Initial Substrate Binding of γ‑Secretase: The Role of Substrate Flexibility

γ-Secretase cleaves transmembrane domains (TMD) of amyloid precursor protein (APP), producing pathologically relevant amyloid-β proteins. Initial substrate binding represents a key step of the γ-secretase cleavage whose mechanism remains elusive. Through long time scale coarse-grained and atomic simulations, we have found that the APP TMD can bind to the catalytic subunit presenilin 1 (PS1) on an extended surface covering PS1’s TMD2/6/9 and PAL motif that are all known to be essential for enzymatic activity. This initial substrate binding could lead to reduction in the vertical gap between APP’s ε-cleavage sites and γ-secretase’s active center, enhanced flexibility and hydration levels around the ε-sites, and the presentation of these sites to the enzyme. There are heterogeneous substrate binding poses in which the substrate is found to bind to either the N- or C-terminal parts of PS1, or both. Moreover, we also find that the stability of the binding poses can be modulated by the flexibility of substrate TMD. Especially, the APP substrate, when deprived of bending fluctuation, does not bind to TMD9 at PS1’s C-terminus. Our simulations have revealed further that another substrate of γ-secretase, namely, notch receptors, though bearing a rigid TMD, can still bind to PS1 TMD9, but by a different mechanism, suggesting that the influence of substrate flexibility is context-dependent. Together, these findings shed light on the mechanism of initial substrate docking of γ-secretase and the role of substrate flexibility in this process

The up-version of the response scale for the ranking question in Experiment 3.

<p>The up-version of the response scale for the ranking question in Experiment 3.</p

The down-version of the response scale for the ranking question in Experiment 3.

<p>The down-version of the response scale for the ranking question in Experiment 3.</p

Unraveling the Interplay of Extracellular Domain Conformational Changes and Parathyroid Hormone Type 1 Receptor Activation in Class B1 G Protein-Coupled Receptors: Integrating Enhanced Sampling Molecular Dynamics Simulations and Markov State Models

Parathyroid hormone (PTH) type 1 receptor (PTH1R), as a typical class B1 G protein-coupled receptor (GPCR), is responsible for regulating bone turnover and maintaining calcium homeostasis, and its dysregulation has been implicated in the development of several diseases. The extracellular domain (ECD) of PTH1R is crucial for the recognition and binding of ligands, and the receptor may exhibit an autoinhibited state with the closure of the ECD in the absence of ligands. However, the correlation between ECD conformations and PTH1R activation remains unclear. Thus, this study combines enhanced sampling molecular dynamics (MD) simulations and Markov state models (MSMs) to reveal the possible relevance between the ECD conformations and the activation of PTH1R. First, 22 intermediate structures are generated from the autoinhibited state to the active state and conducted for 10 independent 200 ns simulations each. Then, the MSM is constructed based on the cumulative 44 μs simulations with six identified microstates. Finally, the potential interplay between ECD conformational changes and PTH1R activation as well as cryptic allosteric pockets in the intermediate states during receptor activation is revealed. Overall, our findings reveal that the activation of PTH1R has a specific correlation with ECD conformational changes and provide essential insights for GPCR biology and developing novel allosteric modulators targeting cryptic sites

Differences in the activation extent in the seed regions of the functional connectivities.

<p>(A) Clusters showing the differences in activation extent are in red, and the seed regions for the functional connectivities are in yellow. (B) The parametric estimates of these clusters showing the differences in activation extent during each task condition are also shown. Abbreviations: see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0041048#pone-0041048-t001" target="_blank">Table 1</a>.</p

A decision tree employed to characterize reading options.

<p>A decision tree employed to characterize reading options.</p

The mean r-value matrices (A) and hierarchical clustering analyses (B) for the four task conditions: the preferential choice in the gain domain, the preferential choice in the loss domain, the trade-off instruction choice in the gain domain and the trade-off instruction choice in the loss domain.

<p>(A): Each figure shows a 19×19 square matrix in which the x and y axes correspond to the regions listed in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0041048#pone-0041048-t001" target="_blank">Table 1</a> and in which each entry indicates the mean strength of the functional connectivity between each pair of brain regions. The z score of the functional connectivity is indicated with a colored bar. (B): The vertical axis represents distance. The numbers in the horizontal axis represent the seed regions. Please see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0041048#pone-0041048-t001" target="_blank">Table 1</a> for a detailed interpretation of the numbers.</p

Seed regions for the interregional functional connectivity analyses.

*<p>Seed regions were generated from 12-mm diameter spheres centered on the peak foci of the region. The other seed regions were generated from 18-mm diameter spheres centered on the peak foci. For details, please see the main text. Abbreviations: L: left; R: right; aPFC: anterior prefrontal cortex; aINS: anterior insula; BA: Brodmann area; dSTR: dorsal striatum; IFG: inferior frontal cortex; IPL: inferior parietal lobe; MFG: middle frontal cortex; PAL: pallidum; pIFS: posterior inferior frontal sulcus; SPL: superior parietal lobe; THA: thalamus; vSTR: ventral striatum.</p

Mean ratings of agreement with each point supporting either the psychological waste account or the endowment account (1 definitely disagree, 7 definitely agree).

<p>Mean ratings of agreement with each point supporting either the psychological waste account or the endowment account (1 definitely disagree, 7 definitely agree).</p

Activated regions across the four conditions obtained by conjunction analysis.

<p>The activated regions are shown in red. For the presentation purposes, a threshold of p<0.01 (corrected by FDR) was used. The seed regions for functional connectivity are shown in purple. Please see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0041048#pone-0041048-t001" target="_blank">Table 1</a> for a detailed interpretation of the numbers.</p