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Ensembles of a small number of conformations with relative populations

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Abstract

In our previous work, we proposed a new way to represent protein native states, using ensembles of a small number of conformations with relative Populations, or ESP in short. Using Ubiquitin as an example, we showed that using a small number of conformations could greatly reduce the potential of overfitting and assigning relative populations to protein ensembles could significantly improve their quality. To demonstrate that ESP indeed is an excellent alternative to represent protein native states, in this work we compare the quality of two ESP ensembles of Ubiquitin with several well-known regular ensembles or average structure representations. Extensive amount of significant experimental data are employed to achieve a thorough assessment. Our results demonstrate that ESP ensembles, though much smaller in size comparing to regular ensembles, perform equally or even better sometimes in all four different types of experimental data used in the assessment, namely, the residual dipolar couplings, residual chemical shift anisotropy, hydrogen exchange rates, and solution scattering profiles. This work further underlines the significance of having relative populations in describing the native states.

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Acknowledgments

Funding from National Science Foundation (CAREER award, CCF-0953517) is gratefully acknowledged. The authors would also like to thank Dr. LeMaster for his invaluable help in the initial phase of hydrogen exchange calculations. The authors would also like to extend thanks to Dr. Grishaev for his invaluable advice and help in computing solution scattering profiles.

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Authors and Affiliations

  1. Bioinformatics and Computational Biology Program, Department of Computer Science, Iowa State University, 226 Atanasoff Hall, Ames, IA, 50011, USA

    Vijay Vammi & Guang Song

  2. Baker Center for Bioinformatics and Biological Statistics, Iowa State University, Ames, IA, USA

    Guang Song

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  1. Vijay Vammi
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  2. Guang Song
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Correspondence to Vijay Vammi.

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Vammi, V., Song, G. Ensembles of a small number of conformations with relative populations. J Biomol NMR 63, 341–351 (2015). https://doi.org/10.1007/s10858-015-9993-9

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