Macromolecular Structural Biology
A.Y. 2026/2027
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.
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.
Lesson period: Second semester
Assessment methods: Esame
Assessment result: voto verbalizzato in trentesimi
Single course
This course cannot be attended as a single course. Please check our list of single courses to find the ones available for enrolment.
Course syllabus and organization
Single session
Responsible
Course syllabus
The course focuses on the determination and analysis of the three-dimensional structures of macromolecules and macromolecular complexes at high resolution, using macromolecular crystallography and single-particle cryo-electron microscopy.
Experimental techniques for macromolecular crystallization will be described in detail, including practical sessions in the bio-crystallography laboratory, with applications to both soluble and membrane proteins. X-ray diffraction from macromolecular crystals will be extensively discussed. Topics will include X-ray sources, synchrotron radiation, atomic scattering factors, structure factors, the phase problem, phasing by molecular replacement and heavy-atom methods, and crystallographic refinement.
Structural model validation methods will also be analysed, together with the main features and use of the Protein Data Bank.
The theoretical basis and practical applications of single-particle cryo-electron microscopy will be covered, with particular emphasis on sample preparation, transmission electron microscope architecture, data acquisition, and image processing.
At the end of the lectures and practical sessions, students will be able to design and perform experiments aimed at obtaining high-resolution structures of macromolecules using macromolecular crystallography and cryo-electron microscopy. They will also acquire a critical understanding of the design and execution of structural biology experiments aimed at investigating the structure, function, interactions, and modifications of macromolecules in the cellular context.
The course also includes a Journal Club activity aimed at providing students with tools for the critical analysis of structural biology research through the discussion of selected examples from the scientific literature.
Experimental techniques for macromolecular crystallization will be described in detail, including practical sessions in the bio-crystallography laboratory, with applications to both soluble and membrane proteins. X-ray diffraction from macromolecular crystals will be extensively discussed. Topics will include X-ray sources, synchrotron radiation, atomic scattering factors, structure factors, the phase problem, phasing by molecular replacement and heavy-atom methods, and crystallographic refinement.
Structural model validation methods will also be analysed, together with the main features and use of the Protein Data Bank.
The theoretical basis and practical applications of single-particle cryo-electron microscopy will be covered, with particular emphasis on sample preparation, transmission electron microscope architecture, data acquisition, and image processing.
At the end of the lectures and practical sessions, students will be able to design and perform experiments aimed at obtaining high-resolution structures of macromolecules using macromolecular crystallography and cryo-electron microscopy. They will also acquire a critical understanding of the design and execution of structural biology experiments aimed at investigating the structure, function, interactions, and modifications of macromolecules in the cellular context.
The course also includes a Journal Club activity aimed at providing students with tools for the critical analysis of structural biology research through the discussion of selected examples from the scientific literature.
Prerequisites for admission
Students are expected to have basic knowledge of the biochemistry of proteins and nucleic acids, with particular reference to their structural organization at different levels.
Teaching methods
Teaching activities include classroom lectures supported by projected material, Journal Club sessions, and practical sessions in bio-crystallography, cryo-electron microscopy, and bioinformatics. Attendance is not mandatory but is strongly recommended in order to fully benefit from the theoretical and practical components of the course.
Teaching Resources
Given the broad conceptual and practical scope of the topics covered in the course, there is no single textbook that includes all the material discussed. Moreover, structural biology is a rapidly evolving field, and students will therefore be guided towards selected textbooks, websites, and scientific review articles relevant to specific topics.
Study material will be provided mainly through lecture slides and additional resources made available through the course website on the myARIEL platform of the University of Milan. This material includes copies of the slides projected during lectures, as well as selected supplementary resources. However, these materials are intended to support, and not replace, attendance at lectures or consultation of textbooks.
The material provided through the course website is made available exclusively to students enrolled in the Degree Course in Molecular Biotechnology and Bioinformatics and must not be distributed to others.
