Journal of Biomolecular NMR

, Volume 63, Issue 1, pp 85–95 | Cite as

MERA: a webserver for evaluating backbone torsion angle distributions in dynamic and disordered proteins from NMR data

  • Alexey B. Mantsyzov
  • Yang Shen
  • Jung Ho Lee
  • Gerhard Hummer
  • Ad Bax
Article

Abstract

MERA (Maximum Entropy Ramachandran map Analysis from NMR data) is a new webserver that generates residue-by-residue Ramachandran map distributions for disordered proteins or disordered regions in proteins on the basis of experimental NMR parameters. As input data, the program currently utilizes up to 12 different parameters. These include three different types of short-range NOEs, three types of backbone chemical shifts (15N, 13Cα, and 13C′), six types of J couplings (3JHNHα, 3JC′C′, 3JC′Hα, 1JHαCα, 2JCαN and 1JCαN), as well as the 15N-relaxation derived J(0) spectral density. The Ramachandran map distributions are reported in terms of populations of their 15° × 15° voxels, and an adjustable maximum entropy weight factor is available to ensure that the obtained distributions will not deviate more from a newly derived coil library distribution than required to account for the experimental data. MERA output includes the agreement between each input parameter and its distribution-derived value. As an application, we demonstrate performance of the program for several residues in the intrinsically disordered protein α-synuclein, as well as for several static and dynamic residues in the folded protein GB3.

Keywords

Coil library IDP Karplus curve Random coil Short-range NOE α-Synuclein 

Notes

Acknowledgments

This work was supported by the Russian Science Foundation (Grant 14-14-00598) and by the Intramural Research Program of the National Institute of Diabetes and Digestive and Kidney Diseases and the Intramural Antiviral Target Program of the Office of the Director, NIH, and by the Max Planck Society. JHL is the recipient of a KVSTA fellowship.

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Copyright information

© Springer Science+Business Media Dordrecht (outside the USA) 2015

Authors and Affiliations

  • Alexey B. Mantsyzov
    • 1
  • Yang Shen
    • 2
  • Jung Ho Lee
    • 2
  • Gerhard Hummer
    • 3
  • Ad Bax
    • 2
  1. 1.Faculty of Fundamental MedicineM.V. Lomonosov Moscow State UniversityMoscowRussian Federation
  2. 2.Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney DiseasesNational Institutes of HealthBethesdaUSA
  3. 3.Max Planck Institute of BiophysicsFrankfurt am MainGermany

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