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Structural Biology

By Prof. Saugata Hazra   |   IIT Roorkee
Learners enrolled: 194
ABOUT THE COURSE : Post NGS (Next Generation Sequencing) era has completely changed the way of understanding research, especially in the field of biomedical science. Today the complete genome sequencing of an organism is done in a few days providing the researchers with thousands of genes hence thousands of protein sequences. But to proceed further we need to understand the three-dimensional architecture of the protein molecules. The current course would take an initiative to educate the students in gathering knowledge about the structural units forming biological macromolecules, their architectural hierarchies, the basics of the structural biology techniques, their pros and cons, how to read and visualize 3D structure files, etc. The course also include introduction to molecular dynamics and case studies explaining the probable application of the acquired knowledge. But most importantly this course is an attempt to help linking the biological events to understand how biological macromolecules are generated, folded and get functional. Understanding those fundamentals would help students towards studying follow up advanced courses like Advanced structural biology, Macromolecular crystallography, Cryo-Electron Microscopy, Nuclear Magnetic Resonance, Structure-based drug designing, protein engineering, etc. In summary, this course would open up the gate of modern research-related courses in the field of Drug Designing and macromolecule based engineering.

INTENDED AUDIENCE: 
Biotechnology/ Pharmaceuticals/ Bioinformatics / Chemistry and related programs Also it would be a nice introductory course to, research scientists in biotechnology, pharma industry, veterinarians and clinicians/medical people involved in basic research.
PREREQUISITES: This is an introductory course so anyone should follow it, basic knowledge of biology might be helpful
INDUSTRIES SUPPORT: Pharmaceutical, Biotechnology, Biochemical Engineering
Summary
Course Status : Upcoming
Course Type : Core
Duration : 12 weeks
Start Date : 23 Jan 2023
End Date : 14 Apr 2023
Exam Date : 30 Apr 2023 IST
Enrollment Ends : 30 Jan 2023
Category :
  • Biological Sciences & Bioengineering
  • Biosciences
Credit Points : 3
Level : Undergraduate/Postgraduate

Page Visits



Course layout

Week 1: Introduction: Flow of the history of biological inventions, basic Biological Macromolecules of life, i.e., Protein, Nucleic Acid, Carbohydrates & Lipid/Fat, and a comparison between polymers and "3C"ecrets of covalent bond, nucleic acid, DNA sequencing, PCR innovation, gene sequencing to genome sequencing, introduction to NGS and its different platforms, arrival of Post Genomic Era, the effect of HGP, and experimental three-dimensional structure determination techniques.

Week 2: Protein: Amino acids and their properties, Protein Chemistry, Chirality, Peptide bond, and Levels of protein structures, Dihedral angles, Peptide bond, and Ramachandran Plot, Super Secondary Structures, Motif, Domains, Non-covalent interactions, Folding of Protein, Thermodynamics, and Kinetics of protein folding, Characterization of Proteins.

Week 3: Introduction to Structural Biology Techniques: cellular organization,  resolution structure determining technique with their ranges of the resolution, the success of X-ray crystallography from single molecule to a crystal, X-ray Crystallography, Crystallization in X-ray Crystallography, Crystal mounting in X-ray Crystallography.

Week 4: X-ray Crystallography: Production of X-ray and its properties, unit cell, symmetry, and lattice, the geometry of the crystal system, Crystal Symmetry, Instrumentation in X-ray Crystallography, Data collection, and processing

Week 5: X-ray Crystallography: Data Analysis of  X-ray Crystallography - Diffraction Patterns, Indexing, Bragg's Law, Laue equation, Relation between "Laue equation and Bragg's Law", Lattice Transformation, Ewald Sphere, Laue Condition for Diffraction and Ewald Sphere, Structure Factors and Diffraction Pattern, Atomic Scattering Factor, Anomalous Dispersion, Analytical expression of the phase, Fourier Transformation, introduction to Phase Problem. Phase problem - Phase Problem, Patterson Function, How to solve phase problem, Heavy atom replacement methods, Isomorphous replacement, Anomalous dispersion, phase problem associated with crystal diffraction and common techniques to recover phase resolving different phase improvement methods. Refinement and Structure deposition to PDB - aspects of structure refinement, motivation, application, the procedure of simulated annealing, PDB repository, atomic model deposition as well as different PDB validation suites.

Week 6: NMR: Introduction to 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.

Week 7: Spectroscopy: 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.

