scholarly journals Modeling Hsp70/Hsp40 interaction by multi-scale molecular simulations and co-evolutionary sequence analysis

2016 ◽  
Author(s):  
Duccio Malinverni ◽  
Alfredo Jost Lopez ◽  
Paolo De Los Rios ◽  
Gerhard Hummer ◽  
Alessandro Barducci
Keyword(s):  
Sequence Analysis ◽  
Structural Model ◽  
Molecular Simulations ◽  
Evolutionary Sequence ◽  
Multi Scale ◽  
Atomistic Models ◽  
Structural Details ◽  
Shock Proteins ◽  
Interaction Surface ◽  
Shed Light

AbstractThe interaction between the Heat Shock Proteins 70 and 40 is at the core of the ATPase regulation of the chaperone machinery that maintains protein homeostasis. However, the structural details of this fundamental interaction are still elusive and contrasting models have been proposed for the transient Hsp70/Hsp40 complexes. Here we combine molecular simulations based on both coarsegrained and atomistic models with co-evolutionary sequence analysis to shed light on this problem by focusing on the bacterial DnaK/DnaJ system. The integration of these complementary approaches resulted into a novel structural model that rationalizes previous experimental observations. We identify an evolutionary-conserved interaction surface formed by helix II of the DnaJ J-domain and a groove on lobe IIA of the DnaK nucleotide binding domain, involving the inter-domain linker.

scholarly journals Modeling Hsp70/Hsp40 interaction by multi-scale molecular simulations and coevolutionary sequence analysis

eLife ◽  
2017 ◽  
Vol 6 ◽  
Author(s):  
Duccio Malinverni ◽  
Alfredo Jost Lopez ◽  
Paolo De Los Rios ◽  
Gerhard Hummer ◽  
Alessandro Barducci
Keyword(s):  
Sequence Analysis ◽  
Structural Model ◽  
Molecular Simulations ◽  
Binding Domain ◽  
Coarse Grained ◽  
Multi Scale ◽  
Atomistic Models ◽  
Evolutionarily Conserved ◽  
Structural Details ◽  
Shock Proteins

The interaction between the Heat Shock Proteins 70 and 40 is at the core of the ATPase regulation of the chaperone machinery that maintains protein homeostasis. However, the structural details of the interaction remain elusive and contrasting models have been proposed for the transient Hsp70/Hsp40 complexes. Here we combine molecular simulations based on both coarse-grained and atomistic models with coevolutionary sequence analysis to shed light on this problem by focusing on the bacterial DnaK/DnaJ system. The integration of these complementary approaches resulted in a novel structural model that rationalizes previous experimental observations. We identify an evolutionarily conserved interaction surface formed by helix II of the DnaJ J-domain and a structurally contiguous region of DnaK, involving lobe IIA of the nucleotide binding domain, the inter-domain linker, and the β-basket of the substrate binding domain.

scholarly journals Author response: Modeling Hsp70/Hsp40 interaction by multi-scale molecular simulations and coevolutionary sequence analysis

2017 ◽  
Author(s):  
Duccio Malinverni ◽  
Alfredo Jost Lopez ◽  
Paolo De Los Rios ◽  
Gerhard Hummer ◽  
Alessandro Barducci
Keyword(s):  
Sequence Analysis ◽  
Molecular Simulations ◽  
Author Response ◽  
Multi Scale ◽  
Response Modeling

Skin and dry adhesion

2018 ◽  
Author(s):  
Changhyun Pang ◽  
Chanseok Lee ◽  
Hoon Eui Jeong ◽  
Kahp-Yang Suh
Keyword(s):  
Material Properties ◽  
Structural Features ◽  
Mechanical Interlocking ◽  
Multi Scale ◽  
Skin Patch ◽  
Reversible Adhesion ◽  
Dry Adhesion ◽  
Close Observation ◽  
Dry Adhesives ◽  
Shed Light

Close observation of various attachment systems in animal skins has revealed various exquisite multi-scale architectures for essential functions such as locomotion, crawling, mating, and protection from predators. Some of these adhesion systems of geckos and beetles have unique structural features (e.g. high-aspect ratio, tilted angle, and hierarchical nanostructure), resulting in mechanical interlocking mediated by van der Waals forces or liquid secretion (capillary force). In this chapter, we present an overview of recent advances in bio-inspired, artificial dry adhesives, and biomimetics in the context of nanofabrication and material properties. In addition, relevant bio-inspired structural materials, devices (clean transportation device, interlocker, biomedical skin patch, and flexible strain-gauge sensor) and microrobots are briefly introduced, which would shed light on future smart, directional, and reversible adhesion systems.

