Measurement and correlation of microstructures: the case of foliation intersection axes

Recent studies have used the relative rotation axis of sigmoidal and spiral-shaped inclusion trails, known as Foliation Inflexion/Intersection Axis (FIA), to investigate geological processes such as fold mechanisms and porphyroblast growth. The geological usefulness of this method depends upon the accurate measurement of FIA orientations and correct correlation of temporally related FIAs. This paper uses new data from the Canton Schist to assess the variation in FIA orientations within and between samples, and evaluates criteria for correlating FIAs. For the first time, an entire data set of FIA measurements is published, and data are presented in a way that reflects the variation in FIA orientations within individual samples and provides an indication of the reliability of the data. Analysis of 61 FIA trends determined from the Canton Schist indicate a minimum intrasample range in FIA orientations of 30°. Three competing models are presented for correlation of these FIAs, and each of the models employ different correlation criteria. Correlation of FIAs in Model 1 is based on relative timing and textural criteria, while Model 2 uses relative timing, orientation and patterns of changing FIA orientations, and Model 3 uses relative timing and FIA orientation as correlation criteria. Importantly, the three models differ in the spread of FIA orientations within individual sets, and the number of sets distinguished in the data. Relative timing is the most reliable criterion for correlation, followed by textural criteria and patterns of changing FIA orientations from core to rim of porphyroblasts. It is proposed that within a set of temporally related FIAs, the typical spread of orientations involves clustering of data in a 60° range, but outliers occur at other orientations including near-normal to the peak distribution. Consequently, in populations of FIA data that contain a wide range of orientations, correlation on the basis of orientation is unreliable in the absence of additional criteria. The results of this study suggest that FIAs are best used as semiquantitative indicators of bulk trends rather than an exact measurement for the purpose of quantitative analyses

Computational studies of Family A and Family B GPCRs

A full picture of the similarities between Family A and Family B GPCRs (G-protein coupled receptors) has been frustrated by the lack of clear homology between the respective sequences. Here, we review previous computational studies on GPCR dimerization in which the putative dimerization interfaces have been analysed using entropy, the ET (evolutionary trace) method and related methods. The results derived from multiple sequence alignments of Family A subfamilies have been mapped on to the rhodopsin crystal structure using standard alignments. Similarly, the results for the Family B alignments have been mapped on to the rhodopsin crystal structure using the ‘cold-spot’ alignment. For both Family A and Family B GPCRs, the sequence analysis indicates that there are functional sites on essentially all transmembrane helices, consistent with the parallel daisy chain model of GPCR oligomerization in which each GPCR makes interactions with a number of neighbouring GPCRs. The results are not too sensitive to the quality of the alignment. Molecular Dynamics simulations of the activation process within a single transmembrane bundle of the rhodopsin and the β2-adrenergic receptor have been reviewed; the key observation, which is consistent with other computational studies, is that there is a translation and bending of helix 6, which contributes to a significant opening out of the intracellular face of the receptor, as shown in the accompanying movies. The simulations required the application of specific experiment-derived harmonic and half-harmonic distance restraints and so the application of such simulations to Family B GPCRs requires considerable care because of the alignment problem. Thus, in order to address the alignment problem, we have exploited the observation that GCR1, a plant GPCR, has homology with Family A, Family B and Family E GPCRs. The resulting alignment for transmembrane helix 3 is presented