Water environment

About: Water environment is a research topic. Over the lifetime, 13384 publications have been published within this topic receiving 125138 citations.

Conformational study of the protegrin-1 (PG-1) dimer interaction with lipid bilayers and its effect

Abstract: Protegrin-1 (PG-1) is known as a potent antibiotic peptide; it prevents infection via an attack on the membrane surface of invading microorganisms. In the membrane, the peptide forms a pore/channel through oligomerization of multiple subunits. Recent experimental and computational studies have increasingly unraveled the molecular-level mechanisms underlying the interactions of the PG-1 β-sheet motifs with the membrane. The PG-1 dimer is important for the formation of oligomers, ordered aggregates, and for membrane damaging effects. Yet, experimentally, different dimeric behavior has been observed depending on the environment: antiparallel in the micelle environment, and parallel in the POPC bilayer. The experimental structure of the PG-1 dimer is currently unavailable. Although the β-sheet structures of the PG-1 dimer are less stable in the bulk water environment, the dimer interface is retained by two intermolecular hydrogen bonds. The formation of the dimer in the water environment implies that the pathway of the dimer invasion into the membrane can originate from the bulk region. In the initial contact with the membrane, both the antiparallel and parallel β-sheet conformations of the PG-1 dimer are well preserved at the amphipathic interface of the lipid bilayer. These β-sheet structures illustrate the conformations of PG-1 dimer in the early stage of the membrane attack. Here we observed that the activity of PG-1 β-sheets on the bilayer surface is strongly correlated with the dimer conformation. Our long-term goal is to provide a detailed mechanism of the membrane-disrupting effects by PG-1 β-sheets which are able to attack the membrane and eventually assemble into the ordered aggregates. In order to understand the dimeric effects leading to membrane damage, extensive molecular dynamics (MD) simulations were performed for the β-sheets of the PG-1 dimer in explicit water, salt, and lipid bilayers composed of POPC lipids. Here, we studied PG-1 dimers when organized into a β-sheet motif with antiparallel and parallel β-sheet arrangements in an NCCN packing mode. We focus on the conformations of PG-1 dimers in the lipid bilayer, and on the correlation between the conformations and the membrane disruption effects by PG-1 dimers. We investigate equilibrium structures of the PG-1 dimers in different environments in the early stage of the dimer invasion. The dimer interface of the antiparallel β-sheets is more stable than the parallel β-sheets, similar to the experimental observation in micelle environments. However, we only observe membrane disruption effects by the parallel β-sheets of the PG-1 dimer. This indicates that the parallel β-sheets interact with the lipids with the β-sheet plane lying obliquely to the bilayer surface, increasing the surface pressure in the initial insertion into the lipid bilayer. Recent experimental observation verified that parallel PG-1 dimer is biologically more active to insert into the POPC lipid bilayer.

Surface water quality and cropping systems sustainability under a changing climate in the Upper Mississippi River Basin

Abstract: Agricultural nonpoint source pollution is the main source of nitrogen (N) and phosphorus (P) in the intensely row-cropped Upper Mississippi River Basin (UMRB) stream system and is considered the primary cause of the northern Gulf of Mexico hypoxic zone according to the US Environmental Protection Agency. A point of crucial importance in this region is therefore how intensive corn (Zea mays L.)-based cropping systems for food and fuel production can be sustainable and coexist with a healthy water environment, not only under existing climate conditions but also under a changed climate in the future. To address this issue, a UMRB integrated modeling system has been built with a greatly refined 12-digit subbasin structure based on the Soil and Water Assessment Tool (SWAT) water quality model, which is capable of estimating landscape and in-stream water and pollutant yields in response to a wide array of alternative cropping and/or management strategies and climatic conditions. The effects of the following four agricultural management scenarios on crop production and pollutant loads exported from the cropland of the UMRB to streams and rivers were evaluated: (1) expansion of continuous corn across the entire basin, (2) adoption of no-till on all corn and soybean (Glycine max L.) fields in the region, (3) substitution of the traditional continuous corn and corn–soybean rotations with an extended five-year rotation consisting of corn, soybean, and three years of alfalfa (Medicago sativa L.), and (4) implementation of a winter cover crop within the baseline rotations. The effects of each management scenario were evaluated both for current climate and a projected midcentury (2046 to 2065) climate from a General Circulation Model (GCM). All four scenarios behaved similarly under the historical and future climate, generally resulting in reduced erosion and nutrient loadings to surface water bodies compared to the baseline agricultural management. Continuous corn was the only scenario which resulted in increased N pollution while no-till was the most environmentally effective and able to sustain production at almost the same levels. Rye (Secale cereale L.) cover crop within the fallow period was also effective in reducing erosion and both sediment-bound and soluble forms of nutrients. The results indicated that alternative management practices could reduce sediment, N, and P exports from UMRB cropland by up to 50% without significantly affecting yields. Results for the climate change scenario showed that the effectiveness of the management scenarios was strongly linked to the reduced water availability predicted under the future climate, which assisted in mitigating pollutant transport, although with a small loss of production.

An SCC-DFTB/MD Study of the Adsorption of Zwitterionic Glycine on a Geminal Hydroxylated Silica Surface in an Explicit Water Environment

Abstract: Theoretical work on amino acid monomers interact- ing with a silica surface is very important in the field of biomaterials. However, the adsorption of an amino acid monomer on the geminal silanols of silica surfaces has rarely been studied. In this work, we study zwitterionic glycine adsorption on an edingtonite surface covered by geminal silanols using molecular dynamics simulations based on the density functional tight-binding method. By introdu- cing 140 water molecules into the systems, we directly considered the solvent effect. We found that both the amino (NH3 þ ) and the carboxylic (COO � ) groups of glycine can directly form hydrogen bonds with geminal silanols. However, unlike the COOgroup, the NH3 þ group cannot be persistently sustained on the surface. Therefore, thedominant configurationisthe COOgroup pointing toward the surface. Our study not only provides a molecular level understanding of the interactions between inorganic materials and biochemical molecules but also demonstrates a feasible theoretical method on a quantum level for studying these interactions in biomaterial engineering.