Polymorphism of fibrillar structures depending on the size of assembled A beta(17-42) peptides

The size of assembled Aβ17-42 peptides can determine polymorphism during oligomerization and fibrillization, but the mechanism of this effect is unknown. Starting from separate random monomers, various fibrillar oligomers with distinct structural characteristics were identified using discontinuous molecular dynamics simulations based on a coarse-grained protein model. From the structures observed in the simulations, two characteristic oligomer sizes emerged, trimer and paranuclei, which generated distinct structural patterns during fibrillization. A majority of the simulations for trimers and tetramers formed non-fibrillar oligomers, which primarily progress to off-pathway oligomers. Pentamers and hexamers were significantly converted into U-shape fibrillar structures, meaning that these oligomers, called paranuclei, might be potent on-pathway intermediates in fibril formation. Fibrillar oligomers larger than hexamers generated substantial polymorphism in which hybrid structures were readily formed and homogeneous fibrillar structures appeared infrequently. © 2016 The Author(s).1

Impaired formation of high-order gephyrin oligomers underlies gephyrin dysfunction-associated pathologies

Gephyrin is critical for the structure, function, and plasticity of inhibitory synapses. Gephyrin mutations have been linked to various neurological disorders; however, systematic analyses of the functional consequences of these mutations are lacking. Here, we performed molecular dynamics simulations of gephyrin to predict how six reported point mutations might change the structural stability and/or function of gephyrin. Additional in silico analyses revealed that the A91T and G375D mutations reduce the binding free energy of gephyrin oligomer formation. Gephyrin A91T and G375D displayed altered clustering patterns in COS-7 cells and nullified the inhibitory synapse-promoting effect of gephyrin in cultured neurons. However, only the G375D mutation reduced gephyrin interaction with GABAA receptors and neuroligin-2 in mouse brain; it also failed to normalize deficits in GABAergic synapse maintenance and neuronal hyperactivity observed in hippocampal dentate gyrus-specific gephyrin-deficient mice. Our results provide insights into biochemical, cell-biological, and network-activity effects of the pathogenic G375D mutation. © 2021 The Author(s)1

Structural and molecular insight into the pH-induced low-permeability of the voltage-gated potassium channel Kv1.2 through dewetting of the water cavity.

Understanding the gating mechanism of ion channel proteins is key to understanding the regulation of cell signaling through these channels. Channel opening and closing are regulated by diverse environmental factors that include temperature, electrical voltage across the channel, and proton concentration. Low permeability in voltage-gated potassium ion channels (Kv) is intimately correlated with the prolonged action potential duration observed in many acidosis diseases. The Kv channels consist of voltage-sensing domains (S1-S4 helices) and central pore domains (S5-S6 helices) that include a selectivity filter and water-filled cavity. The voltage-sensing domain is responsible for the voltage-gating of Kv channels. While the low permeability of Kv channels to potassium ion is highly correlated with the cellular proton concentration, it is unclear how an intracellular acidic condition drives their closure, which may indicate an additional pH-dependent gating mechanism of the Kv family. Here, we show that two residues E327 and H418 in the proximity of the water cavity of Kv1.2 play crucial roles as a pH switch. In addition, we present a structural and molecular concept of the pH-dependent gating of Kv1.2 in atomic detail, showing that the protonation of E327 and H418 disrupts the electrostatic balance around the S6 helices, which leads to a straightening transition in the shape of their axes and causes dewetting of the water-filled cavity and closure of the channel. Our work offers a conceptual advancement to the regulation of the pH-dependent gating of various voltage-gated ion channels and their related biological functions

