Comparing NMR and X-ray protein structure: Lindemann-like parameters and NMR disorder.
J Biomol Struct Dyn
; 36(9): 2331-2341, 2018 Jul.
Article
em En
| MEDLINE
| ID: mdl-28714803
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 see text] for the best correspondence between X-ray and NMR derived order/disorder assignment, judged by maximizing the Matthews correlation, and a critical value [Formula see text] 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.
Palavras-chave
Texto completo:
1
Coleções:
01-internacional
Base de dados:
MEDLINE
Assunto principal:
Conformação Proteica
/
Raios X
/
Espectroscopia de Ressonância Magnética
/
Proteínas
Tipo de estudo:
Prognostic_studies
Idioma:
En
Revista:
J Biomol Struct Dyn
Ano de publicação:
2018
Tipo de documento:
Article
País de afiliação:
Estados Unidos