An analysis of conformational changes on protein-protein association: implications for predictive docking.

Conformational changes on complex formation have been measured for 39 pairs of structures of complexed proteins and unbound equivalents, averaged over interface and non-interface regions and for individual residues. We evaluate their significance by comparison with the differences seen in 12 pairs of independently solved structures of identical proteins, and find that just over half have some substantial overall movement. Movements involve main chains as well as side chains, and large changes in the interface are closely involved with complex formation, while those of exposed non-interface residues are caused by flexibility and disorder. Interface movements in enzymes are similar in extent to those of inhibitors. All eight of the complexes (six enzyme-inhibitor and two antibody-antigen) that have structures of both components in an unbound form available show some significant interface movement. However, predictive docking is successful even when some of the largest changes occur. We note however that the situation may be different in systems other than the enzyme-inhibitors which dominate this study. Thus the general model is induced fit but, because there is only limited conformational change in many systems, recognition can be treated as lock and key to a first approximation.     

Wild bee diversity is enhanced by experimental removal of timber harvest residue within intensively managed conifer forest

The use of timber harvest residue as an energy source is thought to have environmental benefits relative to food‐based crops, yet the ecological impact of this practice remains largely unknown. We assessed whether the abundance and diversity of wild bees (Apoidea) were influenced by the removal of harvest residue and associated soil compaction within managed conifer forest in western Oregon, USA. We sampled bees over two years (2014–2015) on study plots that were subjected to five treatments representing gradients in removal of harvest residue and soil compaction. We collected >7,500 bee specimens from 92 distinct species/morphospecies that represented five of the seven bee families. We trapped 3x more individuals in the second year of the study despite identical sampling effort in both years, with most trapped bees classified as ground‐nesting species. Members of the sweat bee family (Halictidae) comprised more than half of all specimens, and the most abundant genus was composed of metallic green bees (Agapostemon, 33.6%), followed by long‐horned bees (Melissodes, 16.5%), sweat bees (Halictus, 15.9%), and bumble bees (Bombus, 13.6%). In both years, abundance and observed species richness were greatest in the most intensive harvest residue treatment, with other treatments having similar values for both measures. Our study indicates that early successional managed conifer forest that has experienced removal of harvest residue can harbor a surprising diversity of wild bees, which are likely to have important contributions to the broader ecological community through the pollination services they provide.     

Growth Pattern and Dietary Intake of Children with Chronic Renal Insufficiency

The growth pattern and dietary intake of 33 children with varying degrees of renal insufficiency has been investigated. The development of impaired renal function in infancy has a more deleterious effect on linear growth than has its onset in later years. A reduction in growth velocity may occur once the glomerular filtration rate falls below 25 ml/min/1·73m². There was a significant reduction of the energy, protein, and vitamin D intakes of children with renal insufficiency compared with those recommended for their age, and of energy intake compared with that of normal children of their own height. Reduced growth velocity occurred when energy intake fell below 80% of that recommended. The reduction in the intake of energy and nutrients in these children may in part be responsible for their growth retardation.     

Effects of Four Commonly-used Tranquillizers on Low-speed Driving Performance Tests

A double-blind controlled comparison of four commonly-used tranquillizing drugs (haloperidol, amylobarbitone sodium, chlordiazepoxide, and trifluoperazine) against placebo was made in their effects on the performance of volunteers during three low speed vehicle-handling tests. The drugs (with the exception of haloperidol) significantly altered driving behaviour though they did not seem to interact significantly with alcohol. There is, therefore, a strong possibility that such drugs will similarly alter driving performance in patients taking them for therapeutic purposes. Since, as these experiments also show, those affected may be subjectively unaware of it, and routine clinical screening is not sensitive enough to detect them, physicians should warn patients of the probability that their driving performance will be affected by such drugs, particularly during the first few days that they are taken.     

Modelling species distributions without using species distributions: the cane toad in Australia under current and future climates

Accurate predictions of the potential distribution of range-shifting species are required for effective management of invasive species, and for assessments of the impact of climate change on native species. Range-shifting species pose a challenge for traditional correlative approaches to range prediction, often requiring the extrapolation of complex statistical associations into novel environmental space. Here we take an alternative approach that does not use species occurrence data, but instead captures the fundamental niche of a species by mechanistically linking key organismal traits with spatial data using biophysical models. We demonstrate this approach with a major invasive species, the cane toad Bufo marinus in Australia, assessing the direct climatic constraints on its ability to move, survive, and reproduce. We show that the current range can be explained by thermal constraints on the locomotor potential of the adult stage together with limitations on the availability of water for the larval stage. Our analysis provides a framework for biologically grounded predictions of the potential for cane toads to expand their range under current and future climate scenarios. More generally, by quantifying spatial variation in physiological constraints on an organism, trait-based approaches can be used to investigate the range-limits of any species. Assessments of spatial variation in the physiological constraints on an organism may also provide a mechanistic basis for forecasting the rate of range expansion and for understanding a species' potential to evolve at range-edges. Mechanistic approaches thus have broad application to process-based ecological and evolutionary models of range-shift.     

There's a right way and a wrong way: in vivo and in vitro folding, misfolding and subunit assembly of the P22 tailspike.

The in vivo and in vitro folding, assembly and misfolding of an elongated protein, the thermostable tailspike adhesin of phage P22, reveals important aspects of the sequence control of chain folding as well as its failure mode, inclusion body formation.