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The centromere-like parC locus of plasmid R1 总被引:1,自引:0,他引:1
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Dominik Budday Rasmus Fonseca Sigrid Leyendecker Henry van den Bedem 《Proteins》2017,85(10):1795-1807
Proteins exist as conformational ensembles, exchanging between substates to perform their function. Advances in experimental techniques yield unprecedented access to structural snapshots of their conformational landscape. However, computationally modeling how proteins use collective motions to transition between substates is challenging owing to a rugged landscape and large energy barriers. Here, we present a new, robotics‐inspired motion planning procedure called dCC‐RRT that navigates the rugged landscape between substates by introducing dynamic, interatomic constraints to modulate frustration. The constraints balance non‐native contacts and flexibility, and instantaneously redirect the motion towards sterically favorable conformations. On a test set of eight proteins determined in two conformations separated by, on average, 7.5 Å root mean square deviation (RMSD), our pathways reduced the Cα atom RMSD to the goal conformation by 78%, outperforming peer methods. We then applied dCC‐RRT to examine how collective, small‐scale motions of four side‐chains in the active site of cyclophilin A propagate through the protein. dCC‐RRT uncovered a spatially contiguous network of residues linked by steric interactions and collective motion connecting the active site to a recently proposed, non‐canonical capsid binding site 25 Å away, rationalizing NMR and multi‐temperature crystallography experiments. In all, dCC‐RRT can reveal detailed, all‐atom molecular mechanisms for small and large amplitude motions. Source code and binaries are freely available at https://github.com/ExcitedStates/KGS/ . 相似文献
5.
Christina Lehmkuhl Noer Esther Kj?r Needham Ann-Sophie Wiese Thorsten Johannes Skovbjerg Balsby Torben Dabelsteen 《PloS one》2015,10(6)
Animal personality research is receiving increasing interest from related fields, such as evolutionary personality psychology. By merging the conceptual understanding of personality, the contributions to both fields of research may be enhanced. In this study, we investigate animal personality based on the definition of personality traits as underlying dispositional factors, which are not directly measurable, but which predispose individuals to react through different behavioural patterns. We investigated the shyness-boldness continuum reflected in the consistency of inter-individual variation in behavioural responses towards novelty in 47 farmed American mink (Neovison vison), which were raised in identical housing conditions. Different stages of approach behaviour towards novelty, and how these related within and across contexts, were explored. Our experimental design contained four tests: two novel object tests (non-social contexts) and two novel animated stimuli tests (social contexts). Our results showed consistency in shyness measures across multiple tests, indicating the existence of personality in farmed American mink. It was found that consistency in shyness measures differs across non-social and social contexts, as well as across the various stages in the approach towards novel objects, revealing that different aspects of shyness exist in the farmed American mink. To our knowledge this is the first study to reveal aspects of the shyness-boldness continuum in the American mink. Since the mink were raised in identical housing conditions, inherited factors may have been important in shaping the consistent inter-individual variation. Body weight and sex had no effect on the personality of the mink. Altogether, our results suggest that the shyness-boldness continuum cannot be explained by a simple underlying dispositional factor, but instead encompasses a broader term of hesitating behaviour that might comprise several different personality traits. 相似文献
6.
Linser R 《Journal of biomolecular NMR》2012,52(2):151-158
For micro-crystalline proteins, solid-state nuclear magnetic resonance spectroscopy of perdeuterated samples can provide spectra
of unprecedented quality. Apart from allowing to detect sparsely introduced protons and thereby increasing the effective resolution
for a series of sophisticated techniques, deuteration can provide extraordinary coherence lifetimes—obtainable for all involved
nuclei virtually without decoupling and enabling the use of scalar magnetization transfers. Unfortunately, for fibrillar or
membrane-embedded proteins, significantly shorter transverse relaxation times have been encountered as compared to micro-crystalline
proteins despite an identical sample preparation, calling for alternative strategies for resonance assignment. In this work
we propose an approach towards sequential assignment of perdeuterated proteins based on long-range 1H/13C Cross Polarization transfers. This strategy gives rise to H/N-separated correlations involving Cα, Cβ, and CO chemical shifts of both, intra- and interresidual contacts, and thus connecting adjacent residues independent of
transverse relaxation times. 相似文献
7.
