Structure-oriented methods for protein NMR data analysis

Abstract

The standard approach to nuclear magnetic resonance (NMR) protein structure determination is based on the near complete assignment of the resonances’ chemical shifts to atoms in the molecule, prior to the structure calculation [1]. Computational methods that adhere to this approach are intrinsically assignment-oriented in that first priority is given to solving the assignment problem from which the rest of the process readily follows [2]. More recently, however, an increasing number of researchers have started to question this strategy [3]. Indeed, if the goal is to obtain a protein fold, why should the derivation of assignments be given so much weight upfront? Considerations of this kind have led to the formulation of alternative structure-oriented methods that do not hinge on the availability of complete, accurate assignments; instead, the focus is placed on the structure from the onset by generating initial, often approximate structural models that subsequently can be improved in iterative automated or semi-automated fashion. Thus, by deemphasizing the arduous and time-consuming assignment stage, the aim is to expedite structure determination, an aspect that is particularly important when high throughput is the end. 1.1. Assignment-oriented methods Conventional automated structure determination methods typically tackle the assignment stage as follows [2]: (1) grouping of chemical shifts into spin systems, (2) identification of amino acid type for each spin system, (3) linking sequential spin systems into segments, (4) mapping spin-system segments onto the known protein sequence. To this end, an experimental NMR dataset is recorded that, in the preferred case of isotopically 15N/13C double-labeled samples, provides information on through-bond interactions (via scalar J-couplings) and chemical environments (via chemical shifts). Although such information is relatively limited with regards to the overall molecular topology (for advances in structure calculation from chemical shifts see Refs. [4-6]), its rather exhaustive analysis provides chemical shift assignments required, in turn, for the interpretation of additional, more structurally relevant experiments (e.g., nuclear Overhauser effect spectroscopy; NOESY) in terms of three-dimensional (3D) models.