Standard NMR methods applied to the structural analysis of proteins are based on the measurement of local geometric information between protons. The lack of long range restraints can be limiting factor for the study of the modular proteins, protein complexes and supramolecular assemblies. Perdeuteration of samples is necessary for the study of these large systems. However, the exchange of protons with deuterium limit the number of detectable structural restraints, particularly NOEs distance restraints. To resolve this problem, a strategy based on the protonation of some discrete sites was developed. The specific protonation of methyls in proteins constitutes an optimum choice for detection of long range restraints. Protocols for specific labelling of methyls of Isoleucines, Valines and Leucines were implemented and optimized, and a new method for specific protonation of Alanines was introduced. In moderate size systems, the use of this specific labelling strategy combined with the development of NMR experiments allows the detection of restraints (NOEs and RDCs) between methyls separated by more than 12 Å. A robust method was developed to extract distances with very high precision. This approach can also be applied to large proteins. NOEs have been observed between methyls separated by more than 7 Å in a 468 kDa supramolecular assembly.