Week 8: Microscopy: 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.

Week 9: Molecular Visualizations: 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.

Week 10: Molecular Dynamic Simulation: Why we need MD Simulation, Molecular Dynamic Simulation Process, Build a realistic atomistic model of the system, the algorithm behind simulation process, Concept of Topology and Parameter files, Major components in a force field, the concept of solvation, solvent models, Periodic Boundary Condition, Concept of Central Simulation Box, Phase Space, Concept of Ensembles, Energy Minimization (EM), potential energy surface (PES), Determination of EM, types of EM methods and their algorithms, Steps in MD Simulation, Application of Molecular Dynamic Simulation.

Week 11: Protein Engineering: What, How & Which of Protein Engineering, How to make logical Protein Engineering: Process of Rational design, a 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.

Week 12: Structure-Based Drug Discovery: 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

Books and references

Carl Ivar Branden and John Tooze., “Introduction to Protein Structure” 2nd 2001 Edition, Taylor and Francis
Voet, D. and Voet, J. G., “Biochemistry” 3rd edition, John Wiley and Sons.
Introduction to Protein Architecture: The Structural Biology of Proteins, 2001 Arthur M. Lesk, Oxford University Press; 1st edition
Lubert Stryer, Biochemistry, 4th Edition, WH Freeman & Co
Creighton. T.E., Proteins, Structure and Molecular Properties, 2nd Edition, 1993 W.H. Freeman and Co
McPherson, A. “Introduction to Macromolecular Crystallography", 2nd 2009 edition, Wiley-Blackwell.
Drenth, J., "Principles of Protein X-Ray Crystallography", 3rd edition, 2007 Springer.
Rhodes, G., "Crystallography Made Crystal Clear", 3rd edition, Academic Pres

Instructor bio

Prof. Saugata Hazra

IIT Roorkee
Dr. Saugata Hazra is a Associate Professor in the Department of Biotechnology at the Indian Institute of Technology, Roorkee. An alumnus of IIT Kharagpur, Prof. Hazra has obtained his Ph.D. degree from the University of Illinois; Chicago (2004- 2010) in Structural Biology and Structure based Drug Designing and post-doc from St. Jude Children Research Center, Memphis, USA (2010-2011) and Albert Einstein College of Medicine, NY, USA, in the major area of Structural Biology. He joined IIT Roorkee in 2014. Current research in his group centers on catalytic divergence of enzymes involved in antimicrobial drug resistance and structure based enzyme engineering towards waste valorization. Prof. Hazra is teaching UG/PG courses like Macromolecular Crystallography, Bioinformatics, Computational Biology, and Biochemistry since his joining in IITR. He has published in several peer reviewed journals and recipient of awards like James graduate fellowship, DST-Young Scientist Award and Frontiers of Engineering from Royal Academy of Engineering etc.throughout his career. View Faculty Profile: https://www.saugatahazralab.com/

Course certificate

The course is free to enroll and learn from. But if you want a certificate, you have to register and write the proctored exam conducted by us in person at any of the designated exam centres.
The exam is optional for a fee of Rs 1000/- (Rupees one thousand only).
Date and Time of Exams: 
30 April 2023 Morning session 9am to 12 noon; Afternoon Session 2pm to 5pm.
Registration url: Announcements will be made when the registration form is open for registrations.
The online registration form has to be filled and the certification exam fee needs to be paid. More details will be made available when the exam registration form is published. If there are any changes, it will be mentioned then.
Please check the form for more details on the cities where the exams will be held, the conditions you agree to when you fill the form etc.

CRITERIA TO GET A CERTIFICATE

Average assignment score = 25% of average of best 8 assignments out of the total 12 assignments given in the course.
Exam score = 75% of the proctored certification exam score out of 100

Final score = Average assignment score + Exam score

YOU WILL BE ELIGIBLE FOR A CERTIFICATE ONLY IF AVERAGE ASSIGNMENT SCORE >=10/25 AND EXAM SCORE >= 30/75. If one of the 2 criteria is not met, you will not get the certificate even if the Final score >= 40/100.

Certificate will have your name, photograph and the score in the final exam with the breakup.It will have the logos of NPTEL and IIT Roorkee.It will be e-verifiable at nptel.ac.in/noc.

Only the e-certificate will be made available. Hard copies will not be dispatched.

Once again, thanks for your interest in our online courses and certification. Happy learning.

- NPTEL team


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