NMR structure calculation tutorial

Thanks to several Utrecht NMR Research group lab members

  1. General remarks
  2. The aim of this tutorial is to make you familiar with the basics of NMR structure calculation and validation. We have chosen to lead you through the coarse trajectory that one would follow when working on a biological macromolecule. This means that a lot of the details of structure calculation will be skipped and some of the software will be used as a "black box". Our aim is that from the basic knowledge that is learned throughout the course, you will be able to set up your own structure calculations, and independently expand your knowledge on this topic to higher levels. In practice, this means that instead of running many variations of different types of structure calculation protocols, a simple "standard" structure calculation protocol based on NOE-derived distance restraints and J-coupling-derived dihedral angle restraints will be performed. The calculated structures will then be analysed using various structure validation methods and visual inspection.

  3. Setup
  4. In order to reflect the reality of an NMR structure determination to some extent, we have chosen to take a project-based approach. This means that we are going to calculate a set of structure models for a given protein. From these structures you will select those "good" structures that will make your final ensemble. In this particular case, we are going to calculate the structure for one antifreeze protein . Depending on the time available we will try to investigate their global and local properties, identify possible problems in the structure, etc. For each project the following is provided:

    The general goals for each project are:

  5. Software
    1. Structure calculation.
    2. A large number of programs and protocols can be used to calculate macro-molecular structures from NMR data. In this practical we will however concentrate on the use of one particular program, CNS ( "Crystallographic and NMR System") from Axel Brunger's laboratory. CNS is the follow-up of the widely used program X-PLOR. More information on both programs can be found at through the links at http://atb.slac.stanford.edu/.

    3. Structure validation.
    4. Various different programs are available for structure validation. In this tutorial we will use the two most powerful and widely used packages PROCHECK and WHAT IF (Only if internet access). PROCHECK provides nice illustrative outputs, WHAT IF is more powerful but less user-friendly. Throughout the course you will be made familiar with the strengths of both programs. PROCHECK - Single structure analysis PROCHECK-NMR - Structure ensemble analysis PROCHECK-COMP - Comparison of two structures WHAT IF - Single structure and/or ensemble analysis.

    5. Structure visualization.
    6. Throughout this course we will use molmol as a viewer. Maybe you are already familiar with this program. If not, take some time during this course to read the tutorial on the web. PyMol - is a powerful viewer, specially when preparing pictures and movies of high quality; molmol - is also quite a powerful viewer and contains various analysis commands, but not very intuitive in its use; Rasmol - is a simple and easy to use viewer, nice for quick inspection but rather limited in its capabilities.

  6. Literature
  7. The following papers are good overviews and starting points for reading:

    • P. Guntert. "Structure calculation of biological macromolecules from NMR data".(1998). Quarterly reviews of Biophysics, 31:145-237.
    • C.A.E.M. Spronk , S.B. Nabuurs, E. Krieger, G. Vriend & G.W. Vuister. "Validation of protein structures derived by NMR spectroscopy".(2004). Progress in NMR spectroscopy, 45,:315-337.

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structure calculation tutorial