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Books:
1. Lehninger Principle of Biochemistry ( by Nelson and Cox)
Amino acid
Properties:
1. -carbon is bonded to four different groups except glycine
2. -carbon is a chiral center
3. Two possible stereoisomers (called enantiomers)
4. Optically active (except glycine): rotate plan polarized light
5. Can act as acids and bases
Leucine
Isoleucine
Valine
Histidine
Lysine
6.
7.
8.
9.
Methionine
Phenylalanine
Threonine
Tryptophan
Obtained from
nutrition
Alanine
Arginine
Asparagine
Aspartic acid
Cysteine
Glutamic acid
Glutamine
8.
9.
10.
11.
Glycine
Proline
Serine
Tyrosine
Synthesized by
the body
Gly/G
Ala/A
Leu/L
Pro/P
Ile/I
Val/V
Met/M
Thr/T
Cys/C
Asn/N
Gln/Q
Lys/K
Arg/R
His/H
Asp/D
Glu/E
Aromatic R groups
Phe/F
Tyr/Y
1. Non-polar
2. Hydrophobic
3. Form H-bond
4. Absorb UV light (280 nm)
Trp/W
pI = ?
pI = ?
Protein
1. All protein polymers are constructed from the same set
of 20 amino acids.
2. Polymers of proteins are called polypeptides.
3. A protein consists of one or more polypeptides folded
and coiled into a specific conformation
4. The physical and chemical characteristics of the R group
determine the unique characteristics of a particular
amino acid.
Peptide Bond
trans-Peptide group
cis-Peptide group
Protein:
1. A functional, polypeptide chain composed of at
least around fifty amino acids put together.
2. They play a critical role in biochemical reactions
within cells.
Types of Protein
1. Simple protein: contain only amino acid residues
2. Conjugated proteins: contain permanently associated chemical
components in addition to amino acids
(a) Lipoproteins: contain lipid
(b) glycoproteins: contain sugar
(c) metalloprotein: contain specific metal
Structure of Protein
Primary Structure
I.
1.
2.
3.
4.
5.
6.
7.
Elongated
Dynamic, heterogeneous
Very rich in H-bond
Every protein has unique amino acid sequence
Sequence decide the mechanism of action
Sequence determine the 3-D structure
Sequence reveals about its evolutionary history
Human insulin
Molecular interactions
1. Strong interactions
(a) Covalent bonding
(b) Ionic bonding
(c) Resonance bonding
2. Weak Interaction
(a) Van der Waals interaction
(i) Polar-polar
(ii) Polar-non polar
(iii) Non polar- non polar
(b) Hydrogen bonding
3. Effect of medium
(a) Screening of field
(b) Surface interaction
(c) Hydrophobic environment
(d) Hydrophilic environment
Alpha-helix
1. It is coiled structure stabilized by intra-chain H-bonds
between NH and CO groups (situated 4 residue ahead in
the sequence) except end terminal groups
2. Pitch of alpha-helix 5.4 A
3. Both right handed and left handed helix are allowed ,
however right handed alpha-helices are energetically
more favourable because there is less steric clash
between the side chain and backbone
4. Content in the protein: alpha-helices may be 100%
5. Glycine, serine and threonine make amino terminal
residue (N-cap) in alpha-helix
6. Glycine and asparagine makes carboxyl terminal (C-cap)
of alpha-helix
-helices
H bond between residues i, i+4
The Dipoles of
peptide units are
aligned along the
helical axis
Beta- sheet/strand
1. It is stabilized by H-bonding between chains
2. This secondary structure may associated through side chain interactions
and form super-secondary structure called motif
3. Beta-sheet is almost fully extended
4. The distance between adjacent amino acids along a beta-strand is
roughly 3.5 A (in contrast to 1.5 A in alpha-helix)
5. A beta- sheet is formed by linking two pr more beta strands by H-bonds
6. Beta strand represented by broad arrows pointing in the direction of Cterminal
7. Beta sheet formation is important in fatty acid-binding proteins and
lipid metabolism
-Strand
The side chain (green) are alternatively above and below the plane of the strand
Anti-parallel -sheet
C
C
Adjacent -strand run in opposite direction. H-bond between
NH and CO groups connect each amino acid on an
adjacent strand and stabilize the structure
Parallel -sheet
C
Adjacent -strand run in same direction. H-bond between NH
and CO groups connect each amino acid on one strand with
two different amino acids on the adjacent strand
Mixed -sheet
Ramachandran plot
Psi ()
no steric
clashes
Phi ()
permitted
if atoms are
more closely
spaced
Description
primary structure
secondary structure
domain
tertiary structure
quaternary structure
Structure of proteins
Domain structures core is exclusively built from
helices
Domain structures core comprises of antiparallel
sheets, usually two sheets packed against each other
/ Domain structures made from combinations of
-- motifs that form a predominantly parallel
sheets surrounded by helices
Structure of proteins
Triosephosphate
isomerase
Function
Structure
Mechanism
Structure
Origins/Evolution
QHTAWCLTSEQHTAAVIWDCETPGKQNGAYQEDCA
HHHHHHCCEEEEEEEEEEECCHHHHHHHCCCCCCC
10
Protein Structure
solved by X-ray crystallography
Total
Yearly
Protein folding
Hydrophobic effect
Conformational entropy
Electrostatics
Hydrogen bonding
van der Waals interaction
Protein folding
Insulin
?
Compact (in general)
Defined structure
Molten Globule
1. Secondary structure that is present in a native
protein forms within a few microsecond
2. This is because of hydrophobic collapse
3. It is larger by (5-15%) in size of native conformations
4. Side chains are not ordered/packed
5. Structure fluctuation is much larger
6. Not thermodynamically stable
100 kBT
Degree of
nativeness
Folding protein
moves over energy
surface from
unfolded to
folded state:
folded
Structure
Function
Disease
Huntingtons Disease
Huntingtin protein
Amyotrophic Lateral Sclerosis
Superoxide dismutase
Type II Diabetes
Amylin
unfolded
partially
unfolded
natively
folded
ribosome
amyloid
fibrils
misfolded
partially-unfolded
and aggregated
degraded
fragments
disordered
aggregates
non-native
structured
aggregates
Chiti & Dobson, Annu. Rev. Biochem., (2006)
Force-extension curves
Move traps apart at constant rate to stretch
handles and apply force to a single-molecule:
unfolding
molecule unfolds
Apparently
two-state
folding
refolding
stretching
handles
molecule unfolds
Force
But energy
is dissipated!
Work
Geqm W
Distance
Probability
Geqm
W
Work
Jarzynski equality:
Geqm
W
= exp noneqm
exp
k BT
k BT
G ( x ) =
k BT log P ( x )
Time (s)
Probability density
Extension (nm)
Invert
G ( x )
P ( x ) exp
k
T
B
Thousands of
transitions!
Extension (nm)
Woodside et al., Science (2006)
G(x)
raw data
Extension (nm)
parameterfree model
for folding
Residual
Probability
deconvolution
Woodside et al.,
PNAS (2006)
Extension (nm)
Protein folding/unfolding
Denaturants
high temperatures
- cause protein unfolding, aggregation
low temperatures
- some proteins are sensitive to cold denaturation
heavy metals (e.g., lead, cadmium, etc.)
- highly toxic; efficiently induce the stress response
proteotoxic agents (e.g., alcohols, cross-linking agents, etc.)
oxygen radicals, ionizing radiation
- cause permanent protein damage
chaotropes (urea, guanidine hydrochloride, etc.)
- highly potent at denaturing proteins;
often used in protein folding studies
Force spectroscopy
AFM
Optical Tweezers