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
Overview
Syllabus
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 moleculeWeek 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 foldingWeek 3:Bonds and energies in macromolecules- Covalent, Ionic, coordinate, hydrophobic and Vander walls interactionsWeek 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 discussionWeek 6: Macromolecular Crystallography: Crystallization and Data Collection Crystallization, method of protein crystallization, thermodynamics and kinetics of protein crystallization, structural genomics projectWeek 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 techniqueWeek 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 CootWeek 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 programsWeek 11:Applicative measures01: Case studies: Structure based drug designingWeek 12: Applicative measures02: Case studies: Protein Engineering
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 discussionWeek 6: Macromolecular Crystallography: Crystallization and Data Collection Crystallization, method of protein crystallization, thermodynamics and kinetics of protein crystallization, structural genomics projectWeek 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 techniqueWeek 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 CootWeek 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 programsWeek 11:Applicative measures01: Case studies: Structure based drug designingWeek 12: Applicative measures02: Case studies: Protein Engineering
Taught by
Prof. Saugata Hazra
