66473 - BIOCHIMICA CELLULARE E STRUTTURALE CON LABORATORIO DI BIOINFORMATICA

Learning outcomes

At the end of this tutorial, the student will acquire deepened knowledge on: protein structural changes involved in important biochemical functions like catalysis, signal transduction, DNA-protein interactions. The student will be able to advantageously discuss about cellular biochemistry, to understand the methodology utilized in cellular biochemistry, to propose experimental protocols for the study of specific cellular functions

In the informatics hall, the student will get a basic know how of the molecular graphic program Deep View for the analysis of PDB files and for planning mutagenesis experiments based on the detailed study of the proteins structure.

Course contents

Part of the tutorial will take place in the informatics hall and dedicated to the following topics:

-know how of the main nucleic acid and protein databank and retrieval of the searched information (structure, function, sequence, omology)

-learning of the basic functions of the program Deep View to visualize and manipulate crystalloghraphic data

-key factors of secondary, tertiary and quaternary protein structure organization, Ramachandran plot; super-secondary structure; ligand induced conformational changes; manipulation of structure to evaluate in silico induced mutations; structural comparison between homologous proteins.

-studies on the molecular mechanism utilized by proteins mentioned in the associated lessons of Cellular and Molecular Biochemistry (hold by Prof. Anna Maria Porcelli), that will treat the following arguments:

-7TM receptors signalling strategies independent of G proteins . Mechanisms of receptor inactivation: the GRK family. Arrestins: role as molecular switch and signalling scaffold in endocytosis and MAP kinases activation. Differences between the class A and B receptors.Trans-activation of tyrosin-kinase receptors; arrestin and tyrosin-kinase receptors.

-Adenylate cyclase and lipid rafts. In vivo evaluation of cAMP. PKA: structure and localization. AKAPs.

-Phospholipases C: the phosphoinositide cycle, multi-domain organization of PLC beta/ gamma/delta/epsilon. DAG measurements in vivo. The very special case of PLC epsilon: dual activity and activation mechanisms involving G proteins, EPAC and Rap GTPases.

-PKC: isoforms structure, activation.

-Calcium an universal intracellular messenger: Ca2+ signalling toolkit, spatial-temporal aspects, waves, oscillations and possible mechanisms. Ca2+ and mitochondria; Ca2+ micro-domains in cell signalling: the ER/mitochondria relationship.

-Mitochondria. Ultra-structural details of mitochondria. Morphological and functional heterogeneity of the mitochondrial reticulum. Mitochondria biogenesis: targeting signals, TOM, TIM23/PAM, TIM23/SORT, TIM22, OXA1, MIA complexes, MDM complex. Dynamics: mitofusins, OPA1 e DRP1 in the fusion/fission processes.

Readings/Bibliography

Scientific papers provided by the teacher.

Teaching methods

Lectures and practices in the informatics hall.

Assessment methods

Oral and practical test using the molecular graphics program Deep View. Students must prepare a commentary on a crystal structure at their choice.

Teaching tools

Power point lectures, Deep View guide, practical exercises in informatics hall.

Office hours

See the website of Francesco Francia

See the website of Anna Maria Porcelli