Recommended reference material:
Principles of Protein X-ray Crystallography, 2nd edition — J. Drenth, Springer
Crystallization of Nucleic Acids and Proteins: A Practical Approach — edited by A. Ducruix and R. Giegé, Oxford University Press
Crystallography Made Crystal Clear: A Guide for Users of Macromolecular Models — Gale Rhodes, Elsevier
Single-particle Cryo-EM of Biological Macromolecules — Eva Nogales, Biophysical Society
Useful online resources:
https://www.xtal.iqfr.csic.es/Cristalografia/index-en.html
https://cryoem101.org/
https://pdb101.rcsb.org/
https://www.thermofisher.com/it/en/home/electron-microscopy/life-sciences/learning-center/cryo-em-university.html
Study material will be provided mainly through lecture slides and additional resources made available through the course website on the myARIEL platform of the University of Milan. This material includes copies of the slides projected during lectures, as well as selected supplementary resources. However, these materials are intended to support, and not replace, attendance at lectures or consultation of textbooks.
The material provided through the course website is made available exclusively to students enrolled in the Degree Course in Molecular Biotechnology and Bioinformatics and must not be distributed to others.
Recommended reference material:
Principles of Protein X-ray Crystallography, 2nd edition — J. Drenth, Springer
Crystallization of Nucleic Acids and Proteins: A Practical Approach — edited by A. Ducruix and R. Giegé, Oxford University Press
Crystallography Made Crystal Clear: A Guide for Users of Macromolecular Models — Gale Rhodes, Elsevier
Single-particle Cryo-EM of Biological Macromolecules — Eva Nogales, Biophysical Society
Useful online resources:
https://www.xtal.iqfr.csic.es/Cristalografia/index-en.html
https://cryoem101.org/
https://pdb101.rcsb.org/
https://www.thermofisher.com/it/en/home/electron-microscopy/life-sciences/learning-center/cryo-em-university.html
Assessment methods and Criteria
The evaluation of the student's performance is based on a written examination consisting of 5-6 open-answer questions covering all topics discussed during the course. The written examination lasts 2 hours and allows students to demonstrate their ability to describe and critically discuss the theoretical bases and practical applications of the structural biology methods learned during the course, including the use of diagrams, graphs, and equations where appropriate.
Attendance at lectures and practical sessions is not mandatory; therefore, absence from any lecture or practical activity does not penalize the student, and all students can obtain the maximum score in the written examination.
Students who participate in the Journal Club activity will receive 1 additional point added to their final mark and will be required to answer one fewer question in the written examination.
The description and analysis of the practical experiences developed during the second half of the course, in the form of students' reports, can contribute up to 2 additional points to the final mark. The report format is free, but reports should be clear, concise, and focused. They should include a brief introduction to the experiment, the results obtained, and a short discussion of those results, supported by figures and images when appropriate. Reports must be submitted by the deadline indicated by the lecturer; reports submitted after the deadline will not be considered for the final mark.
Electronic devices are not allowed during the written examination. Any violation of this rule may result in cancellation of the examination.
Attendance at lectures and practical sessions is not mandatory; therefore, absence from any lecture or practical activity does not penalize the student, and all students can obtain the maximum score in the written examination.
Students who participate in the Journal Club activity will receive 1 additional point added to their final mark and will be required to answer one fewer question in the written examination.
The description and analysis of the practical experiences developed during the second half of the course, in the form of students' reports, can contribute up to 2 additional points to the final mark. The report format is free, but reports should be clear, concise, and focused. They should include a brief introduction to the experiment, the results obtained, and a short discussion of those results, supported by figures and images when appropriate. Reports must be submitted by the deadline indicated by the lecturer; reports submitted after the deadline will not be considered for the final mark.
Electronic devices are not allowed during the written examination. Any violation of this rule may result in cancellation of the examination.
BIOS-07/A - Biochemistry - University credits: 6
Exercises: 32 hours
Lectures: 32 hours
Lectures: 32 hours
Professor:
Chaves Sanjuan Antonio
Professor(s)
Reception:
9:00-17:00 (please, send an email for confirmation)
tower C, floor 5