Structural Biochemistry A

General characterization

Prerequisites

Available soon

Bibliography

• Structural Biology, Practical NMR applications, Quincy Teng, Springer (2005)
• H.J. Dyson, A.G. Palmer, “1.9 Introduction to Solution State NMR Spectroscopy”, Comprehensive Biophysics, 136-159, Edward H. Egelman, Eds, Elsevier (2012)
• “Introduction to Protein Structure”   Branden, C.-I. & Tooze, J. Garland Pub. (1999)
• “Crystallography made Crystal Clear- A Guide for users of Macromolecular Models” G. Rhodes, 2^nd Ed., Academic Press: San Diego, London (2000)
• Recent publications (articles and reviews) will be made available each year

Teaching method

T + P classes

T - presentation of contents with slide support (ppt) this year on an online platform (Zoom) + student work with bibliography support and self-assessment mini-tests

P - group work sessions, with a protocol provided by the professors. The work will be developed in a laboratory environment (1 session) and classroom (virtual or in person) with the support of online platforms and dedicated software, with exercises for applying the contents presented in the T classes

Student Work - includes answering quizzes for preparing and preparing quizzes and group monographs. Each group will have to do a research to choose 2 scientific articles (with case studies of application of the contents) to be presented in a seminar.

Evaluation method

A - Practice: NMR (questionnaires) + crystallography (monography) (20%)

B - Seminars and discussion S1+S2 (40%)

C - NMR Test (20%) + Crystallography/CryoEM/SAXS Test (15%) and average weekly quizzes 5%) - minimum score in each test = 9.5 values OR Exam (Possibility of repeating only one of the tests at the time of appeal).

Final grade = (Ax0.2) + (Bx0.4) + (Cx0.4)

- Seminar

Examples of AI applications in Structural Biochemistry: Preparation of a seminar analyzing a scientific article / “case study” in Structural Biochemistry. The final oral presentation and discussion of the “case study” should be preceded by a presentation to share these topics with secondary school students (10th- 12th grade). To do this, they must travel to a secondary school in the Faculty''s area and give a presentation during a class. The experience should be presented in the final discussion of the seminar, with the UC''s teachers.

The details and objectives of the seminar evaluation were presented in class and are available on the UC page on Moodle platform

- Practical classes take place in a single shift and are mandatory; the Monograph will be developed in groups of 3 students (the same applies to the Seminars)

Subject matter

Part I

- Basic Concepts in NMR (review); 1D and 2D spectra (homo-and hetero-nuclear): applications to proteins

- Identification and assignment of signals in protein 2D spectra; secondary structural elements determination based on chemical shifts

- Backbone assignment of proteins using triple resonance experiments - methodology

- Determination of protein structures in solution; NMR constraints and methodology for structure calculations

- Relaxation and protein dynamics

- NOE effect and Saturation Transfer Difference experiments: application to protein - ligand interactions

- NH exchange and protein structural information.

Part II

- Introduction to protein crystallography; review

- Crystallization of proteins; Lattice, Symmetry and Space Groups

- X-ray sources and detectors; diffraction; reciprocal space

- Diffraction and Fourier transform; The Phase Problem and how to solve it.

- Model building and Refinement; Methods of Validation

- Molecular Electron Microscopy 

Practical Classes

NMR solution structure

- P1 : The NMR spectrometer ; 2D heteronuclear experiments.

- P2 : Resonance assignment using 3D spectra. Introduction to BMRB  - Biological Magnetic Resonance Data Bank.

- P3 : Solution structures determination using Cyana software - input data preparation,  output data (violations detection & iterative process) and validation results (online tools). NMR vs X-ray structures.

- P4 : Protein ligand interactions; titrations followed by HSQC and data obtained by STD (eg CBM11 )

- S : Case study Oral presentation and discussion

X-Ray Crystallography

- P1: databases, PDB revisited

- P2: Preparation and optimization of protein crystals (Q1)

- P3: The X-ray diffractometer and diffraction experiment. Processing and analysis of data.

- P4: Solving a structure by MR method (Q2)

- P5: Analysis of electron density and model building; Model quality and validation criteria. (Q3)

- S: Seminars – Case study : Oral presentation and discussion

Programs

Programs where the course is taught: