Cross- and axial-peak intensities in 2D-SLF experiments based on cross-polarization--the role of the initial density matrix.
ABSTRACT Simulations and experiments on simple oriented systems have been used to estimate the relative ratio of cross-peak to axial-peak intensities in 2D-SLF experiments based on dipolar oscillations during cross-polarization (CP). The density matrix prior to dipolar evolution is considered and for an isolated spin pair, it is shown that direct calculations of the ratios match well with simulations and experimental results. Along with the standard CP pulse sequence, two other pulse sequences namely CP with polarization inversion (PI-CP) and another novel variation of the standard CP experiment (EXE-CP) reported recently have been considered. Inclusion of homonuclear dipolar coupling has been observed to increase the axial-peak intensities. In combination with Lee-Goldburg (LG) decoupling, experiments on an oriented liquid crystalline sample have been carried out and the performance of the pulse schemes have been compared. The applicability of the new pulse sequence for different samples and different nuclei is discussed. Such studies are expected to lead to a better understanding of the experiments and to the design of useful pulse sequences.
Article: Glycines: role in α-helical membrane protein structures and a potential indicator of native conformation.[show abstract] [hide abstract]
ABSTRACT: Among the growing number of membrane protein structures in the Protein Data Bank, there are many transmembrane domains that appear to be native-like; at the same time, there are others that appear to have less than complete native-like character. Hence, there is an increasing need for validation tools that distinguish native-like from non-native-like structures. Membrane mimetics used in protein structural characterizations differ in numerous physicochemical properties from native membranes and provide many opportunities for introducing non-native-like features into membrane protein structures. One possible approach for validating membrane protein structures is based on the use of glycine residues in transmembrane domains. Here, we have reviewed the membrane protein structure database and identified a set of benchmark proteins that appear to be native-like. In these structures, conserved glycine residues rarely face the lipid interstices, and many of them participate in close helix-helix packing. Glycine-based validation allowed the identification of non-native-like features in several membrane proteins and also shows the potential for verifying the native-like character for numerous other membrane protein structures.Biochemistry 05/2012; 51(24):4779-89. · 3.42 Impact Factor