NMR structure validation in relation to dynamics and structure determination

TitleNMR structure validation in relation to dynamics and structure determination
Publication TypeJournal Article
Year of Publication2014
AuthorsVranken, WF
JournalProgress in nuclear magnetic resonance spectroscopy
Volume82
Pagination27–38
Abstract

NMR spectroscopy is a key technique for understanding the behaviour of proteins, especially highly dynamic proteins that adopt multiple conformations in solution. Overall, protein structures determined from NMR spectroscopy data constitute just over 10% of the Protein Data Bank archive. This review covers the validation of these NMR protein structures, but rather than describing currently available methodol- ogy, it focuses on concepts that are important for understanding where and how validation is most rel- evant. First, the inherent characteristics of the protein under study have an influence on quality and quantity of the distinct types of data that can be acquired from NMR experiments. Second, these NMR data are necessarily transformed into a model for use in a structure calculation protocol, and the protein structures that result from this reflect the types of NMR data used as well as the protein characteristics. The validation of NMR protein structures should therefore take account, wherever possible, of the inher- ent behavioural characteristics of the protein, the types of available NMR data, and the calculation pro- tocol. These concepts are discussed in the context of ‘knowledge based’ and ‘model versus data’ validation, with suggestions for questions to ask and different validation categories to consider. The prin- cipal aim of this review is to stimulate discussion and to help the reader understand the relationships between the above elements in order to make informed decisions on which validation approaches are the most relevant in particular cases.

DOI10.1016/j.pnmrs.2014.08.001