids that join two units of secondary
structure, such as two adjacent strands of an
antiparallel β sheet.
• Irregular in conformation, loops nevertheless
serve key biologic roles except in certain
enzymes for binding the substrates.
• reside on the surface of proteins, thus are
helpful in recognition and binding of
antibodies.
 2-10

Protein structure: turns/loops

alpha-helix beta-sheet
- thereare various
types of turns, differing
in the number of
residues and
H-bonding pattern

- loops are typically

longer;
they are often called
coils and do not have a
‘regular’,
or repeating, structure
ribonuclease A

loop
(usually exposed on surface)
 β-Bends (reverse turns, β-
turns)
• β-Bends reverse the direction of a
polypeptide chain, helping it form a
compact, globular shape.
• β-Bends were given this name because
they often connect successive strands of
antiparallel β-sheets
• β-Bends are stabilized by the formation of
hydrogen and ionic bonds.
 Supersecondary Structures
(Motifs)
• Usually produced by packing side chains
from adjacent secondary structural elements
• These form primarily the core region—that is,
the interior of the molecule
• They are connected by loop regions (for
example, β-bends) at the surface of the
protein
• Thus, α-helices and β-sheets that are
adjacent in the amino acid sequence are also
usually(but not always) adjacent in the final,
folded protein.
 Motifs (folds)

Arrangements of several secondary

structure elements
TERTIARY
STRUCTURE
OF
GLOBULAR
PROTEINS
 Protein Tertiary Structure
Refers to the entire three dimensional
conformation of a polypeptide i.e. how
secondary structural features—helices, sheets,
bends, turns, and loops—assemble to form
domains
 Domains
• A domain is a basic structural unit of a protein –
a section of protein structure sufficient to
perform a particular chemical or physical task
such as binding of a substrate
• Other domains may anchor a protein to a
membrane or interact with a regulatory
molecule that modulates its function.
• Different domains can impart different functions
to proteins
• Proteins can have one to many domains
depending on protein size; chains greater than
200 amino acids in length generally consist of
two or more domains
Interactions Stabilizing Tertiary Structure
• Disulfide bonds (e.g. cysteine-cysteine
disulphide bridge)
• Hydrophobic interactions (amino acids with
nonpolar side chains tend to be located in the
interior of the polypeptide molecule)
• Hydrogen bonds (amino acid side chains
containing oxygen- or nitrogen-bound
hydrogen)
• Ionic interactions ( negatively charged
groups, such as the carboxylate group (–
COO–) can interact with positively charged
groups, such as the amino group (– NH3+)
QUATERNARY
STRUCTURE
OF PROTEINS
Quaternary structure
defines the polypeptide
composition of a protein
and, for an oligomeric
protein, the spatial
relationships
between its subunits or
protomers.
• Many proteins consist of a single polypeptide
chain. However, others may consist of two or
more polypeptide chains that may be
structurally identical or totally unrelated.
• The arrangement of these polypeptide
subunits is called the quaternary structure of
the protein.
• Subunits are held together by noncovalent
interactions (for example, hydrogen bonds,
ionic bonds, and hydrophobic interactions).
 Proteins – Multiple Peptides
• Monomeric proteins
-consist of a single polypeptide chain.
Dimeric proteins -contain two polypeptide chains.
• Homodimers -contain two copies of the same
polypeptide chain eg: α α or α2
• Heterodimer the polypeptides differ.
• Greek letters (α, β, γ etc) are used to distinguish
different subunits of a heterodimers and subscripts
indicate the number of each subunit type
• For example, α4 designates a homotetrameric
protein, and α2β2γ a protein with five subunits of
three different types.
• Hemoglobin
– 2  globin
subunits
– 2  globin
subunits
 Protein Denaturation
• Protein denaturation results in the unfolding
and disorganization of the protein’s
secondary and tertiary structures, which
are not accompanied by hydrolysis of
peptide bonds.
• Denaturing agents include heat, organic
solvents, mechanical mixing, strong acids
or bases, detergents, and ions of heavy
metals such as lead and mercury.