PEPTIDES AND PROTEINS

M.Prasad Naidu
MSc Medical Biochemistry, Ph.D,.
ABSTRACT
Overview of amino acids, peptides and the
peptide bond

Discuss the levels of protein structure

Describe techniques used for analysis of
proteins
Planar nature of the peptide bond. The partial
double bond characteristic prevents free
rotation around the C-N bond; keeping it in
the same plane with the attached O and H
atoms. These planar bonds can pivot around
the shared Ca atom
LEVELS OF PROTEIN STRUCTURE
PROTEIN STRUCTURE LEVELS
PRIMARY: the linear sequence of amino
acids linked together by peptide bonds

SECONDARY: regions within polypeptide
chains with regular, recurring, localized
structure stabilized by H-bonding between
constituent amino acid residues
PROTEIN STRUCTURE LEVELS (CONT)
TERTIARY: the overall three-dimensional
conformation of a protein

QUATERNARY: the three-dimensional
conformation of a protein composed of
multiple polypeptide subunits

THE PRIMARY AMINO ACID SEQUENCE
IS THE ULTIMATE DETERMINANT OF
FINAL PROTEIN STRUCTURE
Ex: INSULIN
Disulfide bonds
Form between two intra-
or interchain cysteine
residues, product called
cystine
- Stabilizes/creates protein
conformation
- Prevalent in extracellular/
secreted proteins
STABILIZING FORCES
1. Electrostatic/ionic 3. Hydrophobic interactions
2. Hydrogen bonds 4. Disulfide bonds
2
o
Structure: a-helix

each oxygen of a carbonyl
group of a peptide bond
forms a H-bond with the
hydrogen atom attached to
a nitrogen in a peptide
bond 4 amino acids further
along the chain; very stable
structurally; prolines will
disrupt helix formation
END-ON VIEW OF A-HELIX
Parallel
Anti-Parallel
B-SHEET
In this secondary structure, each amino acid residue is rotated
180
o
relative to its adjacent residue. Occur most commonly in
anti-parallel directions, but can also be found in parallel. H-bonds
between adjacent chains aid in stabilizing the conformation.
b-bend
SUPER-SECONDARY STRUCTURE
EXAMPLES
Super-secondary structures
commonly found in some
DNA-binding proteins
DOMAINS, EXAMPLES:
Saddle
b-Barrel
Bundle
Ex: Tertiary Structure Ex: Quaternary Structure
Myoglobin b-subunit Hemoglobin
STRUCTURE OF MYOGLOBIN AND
HEMOGLOBIN
The amino acid sequences of
myoglobin and hemoglobin are similar
(or, highly conserved) but not identical
Their polypeptide chains fold in a similar
manner
Myoglobin is found in muscles as a
monomeric protein; hemoglobins are
found in mature erythrocytes as multi-
subunit tetrameric proteins. Both are
localized to the cytosol
SEQUENCE COMPARISON EXAMPLES
Myoglobin
Hba (horse)
Hbb (horse)
Hba (human)
Hbb (human)
Hbg (human)
Hbd (human)

Myoglobin
Hba (horse)
Hbb (horse)
Hba (human)
Hbb (human)
Hbg (human)
Hbd (human)

(Internal helix)
(Surface helix)
MYOGLOBIN PROPERTIES
At the tertiary level, surface residues prevent
one myoglobin from binding complementarily
with another myoglobin; thus it only exists as a
monomer.
Each monomer contains a heme prosthetic
group: a protoporphryin IX derivative with a
bound Fe
2+
atom.
Can only bind one oxygen (O
2
) per monomer
The normal physiological [O
2
] at the muscle is
high enough to saturate O
2
binding of
myoglobin.
Heme-Fe2+
Protein-Heme Complex
with bound oxygen
HEME STRUCTURE
HEMOGLOBIN PROPERTIES
At the tertiary level, the surface residues of the
a and b subunits form complementary sites that
promote tetramer formation (a
2
b
2
), the normal
physiological form of hemoglobin.
Contains 4 heme groups, so up to 4 O
2
can be
bound
Its physiological role is as a carrier/transporter
of oxygen from the lungs to the rest of the body,
therefore its oxygen binding affinity is much
lower than that of myoglobin.
If the Fe2+ becomes oxidized to Fe3+ by
chemicals or oxidants, oxygen can no longer
bind, called Methemoglobin
BIOCHEMICAL METHODS TO ANALYZE
PROTEINS
Electrophoresis
Chromatography: Gel filtration, ion
exchange, affinity
Mass Spectrometry, X-ray
Crystallography, NMR
You will not be tested on the sections in
your textbook describing amino acid
separations (Ch 4), peptide/protein
sequencing and synthesis (Ch 5), and
X-ray crystallography/NMR (Ch 6)
PROTEIN SEPARATION BY SDS-
POLYACRYLAMIDE GEL
ELECTROPHORESIS
Presence of SDS, a detergent,
denatures and linearizes a protein
(Na and sulfate bind to charged
amino acids, the hydrocarbon chain
interacts with hydrophobic residues).
An applied electric field leads to
separation of proteins based on size
through a defined gel pore matrix.

For electrophoresis in the absence
of SDS, separation is based on size,
charge and shape of the protein
(proteins are not denatured and can
potentially retain function or activity)
SDS-POLYACRYLAMIDE GEL (CONT)
Separation of proteins
based on their size is
linear in relation to the
distance migrated in the
gel. Using protein
standards of known
mass and staining of the
separated proteins with
dye, the mass of the
proteins in the sample
can be determined. This
is useful for purification
and diagnostic purposes.
GEL FILTRATION
Separation is based on protein size.
Dextran or polyacrylamide beads of
uniform diameter are manufactured
with different pore sizes. Depending
on the sizes of the proteins to be
separated, they will enter the pore if
small enough, or be excluded if they
are too large.
Hydrophobic Chromatography
Proteins are separated based on their
net content of hydrophobic amino
acids. A hydrocarbon chain of 4-16
carbons is the usual type of resin.
Separation of proteins based on
the net charge of their constituent
amino acids. Different salt
concentrations can be used to elute
the bound proteins into tubes in a
fraction collector. As shown below,
resins for binding (+) or (-) charged
proteins can be used
ION EXCHANGE CHROMATOGRAPHY
AFFINITY CHROMATOGRAPHY
Based on the target proteins ability to bind a
specific ligand, only proteins that bind to this
ligand will be retained on the column bead.
This is especially useful for immunoaffinity
purification of proteins using specific
antibodies for them.
Example:
PROTEIN STRUCTURE METHODS
The sequence of a protein (or peptide) is
determined using sophisticated Mass
Spectrometry procedures. The three dimensional
structures of proteins are determined using X-ray
crystallographic and NMR (nuclear magnetic
resonance) spectroscopic methods.
Protein sequence data banks useful for structural
and sequence comparisons
Please note that the new discipline termed
Proteomics is evolving to incorporate cross-
over analysis of sequence data banks, Mass
Spec methodology, and living cells
THANK Q