Protein engineering and proteomics

A.Y. 2020/2021
Overall hours
Learning objectives
The course provides an introduction to protein biotechnology and the basic knowledge required for set up large-scale protein production within biotechnological industry, from cell cultivation in bioreactors up to protein purification in a preparative scale and includes different modern bioanalytical techniques. The course is aimed at giving students in-depth understanding of 1) the structure-function relationship of proteins and of 2) the methodologies used to produce, characterize and use proteins, enzymes included, and 3) the molecular basis and protein engineering tools available for designing enzymes or proteins with new or desirable functions. The course will have a strong hands-on connotation based on practical sessions either of experimental design in classroom and of bioinformatics.
Expected learning outcomes
At the end of the course the student will be able to implement the notions of molecular biology, proteomics and genetic engineering for the production and improvement of proteins and enzymes. The student will be able to analyze the structure of proteins and their post-translational modifications; review the main factors that are significant for protein folding processes and stability; explain how proteins can be used for different industrial applications, carry out mutagenesis approaches to improve protein stability and to confer on them new functions.
Course syllabus and organization

Single session

Lesson period
Second semester
Teaching methods: The lessons will be held on the Microsoft Teams platform and can be followed both synchronously on the basis of the second semester timetable and asynchronously because they will be recorded and left available to students on the same platform. The schedule of lessons and all the details of the activities will be published through notices on the ARIEL board. before the start of the lessons. Any updates will also be communicated through notices on the ARIEL board.
The methods and criteria for participating to any possible in classroom lessons and practical labs as established by the University, will be published in due time on the ARIEL notice board of the course. The exercises will take place partly in person and partly online, both asynchronously (providing the material with audio commentary through the Ariel site) and with synchronous mode to critically discuss publications and scientific reports of interest (through the Microsoft Teams platform ).
Program and reference material: The program and reference material will not change.
Learning verification procedures and assessment criteria: The exam will take place orally using the Microsoft Teams platform, according to the indications provided by the University.
Course syllabus
Structural/functional molecular characteristics of proteins: from biosynthesis to folding. Structural and functional dynamics of proteins. Modern approaches for the study of the proteins. Implementation of protein purification procedures. Proteome analyses for protein and enzyme identification and exploitation. Recombinant protein technologies; gene expression: vectors, expression in bacteria, yeasts, plants, insect and mammalian cells. Cell-Free translation systems. Inclusion bodies, their solubilization; protein refolding. Co-expression and use of chaperones. Storage stabilization of proteins. Hints of evolutionary biotechnology (rational design and directed evolution). Examples of tailored enzymes in industrial biocatalysis. Production and applications of polyclonal and monoclonal antibodies. Strategies to set up a protein engineering project. Proteomics: principles and methodologies.
Prerequisites for admission
Prerequisites: general knowledge of structural biochemistry (protein primary, secondary, tertiary quaternary structures, including basics of protein folding) and cell protein synthesis. Enzymatic activities. Basics of gene cloning and heterologous gene expression. For any question and further details please contact the teacher at
Teaching methods
Frontal lessons, laboratories, numerical exercises in classroom and simulations in computer room.
Teaching Resources
Slides of the lessons will be available to students through ARIEL platform.
"Protein Engineering" by Moody P C E and Wilkinson A J,
"Proteins" by Creighton T E,
"Introduction to Protein Structure" by Branden C and Tooze J.,
"Biochemistry" by Voet D and Voet G,
"Protein Engineering" by Kurra Venkata Gopaiah, "Medicinal Protein Engineering" by Yury E Khudyakov, "Protein Engineering: Design, Selection and Applications (Protein Biochemistry, Synthesis, Structure" by Mallorie N Sheehan, "Protein Engineering: Principles and Practice" by Jeffrey L Cleland and Charles S Craik
"Protein Engineering Handbook", 1 & Volume 2, by Lutz and Bornscheuer
Assessment methods and Criteria
Oral. At least 7 exam sessions per year will be guaranteed. The date of the exam will be published on SIFA platform.
Written exam based on questions about the topics covered during the course.
The learning verification will be evaluated according to the following criteria:
1. Proof of understanding of the topics covered during lectures and laboratory practices
2. Ability to expose, in a critical and integrated way, the molecular determinant of proteins structure and their post-translational modifications; the main factors that are significant for protein folding processes and stability; how proteins can be used for different industrial applications; how to carry out mutagenesis interventions to improve protein stability and to confer on them new functions.
3. Knowledge of laboratory methodologies to assess protein structure, functionality and stability.
4. Correct terminology
5. Completeness of the answers
BIO/10 - BIOCHEMISTRY - University credits: 6
Practicals: 16 hours
Laboratories: 8 hours
Lessons: 36 hours
Professor: Scarafoni Alessio
Thursday afternoon only by appointment (by e-mail)
Building 21040, first floor