4,4'-Diisothiocyanato-2,2'-Stilbenedisulfonic Acid (DIDS) Modulates the Activity of KCNQ1/KCNE1 Channels by an Interaction with the Central Pore Region

Biopore surface is often characterized by finer particles and increased concentration of polysaccharides from root and earthworm exudates, presenting physico-chemical properties different from those of the soil matrix. Such exudates controls not only the wettability or sorption properties but also the adhesive forces of the surrounding soil particles. Thus, increased mechanical stability may be expected on biopore-matrix interface affecting preferential flow and transport processes, as well. However, it is still unknown (i) to what extent the particle cohesion in the coated region is able to increase the resilience of the biopore to an external loading and (ii) how it affects the permeability of the biopore-matrix pore region. We created a discrete element model (DEM) model of a hollow cylindrical soil sample with a coated biopore in the center (i.e., 1 cm height, 1 cm outer and 0.6 cm inner diameter). The spherical particles in the model presented diameter of 0.13 mm for the coated material and 0.22 mm for the soil matrix. The cohesion among particles in the soil matrix was set to a constant value of 10.9 MPa while the cohesion among particles in the coated region varied between 10.9 and 50.9 MPa. The sample was subjected to axial compression and the force and cracks recorded. The permeability in the radial direction from the biopore to soil matrix was calculated using ImageJ and a 3D stokes solver (FDMMS). The increment in the coating cohesion increased the overall soil stiffness in terms of the Young&#8217;s modulus. Before axial compression, the calculated hydraulic permeability for the interface coating and matrix was 182 &#956;m2. After compression, although the lower coating cohesion resulted in a larger number of cracks, permeability increased with coating cohesion. This suggests that with increasing soil stiffness, the cracks decrease in number but increase in length (i.e. improved connectivity).

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Hydrogen exchange reveals Hsp104 architecture, structural dynamics, and energetics in physiological solution

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1816184116 ◽

2019 ◽

Vol 116 (15) ◽

pp. 7333-7342 ◽

Cited By ~ 12

Author(s):

Xiang Ye ◽

Jiabei Lin ◽

Leland Mayne ◽

James Shorter ◽

S. Walter Englander

Keyword(s):

Hydrogen Exchange ◽

Atp Hydrolysis ◽

Physiological Solution ◽

Mass Spectrometry Analysis ◽

Structural Element ◽

Spectrometry Analysis ◽

Exchange Mass Spectrometry ◽

Substrate Protein ◽

Central Pore ◽

The One

Hsp104 is a large AAA+ molecular machine that can rescue proteins trapped in amorphous aggregates and stable amyloids by drawing substrate protein into its central pore. Recent cryo-EM studies image Hsp104 at high resolution. We used hydrogen exchange mass spectrometry analysis (HX MS) to resolve and characterize all of the functionally active and inactive elements of Hsp104, many not accessible to cryo-EM. At a global level, HX MS confirms the one noncanonical interprotomer interface in the Hsp104 hexamer as a marker for the spiraled conformation revealed by cryo-EM and measures its fast conformational cycling under ATP hydrolysis. Other findings enable reinterpretation of the apparent variability of the regulatory middle domain. With respect to detailed mechanism, HX MS determines the response of each Hsp104 structural element to the different bound adenosine nucleotides (ADP, ATP, AMPPNP, and ATPγS). They are distinguished most sensitively by the two Walker A nucleotide-binding segments. Binding of the ATP analog, ATPγS, tightly restructures the Walker A segments and drives the global open-to-closed/extended transition. The global transition carries part of the ATP/ATPγS-binding energy to the somewhat distant central pore. The pore constricts and the tyrosine and other pore-related loops become more tightly structured, which seems to reflect the energy-requiring directional pull that translocates the substrate protein. ATP hydrolysis to ADP allows Hsp104 to relax back to its lowest energy open state ready to restart the cycle.

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