Mechanistic analysis of light-driven overcrowded alkene-based molecular motors by multiscale molecular simulations

2021 ◽  
Vol 23 (14) ◽  
pp. 8525-8540
Author(s):  
Mudong Feng ◽  
Michael K. Gilson
Keyword(s):  
Molecular Dynamics ◽  
Excited State ◽  
Molecular Dynamics Simulations ◽  
Ground State ◽  
Molecular Motors ◽  
Motor Performance ◽  
Molecular Simulations ◽  
Mechanistic Analysis ◽  
Dynamics Simulations ◽  
Shed Light

Ground-state and excited-state molecular dynamics simulations shed light on the rotation mechanism of small, light-driven molecular motors and predict motor performance. How fast can they rotate; how much torque and power can they generate?

Structural, chemical and spectroscopic re-examination of type uklonskovite leads to its redefinition

2017 ◽  
Vol 81 (6) ◽  
pp. 1397-1404 ◽  
Author(s):  
S. Menchetti ◽  
L. Bindi ◽  
D. Belakovskiy ◽  
F. Zaccarini
Keyword(s):  
Crystal Structure ◽  
Scientific Literature ◽  
Careful Analysis ◽  
Chemical Formula ◽  
International Mineralogical Association ◽  
Mineralogical Association ◽  
Structural Details ◽  
First Time ◽  
Shed Light

AbstractThe crystal structure and the chemical composition of uklonskovite from the holotype material was reinvestigated to shed light on its correct chemical formula. On the basis of information gained from this characterization, we revised the formula from NaMg(SO4)OH·2H2O to NaMg(SO4)F·2H2O (F instead of OH). A careful analysis of the structural details together with a critical review of all the chemical data listed in the scientific literature for uklonskovite support our redefinition. We also present Raman data for the mineral for the first time. Our proposal was approved by the Commission on New Minerals, Nomenclature and Classification of the International Mineralogical Association (voting proposal 16-J).

The thermal field across the Alpine orogen and its forelands and the relation to seismicity

2020 ◽  
Author(s):  
Cameron Spooner ◽  
Magdalena Scheck-Wenderoth ◽  
Mauro Cacace ◽  
Hans-Jürgen Götze ◽  
Elco Luijendijk
Keyword(s):  
Thermal Field ◽  
Structural Model ◽  
Seismogenic Zone ◽  
Thermally Activated ◽  
Brittle Ductile Transition ◽  
Region Temperature ◽  
Crustal Strength ◽  
Modelling Techniques ◽  
The Alps ◽  
Shed Light

<p>The Alpine orogen and its forelands comprise a multitude of crustal blocks from different tectonic providences and different physical properties. This implies that the thermal configuration of the lithosphere would also be expected to vary significantly throughout the region. Temperature is a key controlling factor for rock strength via thermally activated creep and it exerts a first order influence on the depth of the brittle-ductile transition zone, the lower bound to the seismogenic zone and the spatial distribution of seismicity. Here we present new results from INTEGRATE, a project in the DFG priority program Mountain Building in 4 Dimensions, as part of the AlpArray initiative, which aims to gain a better understanding of the structure, temperature and rheology of the crust and the uppermost mantle beneath the Alps and their forelands using multiple 3D modelling techniques. The overall goal is to test different hypotheses on the configuration of the lithosphere and its relation to the distribution of deformation and related seismicity in the Alpine region. We build on previous work of a 3D density differentiated structural model of the region that is consistent with deep seismic data and gravity, to calculate the 3D conductive steady state thermal field of the Alps and their forelands. The model is unique in using different thermal parameters for different tectonic domains and is validated with a dataset of wellbore temperatures from across the region. Comparing recorded seismicity to the calculated thermal field we find a systematic clustering of the deep seismic activity that correlates with different isotherms within individual crustal blocks, reflecting the presence of different dominant lithologies. These inferred lithologies in conjunction with the calculated temperatures and the previous 3D density-structural model of the region, can be used to shed light on the lateral changes in crustal strength within the Alps and their forelands, helping to explain the observed patterns of deformation.  </p>

scholarly journals Multi-scale analysis and Modeling of aeromagnetic data over the Bétaré-Oya area in the Eastern Cameroon, for structural evidences investigations

