Structural Biochemistry A
Maria dos Anjos Lopes de Macedo, Maria João Lobo de Reis Madeira Crispim Romão
Weekly - 4
Total - Available soon
- 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.
- 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
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
- 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 where the course is taught: