Docking and molecular dynamics simulations of the ternary complex nisin2:lipid II

Lanthionine antibiotics are an important class of naturally-occurring antimicrobial peptides. The best-known, nisin, is a commercial food preservative. However, structural and mechanistic details on nisin/lipid II membrane complexes are currently lacking. Recently, we have developed empirical force-field parameters to model lantibiotics. Docking and molecular dynamics (MD) simulations have been used to study the nisin2:lipid II complex in bacterial membranes, which has been put forward as the building block of nisin/lipid II binary membrane pores. A Ile1Trp mutation of the N-terminus of nisin has been modelled and docked onto lipid II models; the computed binding affinity increased compared to wildtype. Wild-type nisin was also docked onto three different lipid II structures and a stable 2:1 nisin:lipid II complex formed. This complex was inserted into a membrane. Six independent MD simulations revealed key interactions in the complex, specifically the N terminal engagement of nisin with lipid II at the pyrophosphate and C-terminus of the pentapeptide chain. Nisin2 inserts into the membrane and we propose this is the first step in pore formation, mediated by the nisin N-terminus–lipid II pentapeptide hydrogen bond. The lipid II undecaprenyl chain adopted different conformations in the presence of nisin, which may also have implications for pore formation

New evidence of bones used as fuel in the Gravettian level at Coímbre cave, northern Iberian Peninsula

The use of bone as fuel has been already documented in some sites dated to the Middle and Upper Palaeolithic. They contribute to a longer combustion time due to their durability; consequently, they are useful to reduce the need for firewood, a good advantage in open palaeoenvironmental contexts with limited arboreal vegetation. The use of bones as fuel can be identified by several lines of evidence. The main one is a large number of burned bones, with an intense cremation–charring or calcination, together with high fragmentation resulting from the long contact with the fire. Other features may be present, although they can also result from individual circumstances. They include either the presence of complete skeletal profiles–which implies using all the bones of the animal–or a selection of the anatomical parts which contribute better to combustion, i.e. epiphyses and axial elements. In this article, we argue that the faunal assemblage of level Co.B.6 of Coímbre cave fully corresponds to this model. Moreover, this level coincides with a cold palaeoclimatic event, which was correlative to the climatic deterioration that occurred at the end of MIS 3, and an open environment. Thus, we propose that this level contains the first known use of bones as fuel in the Cantabrian Gravettian

Microscopic Charcoal Signal in Archaeological Contexts

The recovery of archaeological wood charcoals from combustion features provides insights into the exploitation and use of wood fuel resources and past landscapes. The quality of our interpretation based on wood charcoals, however, depends on reliable information about the charcoal assemblages resulting from taphonomy. Charcoal is very fragile in comparison to other combustion residues such as burnt bones. In archaeological contexts, charcoal can easily be fragmented into small pieces (<0.25 mm) due to their fragile property. The investigation of small fragments and particles is particularly important for the interpretation of combustion residues when large pieces of charcoal are rare or apparently absent in archaeological sites, which is mainly true for many European Palaeolithic sites. Here, archaeologists get incomplete information when only the largest pieces and fragments are considered. In this chapter, we present a method for extracting and quantifying charcoal pieces, fragments, and particles. This approach can be considered as a strategy to minimize the impact of sample incompleteness and biases related to combustion residues in archaeological contexts. We further provide (1) a definition of what the charcoal signal means in an archaeological context; (2) an overview of taphonomy that causes charcoal fragmentation; (3) a review of charcoal sampling, extraction, observation and quantification protocols; (4) a manual (pictures and descriptions) for the observation of charcoal, from large pieces to the smallest particles; and (5) a discussion about why the charcoal signal is useful for archaeologists. By taking into account the consequences of taphonomy, the microscopic charcoal analysis in archaeological contexts provides a reliable assessment of firewood and fuel management practices and the related resilience of societies through time. The microscopic charcoal analysis can further offer additional information about the intensity of taphonomical processes and dating