C6770 NMR Spectroscopy of Biomolecules

Faculty of Science
Autumn 2020
Extent and Intensity
2/0/0. 2 credit(s) (fasci plus compl plus > 4). Recommended Type of Completion: zk (examination). Other types of completion: k (colloquium).
Taught online.
Teacher(s)
prof. Mgr. Lukáš Žídek, Ph.D. (lecturer)
doc. RNDr. Radovan Fiala, CSc. (lecturer)
Mgr. Pavel Kadeřávek, Ph.D. (lecturer)
Guaranteed by
prof. Mgr. Lukáš Žídek, Ph.D.
National Centre for Biomolecular Research - Faculty of Science
Contact Person: prof. Mgr. Lukáš Žídek, Ph.D.
Supplier department: National Centre for Biomolecular Research - Faculty of Science
Timetable
Tue 9:00–10:50 C04/211
Prerequisites
The course is offered to students interested in NMR methods applied to biomacromolecules. Basic knowledge of structure of proteins and nucleic acids is expected.
Course Enrolment Limitations
The course is also offered to the students of the fields other than those the course is directly associated with.
fields of study / plans the course is directly associated with
there are 9 fields of study the course is directly associated with, display
Course objectives
The course will provide introduction to modern NMR techniques which can be applied to extract structural information for small and mid-size biological macromolecules - peptides, proteins, DNA and RNA oligonucleotides. Experimental procedures and computational protocols for determination of three-dimensional structures and dynamics based on NMR data will be discussed. Students who finish the course successfully will understand principles of NMR and its applications to biochemical problems described in original research articles, to analyze NMR experiments and design their modification, to chose the correct approach of solving a given problem, and to combine results of individual approaches to obtain a complex picture of the studied problem. The course is designed so that students who continue to study in a PhD program will be able to apply the learned skills in their own research projects.
Syllabus
  • 1. NMR as a tool for structure biology; Origin of magnetism. Structure determination based on NMR-derived distance restraints, comparison with diffraction techniques (advantages and disadvantages). Other biomolecular applications of NMR spectroscopy: quick quality control, intermolecular interactions, molecular motions (overall, internal), kinetics and thermodynamics, in-vivo measurements, spatial resolution. Limitations of biomolecular liquid-state NMR spectroscopy. Magnetism of Dirac particles, nuclear magnetism, magnetic dipole moment and its precession in a homogeneous magnetic field, relation between angular momentum and magnetic moment, energy and precession frequency of a magnetic moment in a magnetic field.
  • 2. What is going on inside the magnet. Macroscopic magnetization and distribution of magnetic moments in thermodynamic equilibrium, polarization, coherence. Basic NMR experiment. NMR spectrometer, radio-wave irradiation, signal detection. Local magnetic fields in a molecule (caused by nuclei, electrons), chemical shift, dipole-dipole interactions, J-coupling, modulation of carrier frequency, Fourier transformation, spectrum.
  • 3. 2D NMR experiments (correlated spectroscopy). Basic idea (NOESY as an example), heteronuclear spectroscopy. Spin echoes, INEPT, HSQC.
  • 4. NMR of proteins I. Spin systems in proteins. 3D experiments for sequential resonance assignment, HNCA, HN(CO)CA, HNCACB, CBCA(CO)NH. Side-chain assignment.
  • 5. NMR of proteins II. Strong coupling and isotropic mixing, TOCSY. Side-chain assignment from HSQC-TOCSY.
  • 6. NMR of proteins III. Technical issues. Pulses and delays, offset effects and selective pulses, quadrature detection, pulsed-field gradients, phase cycling, suppression of water signal.
  • 7. NMR of proteins IV. Structure determination. Structural parameters (inter-proton distances from NOE, torsion angles from J-coupling, orientation from residual dipolar coupling). Calculation of 3D structure by restrained molecular dynamics simulation.
  • 8. NMR of nucleic acids I. Spin systems in nucleic acids, 1D spectroscopy in water and deuterium oxide, homonuclear correlations in bases and sugar-phosphate backbone.
  • 9. NMR of nucleic acids II. Isotope labeling and heteronuclear spectroscopy of nucleic acids, structural parameters, structure determination.
  • 10. NMR relaxation and dynamics of molecules I - theory of relaxation. Relaxation mechanisms (chemical shift anisotropy and dipole-dipole interactions). Adiabatic contribution and loss of coherence. Non-adiabatic contributions and return to equilibrium. Correlation function, spectral density function, relaxation rates.
  • 11. NMR relaxation and dynamics of molecules II - measurement and analysis. Relaxation rates R1 and R2, steady-state nuclear Overhauser effect. Model-free analysis and spectral density mapping, limitations.
  • 12. Interactions, exchange. Effect of slow dynamics on relaxation rates and line-shape.
Literature
  • CAVANAGH, John. Protein NMR spectroscopy : principles and practice. 2nd ed. Amsterdam: Elsevier, 2007. xxv, 885. ISBN 9780121644918. info
Teaching methods
Interactive on-line lectures in real time combining explanation of basic ideas with analysis of model examples, computer simulations of the discussed topics.
Assessment methods
Oral examination in a form of discussion of problems solved by the student. On-line possible.
Language of instruction
English
Follow-Up Courses
Further Comments
Study Materials
The course is taught annually.
Teacher's information
http://www.ncbr.chemi.muni.cz/~lzidek/C6770/C6770.html
The course is also listed under the following terms Spring 2008 - for the purpose of the accreditation, Spring 2011 - only for the accreditation, Spring 2000, Spring 2001, Spring 2002, Spring 2003, Spring 2004, Spring 2005, Spring 2006, Spring 2007, Spring 2008, Spring 2009, Spring 2010, Spring 2011, Spring 2012, spring 2012 - acreditation, Spring 2013, Spring 2014, Spring 2015, Spring 2016, Spring 2017, spring 2018, Spring 2019, Autumn 2019.
  • Enrolment Statistics (recent)
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