basic information

1. DEPARTMENT OF MICROBIOLOGY
PROTEOMICS AND PROTEOME : OVERVIEW OF
ANALYTICAL PROTEOMICS, APPLICATIONS
OF PROTEOMICS
 M.Sc. → Sem-1
 Guided by → M.F. Mansuri sir
 Delivered by → Akshay k. Darji (5)
 Date → 3 Oct. 2019

2. Outline
 Introduction
- proteomics and proteome
 Difference between protein biochemistry and
proteomics
 Overview of Analytical proteomics
- protein separation
- protein digestion
- protein identification
 Applications of proteomics

3. What is proteome ?
 Proteome refers to the entire set of expressed protein
in a cell , it is full complement of translated product
of genome
 Every organism has one genome but many
proteomes
 The proteome in any cell thus represents some subset
of all possible gene product

4.  However, this does not mean that the proteome is simples
then the Genome.
 Any protein though a product of single gene, may exist in
multiple forms that very within a particular cell or between
different cell.
 Indeed most proteins exist in several modified forms. These
modifications affect protein structure, localization, functions,
and turnover.
 The proteome in essentially any organism is collection of
some where between 30% and 80% of the possible gene
product

5. WHAT IS PROTEOMICS?
 The qualitative and /or quantitative comparison of
proteomes under different condition further unravel
biological process
 The terms “ proteomics” and “proteome” were coined by
Marc wilkins and colleagues in the early 1990s

6. DNA → Genome
“Genomics”
mRNA
Proteins → Proteome
“proteomics”
Cell functions

7.  The context of proteomics is system biology,
rather then structural biology.
 It involves simultaneous analysis of all
translated proteins
 It is the study of multiprotein system, in which
the focus is on the interplay of multiple, distinct
protein in their roles as part of larger system or
network

8. Difference between protein chemistry and
proteomics .
Protein chemistry Proteomics
- Individual proteins - Complex mixture
- Complex sequence analysis - Partial sequence analysis
- Emphasis on structure and
function
- Emphasis on identification
by database matching
- Structural biology - System biology

9.  Analytical Protein identification is built around one
essential fact; most peptide sequence of approximately six
or more amino acid are largely unique in the proteome of
organism
 Thus, if we can obtain the sequence of the peptide or if we
can accurately measure it’s mass, we can identify the
proteins it came from simple by finding it’s match in
database of protein sequence
 Most analytical proteomics problems begin with a protein
mixture.
 This mixture contains intact proteins of varying in
molecular weights, modification and solubilities.

10.  Analytical proteomics is essentially one assay, in which
protein mixtures are converted to peptide mixture
 Peptide MS data are obtained , and the corresponding
proteins are identified by software – assisted database
searching.
 What makes proteomics so powerful is that this one assay
can be applied to many different protein sample generated
from a variety of experimental designs.

12. (1) Protein separation → 1D-SDS-PAGE
→ 2D-SDS-PAGE
→ Preparative IEF
(2) protein digestion → Proteases
(3) protein identification → Mass spectrometry
Methods for proteomic analysis

14.  Before we get into the approaches to
separation and digestion , let’s consider
why the problem of complex protein
mixture is an issue ?

15.  Analytical protein separation that are done before the protein
digested.
 The three principle separation approaches used with intact
proteins are 1D & 2D-SDS-PAGE and preparative
isoelectric focusing (IEF)
 The idea behind separating intact proteins is to take
advantage of their diversity in physical properties, especially
isoelectric point and molecular weight.
 The mixture may be separated into relatively small number
of fractions (as in 1D-SDS-PAGE & Preparative IEF)
OR
 Into many fractions (as many spots in 2D-SDS-PAGE)
Protein separation

16. Extracting protein from biological sample
 With the aid of……..
 Detergents → SDS, 3-( [3-cholamido-propyl]-1-propane
sulfonat) ,cholat, tween… which help to solublize
membrane protein and aid their separation from lipids
 Reductants → Dithiotheitol (DTT) , Mecaptorthanol ,
thiourea … which reduces disulfide bonds or prevent
protein oxidation .