Measuring the scattering tensor of a disordered nonlinear medium

Disordered media with their numerous scattering channels can be used as optical operators. Measurements of the scattering tensor of a second-harmonic medium extend this computing application to the nonlinear regime. A complex scattering medium offers spatial mixing of the incoming waves via numerous randomly wired channels, making it act as a unique linear optical operator. However, its use as a nonlinear operator has been unexplored due to the difficulty in formulating the nonlinear wave-medium interaction. Here we present a theoretical framework and experimental proof that a third-order scattering tensor completely describes the input-output response of a nonlinear scattering medium made of second-harmonic-generation nanoparticles. The rank of the nonlinear scattering tensor is higher than that of a second-order scattering tensor describing a linear scattering medium, scaling with the number of the spatially orthogonal illumination channels. We implement the inverse of the nonlinear scattering tensor by tensor reshaping and minimization operation, which enables us to retrieve the original incident wave from the speckled nonlinear wave. Using the increased rank of the scattering tensor along with its inverse operation, we demonstrate that the disordered nonlinear medium can be used as a highly scalable nonlinear optical operator for optical encryptions, all-optical multichannel logic AND gates, and optical kernel methods in machine learning.11Nsciescopu

Time-resolved detection of early-arriving ballistic waves in a quasi-diffusive regime

© 2021 Optical Society of America under the terms of the OSA Open Access Publishing AgreementBallistic waves directly carry image information in imaging through a scattering medium, but they are often obscured by much intense multiple-scattered waves. Detecting early arriving photons has been an effective method to extract ballistic waves in the transmission-mode imaging. However, it has been difficult to identify the temporal distribution of ballistic waves relative to the multiple scattering waves in the quasi-diffusive regime. Here, we present a method to separately quantify ballistic and multiple-scattered waves at their corresponding flight times even when multiple scattering is much stronger than the ballistic waves. This is realized by measuring the transmission matrix of an object embedded within scattering medium and comparing the coherent accumulation of ballistic waves with their incoherent addition. To further elucidate the temporal behavior of ballistic waves in quasi-diffusive regime, we analyze the flight time difference between ballistic and multiple-scattered waves and the effect of coherence gating on their relative intensities for the scattering medium of different thicknesses. The presented method to distinctively detect the temporal behavior of ballistic and multiple-scattered waves will lay a foundation to exploit multiple-scattered waves for deep-tissue imaging.11Nsciescopu

Deep optical imaging within complex scattering media

© 2020, Springer Nature Limited.Optical imaging has had a central role in elucidating the underlying biological and physiological mechanisms in living specimens owing to its high spatial resolution, molecular specificity and minimal invasiveness. However, its working depth for in vivo imaging is extremely shallow, and thus reactions occurring deep inside living specimens remain out of reach. This problem originates primarily from multiple light scattering caused by the inhomogeneity of tissue obscuring the desired image information. Adaptive optical microscopy, which minimizes the effect of sample-induced aberrations, has to date been the most effective approach to addressing this problem, but its performance has plateaued because it can suppress only lower-order perturbations. To achieve an imaging depth beyond this conventional limit, there is increasing interest in exploiting the physics governing multiple light scattering. New approaches have emerged based on the deterministic measurement and/or control of multiple-scattered waves, rather than their stochastic and statistical treatment. In this Review, we provide an overview of recent developments in this area, with a focus on approaches that achieve a microscopic spatial resolution while remaining useful for in vivo imaging, and discuss their present limitations and future prospects © 2020 Springer Nature Limited11Nsciescopu

Molecular Basis of the Membrane Interaction of the β2e Subunit of Voltage-Gated Ca2+ Channels

