Cellular and Molecular Biology

STRUCTURE OF MACROMOLECULES AND PROTEOMICS

STRUCTURE OF MACROMOLECULES AND PROTEOMICS

Academic year 2020/2021

Sommario del corso

• Course objectives
• Results of learning outcomes
• Course delivery
• Learning assessment methods
• Program
• Suggested textbooks and readings
• Teaching tools

Course objectives

This teaching contributes to the learning objectives included into the Biomolecular area of the Master in Cellular and Molecular Biology - Biologia Cellulare e Molecolare - providing an in-depth and integrated knowledge of biological systems at molecular level focusing on quantitative and qualitative analysis of biological macromolecules and bioinformatic analyses.

In particular, the course provides the student the fundamental knowledge of:

- protein folding,

- structure and the spectroscopic techniques used to study protein conformation and solve their 3D structure,

- protein crystallography,

- instrumentation and techniques employed in the field of proteomics,

- startegies for the construction of protein arrays and protein chips.

Laboratory-based experiments on protein crystallization and protein stability analysis through calorimetry (DSC) will provide the student a practical overview of the approaches that can be used for protein folding and structure studies. 

Moreover, the student will learn the use of up to date bioinformatics tools for protein modeling and docking. 

Results of learning outcomes

KNOWLEDGE AND UNDERSTANDING .

At the end of the course, the students should know:

- the different levels of protein structure and their graphical representation;

- structural interpretation in terms of polypeptide chain folding;

- structure-function relationships of biological macromolecules,

- the study of protein folding,

- evolution of protein structures and protein modules,

- spectroscopy applied to biological macromolecules,

- X-ray crystallography,

- techniques for the study of the proteome,

- protein arrays and protein chips.

 APPLYING KNOWLEDGE AND UNDERSTANDING. 

At the end of the course, the student will be able to:

- Recognize and classify protein structures

- Select the appropriate spectroscopic technique for structural and functional protein studies

- Understand and apply the techniques of protein immobilization for biochips

- Understand the principles of mass spectrometry applied to protomics

- Use databases of sequences and protein structures

- Visualize, calculate and study the protein structures using molecular graphics software.

JUDGEMENT. Recognition of molecules and structures in the graphical representation in databases. Interpretation of Molecular Biology basic protocols.

COMMUNICATIONS SKILLS. Written test on the practicals part about molecular mechanics approaches .

LEARNING ABILITY. Familiar with protein databases and tools available online.

Course delivery

Lectures: 40 hours; Practicals: 16 hours

Due to COVID-19 emergency, the lectures are held in the classroom and contemporarly available live streaming on webex. They are also recorded and added on the Moodle platform on the day of the lecture.  

Practicals will also be organized in small groups in the laboratory depending on the rules given the sanitary situation and, in any case, live streaming on webex and recorded to be available on the Moodle platform.

Learning assessment methods

Depending on the health emergency conditions, the exam will be written in the classroom with small groups of students, written or oral through the Webex platform, depending on the number of students. 

In any case, there will be 3 open questions:

- one question on the module of Prof. Di Nardo (60% of the final grade)

- one of them on the module of Prof. Sadeghi (30% of the final grade)

- one question on the Lecture and Practicals of "Protein bioinformatics" (10% of the final grade)

Students should gain a sufficient grade (6 out of 10 or more) on all the three questions in order to pass the exam.

The final grade will be expressed in a maximum of 30 cum laude.

The student will be invited to the meeting on the Webex platform through a mail the day before the exam. Possible technical malfunctions (e.g. weak or absent line for video conferencing on Webex or obscuring the video during the test) do not preclude the possibility of taking the test or exam, which will take place, if deemed necessary, by means of a personalized test or a replacement oral.

First session, January-February 2021: the exam will be written in classroom and contemporarly on the webex platform and moodle.

Program

PROTEIN STRUCTURE

• Protein structure classification , superscondary structure, protein domain classification, function and evolution
• Membrane proteins: how the structure supports the function
• Protein folding: Key concepts and methods, Thermodynamics, Kinetics, Effect of denaturants on rates of folding and unfolding, Protein misfolding and chaperons, Proteins misfolding and disease, Principles of calorimetry for the study of protein folding
• Biological spectroscopy: fluorescence, circular dichroism and IR applied to the study of protein structure and dynamics
• Methods to study the 3D structure of macromolecules: NMR, x-ray crystallography and cryo-EM.
• Methods for crystallization adn rtructure resolution by X-ray crystallography
• Practical 1: crystallization of lysozyme and basics on analysis of x-ray diffraction images
• Practical 2: molecular modelling: construction and evaluation of protein models, ligand docking, docking of protein structures and domains

• PROTEOMICS

• Technical background on electrophoretic methods-2DE-DIGE

• Obtaining and scanning gel maps, Image analysis software for matching and semi-quantitative analysis.

• Mass spectrometry (MS) for proteomics (Maldi, ESI, De novo sequencing). Data analysis.

• Examples of application of 2DE and MS for diagnostics and research: presentation of recent papers on various fields of proteomics research.

• Protein array and protein chip: overview on available approaches and detection (SPR, fluorescence).

• Immobilisation strategies for arrays and chips. Nanoarrays and nanotechnologies applied to the development of protein chips. Examples of protein chips applications.

• Functional proteomics: activity based protein profiling (ABPP), theory and examples.

- A.M-Lesk: Introduction to protein science. Architecture, functions and genomics, Oxford University Press
- AC supply Orengo, D.T. Jones & J.M. Thornton: Bioinformatics. Genes, protein & Computers
- BIOS Scientific Publishers Limited It 'strongly advised to use the following material for insights and additions:
- Powerpoint presentations and lecture notes;
- Articles and reviews taken from the literature as shown in class.

• Teaching materials
• Exams and finals
• Go to Moodle
• Visit the forums