Comparing NMR and X-ray protein structure: Lindemann-like parameters and NMR disorder. Issue 9 (4th July 2018)

• Record Type: Journal Article
• Authors: Faraggi, Eshel; Dunker, A. Keith; Sussman, Joel L.; Kloczkowski, Andrzej
• Is Part Of: Journal of biomolecular structure & dynamics. Volume 36:Issue 9(2018)
• Page Start: 2331
• Page End: 2341
• Publication Date: 2018-07-04
• Subjects: Lindemann parameter -- NMR -- X-ray -- Proteins in vivo; Biomolecules -- Periodicals; Molecular structure -- Periodicals; Molecular Biology -- Periodicals; Biomechanics -- Periodicals; 572
• DOI: 10.1080/07391102.2017.1352539
• Languages: English
• ISSNs: 0739-1102

Abstract

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 for the best correspondence between X-ray and NMR derived order/disorder assignment, judged by maximizing the Matthews correlation, and a critical value 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.