Exploring Proteins and Proteomes. Stryer,CHAPTER 3 ppt

1. BS(integrated) BIOCHEMISTRY
Email ID:khair_awkum@yahoo.com
Biochemistry
Sixth Edition
By Khair Ullah
Chapter 3:
Exploring Proteins and Proteomes

2. Methods in Protein Chemistry
These are methods used in isolation, purification,
detection, degradation, analysis and synthesis
of proteins.
As one would expect, most of these involve
aqueous media and require a knowledge of pH,
pKas, and charge on a peptide at various pH
values.
Proteome: defines the compete functional
information about a group of proteins that
work together as a functional unit.

3. Assay of an Enzyme
In this reaction, the increase in absorbance of NADH
at 340 nm is used to follow the formation of pyruvate
This is an oxidation-reduction reaction

4. Enzyme Activity
Total activity in soution use Unit of enzyme activity:
µmol substrate/min or mol S/sec = katal
To follow during purification use Specific activity:
µmol substrate/min-mg E
or mol S/sec-kg E = katal/kg E
To compare different enzymes use Molecular activity
also called turn-over number (TON):
µmol substrate/min-µmol E
or mol S/sec-mol E = katal/mol E

5. Centrifugation
Separation of
a cell homogenate.

6. Solubility of Proteins
Salting in: When proteins are placed in an
aqueous solution, the only ionic species in
solution are the other protein molecules. Water,
although polar, is only slightly ionized so the
proteins tend to aggregate based on ionic
interactions that form between themselves. The
interactions between protein molecules are more
favorable than interactions between water and a
protein.
At low salt concentration (NaCl), other ionic
species are now present to compete with the ionic
protein:protein interactions. As a result, the ionic
interactions between proteins break up and the
proteins dissolve. Both the small ions (from NaCl)

7. Solubility of Proteins
Salting out: At high salt concentration (typically
with (NH4)2SO4 or Na2SO4), water molecules are more
strongly attracted to these small ions (especially
multivalent ions) than to the large protein molecules.
The proteins are left then to seek whatever favorable
interactions exist and these are the protein:protein
associations which result in aggregation and
precipitation.
Isoelectric precipitation: At the pI there is zero net
charge on a protein. At a pH away from the pI, each
protein molecule bears an identical charge (either +
or - depending on the pH) resulting in repulsion
between molecules. At the pI, no repulsion occurs,
and the proteins will aggregate and precipitate.

8. Determining the isoelectric
point (pI)
Isoelectric point: The pI is the pH at which there is
zero net charge on a molecule. Look at Asp.
The zero net charge form is a part of the first two
ionizations. Therefore, the maximum amount of this
is present at a pH of (2.09 + 3.86)/2 = 2.98 = pI.
HOOC-CH2-CH-COOH
NH3
+
HOOC-CH2-CH-COO
-
NH3
+
+ H+
2.09
HOOC-CH2-CH-COO
-
NH3
+
-
OOC-CH2-CH-COO
-
NH3
+
-
OOC-CH2-CH-COO
-
NH3
+
-
OOC-CH2-CH-COO
-
NH2
+ H+
3.86
+ H+
9.82

9. Dialysis
Separation of
very large from
very small
molecules is
based on an
attempt to
equilibrate
concentration.
Osmotic
pressure

10. Gel Filtration – size separation

11. Affinity Chromatography

12. HPLC
(up to 5000 psi)
Proteins can be
detected from
absorbance of the
peptide bonds in the
uv at 220 nm.
However, it is more
commonly done
at 280 nm as seen
earlier.

13. Ion Exchange Chromatography
Depends upon the
charge on each of
the various
molecules being
separated.

14. Ion Exchange Resins

15. Determining the Charge
on a Peptide
Determing the charge on a peptide involves a
knowledge of ionic equilibria, pKas and the
ionic forms present at a given pH.
In a peptide, the amino terminus, the
carboxy terminus and the ionizable side
chains may be charged at a given pH.
The sum of these charges gives the net
peptide charge.

16. Electrophoresis
Separation of molecules by electrophoresis
depends upon:
1. the strength of the electric field (voltage),
2. the charge on each molecule,
3. the frictional coefficient of movement
through the solid support which in turn
depends on the radius or mass of the
molecule.
So, essentially electrophoresis separates
based on a charge/mass ratio.

