Download Amino acids and Protein Structure

Amino Acids and Proteins
Muhammad Jawad Hassan
Assistant Professor
Biochemistry
Objectives
• Structure and Classification of amino acids
• Peptide Bond and Primary structure of protein
• Secondary Structure of protein, Helices and
Sheets
• Tertiary and Quaternary Structure of protein,
domain and motifs
• Structure-function relationship of proteins and
disease
Structure dictates function
Protein structure
allows DNA
replication without
dissociation of
replicating
machinery
3
Protein subunits: amino acids: L & D isomers
Only L amino acids found in proteins.
C chiral, L & D isomers not symmetrical, except glycine
R group = side chains
Amino
group
Carboxylic acid group
Mirror images of each other
The 20 Amino Acids
The amino acids each have their own shape and
charge due to their specific R group.
View the molecular shape of amino acids by
clicking on the URL link below:
http://sosnick.uchicago.edu/amino_acids.html
Would the shape of a protein be affected if the
wrong amino acid were added to a growing
protein chain?
Ionization state as a function of pH
Physiological pH (measure of [H+])
Simplest amino acids
Ball & stick
Stereochemical
Fischer
projections
Aliphatic side chains
M: thioether
(-S-)
Ile: 2nd
chiral center
Aliphatic
side chains
hydrophobic
Proline: cyclic structure
Ring structure: Proline conformationally restricted, marked effect
on protein architecture
Aromatic side chains
Cysteine
Similar to Serine with sulfhydryl, or thiol (-SH) group replacing
hydroxyl (-OH) group
-SH more reactive than -OH. -SH pairs form disulfide bonds
(aka bridges), key role stabilizing proteins
The basic amino acids
Polar side chains
Lys & Arg have
positive charges
at neutral pH
Lys side chain
capped with
amino group
His can be
positively
charged
near
physiological
pH
Carboxylate & Carboxamide side chains
pKa of some amino acids
Amino acid abbreviations
Essential Amino Acids
• 10 amino acids not synthesized by the
body
• arg, his, ile, leu, lys, met, phe, thr, trp,
val
• Must obtain from the diet
• All in diary products
• 1 or more missing in grains
and vegetables
16
Primary structure: Peptide bond,
between AAs
Between -carboxyl group of one AA & -amino group of another
2 amino acids
Dipeptide
Equilibrium favors hydrolysis, hence,
biosynthesis of peptide bonds require free energy input
Peptide bonds are stable kinetically
Loss of
H2O
Polypeptide chain has direction
Main chain or backbone
Constant backbone: regularly repeating part
Distinctive side chains (R-groups): variable part
AA unit in a polypeptide is called a residue, which contains,
a carbonyl group; good hydrogen-bond acceptor,
an NH group (except Pro); good hydrogen-bond donor
Cross links (disulfide bridges)
Prevalent mainly in extracellular proteins
Bovine insulin: AA sequence
1953, Fred Sanger determined aa sequence of insulin, landmark!
Showed for 1st time, protein has precisely defined aa sequence
Also showed that only L-amino acids were present, linked by
peptide bonds
Now, aa sequence of > 100,000 proteins are known
1950s-1960s studies showed aa sequence genetically determined
Each of 20 aa encoded by one or more specific sequences of
3 nucleotides.
Polypeptide bonds are planar
Six atoms (Ca, C, O, N, H, Ca) lie in a plane, in a pair of aa
Bond lengths in peptide unit
Trans & cis peptides
Cis configuration has steric hindrance; trans strongly favored
Rotation of bonds in a polypeptide
Amino group to C & carbonyl group to C are pure single bonds,
allow rotation
Freedom of rotation allows proteins to fold in different ways
Dihedral angle: measure of rotation about a bond
between -180o & +180o
Ramachandran diagram
Most angle combinations (75%) excluded by steric hindrance
Dark green most favored
Steric exclusion: powerful organizing principle
Limited conformations favor protein folding,
favorable entropy of too many conformations opposes folding
Secondary structure: (1) alpha helix
1951, predicted by Pauling & Corey, 6 years before it was seen!
ball & stick, side
ribbon
end view
space-filling
core
alpha helix stabilized by hydrogen bonds
CO group of residue n forms H-bond with NH group of
Residue n + 4
Ball & stick model of alpha helix
Ribbon and cylindrical depiction
Residues related to
each other by
a rise of 1.5 Å and
a rotation of 100
degrees.
3.6 aa residues / turn
Pitch = 5.4 Å(1.5x3.6)
Ferritin, an iron storage protein
75% alpha helix
Helical content of proteins ranges widely
Super helix: alpha helical coiled coil
Can be as long as 1000 Å, very stable
Helical cables in these proteins serve a mechanical role,
forming stiff bundles of fibers
Found in: • myosin and tropomyosin in muscle,
• fibrin in blood clots,
• keratin in hair, quills, claws, hoofs, & horns
• intermediate filaments
(cytoskeleton or internal scaffolding of cells)
Structure of a beta strand
Also predicted by Pauling & Corey
Side chains are alternately above and below plane of backbone
Distance between adjacent aa = 3.5 A
Contrast to 1.5 A for alpha helix
Antiparallel beta sheet
Strands linked by H-bonding between opposite amino acids
Parallel beta sheet
Strands linked by H-bonding of an aa on one strand to two
different aa on the adjacent strand
Structure of mixed beta sheet
Fatty acid-binding protein
Rich in beta sheets
Arrow pointing
to carboxylterminal end
Tertiary structure, myoglobin
O2 carrier in
muscle,
1st protein in
atomic detail,
153 aa,
X-ray crystals
Tertiary structure, myoglobin, schematic
Mainly alpha helices,
total = 8 helices
(75% of main chain)
Prosthetic (helper)
group to bind O2
Heme group is
protoporphyrin IX,
& central iron atom
Distribution of aa in myoglobin
Surface, mainly charged aa.
Yellow: hydrophobic aa
Blue: charged aa
White: other aa
Interior, mainly hydrophobic aa
Cross-section
Quaternary structure, dimer
Cro protein of bacteriophage lambda
Dimer of identical subunits
Quaternary structure, tetramer
Human
hemoglobin,
two alpha(red)
two beta(yellow)
subunits,
4 heme groups
Covalent bond…..NO
Amino acid sequence determines 3D-structure
Bovine ribonuclease, 1950, C. Anfinsen work
Denature &
renature
4 disulfide bonds
124 amino acids
Primary structure determination
•Acid hydrolysis
•Column chromatography
•Ion exchange chromatography
Reducing disulfied bonds
beta-mercaptoethanol, reduced
oxidized
Denaturing agent, urea
Denaturing agent, guanidinium chloride
Denaturing agent, beta mercaptoethanol
Ribonuclease: reduction & denaturation
Finishing touches: covalent modifications
Proteins covalently modified to augment function
Research Protein
Discuss what you can learn about its
structure, function and the organism it
comes from using the skills you learned
today and website resources.
You can explore a number of proteins using Cn3D. Go to the
following URL:
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=Structure