17.  Denaturing agents → urea and acids.. Which disrupt
protein-protein interaction, Secondary and tertiary structures
by altering solution ionic strength and PH
 Enzymes → DNAs, RNAs… Which digest contaminating
nucleic acids, Carbohydrates & Lipids

18. One Dimensional-SDS-PAGE
 The single most widely used analytical separation in all of
protein chemistry.
 In 1D-SDS-PAGE, the protein sample is dissolved in a
loading buffer that usually contains a thiol reductunts
(meracaptoethanol or DTT) and SDS
 The separation method is based on the binding of SDS to the
protein, which imparts negative change (from theSDSsulfate
group) to the protein in roughly constant proportion to
molecular weight.
 When the Gel is subjected to the high voltage, the protein-
SDS- complex migrate through the cross linked
polycrylamide gel at rates based on their ability to penetrate
the pore matrix of the Gel

20. fig :- 1D-SDS-PAGE

21. Two-Dimensional- SDS-PAGE
 This separation method has become synonymous with
proteomics and remain the single best method for
resolving highly complex protein mixture
 2D-SDS-PAGE is actually combination of two different
types separation.
 In the first, the protein are resolved on the basis, of
isoelectic point by IEF. In the second, focused protein
then are further resolved by electrophoresis on a
polyacrylamide gel.

23.  Thus 2D-SDS-PAGE resolves proteins in first dimension by
isoelectic point and in the second dimension by molecular
weight
 Proteins separated by 2D gels are visualized by
conventional staining technique, including silver,
coomassie, and amido Black staining.Silver-staining and
newer fluroscent dyes are the most sensitive.

24. Problems with 2D-SDS-PAGE
 The first is the difficulty of performing completely
reproducible 2D-SDS-PAGE to compare two sample by
comparing the image of the stained gels.
 This problems becomes importants
 A second problems with 2D-SDS-PAGE is the relative
incompatibility of some protein with the first-dimension
IEF step.

25. Preparative IEF
 This technique is analogous to the first step in 2D-
SDS-PAGE
 In preparative, the separation is carried out on an IPG
strip, in tube gel or in solution.
 The generation of PH gradient is achived with soluble
ampholytes, which are polycarboxylic acid
coumpounds that generate a stable PH gradient when
voltage is applied across the focusing cell.
 The protein sample is then add, voltage again is
applied, and proteins then are separated by isoelctric
point.

26.  In commercially available apparatus, such as the
BioRad Rotofor cell, the focusing cell I divided
by permeable membranes into a series of
chambers.
 After the focusing step, the chambers are
quickly and simultaneously emptied by vaccum
siooer that draws the contents of each section of
the cell into a separate tube with this type of
appartus, the entire protein mixture is separated
into 12-20 fraction.

27. Protein digestion
 The ideal protein digestion approach would cleave
proteins at certain specific amino acid residues to yield
fragments that are most compatible with MS analysis.
 Specifically, peptide fragments of between about 6-20
amino acid are ideal are ideal for MS analysis and
database comparisons.
 Peptide shorter than about 6 amino acid generally are
two short to produce unique sequence matches in
database searches.

28. Proteases :-
 Nature has evolved diverse collection of proteases to
undertake the endless tasks of protein remodeling that
are essential to higher organism.
 Available in limited quantity
 In analytical proteomics we need stable, well
charcterized enzymes with well defined specifities.
 A number of proteases that meet these requirments have
been used in proteomics analysis.

29.  Trypsin → Most widely used protease in proteomic
analysis.
- obtained from porcine or bovin pancreas and is easily
purified
- Trypsin cleaves proteins at lysin and arginine residues
unless either of these is follwed by a proline residues in
the C-teminal direction.
- An advamtage of trypsin for proteomics is that the
enzyme displays good activity both in solution and “ in
gel” digestion protocols.

30.  Glu -C (v8 protease) → It is an endoproteinase that
cleaves at the carboxyl side of glutamate residues in
either ammnium acetate or ammonium biocarbonate
buffer.
 In sodium buffer, however the enzyme cleaves at both
glutamate and aspartate residues.
 Glu-C can be used for in-gel digestion
 An advantage of using Glu-C is that it displays a
markedly different cleavage specificity than trypsin,
which improves the likelihood to obtaining
complementary peptide fragments of a protein

31.  Non specific proteases → Subtilysin, pepsin,
Protainase-k, and pronase.
- These enzymes cleave proteins more or less randomly
to produce multiple overlapping peptides
- The advantages of producing multiple overlapping
peptides is that they increase the likelihood of
obtaining sequence data over a greater percentage of
each protein analyzed.

32. In-Gel digestion
 A commonly used approach to digestion of
protein separated by 1D- or 2D-SDS-PAGE is
referred to as “in-gel” digestion
 The band spot of interest is cut from the gel,
destained, and than treated with protease(most
commonly trypsin).
 The enzyme penetrates the gel matrix and digests
the protein to peptides, which then are eluted from
the gel by washing

34. Mass spectometers for protein and paptide
analysis
 How MS instrument work ?
 Mass spectometers have three essential parts the first is the
source, which resolves ion based on their mass/charge(m/z)
ratio.
 The third part is detactor, which detects the ion resolved by
the mass analyzer.
 The mass spectometer coverts componants of a mixture to
ion and the analyzes thenm on the besis of their m/z
 The data are automatically recorded by the data system can
then be retrived for manual or computer assisted
interpretation.

