NOESY assignment

The structure of this chapter is as follows Section 2.2 introduces the various types of conformational constraints used in NMR structure calculations. Section 2.3 is devoted to modern structure calculation algorithms. Section 2.4 gives an account of the general principles and the practice of automated NOESY assignment. 

In de novo three-dimensional structure determinations of proteins in solution by NMR spectroscopy, the key conformational data are upper distance limits derived from nuclear Overhauser effects (NOEs) [11, 14]. In order to extract distance constraints from a NOESY spectrum, its cross peaks have to be assigned, i.e. the pairs of hydrogen atoms that give rise to cross peaks have to be identified. The basis for the NOESY assignment... 

Semi-automated approaches to NOESY assignment [85-87] use the chemical shifts and a model or preliminary structure to provide the user with the list of possible assignments for each cross peak. The user decides interactively about the assignment and/or temporary removal of individual NOESY cross peaks, possibly taking into account supplementary information such as line shapes or secondary structure data, and performs a structure calculation with the resulting (usually incomplete) input. In practice, several cycles of NOESY assignment and structure calculation are required to obtain a high-quality structure. 

Fig. 2.2 General scheme of automated combined NOESY assignment and structure calculation.

The latest approach to automated NOESY assignment is the Candid algorithm [26], which will be explained in detail in the following sections. 

---