Proteins fold into unique native structures stabilized by thousands of weak interactions that collectively overcome the entropic cost of folding. Although these forces are "encoded" in the thousands of known protein structures, "decoding" them is challenging because of the complexity of natural proteins that have evolved for function, not stability. We combined computational protein design, next-generation gene synthesis, and a high-throughput protease susceptibility assay to measure folding and stability for more than 15,000 de novo designed miniproteins, 1000 natural proteins, 10,000 point mutants, and 30,000 negative control sequences. This analysis identified more than 2500 stable designed proteins in four basic folds-a number sufficient to enable us to systematically examine how sequence determines folding and stability in uncharted protein space. Iteration between design and experiment increased the design success rate from 6% to 47%, produced stable proteins unlike those found in nature for topologies where design was initially unsuccessful, and revealed subtle contributions to stability as designs became increasingly optimized. Our approach achieves the long-standing goal of a tight feedback cycle between computation and experiment and has the potential to transform computational protein design into a data-driven science.

In nature, structural specificity in DNA and proteins is encoded quite differently: in DNA, specificity arises from modular hydrogen bonds in the core of the double helix, whereas in proteins, specificity arises largely from buried hydrophobic packing complemented by irregular peripheral polar interactions. Here we describe a general approach for designing a wide range of protein homo-oligomers with specificity determined by modular arrays of central hydrogen bond networks. We use the approach to design dimers, trimers, and tetramers consisting of two concentric rings of helices, including previously not seen triangular, square, and supercoiled topologies. X-ray crystallography confirms that the structures overall, and the hydrogen bond networks in particular, are nearly identical to the design models, and the networks confer interaction specificity in vivo. The ability to design extensive hydrogen bond networks with atomic accuracy is a milestone for protein design and enables the programming of protein interaction specificity for a broad range of synthetic biology applications.

Antidepressants are among the most commonly detected human pharmaceuticals in the aquatic environment. Since their mode of action is by modulating the neurotransmitters serotonin, dopamine, and norepinephrine, aquatic invertebrates who possess transporters and receptors sensitive to activation by these pharmaceuticals are potentially affected by them. We review the various types of antidepressants, their occurrence and concentrations in aquatic environments, and the actions of neurohormones modulated by antidepressants in molluscs and crustaceans. Recent studies on the effects of antidepressants on these two important groups show that molluscan reproductive and locomotory systems are affected by antidepressants at environmentally relevant concentrations. In particular, antidepressants affect spawning and larval release in bivalves and disrupt locomotion and reduce fecundity in snails. In crustaceans, antidepressants affect freshwater amphipod activity patterns, marine amphipod photo- and geotactic behavior, crayfish aggression, and daphnid reproduction and development. We note with interest the occurrence of non-monotonic dose responses curves in many studies on effects of antidepressants on aquatic animals, often with effects at low concentrations, but not at higher concentrations, and we suggest future experiments consider testing a broader range of concentrations. Furthermore, we consider invertebrate immune responses, genomic and transcriptomic sequencing of invertebrate genes, and the ever-present and overwhelming question of how contaminant mixtures could affect the action of neurohormones as topics for future study. In addressing the question, if antidepressants affect aquatic invertebrates at concentrations currently found in the environment, there is strong evidence to suggest the answer is yes. Furthermore, the examples highlighted in this review provide compelling evidence that the effects could be quite multifaceted across a variety of biological systems.

The structure of North Sea benthic invertebrate and fish communities is an important indicator of anthropogenic and environmental impacts. Although North Sea fish stocks are monitored regularly, benthic fauna are not. Here, we report the results of a survey carried out in 2000, in which five nations sampled the epibenthic and fish fauna at 270 stations throughout the North Sea. The aim of the survey was to investigate the diversity and community structure of epibenthic and fish communities and to identify relationships with environmental factors, including the frequency of commercial otter and beam trawling disturbance. Epibenthic species diversity was lower in the southern North Sea than in central and northern areas. Fish, conversely, were more diverse in the south. The 50 m, 100 m and 200 m depth contours broadly defined the boundaries of benthic and fish communities. The abundance of epibenthos of the southern North Sea was dominated by free-living species, whilst north of the 50 m contour sessile species prevailed. A hybrid area, with sessile species typical of the north and free-living species characteristic of the south, was found off the Norfolk and Flamborough coast stretching towards the Dogger Bank. Large-scale hydrodynamic phenomena were most likely to be responsible for the main divisions between communities, especially the boundary between mixed and stratified water masses. However, bottom temperature, sediment parameters and beam trawling were closely correlated with species richness and diversity, as well as community patterns, and may modify regional species composition. Our study shows that effective large-scale sampling of benthic communities can be conducted during existing fisheries surveys. Since annual fisheries surveys are conducted throughout the northeast Atlantic shelf seas, concurrent benthic surveys would allow benthic sampling on unprecedented spatial and temporal scales. The samples would help to monitor the environmental impacts of trawling disturbance, climate change, pollution and other natural and anthropogenic factors