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SDSL-ESR-based protein structure characterization

Abstract

As proteins are key molecules in living cells, knowledge about their structure can provide important insights and applications in science, biotechnology, and medicine. However, many protein structures are still a big challenge for existing high-resolution structure-determination methods, as can be seen in the number of protein structures published in the Protein Data Bank. This is especially the case for less-ordered, more hydrophobic and more flexible protein systems. The lack of efficient methods for structure determination calls for urgent development of a new class of biophysical techniques. This work attempts to address this problem with a novel combination of site-directed spin labelling electron spin resonance spectroscopy (SDSL-ESR) and protein structure modelling, which is coupled by restriction of the conformational spaces of the amino acid side chains. Comparison of the application to four different protein systems enables us to generalize the new method and to establish a general procedure for determination of protein structure.

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Abbreviations

NMR:

Nuclear magnetic resonance

SDSL:

Site-directed spin-labelling

ESR:

Electron spin resonance

EPR:

Electron paramagnetic resonance

GHOST:

Condensation algorithm that filters and groups the solutions found in optimization runs

NTAIL:

C-terminal domain of nucleoprotein of the measles virus

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Acknowledgments

We wish to thank David Stopar and Primoz Ziherl (University of Ljubljana) for many valuable discussions at the very beginning of development of the methodology, Valerie Belle and Bruno Guigliarelli (BIP CNRS Marseille) and Sonia Longhi (AFMB CNRS Marseille) for helping us to develop the algorithm for cleaning the motional pattern profiles on the NTAIL problem. We are also grateful to Jan Premru for important contribution in analysis of the rotamer libraries. This work was carried out with the financial support of the Slovenian Research Agency (program “Experimental biophysics of complex systems”, P1-0060) and COST P15 action support (through a Short Term Scientific Meeting grant).

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Correspondence to Janez Štrancar.

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Štrancar, J., Kavalenka, A., Urbančič, I. et al. SDSL-ESR-based protein structure characterization. Eur Biophys J 39, 499–511 (2010). https://doi.org/10.1007/s00249-009-0510-5

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Keywords

  • Rotational conformational space modelling (CSM)
  • ESR/EPR spectral simulation and optimization
  • GHOST condensation
  • Protein structure optimization
  • Site-directed spin labelling (SDSL)