Ateneo - UPO

The course combines experimental biochemistry activities with structural biology approaches applied to biomedical research. The practical component will focus on the purification of a recombinant protein using chromatographic techniques and on the assessment of protein purity. The second part will introduce students to the three-dimensional analysis of proteins using PyMOL, with particular emphasis on the identification and characterisation of active sites, protein–ligand interactions, and the basic principles of structure-based drug discovery.

No mandatory textbooks are required. Teaching materials, including lecture notes, scientific articles, laboratory protocols, and practical exercise materials, will be provided by the instructor throughout the course.

The course aims to provide students with practical training in experimental biochemistry and structural biology by integrating laboratory activities with computational analysis tools. Through the purification of a recombinant protein and the use of the PyMOL molecular visualization software, students will gain an integrated understanding of the relationship between protein structure and function and appreciate how structural information is applied in biomedical research and rational drug discovery.

Attendance of a Biochemistry course is required, and students are strongly recommended to have successfully passed the corresponding examination before the beginning of the course.

The course is based on laboratory sessions and hands-on practical activities, complemented by short introductory lectures. Students will perform recombinant protein purification experiments and use PyMOL for the structural analysis of proteins, active sites, and protein–ligand interactions. Teaching will follow a learning-by-doing approach, encouraging active participation and discussion of the experimental results.

Students are required to bring their own laptop (PC or Mac) for the structural analysis practical sessions. They should be able to install the free version of PyMOL (or the version specified by the instructor) before the course begins. Students who do not have access to a personal computer will be provided with a workstation by the University.
Students with physical disabilities, Learning Disabilities or Special Education Needs can request specific services and tools via the Staff Sviluppo e Coordinamento Carriere e Servizi alle Studentesse e agli Studenti, consulting the University webpage: https://www.uniupo.it/en/services/servicesstudents-physical-or-learning-disabilities.
Students with disabilities, learning disabilities or special education needs, once they have contacted the University Staff, can refer to the tutor in charge of the course to define the examination modalities, concerning academic aspects.

Assessment will be carried out throughout the course during the practical activities. Evaluation will be based on students' active participation, acquisition of practical and technical skills, ability to interpret and discuss the experimental results, and appropriate use of the laboratory techniques and software introduced during the course.

Module 1 – Recombinant Protein Purification
Overview of recombinant protein expression.
Cell lysis and preparation of protein extracts.
Principles of affinity chromatography.
Purification of a recombinant protein using chromatographic techniques.
Assessment of protein purity by SDS-PAGE.
Discussion of experimental results and common technical challenges.

Module 2 – Introduction to Structural Biology and Drug Discovery
Introduction to protein three-dimensional structure and the Protein Data Bank (PDB).
Introduction to the PyMOL molecular visualization software.
Visualization and analysis of protein structures.
Identification and characterization of protein active sites.
Analysis of protein–ligand interactions.
Principles of structure-based drug discovery and the use of structural information for rational drug design.
Guided hands-on exercises using PyMOL.

At the end of the course, students will be able to:
understand the theoretical principles underlying recombinant protein purification;
perform the main steps of a protein purification protocol and evaluate the obtained results;
use PyMOL to visualize and analyse three-dimensional protein structures;
identify and characterize protein active sites and protein–ligand interactions;
understand the role of structural biology in structure-based drug discovery;
critically interpret and discuss the data generated during the practical activities.