Proteins and Proteomes

1
Proteins and Proteomes

• Debra T. Burhans, Ph.D.
• Director, Bioinformatics Program
• Canisius College
• burhansd_at_canisius.edu
• Bioinformatics Workshop for TeachersUniversity
  at Buffalo
• August 15-19, 2005

2
Outline

• Proteome
• Protein structure
• Protein data
• Textbook reference (Mount) Chapter 10

3
Proteome
4
What is a proteome?

• PROTEin complement to a genOME
• - Expasy (http//us.expasy.org/)

5
What is Proteomics?

• the qualitative and quantitative comparison of
  proteomes under different conditions to further
  unravel biological processes.
• Expasy (http//us.expasy.org/)

6
Central Dogma
DNA ? RNA ? Protein
7
Central Dogmomic
Genomics
? Functional Genomics
? Proteomics
? Functional Proteomics
? Physiomics (Metabolomics)
8
A New Relationship
Genome ? Proteome
9
Protein structure
10
Generic Amino Acid Structure
11
The Peptide Bond
Berg, Tymoczko, Stryer Biochemistry, 5th edition
12
Naming Conventions
Berg, Tymoczko, Stryer Biochemistry, 5th edition
13
Protein Architecture

• 1 Sequence of Amino Acids
• 2 Spatial arrangement of residues near each
  other in the 1 sequence
• 3 Spatial arrangement of residues far from each
  other in the 1 sequence, including disulfides
• 4 Spatial arrangements and contacts between
  peptide chains in proteins containing multiple
  peptide chains

14
Berg, Tymoczko, Stryer Biochemistry, 5th edition
15
a-Helix
Berg, Tymoczko, Stryer Biochemistry, 5th edition
16
b-Strands (b-Pleated Sheet)
Berg, Tymoczko, Stryer Biochemistry, 5th edition
17
b-Strands (b-Pleated Sheet)
Berg, Tymoczko, Stryer Biochemistry, 5th edition
18
Tertiary Structure

• Bonds between groups that are not close to each
  other in the primary structure
• Leads to compact packing of proteins

19
Tertiary Structure
Berg, Tymoczko, Stryer Biochemistry, 5th edition
20
Quaternary Structure

• Interactions between multiple subunits of a
  protein
• Subunits may be identical or different

21
Quaternary Structure
Berg, Tymoczko, Stryer Biochemistry, 5th edition
22
DNA Sequence and Proteins

• A protein sequence can be predicted from an open
  reading frame
• The resulting amino acid sequence can then be
  used to predict
• MW the molecular weight
• pI the isoelectric point

23
Protein data
24
A number of resources

• Protein Data Bank (PDB) http//www.rcsb.org/pdb/
• Worldwide Protein data bank http//www.wwpdb.org/
• SwissProt http//www.expasy.org/sprot/
• Structure at NCBI http//www.expasy.org/sprot/
• There are many protein viewing tools available
• Chime, Cn3D, RasMol