Poulsen JB Andersen KR Kjær KH Vestergaard AL Justesen J Martensen PM 《Biochimie》2012,94(5):1098-1107
The vertebrate 2-5A system is part of the innate immune response and central to cellular antiviral activities. Upon activation by viral double-stranded RNA, 5′-triphosphorylated, 2′-5′-linked oligoadenylate polyribonucleotides (2-5As) are synthesized by one of several 2′-5′ oligoadenylate synthetases. The 2-5As bind and activate RNase L, an unspecific endoribonuclease, resulting in viral and cellular RNA decay. Given that most endogenous RNAs are degraded by RNase L, continued enzyme activity will eventually lead to cell growth arrest and cell death. This is averted, when 2-5As and their 5′-dephosphorylated forms, the so-called 2-5A core molecules, are cleaved and thus inactivated by 2′-5′-specific nuclease(s), e.g. phosphodiesterase 12, thereby turning RNase L into its latent form. In this study, we have characterized the human phosphodiesterase 12 in vitro focusing on its ability to degrade 2-5As and 2-5A core molecules. We have found that the enzyme activity is distributive and is influenced by temperature, pH and divalent cations. This allowed us to determine Vmax and Km kinetic parameters for the enzyme. We have also identified a novel 2′-5′-oligoadenylate nuclease; the human plasma membrane-bound ectonucleotide pyrophosphatase/phosphodiesterase 1, suggesting that 2-5A catabolism may be a multienzyme-regulated process. 相似文献
8.
Hartvig Ida Kosawang Chatchai Kjær Erik Dahl Nielsen Lene Rostgaard 《Biodiversity and Conservation》2021,30(13):3879-3901
Biodiversity and Conservation - The complex biology and specialized relationships between orchids and both fungi and pollinators can complicate orchid conservation and management. Some terrestrial... 相似文献
9.
Eva Ivits Stephanie Horion Rasmus Fensholt Michael Cherlet 《Global Change Biology》2014,20(2):581-593
Drought affects more people than any other natural disaster but there is little understanding of how ecosystems react to droughts. This study jointly analyzed spatio‐temporal changes of drought patterns with vegetation phenology and productivity changes between 1999 and 2010 in major European bioclimatic zones. The Standardized Precipitation and Evapotranspiration Index (SPEI) was used as drought indicator whereas changes in growing season length and vegetation productivity were assessed using remote sensing time‐series of Normalized Difference Vegetation Index (NDVI). Drought spatio‐temporal variability was analyzed using a Principal Component Analysis, leading to the identification of four major drought events between 1999 and 2010 in Europe. Correspondence Analysis showed that at the continental scale the productivity and phenology reacted differently to the identified drought events depending on ecosystem and land cover. Northern and Mediterranean ecosystems proved to be more resilient to droughts in terms of vegetation phenology and productivity developments. Western Atlantic regions and Eastern Europe showed strong agglomerations of decreased productivity and shorter vegetation growing season length, indicating that these ecosystems did not buffer the effects of drought well. In a climate change perspective, increase in drought frequency or intensity may result in larger impacts over these ecosystems, thus management and adaptation strategies should be strengthened in these areas of concerns. 相似文献
10.
Rasmus Revermann Johannes Wallenfang Jens Oldeland Manfred Finckh 《African Journal of Ecology》2017,55(2):152-161
Cross‐border studies offer unique situations to study the impact of different land‐use regimes on ecosystems. Along the Angolan and Namibian border formed by the Okavango River, the environmental conditions and traditional land‐use practises are the same on either side of the river. However, decades of civil war in Angola led to a stagnant development while political stability in Namibia fostered a recent socio‐economic transformation. We investigated the impact of spatially diffuse land use on plant diversity of the dry tropical woodlands covering the vast, sandy hinterlands of the river. As accessibility is the major factor governing land use, we used distance to road as a proxy for land‐use intensity. Based on 58 vegetation plots sized 20 m × 50 m, we showed that species richness increased with distance to road in Angola while in Namibia it remained constant on a lower level. Evenness showed an inverse pattern to species richness and Shannon diversity index showed no response. Analysing diversity patterns according to life forms revealed that these patterns are primarily driven by woody species. The study showed that spatially diffuse land use has a measurable effect on plant diversity and illustrates that roads act as vectors of change. 相似文献