Protein engineering and molecular enzymology

A.Y. 2020/2021
Overall hours
Learning objectives
Protein engineering is a novel and dynamic field, which leads to production of modified proteins used to elucidate biological processes, structure-function relations of proteins, for the development of bioactive compounds and applications of proteins in all domains of biotechnologies. This class mainly aims to provide (i) the theoretical bases for the understanding and design of protein engineering approaches exploiting structural and functional information on the target proteins and (ii) the tools to carry out protein engineering and analyzing engineered proteins.
The course is ideally linked to those dealing with metabolic engineering, structural biology, bioinformatics, nanotechnologies and molecular parasitology.
Expected learning outcomes
At the end of this class , the students are expected to:
(1) have refreshed basic concepts in protein structure-function relations and enzyme catalysis;
(2) have acquired an advanced understanding of theoretical aspects of enzyme catalysis and of the experimental approaches used to correlate structure-function relations with an emphasis on the use of this knowledge to engineer novel enzyme forms in the context of fundamental science projects and biotechnological applications;
(3) have understood the rational of current protein engineering approaches and methods;
(4) have acquired the ability to correlate the theoretical and experimental connections among the disciplines involved and their relevance to biotechnological developments;
(5) have acquired the technical vocabulary needed to critically read research articles and to present them in oral and written forms.
Course syllabus and organization

Single session

Lesson period
Second semester
Teaching methods and delivery methods
Asynchronous lessons will be made available on the ARIEL teaching platform for the whole semester and uploaded to the site according to the class schedule (video lessons consisting of recording of the teacher's desktop with audio commentary), organized to cover the topics of each class. The recorded lectures will be made available according to the schedule of the class. Furthermore, synchronous meetings with students will be organized on a regular basis, using the Microsoft Teams platform, for discussion, complementation of the recorded classes and answers to questions form students. Also the Journal Club, which will consist of the presentation and discussion of research articles by groups of students, will take place via MS Teams.

Learning verification procedures and assessment criteria
The exam will take place orally using the Microsoft Teams platform or, if allowed by rules regarding the COVID sanitary emergency, in a physical classroom in a written form.

The exam, in particular, will be aimed to:
- ensure the achievement of objectives in terms of knowledge and understanding;
- verify the ability to apply knowledge and understanding as well as the autonomy of judgment through the discussion of examples analyzed during classes;
- verify the mastering of the specific language that belongs to the field of biochemistry, in particular enzymology and protein engineering, and the ability to present the topics in a clear and logical fashion with due connections to the content of other classes of the master degree.
Course syllabus
The lectures will first review information on: (i) protein structure, folding and structure-function relations, (ii) the principles of enzyme catalysis and kinetic tools to study enzyme catalytic properties; (iii) spectroscopic techniques for the study of proteins and their function; (iv) techniques and strategies for the overexpression, purification and modification of molecular targets, especially proteins and enzymes.
Lectures will then be largely based on the discussion of articles from specialized journals, and will cover:
- protein engineering goals and strategies
- design, expression, selection, isolation, and characterization of protein variants.
Examples of successful protein engineering experiments will be discussed during classes.
Prof. Nardini (2 CFU) and Prof. Vanoni (4 CFU) will share the teaching of this class by focusing on structural biology (Prof. Nardini) , and enzymology aspects applied to protein engineering, as well as protein engineering methods (Prof. Vanoni)..
Prerequisites for admission
A revision of the topics covered by the basic biochemistry and molecular biology classes included in the bachelor curriculum before attending the course is highly recommended.
Teaching methods
Teaching Mode: Classroom lectures supported by projected material with common discussions on experimental design, data analysis, and specific case studies. Attendance is highly recommended.
Teaching Resources
. Voet, D. & Voet, J.G Biochemistry , 4th Edition, J. Wiley & Sons
· Fersht, A. Structure and mechanism in protein science (Freeman)
· Frey, P.A. & Hegeman, A.D. Enzymatic Reaction Mechanisms, Oxford University Press (2007)
· Petsko, G.A. & Ringe, D. Protein structure and function, New Science Press, 2004
Articles on which lectures will be based.

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.
Assessment methods and Criteria
The evaluation of the student's performance will be based on a "journal club" activity and a written examination with open-answer questions spanning all topics covered in the class (2 hours).
For the "journal club" activity students will work in small groups. Presentations will be done at the end of the class and before the written exam. The evaluation of the Journal club activity will account for up to 2 points of the final grade. After receiving a proposed score resulting from the joint evaluation of the journal club and the written exam by the teachers, students will have the possibility (if they wish) to integrate the written exam with an oral discussion of the written paper to clarify their actual mastering of the topics.
The final grade will result from the joint evaluation of each candidate by the two teachers, and will be communicated through the online UNIMI platform.
BIO/10 - BIOCHEMISTRY - University credits: 6
Lectures: 48 hours
Thursday, 10:30-12:30
Dept. of Biosciences, C tower, 5th floor
Monday, 1 pm -2 pm
Protein Biochemistry Unit, DSBB, Via Celoria 26, 5C