Regulatory mechanism of the light-activable allosteric switch LOV-TAP for the control of DNA binding: a computer simulation study

The spatio-temporal control of gene expression is fundamental to elucidate cell proliferation and deregulation phenomena in living systems. Novel approaches based on light-sensitive multiprotein complexes have recently been devised, showing promising perspectives for the noninvasive and reversible modulation of the DNA-transcriptional activity in vivo. This has lately been demonstrated in a striking way through the generation of the artificial protein construct light-oxygen-voltage (LOV)-tryptophan-activated protein (TAP), in which the LOV-2-Jα photoswitch of phototropin1 from Avena sativa (AsLOV2-Jα) has been ligated to the tryptophan-repressor (TrpR) protein from Escherichia coli. Although tremendous progress has been achieved on the generation of such protein constructs, a detailed understanding of their functioning as opto-genetical tools is still in its infancy. Here, we elucidate the early stages of the light-induced regulatory mechanism of LOV-TAP at the molecular level, using the noninvasive molecular dynamics simulation technique. More specifically, we find that Cys450-FMN-adduct formation in the AsLOV2-Jα-binding pocket after photoexcitation induces the cleavage of the peripheral Jα-helix from the LOV core, causing a change of its polarity and electrostatic attraction of the photoswitch onto the DNA surface. This goes along with the flexibilization through unfolding of a hairpin-like helix-loop-helix region interlinking the AsLOV2-Jα- and TrpR-domains, ultimately enabling the condensation of LOV-TAP onto the DNA surface. By contrast, in the dark state the AsLOV2-Jα photoswitch remains inactive and exerts a repulsive electrostatic force on the DNA surface. This leads to a distortion of the hairpin region, which finally relieves its tension by causing the disruption of LOV-TAP from the DNA.

A novel computer simulation method for simulating the multiscale transduction dynamics of signal proteins

Signal proteins are able to adapt their response to a change in the environment, governing in this way a broad variety of important cellular processes in living systems. While conventional molecular-dynamics (MD) techniques can be used to explore the early signaling pathway of these protein systems at atomistic resolution, the high computational costs limit their usefulness for the elucidation of the multiscale transduction dynamics of most signaling processes, occurring on experimental timescales. To cope with the problem, we present in this paper a novel multiscale-modeling method, based on a combination of the kinetic Monte-Carlo- and MD-technique, and demonstrate its suitability for investigating the signaling behavior of the photoswitch light-oxygen-voltage-2-Jα domain from Avena Sativa (AsLOV2-Jα) and an AsLOV2-Jα-regulated photoactivable Rac1-GTPase (PA-Rac1), recently employed to control the motility of cancer cells through light stimulus. More specifically, we show that their signaling pathways begin with a residual re-arrangement and subsequent H-bond formation of amino acids near to the flavin-mononucleotide chromophore, causing a coupling between β-strands and subsequent detachment of a peripheral α-helix from the AsLOV2-domain. In the case of the PA-Rac1 system we find that this latter process induces the release of the AsLOV2-inhibitor from the switchII-activation site of the GTPase, enabling signal activation through effector-protein binding. These applications demonstrate that our approach reliably reproduces the signaling pathways of complex signal proteins, ranging from nanoseconds up to seconds at affordable computational costs.

Signaling pathway of a photoactivable Rac1-GTPase in the early stages

In modern life- and medical-sciences major efforts are currently concentrated on creating artificial photoenzymes, consisting of light- oxygen-voltage-sensitive (LOV) domains fused to a target enzyme. Such protein constructs possess great potential for controlling the cell metabolism as well as gene function upon light stimulus. This has recently been impressively demonstrated by designing a novel artificial fusion protein, connecting the AsLOV2-Jα-photosensor from Avena sativa with the Rac1-GTPase (AsLOV2-Jα-Rac1), and by using it, to control the motility of cancer cells from the HeLa-line. Although tremendous progress has been achieved on the generation of such protein constructs, a detailed understanding of their signaling pathway after photoexcitation is still in its infancy. Here, we show through computer simulations of the AsLOV2-Jα-Rac1-photoenzyme that the early processes after formation of the Cys450-FMN-adduct involve the breakage of a H-bond between the carbonyl oxygen FMN-C4O and the amino group of Gln513, followed by a rotational reorientation of its sidechain. This initial event is followed by successive events including β-sheet tightening and transmission of torsional stress along the Iβ-sheet, which leads to the disruption of the Jα-helix from the N-terminal end. Finally, this process triggers the detachment of the AsLOV2-Jα-photosensor from the Rac1-GTPase, ultimately enabling the activation of Rac1 via binding of the effector protein PAK1.

Long-term man–environment interactions in the Bolivian Amazon: 8000 years of vegetation dynamics

Only few studies documenting the vegetation history of the Llanos de Moxos, one of the largest seasonally flooded wetland areas in South America, are available and little is known about the environmental impact of pre-Columbian settlements. We use radiocarbon-dated terrestrial plant macrofossils to establish a sound chronology and palynological analyses to reconstruct the vegetation and fire history of the Lago Rogaguado area. The sedimentary pollen and spore record suggests that wetland and wooded savannah (Cerrado) environments occurred around the lake between 8100 and 5800 cal BP. Fire activity was high during this period and was probably connected to the dry Cerrado environments. The pollen evidence suggests early plant cultivation (Zea mays, Annonaceae and Cucurbitaceae) from 6500 cal BP onwards, which is significantly earlier than hitherto assumed for Amazonia. Gallery forests expanded after 5800 cal BP, when fire activity strongly declined. Forest expansion intensified around 2800 cal BP and continued until 2000 cal BP, when forest cover reached its maximum and fire activity its minimum. The late-Holocene forest expansion to the south and the decrease of fire activity may have resulted from a climatic shift to moister conditions (possibly a shorter dry season). New crops (e.g. Avena-type) or adventive plants (e.g. Rumex acetosella-type) document the impact of European economies after ca. 500 cal BP. Land use intensity remained rather stable over the most recent centuries, arguing against a collapse of settlements in response to the arrival of Europeans, as reconstructed from other Amazonian pollen records.

The Interaction Between Forest Fires and Human Activity in Southern Switzerland

The impact of human activities on the fire regime in southern Switzerland was studied using (pre)historical charcoal and pollen data from lake sediments and statistical data from the 20th century. The cultural impact on forest fire was established by correlating charcoal-influx data with pollen percentages of anthropogenic indicators such as Plantago lanceolata, the Cerealia (sum of Avena t., Triticum t. and Hordeum t.) and Secale. During the 20th century, fire frequency was correlated with precipitation, dry and very dry periods and landscape management indicators. The effects of human activity on the fire regime are clearly recognisable since at least the Neolithic period. Using palaeoecological or statistical data, the variations in fire regime originating from anthropogenic actions may be differentiated from those due to climatic changes if they are sufficiently conspicuous.