Structural Biochemistry

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 application in Structural Biochemistry; Preparation of a seminar with the analysis of a scientific article / “case study” in Structural Biochemistry (submission of a 1-page summary); Oral presentation and discussion of the “case study”

- 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: