Computational aspects of membrane protein structure determination using solid state NMR

Lately the structural biology of membrane proteins is of great interest because of their importance in biological function and the urgency for high-resolution structural information to develop drug targets. With the recent developments of membrane protein structure determination by solid state NMR, various computational methods are needed to facilitate the process. Here, computational efforts for membrane protein structure determination using solid state NMR experimental data are presented. The work includes modeling, refinement, and validation procedures using solid state NMR data. An analysis of transmembrane helical geometry and 2D solid state NMR spectra was developed to understand the structural characteristics of the membrane proteins in the lipid bilayer environment. Also the correlation of helical conformation with the spectra was used to model the transmembrane region of M2 protein. M2 is a homo-tetrameric membrane protein located in the envelope of Influenza A virus. M2 functions as an H + channel and participates in the viral uncoating process after viral uptake by endocytosis. The tetramer model structure of M2-TMP was built and searched against the high-resolution structural restraints obtained from the solid state NMR spectra of the uniformly aligned transmembrane region of M2 protein. The refined M2-TMP structure was used to search the conformation of key residues for H+ channel function, His37 and Trp41, combined with a precisely measured distance restraint. The resulting H+ channel structure is validated by the His37 imidazole ring orientational data from a PISEMA experiment and the integrity of pore structure maintained by the close proximity of His and Trp sidechains.