17. Electrophoresis
A classical electrophoresis apparatus.
V
buffer buffer
solid support for sample
cooling plate

18. Sodium Dodecyl Sulfate
SDS is an anionic detergent that
binds uniformly along a protein
chain. About one SDS binds for
every two amino acid residues.
Thus all proteins bear the same
charge/mass ratio and separation
by electrophoresis will be based
on mass alone.

19. SDS Gel Electrophoresis

22. Proteins after Staining

23. Isoelectric Focusing
Electrophoresis on a mixture of polyampholytes.
Each molecule migrates to its point of zero net charge.

24. SDS PAGE after IEF

26. Sequential Purification Steps

27. SDS electrophoresis

28. Ultracentrifugation
The S value is a measure of the rate of sedimentation,
(a sedimentation coefficient) and is not linear with MW
because of molecular shape.

30. In a sucrose or
cesium chloride gradient
a molecule migrates the
buoyant density equal to
its own.

32. Amino Acid Analysis
Determines amino acid composition of a protein.
A protein is hydrolyzed in 6N HCl, 24 hrs at 100o
C.
Separation of AA by ion exchange chromatography.

33. Detecting Amino Acids
Classical reagent for amino
acids. Reaction requires
2-5 min at 100o
C and gives
nanomole level detection.
Ruhemann’s Purple
570 nm
OH
O
O
OH
NH2-CH-COOH
CH3
+
O
O
O
O
NCO2
CH3
CHO
+ +2

34. Detecting Amino Acids
Reacts immediately with primary amines at room
temperature. Detection at picomol level due to
fluorescent products

35. Automated Sequencing

36. Edman’s Method
Edman degradation procedure - Determining one
residue at a time from the N-terminus
(1) Treat peptide with phenyisothiocyanate (PITC) at pH
9.0 which reacts with the N-terminus to form a
phenythiocarbonyl (PTC)-peptide.
(2) Treat the PTC-peptide with anh. trifluoroacetic acid
(TFA) to selectively cleave the N-terminal peptide
bond and form a triazolinone derivative.
(3) Extract N-terminal derivative from the peptide.
(4) Rearrange to a phenylthiohydantoin (PTH)-amino
acid with aq. HCl then chromatograph.

37. Edman’s
Method
Phenylthio-
hydantoin
(PTH)
PITC

38. Edman’s Method
N=C=S
phenylthiocarbamyl-peptide
+ NH2 - CH - C - N - CH -C
O
H O
CH2-OH
CH3
NH - C -
S
NH - CH - C - N - CH -C
O
H O
CH2-OH
CH3
S
N
O
CH3NH -
+
N
N
O
CH3
S
NH2 - CH - C
O
CH2-OH
thiazolinone derivativephenylthiohydantoin derivative

39. Separation of PTH-AAs by HPLC

40. N-Terminal Reagents
DNFB - Sanger’s reagent
(dinitrofluorobenzene)
DANSYL choride
(dimethylaminonaphthalenesulfonyl chloride)
NO2
NO2
F
DNFB
SO2Cl
N(CH3)2
DANSYL-Cl

41. Other Reagents
C-terminal:
Hydrazine
Disulfide reduction:
Dithiothreitol - Cleland’s Reagent
Thiols:
Iodoacetate
5,5’-dithiobis-(2-nitrobenzoic acid) -
Ellman’s reagent
NH2-NH2
HO C H
H C OH
CH2 -SH
CH2 -SH
Cleland's
NO2 S S
COOH
NO2
COOHEllman's
I-CH2-COOH

42. Protein Cleavage
Protein sequencing is most manageable with
small polypeptides.
Therefore, in order to sequence a large protein,
it must be cleaved into smaller pieces.
Cleavage is conducted using either chemical or
enzymatic methods.
The pieces must be separated and purified
before sequencing.

43. Chemical and Enzymatic Cleavage

44. CNBr Cleavage at Met

45. CNBr
Cleavage
at Met

46. Enzymatic cleavage by Trypsin

47. An Example, Peptide overlap

48. Dithiothreitol Reduction of –S-S-

49. Iodoacetate reaction with -SH

50. Performic acid oxidation of –S-S-

51. Sequencing using DNA
Edman’s degradation has been a tremendous
asset in protein sequencing, however, for
larger proteins recombinant DNA technology
is now being used.