AbstractThe auxiliary β subunit plays an important role in the regulation of voltage-gated calcium (CaV) channels. Recently, it was revealed that β2e associates with the plasma membrane through an electrostatic interaction between N-terminal basic residues and anionic phospholipids. However, a molecular-level understanding of β-subunit membrane recruitment in structural detail has remained elusive. In this study, using a combination of site-directed mutagenesis, liposome-binding assays, and multiscale molecular-dynamics (MD) simulation, we developed a physical model of how the β2e subunit is recruited electrostatically to the plasma membrane. In a fluorescence resonance energy transfer assay with liposomes, binding of the N-terminal peptide (23 residues) to liposome was significantly increased in the presence of phosphatidylserine (PS) and phosphatidylinositol 4,5-bisphosphate (PIP2). A mutagenesis analysis suggested that two basic residues proximal to Met-1, Lys-2 (K2) and Trp-5 (W5), are more important for membrane binding of the β2e subunit than distal residues from the N-terminus. Our MD simulations revealed that a stretched binding mode of the N-terminus to PS is required for stable membrane attachment through polar and nonpolar interactions. This mode obtained from MD simulations is consistent with experimental results showing that K2A, W5A, and K2A/W5A mutants failed to be targeted to the plasma membrane. We also investigated the effects of a mutated β2e subunit on inactivation kinetics and regulation of CaV channels by PIP2. In experiments with voltage-sensing phosphatase (VSP), a double mutation in the N-terminus of β2e (K2A/W5A) increased the PIP2 sensitivity of CaV2.2 and CaV1.3 channels by ∼3-fold compared with wild-type β2e subunit. Together, our results suggest that membrane targeting of the β2e subunit is initiated from the nonspecific electrostatic insertion of N-terminal K2 and W5 residues into the membrane. The PS-β2e interaction observed here provides a molecular insight into general principles for protein binding to the plasma membrane, as well as the regulatory roles of phospholipids in transporters and ion channels

The C-Domain of the NAC Transcription Factor ANAC019 Is Necessary for pH-Tuned DNA Binding through a Histidine Switch in the N-Domain

The affinity of transcription factors (TFs) for their target DNA is a critical determinant of gene expression. Whether the DNA-binding domain (DBD) of TFs alone can regulate binding affinity to DNA is an important question for identifying the design principle of TFs. We studied ANAC019, a member of the NAC TF family of proteins in Arabidopsis, and found a well-conserved histidine switch located in its DBD, which regulates both homodimerization and transcriptional control of the TF through H135 protonation. We found that the removal of a C-terminal intrinsically disordered region (IDR) in the TF abolished the pH-dependent binding of the N-terminal DBD to DNA. We propose a mechanism in which long-range electrostatic interactions between DNA and the negatively charged C-terminal IDR turns on the pH dependency of the DNA-binding affinity of the N-terminal DBD (c) 2018 The Authors

Transient anosmia induces depressive-like and anxiolytic-like behavior and reduces amygdalar corticotropin-releasing hormone in a ZnSO4-induced mouse model

Olfactory loss is known to affect both mood and quality of life. Transient anosmia was induced in mice to study the resulting changes in mood, behavior, and on a molecular level. Transient anosmia was induced by a single intranasal instillation of ZnSO4 in BALB/c mice. Hematoxylin and eosin (HE) staining, and potato chip finding test were performed to confirm olfactory loss. Tail suspension, forced swim, and splash tests were performed to evaluate depression-related behavior; while the open field, and elevated plus maze tests were used to evaluate anxiety-related behavior.The mRNA levels of amygdalar corticotropin-releasing hormone (CRH) and hypothalamic glucocorticoid receptor (GR) were quantified using real-time PCR to confirm relevant molecular change. Olfactory loss was confirmed 1-2.5 weeks after induction, and this loss was subsequently reversed over time. The results of the behavioral tests indicated increased depression-like and reduced anxiety-like behavior at week 1. Accordingly, PCR data identified decreased amygdalar CRH expression at week 1. These results suggest that transient anosmia induces both depressive and anxiolytic behavior as a result of decreased amygdalar CRH in a mouse model of anosmia.OAIID:RECH_ACHV_DSTSH_NO:T201733442RECH_ACHV_FG:RR00200001ADJUST_YN:EMP_ID:A079472CITE_RATE:3.235DEPT_NM:의과학과EMAIL:[email protected]_YN:YY

Author Correction: Molecular mechanism of K65 acetylation-induced attenuation of Ubc9 and the NDSM interaction

A correction to this article has been published and is linked from the HTML and PDF versions of this paper. The error has not been fixed in the paper