Structural Biology

Overview

Syllabus 12

1. Unit 1
   • Introduction: Why to Study Structural Biology
   • Introduction to Biological Macromolecules
   • Introduction: Decoding Biological Macromolecules
   • Introduction: Genome Sequencing
   • Introduction: Post Genomic Era
2. Unit 2
   • Amino acids and their properties
   • Protein: Protein Chemistry, Chirality, Peptide bond and Levels of protein structures
   • Protein: Dihedral angles, Peptide bond and Ramachandran Plot
   • Protein: Super Secondary Structures, Motif, Domains, Non-covalent interactions
   • Protein: Folding of Protein, Thermodynamics and Kinetics of protein folding, Characterization of Proteins
3. Unit 3
   • Introduction to Structural Biology Techniques Part I
   • Introduction to Structural Biology Techniques Part II
   • X-ray Crystallography: Crystallization Part I
   • X-ray Crystallography: Crystallization Part II
   • X-ray Crystallography: Crystal Mounting
4. Unit 4
   • X-ray Crystallography: Production of X-ray and its properties
   • X-ray Crystallography: Journey to 3D land
   • X-ray Crystallography: Crystal Symmetry
   • X-ray Crystallography: Instrumentation in X-ray Crystallography
   • X-ray Crystallography: Data collection and processing
5. Unit 5
   • X-ray Crystallography: Data Analysis Part I
   • X-ray Crystallography: Data Analysis Part II
   • X-ray Crystallography: Phase Problem Part I
   • X-ray Crystallography: Phase Problem Part II
   • X-ray Crystallography: Refinement and Structure deposition to PDB
6. Unit 6
   • Introduction to Spectroscopy and NMR
   • Basic Principles of NMR and Instrumentation
   • NMR Sample Preparation and Chemical Shift related concepts
   • Factors effecting NMR Spectra (1D & 2D)
   • 2D & 3D NMR Spectroscopy focusing on protein structure
7. Unit 7
   • Introduction to Spectroscopy.
   • UV-Vis and CD spectroscopy
   • Fluorescence Spectroscopy and Green Fluorescence Protein (GFP)
   • Infrared & Raman Spectroscopy for protein
   • Raman Spectroscopy, Raman Microscopy and Raman Crystallography for studying protein
8. Unit 8
   • Introduction to Microscopy
   • Functioning details of Cryo Electron Microscopy (Cryo EM)
   • Cryo Electron Microscopy: Data Collection and Analysis
   • A concise story of advancement Cryo-EM
   • Protein Data Bank
9. Unit 9
   • History of Molecular Visualizations of Biological Macromolecules
   • Description of structure related files (.pdb, .mmcif, .mtz, etc.)
   • Demonstration of COOT
   • 3D visualization using Pymol
   • Demonstration of Pymol
10. Unit 10
    • Why we need MD Simulation
    • Molecular Dynamic Simulation Process: Part I
    • Molecular Dynamic Simulation Process: Part II
    • Molecular Dynamic Simulation Process: Part III
    • Application of Molecular Dynamic Simulation
11. Unit 11
    • What, How & Which of Protein Engineering
    • How to make logical Protein Engineering: Process of Rational design
    • Success story of Rational Protein designing: Focusing on De Novo Process
    • Designing Protein by mimicking nature: Process of Directed Evolution
    • Achievement, Challenges, and Future direction in the field of Protein Engineering
12. Unit 12
    • Introduction to Structure Based Drug Discovery (SBDD)
    • Rational Drug Discovery
    • Docking Based Virtual Screening: Progress, Challenges and Future perspective
    • What makes a small molecule an ideal drug: Developing in silico ADMETox Model
    • Structure Based Drug Discovery: Case study and Conclusion

Advantages and disadvantages

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Taught by

• Prof. Saugata HazraIIT Roorkee