Macromolecular structural biology

A.Y. 2021/2022
Overall hours
Learning objectives
Structural biology is a field focused on understanding biological macromolecules such as proteins, DNA, and RNA. Deciphering the effects of changes to the structure of these biological macromolecules helps elucidate their function and the part they play in diseases. This ultimately assists in various fields including biotechnology, drug discovery and design of therapeutics.
The course is aiming to provide students with a thorough overview (theoretical and practical) of the most important and recent methods applied to structural biology (i.e. X-ray crystallography, Small Angle X-ray scattering, single-molecule Cryo-electron microscopy), focusing in particular on the scientific objectives that these techniques can help to achieve.
The course is ideally linked to those dealing with protein engineering and structural bioinformatics.
Expected learning outcomes
After following this course, the students will develop a better capability to analyze the correlation between structure and function of macromolecules, and a better understanding of the experimental strategies applied in structural biology. The theoretical and practical approaches that characterize the course will stimulate the critical and judgment skills of the students.
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
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. In particular, copies of the slides projected in the classroom as well as other materials will be made available through the course website on the ARIEL platform of the University of Milano ( By no means, this material replaces the lectures or a textbook. The material is made available only to registered students of the Degree Course in Molecular Biotechnology and Bioinformatics and should not be distributed to others.
Ducruix and R. Giegé (Oxford University press)
Crystallography made crystal clear. A guide for users of macromolecular models. By Gale Rhodes (Elsevier)
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
Lectures: 32 hours
Professor: Nardini Marco
Thursday, 10:30-12:30
Dept. of Biosciences, C tower, 5th floor