BY4017 Protein Structure Analysis Syllabus:
BY4017 Protein Structure Analysis Syllabus – Anna University PG Syllabus Regulation 2021
COURSE OBJECTIVES
1 To impart knowledge on the strategies for identification and analysis of proteins.
2 To provide knowledge on the types of ionization and mass spectrometry in proteomics
3 To impart knowledge on separation and processing of proteins in proteomic analysis
4 To impart knowledge on the comparative proteomic analysis.
5 To impart knowledge on the techniques involved in proteomics
UNIT I PROTEOMICS AND BIOLOGICAL MASS- SPECTROMETRY
Over- view of strategies used for the identification and analysis of proteins; Basics of Mass spectrometry (MS) and bimolecular analysis; One- dimensional (1-D) polyacrylamide gel electrophoresis (PAGE) of proteins; Enzymatic cleavage of proteins in solution; In-gel digestion of protein bands; Electrophoretic transfer of proteins on to membranes (PVDF).
UNIT II MASS-SPECTROMETRY IN PROTEOMICS
Common ionization methods for peptide/protein analysis (MALDI and ESI); Principles of Time of Flight (TOF), Ion Trap (IT), Quadrupole (Q), Fourier Transform-Ion cyclotron Resonance (FT-ICR), and Orbitrap mass analyzers; Collision-Induced Dissociation (CID) of peptides; Introduction to Ion detectors.
UNIT III SEPARATION AND PROCESSING OF PROTEINS FOR PROTEOMICS ANALYSIS
Protein extraction from biological samples (Mammalian Tissues, Yeast, Bacteria, and Plant Tissues); 2-DE of proteins for proteome analysis; Difference in-gel electrophoresis (DIGE); Liquid chromatography separations in proteomics (Affinity, Ion Exchange, Reversed-phase, and size exclusion); Strategies for multidimensional liquid chromatography in proteomics; Analysis of complex protein mixtures using Nano-liquid chromatography (Nano-LC) coupled to Mass-spectrometry analysis.
UNIT IV COMPARATIVE AND QUANTITATIVE PROTEOMICS
Rapid identification of Bacteria based on spectral patterns using MALDI- TOF- MS. Comparative proteomics based on global in-vitro andin-vivo labeling of proteins/peptides followed by Mass spectrometry analysis: ICAT, iTRAQ, SILAC. Analysis of Post-translational modification (PTM) of proteins; Enrichment and analysis of phospho- and glyco- proteins; Characterization of protein interactions using yeast two-hybrid system, Co- immunoprecipitation followed by MS, and Protein micro arrays.
UNIT V PROTEOMICS INFORMATICS
Identification of proteins by PMF and MS/MS data; Database search engines for MS data analysis (Mascot, Sequest, and others); Proteomics informatics strategies for biomarker discovery, analysis of protein functions and pathways. Applications of proteomics (Disease diagnosis, drug development, and plant biotechnology)
TOTAL : 45 PERIODS
COURSE OUTCOMES:
At the end of the course, the students will be able
CO1 To gain knowledge on various areas of proteomics including gel-based and nongel based separation of proteins, strategies for protein labeling and analysis of post-translational modifications of proteins
CO2 To gain knowledge on mass-spectrometry based sequencing and identification..
CO3 To gain knowledge on proteomic techniques
CO4 To gain skills in performing comparative and proteomics analyses.
CO5 To gain skills on proteomics informatics
REFERENCES
1. Simpson R.J., “Proteins and Proteomics: A Laboratory Manual.” I.K. International Pvt. Ltd, 1st Edition,2003.
2. Pennington S. R., Dunn M.J., “Proteomics: From Protein Sequence to Function.” Viva Books, 1st Edition,2002.
3. Twyman R. M., “Principles of Proteomics.” Taylor & Francis, 1st Edition,2004.
4. O’Connor C. D. and Hames B. D. “Proteomics” Scion Publishing, 1st Edition,2008.
5. Dassanayake R. S., Gunawardene Y.I.N. S.” Genomic and Proteomic Techniques.” Narosa, 1st Edition,2011.
6. SiuzdakG.“Mass Spectrometry for Biotechnology.”Academic Press, 1st Edition, 1996.
7. Hoffman E. D., Stroobant V., “Mass Spectrometry – Principles and Applications”, John Wiley& Sons, 1st Edition,2007.
8. Chapman J.R., “Mass Spectrometry of Proteins and Peptides”, (Methods in Molecular Biology Series Vol 146),Humana, 1st Edition, 2000.
9. Rosenberg I. M. “Protein analysis and Purification – Benchtop Techniques.”, Springer, 1st Edition, 2005.
10. Scopes R. K.,” Protein Purification: Principles and Practice.”, Springer, 1st Edition, 1994
11. Chibbal D., LMcLafertty L., Schena M., “Protein Microarrays.”, Jones and Bartlett, 1st Edition, 2005.
12. Smejkal G. B. and Lazarev A. V. “Separation methods in Proteomics.” CRC Press, 1st Edition, 2006.