Comparing NMR and X-ray protein structure: Lindemann-like parameters and NMR disorder

Eshel Faraggi, A. Dunker, Joel L. Sussman, Andrzej Kloczkowski

Research output: Contribution to journalArticle

2 Scopus citations

Abstract

Disordered protein chains and segments are fast becoming a major pathway for our understanding of biological function, especially in more evolved species. However, the standard definition of disordered residues: the inability to constrain them in X-ray derived structures, is not easily applied to NMR derived structures. We carry out a statistical comparison between proteins whose structure was resolved using NMR and using X-ray protocols. We start by establishing a connection between these two protocols for obtaining protein structure. We find a close statistical correspondence between NMR and X-ray structures if fluctuations inherent to the NMR protocol are taken into account. Intuitively this tends to lend support to the validity of both NMR and X-ray protocols in deriving biomolecular models that correspond to in vivo conditions. We then establish Lindemann-like parameters for NMR derived structures and examine what order/disorder cutoffs for these parameters are most consistent with X-ray data and how consistent are they. Finally, we find critical value of (Formula presented.) for the best correspondence between X-ray and NMR derived order/disorder assignment, judged by maximizing the Matthews correlation, and a critical value (Formula presented.) if a balance between false positive and false negative prediction is sought. We examine a few non-conforming cases, and examine the origin of the structure derived in X-ray. This study could help in assigning meaningful disorder from NMR experiments.

Original languageEnglish (US)
Pages (from-to)1-11
Number of pages11
JournalJournal of Biomolecular Structure and Dynamics
DOIs
StateAccepted/In press - Aug 8 2017

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Keywords

  • Lindemann parameter
  • NMR
  • Proteins in vivo
  • X-ray

ASJC Scopus subject areas

  • Structural Biology
  • Molecular Biology

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