Structural biology
Summary
The main focus of this course is on the molecular interactions defining the structure, dynamics and function of biological systems. The principal experimental and computational techniques used in structural biology, as well as molecular modeling and design will be introduced and practiced.
Content
The course will focus on the following topics:
1. Structure: intermolecular interactions, structure of biomolecules, experimental methods in structural biology (i.e., X-ray crystallography, NMR, cryo-electron microscopy), structural classification, protein structure prediction using genomic data and machine learning.
2. Dynamics: elements of statistical mechanics, molecular mechanics of biomolecules, molecular simulations, molecular binding and free energy calculations.
3. Selected topics: protein design and engineering; protein folding, molecular docking, integrative modeling; structure-based drug discovery, machine learning for structural biology.
Practicals and projects will run in parallel to lectures to have a first-hand experience on molecular visualization, major structural biology techniques, molecular modeling, protein design, biomolecular mechanics and dynamics, structure-based drug design, protein interaction networks, macromolecular assemblies, protein structure predictions using AlphaFold.
Keywords
Structural biology, X-ray crystallography, cryo-EM, NMR, AlphaFold, SAXS, integrative modeling, molecular modeling, molecular mechanics, molecular simulation, protein structure prediction, protein folding, protein design, drug discovery, machine learning.
Learning Prerequisites
Required courses
None in particular, but some are recommneded (see below)
Recommended courses
Basic bachelor courses on Maths, Physics, Molecular Biology and Biochemistry
Important concepts to start the course
Structural biology and biochemistry of biomoleculaes. Classical mechanics, themodynamics, and electrostatics (Physics I, II, III), Organic Chemistry.
Learning Outcomes
By the end of the course, the student must be able to:
- Explore the structure of biomolecules (and their interactions)
- Predict the structure and dynamics of proteins
- Design the structure of proteins
- Visualize biomolecules
- Interpret structural data
- Choose the appropriate method to tackle a problem
- Design a project in structural biology
- Make a scientific report and presentation
Transversal skills
- Make an oral presentation.
- Write a scientific or technical report.
- Use a work methodology appropriate to the task.
- Demonstrate the capacity for critical thinking
- Use both general and domain specific IT resources and tools
Teaching methods
Half of the course is based on lectures, while in the other half practical experiences and projects (computational and experimental) are provided to the students.
Expected student activities
Attending lectures, completing practical experiences, reading assignments, presenting a scientific paper, developing a project, writing a report, presenting the results of a project
Assessment methods
Assignments and projects assessment during the semester
Supervision
| Office hours | Yes |
| Assistants | Yes |
| Forum | Yes |
In the programs
- Semester: Spring
- Exam form: During the semester (summer session)
- Subject examined: Structural biology
- Courses: 2 Hour(s) per week x 14 weeks
- Exercises: 2 Hour(s) per week x 14 weeks
- Type: optional
- Semester: Spring
- Exam form: During the semester (summer session)
- Subject examined: Structural biology
- Courses: 2 Hour(s) per week x 14 weeks
- Exercises: 2 Hour(s) per week x 14 weeks
- Type: optional
- Semester: Spring
- Exam form: During the semester (summer session)
- Subject examined: Structural biology
- Courses: 2 Hour(s) per week x 14 weeks
- Exercises: 2 Hour(s) per week x 14 weeks
- Type: optional
- Semester: Spring
- Exam form: During the semester (summer session)
- Subject examined: Structural biology
- Courses: 2 Hour(s) per week x 14 weeks
- Exercises: 2 Hour(s) per week x 14 weeks
- Type: optional
- Semester: Spring
- Exam form: During the semester (summer session)
- Subject examined: Structural biology
- Courses: 2 Hour(s) per week x 14 weeks
- Exercises: 2 Hour(s) per week x 14 weeks
- Type: optional
- Semester: Spring
- Exam form: During the semester (summer session)
- Subject examined: Structural biology
- Courses: 2 Hour(s) per week x 14 weeks
- Exercises: 2 Hour(s) per week x 14 weeks
- Type: optional
- Semester: Spring
- Exam form: During the semester (summer session)
- Subject examined: Structural biology
- Courses: 2 Hour(s) per week x 14 weeks
- Exercises: 2 Hour(s) per week x 14 weeks
- Type: optional