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Bak, J.

Publications and source records attributed to Bak, J..

3 recordsLinked to original sources

Disentangling the CHAOS of intrinsic disorder in human proteins

Most proteins consist of both folded domains and Intrinsically Disordered Regions (IDRs). However, the widespread occurrence of intrinsic disorder in human proteins, along with its characteristics, is often overlooked by the broader communities of structural and molecular biologists. Building on the MobiDB database of intrinsic disorder in proteins, here we develop a comprehensive dataset (Comprehensive analysis of Human proteins And their disOrdered Segments - CHAOS). We implement internally consistent definitions of disordered regions, and annotate general characteristics such as cellular location, essentiality, post-translational modifications, and predicted pathogenicity. Further, we cross-reference to structure predictions from AlphaFold. We find that most human proteins contain at least one disordered region, predominantly located at the protein termini. IDRs are less hydrophobic, enriched in post-translational modifications, and mutations in IDRs are predicted to be less pathogenic than in non-IDRs. Additionally, we discovered that proteins residing in different cellular locations possess distinct disorder profiles. Finally, the predicted AlphaFold models of proteins in CHAOS suggest that disordered regions and proteins are often predicted to adopt secondary structure. Hereby we enhance the visibility and understanding of intrinsic disorder in human proteins. Key messagesO_LIFour out of five human proteins contain one or more intrinsically disordered regions (IDRs). C_LIO_LIHalf of the IDRs are located at protein termini, but three quarters of all human proteins contain a terminal IDR. C_LIO_LIThe amount and location of disordered regions differs throughout cellular compartments. C_LIO_LIOne in five missense mutations in IDRs are likely pathogenic. C_LIO_LIAlphaFold predicts secondary structure elements within intrinsically disordered regions and fully disordered proteins. C_LI

bioinformatics↗

Maternal fluoxetine impairs synaptic transmission and plasticity in the medial prefrontal cortex and alters the structure and function of dorsal raphe nucleus neurons in offspring mice

Selective serotonin (5-HT) reuptake inhibitors (SSRIs) are a class of antidepressant drugs commonly prescribed to women during pregnancy and breastfeeding to treat depression. There is evidence that prenatal exposure to SSRIs may be associated with a higher risk of adverse cognitive outcomes and affective disorders in later life. In animal models, exposure to SSRIs during brain development results in behavioral alterations as well as structural abnormalities of cerebral cortical neurons. Little is known about the consequences of SSRI- induced excess of 5-HT during development on the brain serotonergic system itself. In this study, an SSRI - fluoxetine (FLX) - was administered to C57BL/6J mouse dams during pregnancy and lactation. We found that maternal FLX decreased field potentials, impaired long-term potentiation, facilitated induction of long-term depression and tended to increase the density of 5-HTergic fibers in the medial prefrontal cortex (mPFC) of female but not male adolescent offspring. These effects were accompanied by deteriorated performance in the temporal order memory task and reduced sucrose preference with no change in marble burying behavior in FLX-exposed female offspring. We also found that maternal FLX reduced the axodendritic tree complexity of 5-HT dorsal raphe nucleus (DRN) neurons in female but not male offspring. Whole-cell recordings demonstrated no changes in the excitability of DRN 5-HT neurons in FLX-exposed offspring of either sex. While no effects of maternal FLX on inhibitory postsynaptic currents (sIPSCs) in DRN neurons were found, we observed a significant influence of FLX exposure on kinetic characteristics of spontaneous excitatory postsynaptic currents (sEPSCs) in DRN neurons. Finally, we report that no changes in field potentials and synaptic plasticity were evident in the mPFC of the offspring after maternal exposure during pregnancy and lactation to a new antidepressant, vortioxetine. These findings show that in contrast to the mPFC, long-term consequences of maternal FLX exposure on the structure and function of DRN 5-HT neurons are mild and suggest a sex-dependent, distinct sensitivity of cortical and brainstem neurons to FLX exposure in early life. Regarding side effects on brain development, vortioxetine might be a safer alternative to FLX.

neuroscience↗

Cadherin-13 is a critical regulator of GABAergic modulation in human stem cell derived neuronal networks

Activity in the healthy brain relies on concerted interplay of excitation (E) and inhibition (I) via balanced synaptic communication between glutamatergic and GABAergic neurons. A growing number of studies imply that disruption of this E/I balance is a commonality in many brain disorders, however, obtaining mechanistic insight into these disruptions, with translational value for the human patient, has typically been hampered by methodological limitations. Cadherin-13 (CDH13) has strongly been associated to attention-deficit/hyperactivity disorder and comorbid disorders such as autism and schizophrenia. CDH13 localises at inhibitory presynapses, specifically of parvalbumin (PV) and somatostatin (SST) expressing GABAergic neurons. However, the mechanism by which CDH13 regulates the function of inhibitory synapses in human neurons remains unknown. Starting from human induced pluripotent stem cells, we established a robust method to generate a homogenous population of SST and PV expressing GABAergic neurons (iGABA) in vitro, and co-cultured these with glutamatergic neurons at defined E/I ratios on micro-electrode arrays. We identified functional network parameters that are most reliably affected by GABAergic modulation as such, and through alterations of E/I balance by reduced expression of CDH13 in iGABAs. We found that CDH13-deficiency in iGABAs decreased E/I balance by means of increased inhibition. Moreover, CDH13 interacts with Integrin-{beta}1 and Integrin-{beta}3, which play opposite roles in the regulation of inhibitory synaptic strength via this interaction. Taken together, this model allows for standardized investigation of the E/I balance in a human neuronal background and can be deployed to dissect the cell-type specific contribution of disease genes to the E/I balance.

neuroscience↗