Introduction to
Proteomics and
Structural Biology
Assoc. Prof. Trinh Hong Thai
VNU University of Science
Proteomics and Structural Biology
▪ Proteomics is the study of proteome, the protein
complement of the genome
▪ Structural Biology
▪ 3 Developments:
✓ Growth of gene, expressed sequence tag (EST),
protein sequence databases.
✓ Bioinformatics
✓ Oligonucleotide microarray
Functional genomics and proteins
▪ Succeed in HGP (Human Genome Project, 1990-2001) with
completing human genome – DNA sequence
▪ Many other organisms’ genomes completed
▪ Genome defines genes of an organism; proteins decoded from
the genome are the function bodies of the genes.
▪ However, a genome sequence does tell how the organism work.
▪ There is not a linear relationship between genome and
proteome for an organism.
▪ Gene expression is highly dynamic and cell dependent
▪ Gene cannot predict the function of decode proteins
▪ Study on proteins – the executive of life is essential in
understanding of biochemical processes, diseases etc
Proteome and Proteomics
▪ PROTEin + GenOME = PROTEOME
▪ Proposed by Wilkins M.R. in 1994
▪ A proteome: “all proteins of a genome” or “all proteins
decoded by all genes of a genome”
▪ A proteome should include all proteins of the organism,
including all decode proteins and various modifications
▪ Proteomics: the large-scale study of proteins, particularly
their structures and functions.
Proteomics : Understanding the structure and function of proteins
encoded by a particular genome and their modifications
Environment Active Cellular
DNA RNA Protein
Protein
GENOMICS PROTEOMICS
Proteome and Proteomics (cont.)
▪ The proteome is much more complex than the genome. This is
because each protein can be chemically modified in different
ways after synthesis:
✓ Many proteins have carbohydrate groups added to them.
✓ Others are phosphorylated or acetylated or methylated.
▪ The proteome is also very dynamic.
✓ Most of our cells contain the same genome regardless of the
cell type, developmental stage or environmental conditions.
✓ The proteome, however, varies considerably in these differing
circumstances due to different patterns of gene expression
and different patterns of protein modification.
Proteome and Proteomics (cont.)
▪ Proteomics, the study of the proteome, is important because
proteins represent the actual functional molecules in the cell.
✓ When mutations occur in the DNA, it is the proteins that
are ultimately affected.
✓ Drugs, when they have beneficial effects, do so by
interacting with proteins.
▪ Proteomics therefore covers a number of different aspects of
protein function, including the following:
✓ Structural proteomics
✓ Expression proteomics
✓ Interaction proteomics
Proteome and Proteomics (cont.)
▪ Structural proteomics, the large-scale analysis of
protein structures:
✓ Protein structure comparisons can help to identify the
functions of newly discovered genes.
✓ Structural analysis can also show where drugs bind to
proteins and where proteins interact with each other.
✓ This is achieved using technologies such as X-ray
crystallography and NMR spectroscopy.
Proteome and Proteomics (cont.)
▪ Expression proteomics, the large-scale analysis of
protein expression:
✓ Identify the main proteins found in a particular sample
and proteins differentially expressed in related samples,
such as diseased vs healthy tissue.
✓ A protein found only in a diseased sample may
represent a useful drug target or diagnostic marker.
✓ Proteins with similar expression profiles may also be
functionally related.
✓ Technologies such as 2D-PAGE and mass
spectrometry are used here.
Proteome and Proteomics (cont.)
▪ Interaction proteomics, the large-scale analysis of
protein interactions:
✓ The characterization of protein-protein interactions
helps to determine protein functions and can also show
how proteins assemble in larger complexes.
✓ Technologies such as affinity purification, mass
spectrometry and the yeast two-hybrid system are
particularly useful.
Proteome and Proteomics (cont.)
▪ The techniques for proteome analysis are not as
straightforward as those used in transcriptomics.
▪ The advantage of proteomics is that the real functional
molecules of the cell are being studied.
▪ Strong gene expression, resulting in an abundant
mRNA, does not necessarily mean that the
corresponding protein is also abundant or indeed active
in the cell.
(from [Link])
Aim of Proteomics
▪ Separate, identify and characterize protein on a large
scale
▪ Define levels of proteins in cells and tissue and how these
change
▪ Investigate protein complexes
▪ Elucidate protein functions, pathways and
interrelationship
Traditional Protein chemistry
▪ One protein at a time
▪ Purification via
chromatography (ion
exchange or reversed
phase)
▪ Purification is a long and
tedious process
▪ Characterization may
takes months
Proteomics: handle entire proteome
▪ Based on large scale purification / separation techniques
– 2 D gel electrophoresis, 2D-HPLC
▪ Separate hundreds to thousands protein at one time
▪ MS used for rapid identification
Major Topics in Proteomics
▪ Separation and visualization of a proteome
▪ Rapid identification of proteins separated
▪ Detailed characterization of proteins
▪ The need for bioinformatics
▪ Study of protein complex