Vai al contenuto principale
Oggetto:
Oggetto:

STRUCTURE OF MACROMOLECULES AND PROTEOMICS

Oggetto:

STRUCTURE OF MACROMOLECULES AND PROTEOMICS

Oggetto:

Academic year 2017/2018

Course ID
SVB0049
Teaching staff
Dott. Giovanna Di Nardo
Prof. Sheila Sadeghi
Degree course
Cellular and Molecular Biology
Year
2nd year
Type
Distinctive
Credits/Recognition
6
Course disciplinary sector (SSD)
BIO/10 - biochimica
Delivery
Formal authority
Language
English
Attendance
Lessons optional and laboratories mandatory
Type of examination
Written and oral (optional)
Oggetto:

Sommario del corso

Oggetto:

Course objectives

The course contributes to the realization of the Master degree in Cellular and Molecular Biology by 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. 

Oggetto:

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.

Oggetto:

Course delivery

Lectures: 36 hours; Practicals: 24 hours

Lecture attendance is optional, while practicals is compulsory.

Oggetto:

Learning assessment methods

Final written exam with 3 open questions:

- one question on the module of Dr. Di Nardo (50% of the final grade)

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

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

The seminars of the students, based on an original research article about a protein structure, are also assessed ( 10% of the final grade ).

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

The examination committee reserves the right to have an oral exam to clarify the preparation of the student before registering the vote.

 

Oggetto:

Program

PROTEIN STRUCTURE

• Protein structure classification according to Linderström-Lang, superscondary structure, protein domain classification

• Membrane proteins

  • Biological spectroscopy: fluorescence, circular dichroism and IR.
  • Structure resolution by X-ray crystallography
  • Practical on crystallization of lysozyme and basics on analysis of x-ray diffraction images

• Protein structure: comparison, classification and prediction. Prediction of protein function from sequence and structure

• Practical class molecular modelling: construction and evaluation of protein models, ligand docking, docking of protein structures and domains

• Protein folding: Key concepts and methods, Thermodynamics, Kinetics, Effect of denaturants on rates of folding and unfolding, The molten globule, Folding funnels, Folding patterns, Protein misfolding and chaperons, Proteins misfolding and disease

 

• 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.

Suggested readings and bibliography

Oggetto:

- 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.



Oggetto:
Last update: 20/07/2017 17:13
Non cliccare qui!