Structural Biochemistry A
Maria dos Anjos Lopes de Macedo, Maria João Lobo de Reis Madeira Crispim Romão
Weekly - 4
Total - 51
- 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, 2nd Ed., Academic Press: San Diego, London (2000)
- Recent publications (articles and reviews) will be made available each year
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.
A - Practice: NMR (questionnaires) + crystallography (monography)
B - Seminars and discussion S1+S2
C - Average NMR Test + Crystallography/CryoEM/SAXS Test (includes Test 40% and average weekly quizzes 10%) - minimum score in each test = 9.5 values
Possibility of repeating only one of the tests at the time of appeal (exam).
Final grade = (Ax0.2) + (Bx0.3) + (Cx0.5)
- 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: