Diploma in Protemics

Subject title : PROTEOMICS
Course number : 07BIC08 Number of lecture hours: 5
Subject description :
This paper deals with protein structure prediction and function and various tools for
analysis of proteins.
Goals:
Proteomics is extensively used in drug discovery, and in learning various tools for analysis
of proteins.
Objectives:
Taxonomy, structure-function relationship and functional aspects of the entire set cell
UNIT - I
Protein classification: Structural elements and terminology, Helix, Sheet, Strand, Loop
and coil, Active site, Architecture, Blocks, Class and Domains, Fold, Motif, PSSM, Profile.
Principles of classification: Based on structural features, Phylogenetic relationship, CATH
- Classification by Class, Architecture, Topology, Homology, SCOP - Structural
Classification of Protein, FSSP - Fold classification based on structure -
structure alignment, MMDB - Molecular Modeling Database, SARF - Spatial
arrangement of backbone fragments
UNIT - II
Protein structure prediction: Use of sequence pattern, leucine zipper, coiled
coil, transmembrane, signal peptide, cleavage site. Secondary structure prediction:
Chou - Fasman / GOR method, Neural network, nearest neighbor method, tertiary
structure prediction, threading profile, contact potential, modeling.
UNIT - III
Analytical protein and peptide separations - Complex protein and peptide mixtures,
Extracting proteins from biological samples, Protein separation before digestion: 1D and 2
D Electrophoresis, Immobilized pH gradient, Sample preparation, First dimension criteria,
second dimension criteria, Stabilization, Detecting protein on gel: Electro blot, Image
analysis, Digital imaging, Spot detection and quantification, Gel matching. Data Analysis -
Database for 2D gel.
UNIT - IV
Tools of Proteomics-
Mass Spectrometry for protein and peptide analysis:
- MALDI-TOF Analyzers
- ESI Tandem MS instrument
- Tandem Mass Analyzers
- The Triple Quadrupole Mass Analyzer
- The Ion Trap Mass Analyzer
- Q-TOF & Fourier Transform-Ion Cyclotron Resonance MS Instrument
UNIT - V
Functional Proteome Analysis: Integrated Proteome Analysis - Phage antibody as tool,
Protein expression analysis, High throughput analysis for proteomics. Automation of
proteomic analysis. Proteomics in plant breeding: Objectives,principles and methods,
Genetic diversity analysis, Distribution of varieties, lines andcultivars, Mutant
characteristics, Variability between organ and developmental stage, Identification of abiotic
stress, Genetic mapping of protein markers.