Graduate School

High-Resolution Nuclear Magnetic Resonance

This course is part of the programme:
Materials (Third Level)

Objectives and competences

The main goal of the course is the introduction of students in the practical work with advanced experiments of high-resolution nuclear magnetic resonance (NMR), which is the most powerful method for determination of conformation and dynamics of molecules in solution. Students acquire knowledge about modern NMR approaches for studies of macromolecules and molecular complexes in solution.

Prerequisites

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Content (Syllabus outline)

    • Multidimensional pulse sequences
    • Determination of three-dimensional structure of molecules and molecular complexes
    • Determination of inter-molecular interactions
    • Studies of conformational flexibility of molecules
    • Determination of dynamic properties of molecules and molecular systems
    • Rational drug design
    • Case studies: application of high-resolution NMR in biophysics, structural, organic and medicinal chemistry and molecular biology
    • Case studies: application of high-resolution NMR in pharmaceutical industry

Intended learning outcomes

Knowledge and understanding:

  • of the broad capabilities of modern high-resolution NMR methods for resolving the research and development tasks in academia and industry
  • of the potentials and limitations of modern NMR methods for studies of molecular structure and dynamics in solution.
  • of the application of experimentally determined conformational and dynamic properties of molecules to unravel research problems.
  • of the operation of the modern NMR equipment with high magnetic fields and cryogenic NMR probe technology.

Readings

    • C. P. Slichter: Principles of Magnetic Resonance, Springer-Verlag. Third Edition 1992.
    • J.Cavanagh, W.J. Fairbrother, A.G. Palmer III, M. Rance, N.J. Skelton: Protein NMR Spectroscopy, Elsevier, Second edition 2007
    • O. Jardetzky, J.F. Lefevre: Dynamics and the Problem of Recognition in Biological Macromolecules, Nato ACI Series, Series A: Life Sciences Vol. 288, 1996
    • Recent scientific literature.

Assessment

Individul project task and oral examination (50/50). A passing grade in the individual project task is required for admittance to the oral examination.

Lecturer's references

Full professor of physics at the University of Nova Gorica.

1.SIMČIČ, Mihael, SOSIČ, Izidor, HODOŠČEK, Milan, BARRETEAU, Hélène, BLANOT, Didier, GOBEC, Stanislav, GOLIČ GRDADOLNIK, Simona. The binding mode of second-generation sulfonamide inhibitors of MurD : clues for rational design of potent MurD inhibitors. PloS One, ISSN 1932-6203, 2012, vol. 7, iss. 12, str. 1-15, e52817, doi: 10.1371/journal.pone.0052817. [COBISS.SI-ID 5145882]

2.MAVROMOUSTAKOS, Thomas, DURDAGI, Serdar, KOUKOULITSA, Catherine, SIMČIČ, Mihael, PAPADOPOULOS, Manthos G., HODOŠČEK, Milan, GOLIČ GRDADOLNIK, Simona. Strategies in the rational drug design. Current Medicinal Chemistry, ISSN 0929-8673, 2011, vol. 18, no. 17, str. 2517-2530, [COBISS.SI-ID 4671770]

3.SIMČIČ, Mihael, HODOŠČEK, Milan, HUMLJAN, Jan, KRISTAN, Katja, URLEB, Uroš, KOCJAN, Darko, GOLIČ GRDADOLNIK, Simona. NMR and molecular dynamics study of the binding mode of naphthalene-N-sulfonyl-D-glutamic acid derivatives: novel MurD ligase inhibitors. Journal of Medicinal Chemistry, ISSN 0022-2623, 2009, vol. 52, no. 9, str. 2899-2908. [COBISS.SI-ID 4121626]

4.POTAMITIS, Konstantinos, ZERVOU, Maria, KATSIARAS, Vassilis, DURDAGI, Serdar, PAPADOPOULOS, Manthos G., HAYES, Joseph M., GOLIČ GRDADOLNIK, Simona, KYRIKOU, Ioanna, ARGYROPOULOS, Dimitris S., VATOUGIA, Georgia, MAVROMOUSTAKOS, Thomas. Antihypertensive drug valsartan in solution and at the AT1 receptor : conformational analysis, dynamic NMR spectroscopy, in silico docking, and molecular dynamics simulations. Journal of Chemical Information and Modeling, ISSN 1549-9596. , 2009, vol. 49, no. 3, str. 726-739. [COBISS.SI-ID 4115994]

5.AVBELJ, Franc, GOLIČ GRDADOLNIK, Simona, GRDADOLNIK, Jože, BALDWIN, Robert Lesh. Intrinsic backbone preferences are fully present in blocked amino acids. Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, 2006, vol. 103, no. 5, str. 1272-1277. [COBISS.SI-ID 3425306]

University course code: 3FIi08*

Year of study: 1

Lecturer:

ECTS: 6

Workload:

  • Lectures: 10 hours
  • Exercises: 40 hours
  • Individual work: 130 hours

Course type: elective

Languages: english

Learning and teaching methods:
lectures, team work under supervision of the lecturer responsible for the course, individual contact hours with the lecturer responsible for the course, team work under supervision of the lecturer responsible for the course, individual contact hours with the lecturer responsible for the course