Photocontrolled Reversible Amyloid Fibril Formation of Parathyroid Hormone-Derived Peptides.

Peptide fibrillization is crucial in biological processes such as amyloid-related diseases and hormone storage, involving complex transitions between folded, unfolded, and aggregated states. We here employ light to induce reversible transitions between aggregated and nonaggregated states of a peptide, linked to the parathyroid hormone (PTH). The artificial light-switch 3-{[(4-aminomethyl)phenyl]diazenyl}benzoic acid (AMPB) is embedded into a segment of PTH, the peptide PTH25-37, to control aggregation, revealing position-dependent effects. Through in silico design, synthesis, and experimental validation of 11 novel PTH25-37-derived peptides, we predict and confirm the amyloid-forming capabilities of the AMPB-containing peptides. Quantum-chemical studies shed light on the photoswitching mechanism. Solid-state NMR studies suggest that ß-strands are aligned parallel in fibrils of PTH25-37, while in one of the AMPB-containing peptides, ß-strands are antiparallel. Simulations further highlight the significance of π-π interactions in the latter. This multifaceted approach enabled the identification of a peptide that can undergo repeated phototriggered transitions between fibrillated and defibrillated states, as demonstrated by different spectroscopic techniques. With this strategy, we unlock the potential to manipulate PTH to reversibly switch between active and inactive aggregated states, representing the first observation of a photostimulus-responsive hormone.

ATRANET - Automated generation of transition networks for the structural characterization of intrinsically disordered proteins.

Intrinsically disordered proteins (IDPs) do not fold into a unique three-dimensional structure but sample different configurations of different probabilities that further change with the surrounding of the IDPs. The structural heterogeneity and dynamics of IDPs pose a challenge for the characterization of their structures by experimental techniques only. Molecular dynamics (MD) simulations provide a powerful complement to experimental approaches for that purpose. However, MD simulations on the micro- to millisecond timescale generate a lot of data of protein motions, necessitating advanced post-processing techniques to extract the relevant information. Here, we demonstrate how transition networks created from MD trajectories allow revealing the configurational ensemble and structural interconversions of IDPs, using the amyloid-ß peptide as example. The construction of transition networks relies on molecular descriptors as input, and we show how the choice of descriptors influences the resulting transition network. The transition networks are generated with the open-source Python script ATRANET, and we explain the usage of ATRANET by providing a detailed workflow and exemplary analysis for amyloid-ß, which can be easily generalized to other IDPs and even protein aggregation.

Transition Networks Unveil Disorder-to-Order Transformations in Aß Caused by Glycosaminoglycans or Lipids.

The aggregation of amyloid-ß (Aß) peptides, particularly of Aß1-42, has been linked to the pathogenesis of Alzheimer's disease. In this study, we focus on the conformational change of Aß1-42 in the presence of glycosaminoglycans (GAGs) and 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) lipids using molecular dynamics simulations. We analyze the conformational changes that occur in Aß by extracting the key structural features that are then used to generate transition networks. Using the same three features per network highlights the transitions from intrinsically disordered states ubiquitous in Aß1-42 in solution to more compact states arising from stable ß-hairpin formation when Aß1-42 is in the vicinity of a GAG molecule, and even more compact states characterized by a α-helix or ß-sheet structures when Aß1-42 interacts with a POPC lipid cluster. We show that the molecular mechanisms underlying these transitions from disorder to order are different for the Aß1-42/GAG and Aß1-42/POPC systems. While in the latter the hydrophobicity provided by the lipid tails facilitates the folding of Aß1-42, in the case of GAG there are hardly any intermolecular Aß1-42-GAG interactions. Instead, GAG removes sodium ions from the peptide, allowing stronger electrostatic interactions within the peptide that stabilize a ß-hairpin. Our results contribute to the growing knowledge of the role of GAGs and lipids in the conformational preferences of the Aß peptide, which in turn influences its aggregation into toxic oligomers and amyloid fibrils.

Domain motions, dimerization, and membrane interactions of the murine guanylate binding protein 2.

Guanylate-binding proteins (GBPs) are a group of GTPases that are induced by interferon-[Formula: see text] and are crucial components of cell-autonomous immunity against intracellular pathogens. Here, we examine murine GBP2 (mGBP2), which we have previously shown to be an essential effector protein for the control of Toxoplasma gondii replication, with its recruitment through the membrane of the parasitophorous vacuole and its involvement in the destruction of this membrane likely playing a role. The overall aim of our work is to provide a molecular-level understanding of the mutual influences of mGBP2 and the parasitophorous vacuole membrane. To this end, we performed lipid-binding assays which revealed that mGBP2 has a particular affinity for cardiolipin. This observation was confirmed by fluorescence microscopy using giant unilamellar vesicles of different lipid compositions. To obtain an understanding of the protein dynamics and how this is affected by GTP binding, mGBP2 dimerization, and membrane binding, assuming that each of these steps are relevant for the function of the protein, we carried out standard as well as replica exchange molecular dynamics simulations with an accumulated simulation time of more than 30 µs. The main findings from these simulations are that mGBP2 features a large-scale hinge motion in its M/E domain, which is present in each of the studied protein states. When bound to a cardiolipin-containing membrane, this hinge motion is particularly pronounced, leading to an up and down motion of the M/E domain on the membrane, which did not occur on a membrane without cardiolipin. Our prognosis is that this up and down motion has the potential to destroy the membrane following the formation of supramolecular mGBP2 complexes on the membrane surface.