36. MASS SPECTROMETER

37. What do we want from MS data ?
 For purposes of proteomics, we want good data on peptide
masses (MALDI-TOF MS) or good data that describe
peptide fragmantation (ESI tadam MS)
 So what makes good data ? We look for 3 things the first
senstivity.
 Second, we need resolution which is measure how well we
can distinguish ions of very similar m/z values.
 Third one is mass accurancy this means that the measured
values for peptide ions or their fragmant ion must as close
as possible to their real values.

40. MALDI-TOF MS INSTRUMENTS
 MALDI-TOF is the standard acronym for matrix assisted
laser desorption ioniztion time of flight.
 The first part (MALDI) refer to the source, whereas the TOF
refer to the mass analyzer.
 The term “MALDI” actually describes a method ionization,
but frequently is used in the proteomics literature as
shorthand for MALDI-TOF however, both MALDI source
and TOF analyzer can be used in other configuration.

42. MALDI-TOF INSTRUMENT

43. THE TOF MASS ANALYZER
 The TOF(time of flight) mass analyzer works just like
it’s name sounds.
 The TOF analyzer measures the time it takes for the ion
to fly from one end of the analyzer to other and strike
the detectors.
 The speed with which the fly down the analyzer tube is
proportional to their m/z ,the faster they fly.
 MALDI-TOF instruments are used in proteomics
primarily to obtain mass measurments of intact peptide
ions , some instruments can analyze fragmentation of
peptide ions as well.

45. ESI TANDEM MS INSTRUMENTS
 ESI Tendom MS (or EST MS-MS) is the standard acronym
for electrospray ionization Tandem mass spectromentry.
 ESI refers to the process by which ions are produced in the
source of the instrument.
 Tandem mass spectrometry refer to mass analyses that are
able to perform two stage(or multistage) mass analysis of
ion.
 Other ex..
 Tandam mass analyzers
 The triple quadrupole mass analyzers
 Ion trap mass analyzers

46. Applications of proteomics
 Mining
 Protein-expression profiling
 Protein network mapping
 Mapping of protein modification

47. - Mining
 Mining is simply the exercise of identifying all of the
proteins in a sample.
 The point of mining is catalog the proteome directly, than to
infer the composition of the proteome from expression data
for genes.
 Mining is the ultimate brute-force exercise in proteomics:
one simply resolves proteins to the greatest extent possible
and then uses MS and associated database and software tools
to identify what is found.
 There are several approaches to mining and each offers is the
ability to confirm advantages.
 What these approaches collectively offer is the ability to
confirm by direct analysis what could only be inferred from
gene-expression data.

48. - Protein-expression profiling
 It is the identification of proteins in a particular sample as a
function of the organism or cell. (eg. Differentiation ,
developmental state, or disease state) or as a function of
exposure to a drug, chemical, or physical stimulus
 Expression profiling is actually a specialized form of
mining. It is most commonly practiced as a differential
analysis , in which two states of particular system
compared.
 For example, normal and diseased cells or tissue can be
compared to determine which proteins are expressed
differently in one state compared to the other.this
information has tremendous appeal as a means detecting
potential targets for drug therapy in disease.

49. - Protein network mapping
 It is the proteomics approaches to determining how protein
interacts with each other in living systems.
 Most protein carry out their function in close association
with other proteins.
 These interactions that determine the functional network,
such as signal-transduction cascades and complex
biosynthesis or degradation pathway
 Protein network profiling would offer the ability to assess at
once the status of all the participants in the pathway.
 As such, protein-network profiling represents one of the
most ambitious and potentially powerful future applications
of proteomics.

50. - Mapping of protein modification
 It is the task of identifying how and where proteins are
modified. Many common posttranslational modifications
govern the targating , structure, function and turn over of
proteins.
 In addition many environmental chemical, drug, and
endogenous chemicals give rise to reactive electrophiles that
modified proteins.
 A variety of analytical tools have been developed to identify
modified proteins and the nature of modifications.
 Modified protein can be detected with antibodies (ef. For
specific phosphorylated amino acid residues), but the precise
sequence sites of specific modification often are not known.

51.  Proteomics approaches offer the best means of establishing
both the nature and sequence specificity to post-trnslational
modification.
 These approaches will provide fresh avenues of approaches to
quations of how chemical modification of the proteome affect
living systems.