Structural Biology

By Prof. Saugata Hazra | IIT Roorkee

Learners enrolled: 2214

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 :	Completed
Course Type :	Core
Language for course content :	English
Duration :	12 weeks
Category :	Biological Sciences & Bioengineering Biosciences
Credit Points :	3
Level :	Undergraduate/Postgraduate
Start Date :	18 Jan 2021
End Date :	09 Apr 2021
Enrollment Ends :	01 Feb 2021
Exam Date :	24 Apr 2021 IST

Note: This exam date is subject to change based on seat availability. You can check final exam date on your hall ticket.

Page Visits

Course layout

Week 1: Introduction: What is post NGS era, why structural biology become so important, How to read biological macromolecules, Sequence to structure to function relationship, Protein as our target study molecule

Week 2: Protein Architecture: amino acids structure and function, Primary, secondary, tertiary and quaternary structure of protein; Motifs and domains of protein structures; Conformational analysis, Protein folding

Week 3: Bonds and energies in macromolecules- Covalent, Ionic, coordinate, hydrophobic and Vander walls interactions

Week 4: Enzymes: introduction to enzymes, how enzyme develop magic pockets, enzyme-ligand interaction, Structure-function relationship,

Week 5: Structural Biology Techniques: Basics of macromolecular crystallography, Nuclear Magnetic Resonance (NMR) and Cryo-Electron microscopy, advantages and disadvantages of all the processes: comparative discussion

Week 6: Macromolecular Crystallography: Crystallization and Data Collection Crystallization, method of protein crystallization, thermodynamics and kinetics of protein crystallization, structural genomics project

Week 7: Macromolecular Crystallography: Data Analysis X-ray diffraction and Bragg equation, scattering factor, Structure factor expression, Phase problem and methods for phase determination, structure determination of macromolecules by crystallography technique

Week 8: Reading and Understanding 3D structure files: Introduction to PDB data, RCSB, reading PDB files, related calculations

Week 9: 3D structure Visualization: Visualization of macromolecules using Pymol and Coot

Week 10: Introduction to Molecular Dynamics Simulation: Need of simulation in studying biology, Building realistic atomistic model, Size and Times scale of macromolecular movements, Atomic Interactions: bonded and non-bonded, General form of all atom force field equations, Steps in molecular dynamics, Topology and parameter files, Periodic boundary conditions, Solvation and solvation methods, Simulation programs

Week 11: Applicative measures01: Case studies: Structure based drug designing

Week 12: Applicative measures02: Case studies: Protein Engineering

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 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: 24 April 2021 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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