52. Merrifield Solid-Phase Synthesis
Merrifield and coworkers at Rockefeller Institute
devised a revolutionary solid phase method of
protein synthesis in 1963. The proved that this
method was effective for larger proteins by
synthesizing ribonuclease, an enzyme with 124
amino acid residues.
A chloromethylated polystyrene polymer (resin)
was used as the solid support.
Dicyclohexylcarbodiimide was used as an amino
acid activator and a water scavenger in the
condensation reaction.
Merrifield received a Nobel Prize in 1984 for this
work.

60. Other Methodologies
Immunochemistry: (omit as this is in section 3.3)
ELISA = Enzyme-linked immunosorbent assay
Western blotting
Fluorescense microscopy
Mass Spectrometry: (section 3.5)
MALDI = matrix-assisted laser desorption-
ionization TOF = time of flight
X-ray Crystallography: (section 3.6)
Nuclear Magnetic Resonance: (section 3.6)
NOESY = nuclear Overhauser enhancement
spectroscopy.

61. • Amino acid sequence data provide a basis for preparing antibodies specific for
a protein of interest.
• Amino acid sequence are valuable for making DNA probes that are specific for
the genes encoding the corresponding proteins.
• The nucleotide sequence of DNA (gene) directly reveals the entire amino acid
sequence of the protein encoded by the gene.
• However, DNA sequence can not disclose the information regarding post-
translational modification.
Practical Usage of Amino Acid and DNA Sequences

62. Antibody
• Antibody (immunoglobulin) is a protein synthesized by an animal in response to
the presence of a foreign substance (antigen).
• Antibodies have specific and high affinity against antigens.
• Proteins, polysaccharides and nucleic acids can be effective antigens.
• Epitope : a specific group or cluster (portion) of antigen to stimulate the
synthesis of an antibody and recognized by a specific antibody (antigenic
determinant)
• Hapten : a small molecule containing epitope attached to a carrier

63. Antibody (continued)
• Each antibody producing cell synthesizes only one type of
antibody recognizing a single kind of epitope.
• The proliferation of a given antibody producing cell is
stimulated by the binding of its designated antigen to the
cell surface receptor of the antibody producing cell .
• Periodic injections of an antigen into the host animal can
raise the antibodies specifically recognizing the injected
foreign substance.
• Blood withdrawn from the immunized host animal 
centrifugation  separation of blood cells (pellet) and
serum (supernatant)  anti-serum
• Anti-serum contains multiple kinds of antibodies each
recognizing a different surface feature of the same
antigen.
• This heterogenic antibodies are called as polyclonal

64. Monoclonal Antibody
• Monoclonal hybridoma
cell lines can generate
large amount of
homogeneous
antibodies.
• Monoclonal antibodies
can serve as precise
analytical, preparative
and therapeutic
reagents.(HCV, HIV,
herceptin) Immuno-
Staining of
Drosophila
Embryo
using
Monoclonal
Antibody
against
Engrailed
Plasma cell
by antigen-antibody interaction

65. Monoclonal antibody drugs?

66. Herceptin Binds to the C-terminus of Domain
Herceptin Fab
I
III
II
IV
N
C
HER2

67. Ribbon Diagram of Her-3 ECD
N
C
“Tethered”
I
II
III
IV
Right-handed β helix
Laminin-like folds
Fig. 14.28 pp397

68. Surface representations of EGFR and
HER2 in Antibody-Bound Conformations
Herceptin

69. ELISA (Enzyme-Linked Immuno-Sorbent Assay)
Antibody detection, anti-HIV antibody
Antigen detection

70. Western Blotting
Radioactive secondary antibody
For protein expression and purification

71. Immuno-Fluorescence
Microscopy
Actin Filament Staining
using α-actin antibody
Immuno-Electron
Microscopy
Detection of a channel protein
from the synaptic vesicles
using antibodies tagged with
electron-dense markers such as gold
or ferritin
(Resolution better than 10 nm)
Fluorescence-labeled antibodies
(resolution 200nm)
ex) Glucocorticoid receptor

72. Time of Flight Mass Spectrometer

73. Nuclear Magnetic Resonance

74. End of
Chapter 3
Thank You