Measuring and modeling diffuse scattering in protein X-ray crystallography

X-ray diffraction has the potential to provide rich information about the structural dynamics of macromolecules. To realize this potential, both Bragg scattering, which is currently used to derive macromolecular structures, and diffuse scattering, which reports on correlations in charge density variations, must be measured. Until now, measurement of diffuse scattering from protein crystals has been scarce because of the extra effort of collecting diffuse data. Here, we present 3D measurements of diffuse intensity collected from crystals of the enzymes cyclophilin A and trypsin. The measurements were obtained from the same X-ray diffraction images as the Bragg data, using best practices for standard data collection. To model the underlying dynamics in a practical way that could be used during structure refinement, we tested translation-libration-screw (TLS), liquidlike motions (LLM), and coarse-grained normal-modes (NM) models of protein motions. The LLM model provides a global picture of motions and was refined against the diffuse data, whereas the TLS and NM models provide more detailed and distinct descriptions of atom displacements, and only used information from the Bragg data. Whereas different TLS groupings yielded similar Bragg intensities, they yielded different diffuse intensities, none of which agreed well with the data. In contrast, both the LLM and NM models agreed substantially with the diffuse data. These results demonstrate a realistic path to increase the number of diffuse datasets available to the wider biosciences community and indicate that dynamics-inspired NM structural models can simultaneously agree with both Bragg and diffuse scattering

Water quality in relation to plankton abundance and diversity in river Ogun, Abeokuta, Southwestern Nigeria

Aims: Plankton abundance and diversity are governed by certain aquatic environmental factors which collectively determine the health of the aquatic ecosystem. This study was aimed at investigating the water quality of lower Ogun River, Abeokuta, in relation to plankton abundance and diversity. Materials and Methods: The dataset consists of physicochemical and plankton data collected for 7 months within the period of December 2011 and June 2012 in four stations. Spatial correlations were determined between physicochemical parameters, plankton abundance, and diversity. Physicochemical parameters that exhibited strong correlation with plankton abundance and diversity were used in the calculation of a water quality index (WQI) for the protection of aquatic life. Results: Results showed highly significant correlations (P ≤ 0.05) between plankton abundance, diversity, and the physicochemical parameters monitored during the study period excluding alkalinity and phosphates. The Canadian Council of Ministers of the Environment WQI showed that the river water quality in all the sampled stations (A, 63; B, 63; C, 56; and D, 64) was marginal in classification. Conclusion: It was concluded that River Ogun is polluted beyond doubt. Hence, corrective measures should be put in place so as to prevent total ecological collapse