Integrated structural biology

A.Y. 2021/2022
Overall hours
Learning objectives
The theoretical and practical grounds of structural biology, a branch of life sciences spanning different methodological approaches, will be presented. Through the lectures and practical sessions, the students will gain an understanding of the principles through which the interaction of X-rays, or of electrons, with the biological matter can unravel the molecular/atomic organization of molecules and macromolecules (proteins and nucleic acids) that build cells and organisms. The theoretical bases of X-ray crystallography, presented in frontal lectures, will guide the understanding of applicative methods. Students will learn crystallization and X-ray diffraction techniques, use of synchrotron radiation, computational approaches to solving the three-dimensional structure of proteins and nucleic acids. A thorough understanding of the fundamental principles of cryo-electron microscopy will allow students learning the state of the art methods of single particle cryo-electron microscopy to gain access to the three-dimensional structures of large macromolecular complexes. Altogether, the lectures will be integrated by lab and computing practicals. In the end the students will gain a thorough view on the methods and potential of structural biology that provides us with unique views and understanding of the way proteins, DNA, RNA and other biological (macro)molecules act. The course is ideally linked to those dealing with protein engineering and computational biology.
Expected learning outcomes
Students will acquire extended knowledge on the methods of X-ray crystallography and single particle cryo-electron microscopy. Such cultural background will enable them to: i) appreciate the complexity of structural biology experiments and of the physical principles on which they rely; ii) understand the limitations posed by each technique, and learn how to properly plan/execute experiments; iii) understand how three-dimensional structures of macromolecules are achieved, their significance and their standing within the domain of biological research.
Course syllabus and organization

Single session

Lesson period
Second semester
More specific information on the delivery modes of training activities for academic year 2021/22 will be provided over the coming months, based on the evolution of the public health situation.
Course syllabus
The course is focused on the 3D structure determination and analysis of proteins by using biocrystallographic and bioinformatic techniques. Experimental techniques for protein crystal growth will be described in details (including practicals in the bio-crystallography lab), with application to soluble and membrane proteins. X-ray diffraction on protein crystals and solution samples (SAXS) will be treated extensively (X-ray sources, synchrotron light, atomic scattering factors, structure factors, the "phase problem", phasing by molecular replacement and heavy atoms, crystallographic refinement). Protein model validation techniques will be analyzed, together with the main features of the Protein Data Bank. In addition, the theoretical basis and the practical applications of single-molecule cryo-EM techniques will be treated. At the end of the lectures and of the practical sessions the students will be able to design and run experiments for crystal growth, electron microscopy sample preparation, processing of data for both techniques. They will also gain a critical view on the design and execution of research experiments in the structural biology context, aiming at understanding structure, function, interactions and modifications that characterize proteins in living cells.
Prerequisites for admission
Students are expected to have preexisting knowledge on: fundamental properties of electromagnetic radiation: energy, frequency, wavelength, interference; basic mathematics and physics. Basic knowledge on biochemistry of proteins and nucleic acids, related to their structural organization levels.
Teaching methods
Teaching mode: classroom lectures supported by projected material, and practical sessions in the bio-crystallography, cryo-EM, and cyber labs. Attendance is highly recommended.
Teaching Resources
Given the conceptual and practical span of the arguments covered, there is no single textbook covering all the topics. Besides, these fields are rapidly evolving. Materials for study will be provided through lecture slides and addressing to specific textbooks, web sites and scientific review papers.
Assessment methods and Criteria
The evaluation of the student's performance is based on a written examination with 4-5 open-answer questions spanning all topics covered in the course. A written examination (2 hours) allows students to show their ability to describe and critically comment (by using diagrams, graphs, equations) the theoretical bases and the practical applications of the structural biology methods learned during the course. No exercises are present in the examination test. Examples of the examination test will be discussed during classes and made available to students. Furthermore, description and analysis of the practical experiences developed in the second half of the class (in the form of students' reports) will build 20% of the final exam score.
BIO/10 - BIOCHEMISTRY - University credits: 6
Practicals: 32 hours
Lessons: 32 hours
Professor: Nardini Marco
Thursday, 10:30-12:30
Dept. of Biosciences, C tower, 5th floor