Hybrid Methods


  • NMR and SAXS Hybrid Methods

The global structural information about molecular shapes provided by small-angle X-ray scattering (SAXS) is highly complementary to the high-resolution structural information that can be obtained by NMR. One of the major challenges of studying biomolecules by NMR is that they become difficult to study as their molecular mass increases. SAXS can be used to help overcome the size limitations of NMR because it is not so limited by the size of systems that can be easily studied. Further, SAXS is highly complimentary to NMR given that samples can be studied under the same temperature and buffer conditions. Thus, the atomic resolution information obtained from NMR can be combined with the low-resolution shape information from SAXS to generate a more complete insight into the structures of biomolecules.

The NMRFAM has a Bruker Nanostar bench top system capable of carrying out SAXS experiments on biomolecules and materials. SAXS experiments require only a small amount of material (40-50 mL of 1-10 mg/mL sample) and a full data set can be collected in a single day at the NMRFAM. The Bruker Nanostar system at the NMRFAM is capable of characterizing molecules up to ~22 nm in maximum end-to-end distance. The Bruker Nanostar system can also be used to carry out temperature dependent studies with a temperature range of -30°C to 100°C. The expert staff at the NMRFAM are capable of assisting users in both data collection and analysis.

One example of an NMR/SAXS hybrid technology developed at the NMRFAM involves determining structures of large RNA molecules [1]. The Butcher group recently solved the solution structure of the 111 nucleotide U2/U6 RNA complex (above) by developing a method that combines NMR structural data (NOE’s and RDC’s) with SAXS. This novel method involves generating a large ensemble of RNA structures based on knowledge of the RNA secondary structure. Models from the large structure pool with the best agreement to the NMR and SAXS data are then selected and further refined against the NMR/SAXS data.

1. Burke JE, Sashital DG, Zuo X, Wang YX, Butcher SE. (2012) Structure of the yeast U2/U6 snRNA Complex. RNA 18(4):673-83.

  • RNA Structures by MSA/Pf1 RDCs, NOEs and SAXS

We are developing a productive approach for RNA structure determination that combines SAXS and Nuclear Overhauser Effect (NOE) data with Pf1 and Magnetic Susceptibility Anisotropy (MSA) induced Residual Dipolar Couplings (RDCs) collected at multiple fields. 

 

 
 

 

 

 

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Biochem 800 – Practical Nuclear Magnetic Resonance Theory

Biochem 801 – Biochemical Applications of Nuclear Magnetic Resonance

"The Future of NMR-Based Metabolomics, Current Opinion in Biotechnology (2017), pp. 34-40

Workshop "Ultrahigh Field NMR and MRI: Science at a Crossroads" November 12-13, NIH

Documents on the use of the Bruker-Axs Nanostar,SAXS instrument and analysis of SAXS data are now available.

NMRFAM-SPARKY Distribution - the popular NMR analysis program SPARKY recompiled (including updated python and Tcl/Tk) with incorporation of PINE-Sparky, enhancements to import/export to the structural analysis program CYANA, and other useful python extensions.

ADAPT-NMR Enhancer: Complete Package for Reduced Dimensionality in Protein NMR Spectroscopy

RNA-PAIRS: RNA Probabilistic Assignment of Imino Resonance Shifts

PACSY, a Relational Database Management System for Protein Structure and Chemical Shift Analysis 

 

Donate to NMRFAM. US tax-deductible donation can be made to NMRFAM
Please write check payable to "UW Foundation, Account 112152802"  
And mail to: 
Attn: Sarah Lynn Traver Saunders
Associate Administrative Program Specialist 
University of Wisconsin-Madison 
433 Babcock Drive 
Madison, WI 53706 
Tel: 608-265-2507 or email 

 

1st: Lai Bergeman 
Rm 171; Phone 262-3173

2nd: Milo Westler
Rm B160; Phone 263-9599

3rd: Mark Anderson
Rm B224; Phone 265-3303

4th: Marco Tonelli
Rm B160; Phone 263-9493

5th: John Markley
Rm 171A; Phone 263-9349

We welcome your questions and feedback!

NMRFAM Established 1987