The OPEP coarse-grained protein model has been applied to a wide range of applications since its first release 15 years ago. The model, which combines energetic and structural accuracy and chemical specificity, allows the study of single protein properties, DNA-RNA complexes, amyloid fibril formation and protein suspensions in a crowded environment. Here we first review the current state of the model and the most exciting applications using advanced conformational sampling methods. We then present the current limitations and a perspective on the ongoing developments.

No abstract

The objectives of the research program reported upon here were (1) to measure ambient levels of UV radiation and determine whichvariables most strongly affected its attenuation in the waters of the estuary and Gulf of St. Lawrence, Canada; and (2) to investigate the potential direct impacts of W radiation on species of crustacean zooplankton and fish whose early life stages are planktonic. In this geographic region, productivity-determining biophysical interactions occur in the upper 0 to 30 m of the water column. Measurements of the diffuse attenuation coefficients for ultraviolet-B radiation ( W -B , 280 to 320 nm) at various locations in this region indicated maximum 10% depths (the depth to which 10% of the surface energy penetrates at a given wavelength) of 3 to 4 m at a wavelength of 310 nm. Organisms residing in this layer-including the eggs and larvae of Calanus finmarchicus and Atlantic cod Gadus morhua-are exposed to biologically damaging levels of W radiation. As a result of these physical and biological characteristics, this system offered a relevant opportunity to assess the impacts of UV on subarctic marine ecosystems. Eggs of C. finmarchicus were incubated under the sun, with and without the W -B and/or UV-A (320 to 400 nm) wavebands. W-exposed eggs exhibited low percent hatchmg compared to those protected from W : W radiation had a strong negative impact on C. finmarchicus eggs. Further, percent hatching in W-B-exposed eggs was not significantly lower than that in eggs exposed to UV-A only: under natural sunlight, UV-A radiation appeared to be more detrimental to C. finmarchicus embryos than was UV-B. In analogous experiments with Atlantic cod eggs, exposure to UV-B produced a significant negative effect. However, UV-A had no negative effect on cod eggs. Additional experiments using a solar simulator (SS) revealed high wavelength-dependent mortality in both C. finmarchicus and cod embryos exposed to UV. The strongest effects occurred under exposures to wavelengths below 312 nm. At the shorter wavelengths (<305 nm) UV-B-induced mortality was strongly dose-dependent, but (for both C. finmarchicus and cod) not significantly influenced by dose-rate. Thus, at least within the limits of the exposures under which the biological weighting functions (BWFs) were generated, reciprocity held. The BWFs derived for UV-B-induced mortality in C. finmarchicus and cod eggs were similar in shape to the action spectrum for UV-B effects on naked DNA. Further, the wavelengthdependence of DNA damage was similar to that for the mortality effect. These observations suggest that W-induced mortality in C. finmarchicus and cod eggs is a direct result of DNA damage. There was no evidence of a detrimental effect of UV-A radiation in these SS-derived results. A mathematical model that includes the BWFs, vertical mixing of eggs, meteorological and hydrographic conditions, and ozone depletion, indicates that W-induced mortality in the C. finmarchicus egg population could be as high as 32.5 %, while the impact on the co...

No abstract

Abstract-Downwelling ultraviolet (UV) irradiance (290-400) nm was measured at 1-nm intervals in the surface waters of the estuary and Gulf of St. Lawrence, Canada, in September 1996 and June and September 1997. Measurements were made with an Optronic Laboratories OL 754-O-PMT spectrophotometer equipped with a fiber-optic cable and an underwater sensor. Fluxes greater than the instrument's noise equivalent irradiance (NEI) level of 1 ϫ 10 Ϫ5 Wm Ϫ2 nm Ϫ1 just below the sea surface were measured at wavelengths of Ն294 nm. At 310 nm, the diffuse attenuation coefficient (K d ) ranged between 0.7 and 4.5 m Ϫ1 , with corresponding 10% depth penetrations between 4 and 0.5 m. This represents close to half of the summer mixed-layer water column in the Gulf of St. Lawrence. The following correlation coefficients were found: 0.81 between dissolved organic carbon (DOC) and K d , 0.73 between chlorophyll a (Chl a) and K d , and 0.73 between Chl a and DOC. The spectral variation of K d suggests that yellow substance, and therefore DOC, is responsible for UV attenuation in these bodies of water.