Search

In solution or solid-state, determining the three-dimensional structure of biomolecules by Nuclear -Magnetic Resonance (NMR) normally requires the collection of distance information. The interpretation of the spectra containing this distance information is a critical step in an NMR structure determination. In this chapter, we present the Ambiguous Restraints for Iterative Assignment (ARIA) program for automated cross-peak assignment and determination of macromolecular structure from solution and solid-state NMR experiments. While the program was initially designed for the assignment of nuclear Overhauser effect (NOE) resonances, it has been extended to the interpretation of magic-angle spinning (MAS) solid-state NMR data. This chapter first details the concepts and procedures carried out by the program. Then, we describe both the general strategy for structure determination with ARIA 2.3 and practical aspects of the technique. ARIA 2.3 includes all recent developments. such as an extended integration of the Collaborative Computing Project for the NMR community (CCPN), the incorporation of the log-harmonic distance restraint potential and an automated treatment of symmetric oligomers.

We present an algorithmic method allowing automatic tracking of NMR peaks in a series of spectra. It consists in a two phase analysis. The first phase is a local modeling of the peak displacement between two consecutive experiments using distance matrices. Then, from the coefficients of these matrices, a value graph containing the a priori set of possible paths used by these peaks is generated. On this set, the minimization under constraint of the target function by a heuristic approach provides a solution to the peak-tracking problem. This approach has been named GAPT, standing for General Algorithm for NMR Peak Tracking. It has been validated in numerous simulations resembling those encountered in NMR spectroscopy. We show the robustness and limits of the method for situations with many peak-picking errors, and presenting a high local density of peaks. It is then applied to the case of a temperature study of the NMR spectrum of the Lipid Transfer Protein (LTP).