This document provides an overview of proteomics, including protein modification and sequencing. It defines the proteome and proteomics, giving a brief history. It describes the main types of proteomics including expression and interaction proteomics. It also outlines some of the key tools and methods used in proteomics, including protein structure databases and the main methods for protein sequencing like N-terminal sequencing. The document concludes by defining and describing different types of protein modification like trimming and covalent attachments. It also lists some related proteomics tools.

1. PROTEOMICS PROTEIN MODIFICATION
AND SEQUENCING
BY:
Abinaya Seshan

2. CONTENTS
• Proteome and proteomics
• History
• Types of proteomics
• Tools of proteomics
• Protein structure
• Applications of proteomics
• Protein sequencing
• Methods of sequencing
• Protein modification
• Types
• Tools related with proteomics
• References

3. PROTEOME & PROTEOMICS
• Proteome is a complement protein found in a single
cell in a particular environment. It is a complete
collection of proteins encoded by a genome of an
organism.
• Proteomics is a study of composition, structure,
function and interaction of proteins directing the
activities of each living cell.

4. HISTORY
• The term proteome and proteomics were coined by
Mark Wilkins and colleagues in early 1900’s

5. TYPES OF PROTEOMICS
• Interaction proteomics-
protein-protein association
• Expression proteomics-
protein quantification

15. STRUCTURAL DATABASES
Primary
structural
database
PDB
CSD
Secondary
structural
database
NDB
SCOP
CATH

17. Protein sequencing

18. DEFINITION
• It is a technique to find out amino acid sequence in
protein.
• Important for understanding cellular process.
• Importance in targetting drugs to specific metabolic
pathways.

19. SEQUENCING METHODS
• N-terminal sequencing
• C-terminal sequencing
• Prediction from DNA sequence

20. N-TERMINAL SEQUENCING
• It is done through:
1. Sanger’s method
2. Dansyl chloride method
3. Edman’s degradation method

21. SANGER’S METHOD
• Treat with DNFB to form a derivative of the amino-
terminal amino acid.
• Acid-hydrolysis
• Extraction of DNP-derivative with organic solvent.
• Identification of DNP-derivative by chromatography
and comparison with standards.

23. DANSYL CHLORIDE METHOD
• Forms a highly fluorescent derivative of the amino-
terminal amino acid.
• Identified by chromatography & fluorescence
detection after acid hydrolysis.
• Highly sensitive.
• Best for small amounts.

25. EDMAN’S SEQUENCING METHOD
• Used to sequence the peptides.
• It removes one amino acid from the N-terminal end
of the peptides.
• Under ideal conditions the sequence of 30-60 amino
acids can be determined.

27. STEPS
• Protein purification
• Protein denaturation
• Protein digestion
• N-terminal labeling
• Separation by chromatography
• Detection by mass spectrometry

28. C-TERMINAL SEQUENCING
• Add carboxypeptidases to a solution of the protein.
• Take samples at regular intervals.
• Determine the terminal amino acid by analyzing a
plot of amino acid concentrations against time.

30. FROM DNA SEQUENCING
• Protein sequence can also be determined indirectly
from the mRNA.
• Design primers from the amino acid sequence and
amplify the gene.
• Sequence the gene and determine the amino acid
sequence of the protein.

31. APPLICATIONS
• Recombinant protein synthesis.
• Drugs production.
• Functional genomics.
• Determine the protein folding patterns.

32. PROTEIN MODIFICATION

33. DEFINITION
• Post-translational modifications (PTMs) occur in
almost all proteins and play an important role in
numerous biological processes by significantly
affecting proteins structure and dynamics.
• Covalent or enzymatic modification of proteins
during or after the synthesis of proteins.

34. TYPES
• Trimming
• Covalent attachments
• Protein folding
• Protein degradation

35. TRIMMING
• Insulin is synthesized in the cells that is in inactive
form where it cannot perform its function.
• For proper functioning its PTM occurs that involves
removing a part of protein to convert it into a three
dimensional and fully active form.

37. COVALENT ATTACHMENTS
• Refers to the addition of transfer of polypeptide
chain that acts as an acceptor region.
• It includes:
 Phosphorylation
Glycosylation
Sulfation
Methylation
Hydroxylation

40. TOOLS RELATED
• Protein analysis:
BLASTX ,Entrez- This will return protein sequences
that are similar to the translation product of your
gene of interest.
• Predictive methods using nucleotide sequences:
Simple translation – no introns
eg:ExPASy, NCBI ORF Finder
Complex methods- predict promoter, splice
sites,translation inititation & termination sites.
eg: GENSCAN,FGENEH

41. CONTDD..
• Predictive methods using protein sequences:
 protein identity based on composition
eg: AACompIdent, SWISS-PROT, TrEMBL
Physical properties based on sequence(compute
pI/MW)
eg: SAPS,peptideMass
ExPASy proteomics tools for prediction of
secondary & tertiary structure of protein

42. REFERENCES
• Proteomics - From Protein Sequence To
Function Paperback – 31 Dec 1899by Pennington S R
• https://www.creative-proteomics.com
• Protein Sequencing Protocols (second edition) by Smith B J
• https://nptel.ac.in/courses/102103017/pdf/lecture%2018.pdf
Proteomics & Genomics. Dr. Vikash Kumar Dubey
• Fundamentals of bioinformatics by Harisha S
• https://www.bioinformatics.org/.../Proteomics_and_
protein_science