Primary sequence and aminoacids. Protein secondary structure elements. Torsion angles and Ramachandran plots. Motifs of protein structure. Alpha-domain structure, Alpha/beta structures and beta structures. Structural classification of protein. PDB. Folding and flexibility. DNA Structures. DNA recognition in procaryotes and eucaryotic transcription factors. Membrane proteins. Principles of NMR spectroscopy and X-ray diffraction for 3D structure determination
Carl Branden &John Tooze Introduction to Protein Structure
Jack Kyte Structure in Protein Chemistry.
Structural features of proteins (Banci, Cantini)- NMR of Biomolecules: Towards Mechanistic Systems Biology -Wiley
Book chapters and review articles on specific subjects will be also provided to the students.
Learning Objectives
The course aims at providing the students with a detailed knowledge of various aspects of structural biology, focusing on the fold and organization of biological macromolecules, particularly of proteins and nucleic acids. The relationship between structure and function for some selected classes of proteins will be discussed. The molecular basis for the protein folding process will be presented. The basic concepts of the spectroscopic and biophysical methods used for structural characterization, as well as of the two major techniques (NMR spectroscopy and X-ray diffraction) for 3D structural determination will be presented.
Prerequisites
Courses required: noneCourses recommended: none
Teaching Methods
Total number of hours for Lectures (hours): 48Total number of hours for Laboratory-field practice : 10
Type of Assessment
The examination involves passing an oral exam on the topics covered in the course.
To take the test is required exam registration on the website of teaching enabled electronic verbalization. The list is
closed two days before the date of the examination.
It is guaranteed a minimum number of appeals and the teachers are available to enter further appeals at the request of students.
The schedule of examinations for the academic year. 2016/2017 is available at:
https://sol.unifi.it/docprenot/docprenot
Examination commission: L. Banci, M. Lelli, F. Cantini, V. Calderone
Course program
The primary sequence: the aminoacids and the peptide bond. Secondary structure. Elements of secondary structure: helices, strands and sheets, turns. Torsion angles and Ramachandran plot. Structural motifs: helix-loop-helix, beta hairpin, Greek key, etc. Tertiary structure. Motis and domains. The most common types of folds, classifies as alpha folds, beta folds, alpha/beta and alfa+beta. Quaternary structure. The structural classification of proteins: the CATH and SCOP databases sono database?? The Protein Data Bank (pdb). The types of non covalent interactions and the folding processes in proteins. Structural stability of proteins. Approaches for characterizing the folding processes. The folding “funnel”. The unstructured states. The transition states in the folding process. The molten globule state. In vivo folding processes. The fuction of molecular chapersons such as GroEL and GroES. Protein aggregation and fibril formation. Protein flexibility. The DNA structure and the interactions protein-DNA, in eukaryotic and in prokaryotic organisms. Membrane proteins. Basic knowledge of NMR spectroscopy and X-ray diffraction for the structural characterization and the determination of 3D structure of biomolecules. NMR spectroscopy for the characterization of the overall and internal dynamics of macromolecules.