D1. Knowledge and understanding: the student will acquire the theoretical foundations and applicative principles of the main methods used in Structural Biology aimed at the biophysical and structural characterization of biological macromolecules and their interactions with other molecules.
D2. Applying knowledge and understanding: the student will be able to use the knowledge acquired to solve problems inherent the study of the structure of biological macromolecules and their interactions with other molecules. The student will be able to understand the structural aspects of biological macromolecules in the scientific context of reference.
D3. Making Judgement : the student will be able to identify the appropriate methodologies, among all those discussed, for the specific study of biostructural problems and biomolecular interactions.
D4. Communication skill: the student will acquire the proper terminology necessary for the understanding and discussion of Structural Biology problems.
D5. Learning skills: ideally, the student will be able to apply the acquired biophysical and biostructural notions, to more complex biostructural problems and more in general to scientific problems where the macromolecular structure or the molecular ability to interact with partners, is relevant for the general understanding.

Basic Chemistry and Physics, Biochemistry, Molecular Biology, Biophysics

Introduction to Integrated Structural Biology: Expression and purification of proteins for structural studies.
Biophysical methods for the characterization of biological macromolecules (stability, secondary structures, aggregation) and the quantitative evaluation of their interactions with ligands.
Overview of biophysical methods for determining the structure of macromolecules (Crystallography, SAXS; NMR, Cryo-EM and computational methods). Theoretical and experimental principles of crystallography of biological macromolecules. Solving the phase problem, construction, refinement and validation of the crystallographic molecular model. Introduction to synchrotron radiation and its use in biocrystallography, SAXS and circular dichroism. Brief introduction to NMR for the study of biological macromolecules. Brief introduction to Cryo-EM in structural biology. Brief introduction to computational methods, AlphaFold2.

Readings:

G. Rhodes – Crystallography Made Crystal Clear, Academic Press (2006)

C. Branden and J. Tooze – Introduction to Protein Structure - 2nd Edition, Garland Publishing (1999)
B. Rupp - Biomolecular Crystallography: Principles, Practice, and Application to Structural Biology, Garland (2010)

Selected articles from the scientific literature; Slides of the lessons presentations (material will be made available to the students through digital platforms).

- Integrative Structural Biology: an overview.
- Protein expression and purification aimed at biophysical and structural studies.
- Modern biophysical methods to characterize biological macromolecules and their interactions (Isothermal Titration Calorimetry, Differential Scanning Calorimetry, Surface Plasmon Resonance, Differential Scanning Fluorimetry)
- Brief introduction of modern biophysical methods aimed at exploring the structure of biological molecules.
- Introduction to crystals.
- Introduction to molecular and crystal symmetry.
- Basic theory and experimental techniques in bio-molecular crystallography.
- The phase problem and its solution in macromolecular crystallography (MIR, MAD, Molecular Replacement).
- Density modification and 3D model building.
- Structure refinement and structure validation of the crystallographic model.
- Introduction to Synchrotron Radiation.
- Synchrotron Radiation in Bio-molecular crystallography.
- Synchrotron Radiation and Small Angle X-ray Scattering (SAXS) of biological macromolecules
- Synchrotron Radiation based UV-VIS Circular Dichroism of biological macromolecules.
- How to “use” a PDB entry
- How to read critically a structural biology paper. Ad hoc selected case studies.
- Introduction to NMR application to the study of biological macromolecules.
- Brief introduction to Cryo-EM for structural determination
- Brief introduction to computational methods used in macromolecular structure studies. AlphaFold.

The Course consists of two-hours lectures, carried out using PowerPoint presentations that illustrate the various aspects of the examined topics.

A laboratory activity concerning the topics described during the theoretical lessons (crystallization and diffraction of macromolecules, biophysical methods for the study of the interaction between molecules) will be carried out at the CNR laboratory of Structural Biology (Area Science Park - Basovizza).

Any changes to these indications, which may become necessary will be directly communicated to the students or through the digital platforms provided by the University (Teams)

Dr Alberto Cassetta, Istituto di Cristallografia, CNR – Area Science Park Basovizza (Trieste) Building Q1, II floor, Office 105B, SS. N° 14, Km 163.5, I-34149 Trieste.

E-mail: alberto.cassetta@ic.cnr.it ; Phone: +39-040-3757525; Office Hours: Monday-Thursday 8.30-12.30; 13.30-17.30

Sonia Covaceuszach, PhD, Istituto di Cristallografia, CNR – Area Science Park Basovizza (Trieste) Building Q1, II floor, Office 105B, SS. N° 14, Km 163.5, I-34149 Trieste.

E-mail: sonia.covaceuszach@ic.cnr.it ; Phone: +39-040-3757526; Office Hours: Monday-Thursday 8.30-12.00; 13.00-17.00

To be admitted to the evaluation exam, the student must have attended the compulsory laboratories. There is no evaluation of the laboratory activity

The student's assessment includes an oral test divided into the presentation of a scientific article relating to the topics of the course, chosen by the course teachers and communicated at least 20 days before the exam date upon request by the student via email. The presentation must have a duration between 15 and 30 minutes, at the discretion of the student, that can use a computer aid (PowerPoint). After the presentation of the article, questions relating to the presented article may follow. 6 questions will then be asked on the topics illustrated during the course, 3 for each of the two modules of the course. The student must demonstrate adequate knowledge of the topics covered by the course, in line with the learning descriptors listed above. The score of the exam is attributed through a mark expressed out of thirty calculated as follows: up to a maximum of 12 points are attributed to the presentation, up to a maximum of 3 points are attributed to each of the six general questions.
The final score is awarded on the basis of the following evaluation:
-Excellent (30 -30 cum laude): excellent knowledge of the topics, excellent language skills, excellent analytical skills; the student is able to brilliantly apply theoretical knowledge to concrete cases.
-Very good (27 -29): good knowledge of the topics, remarkable language skills, good analytical skills; the student is able to correctly apply theoretical knowledge to concrete cases.
-Good (24-26): good knowledge of the main topics, good command of the language; the student shows an adequate ability to apply theoretical knowledge to concrete cases.
- Satisfactory (21-23): the student does not show full command of the main topics, while possessing the fundamental knowledge; however, it is showed a satisfactory language skills and sufficient ability to apply theoretical knowledge to concrete cases.
-Sufficient (18-20): minimum knowledge of the main topics and of the technical language, limited ability to adequately apply theoretical knowledge to concrete cases.
- Insufficient (<18): the student does not have an acceptable knowledge of the contents of the various topics of the program.

This course explores topics closely related to one or more objectives of the 2030 Agenda for the Sustainable Development of
United Nations