2020 ◽  
Author(s):  
Christian Emile Nyaban ◽  
Théophile Ndougsa-Mbarga ◽  
Marcelin Bikoro-Bi-Alou ◽  
Stella Amina Manekeng Tadjouteu ◽  
Stephane Patrick Assembe
Keyword(s):  
Central African Republic ◽  
Structural Model ◽  
Scale Analysis ◽  
Aeromagnetic Data ◽  
Euler Deconvolution ◽  
Multi Scale ◽  
Tilt Derivative ◽  
Local Tectonics ◽  
Multi Scale Analysis ◽  
Eastern Cameroon

Abstract. This study was carried out in the Lom series in Cameroun, at the border with Central African Republic located between the latitudes 5°30′–6° N and the longitudes 13°30′–14°45′ E. A multi-scale analysis of aeromagnetic data combining tilt derivative, Euler deconvolution, upward continuation and the 2.75D modelling was used. The following conclusion were drawn: 1 – Several major families of faults were mapped. Their orientations are ENE-WSW, E-W, NW-SE, N-S with a NE-SW prevalence. The latter are predominantly sub-vertical with NW and SW dips and appear to be prospective for the future mining investigation. 2 – The evidence of compression, folding and shearing axis, was concluded from superposition of null contours of the tilt-derivative and Euler deconvolution. The evidence of the local tectonics principally due to several deformation episodes (D1, D2 and D4) associated with NE-SW, E-W, and NW-SE events respectively. 3 – Depths of interpreted faults ranges from 1000 to 3400 m. 4 – Several linear structures correlating with known mylonitic veins were identified. These are associated with the Lom faults and represent the contacts between the Lom series and the granito-gneissic rocks; we concluded the intense foldings caused by senestral and dextral NE-SW and NW-SE stumps; 5 – We propose a structural model of the top of the crust (schists, gneisses, granites) that delineates principal intrusions (porphyroid granite, garnet gneiss, syenites, micaschists, Graphite and Garnet gneiss) responsible for the observed anomalies. The 2.75D modelling revealed; many faults with a depth greater than 1200 m and confirmed the observations from RTE-TMI, Tilt derivative and Euler deconvolution; 6 – We developed lithologic profile of Betare Oya basin.

scholarly journals The DegU Orphan Response Regulator Contributes to Heat Stress Resistance in Listeria monocytogenes

2021 ◽  
Vol 11 ◽  
Author(s):  
Changyong Cheng ◽  
Feng Liu ◽  
Haobo Jin ◽  
Xiangfei Xu ◽  
Jiali Xu ◽  
...  
Keyword(s):  
Heat Stress ◽  
Listeria Monocytogenes ◽  
Heat Shock ◽  
Heat Resistance ◽  
Foodborne Pathogens ◽  
Response Regulator ◽  
Heat Shock Stress ◽  
Heat Stress Resistance ◽  
Shock Proteins ◽  
Shed Light

Listeria monocytogenes is more heat-resistant than most other non-spore-forming foodborne pathogens, posing a severe threat to food safety and human health, particularly during chilled food processing. The DegU orphan response regulator is known to control heat resistance in L. monocytogenes; however, the underlying regulatory mechanism is poorly understood. Here, we show that DegU contributes to L. monocytogenes exponential growth under mild heat-shock stress. We further demonstrate that DegU directly senses heat stress through autoregulation and upregulates the hrcA-grpE-dnaK-dnaJ operon, leading to increased production of heat-shock proteins. We also show that DegU can directly regulate the expression of the hrcA-grpE-dnaK-dnaJ operon. In conclusion, our results shed light on the regulatory mechanisms underlying how DegU directly activates the hrcA-grpE-dnaK-dnaJ operon, thereby regulating heat resistance in L. monocytogenes.

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