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NMR: prediction of molecular alignment from structure using the PALES software

Abstract

Orientational restraints such as residual dipolar couplings promise to overcome many of the problems that traditionally limited liquid-state nuclear magnetic resonance spectroscopy. Recently, we developed methods to predict a molecular alignment tensor and thus residual dipolar couplings for a given molecular structure. This provides many new opportunities for the study of the structure and dynamics of proteins, nucleic acids, oligosaccharides and small molecules. This protocol details the use of the software PALES (Prediction of AlignmEnt from Structure) for prediction of an alignment tensor from a known three-dimensional (3D) coordinate file of a solute. The method is applicable to alignment of molecules in many neutral and charged orienting media and takes into account the molecular shape and 3D charge distribution of the molecule.

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Figure 1: Schematic outline of the PALES algorithm for the prediction of molecular alignment in the case of steric obstruction.
Figure 2: Schematic outline of the PALES algorithm simulating weak ordering of molecules in charged alignment media.
Figure 3: Comparison between experimental one-bond 1H-15N RDCs and values predicted from the 3D charge distribution and shape of the 76-residue protein ubiquitin (PDB code: 1D3Z; mean structure).

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Acknowledgements

I am grateful to Ad Bax for his guidance during my postdoctoral stay in his lab and his continuous support to develop PALES. Many thanks also to Frank Delaglio for useful discussions and access to source code handling input/output of dipolar couplings and PDB files, as well as best-fit of dipolar couplings to PDB files. This work was supported by the Max Planck Society and the DFG through grants ZW71/1-1 to 3-1.

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Correspondence to Markus Zweckstetter.

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Supplementary Data

A document containing (1) a shell script to run the PALES commands outlined in the protocol, (2) input and output files of the protocol, and (3) some comments regarding the information reported in the files. (PDF 106 kb)

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Zweckstetter, M. NMR: prediction of molecular alignment from structure using the PALES software. Nat Protoc 3, 679–690 (2008). https://doi.org/10.1038/nprot.2008.36

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