Conformational States of the CXCR4 Inhibitor Peptide EPI-X4—A Theoretical Analysis

EPI-X4, an endogenous peptide inhibitor, has exhibited potential as a blocker of CXCR4—a G protein-coupled receptor. This unique inhibitor demonstrates the ability to impede HIV-1 infection and halt CXCR4-dependent processes such as tumor cell migration and invagination. Despite its promising effects, a comprehensive understanding of the interaction between EPI-X4 and CXCR4 under natural conditions remains elusive due to experimental limitations. To bridge this knowledge gap, a simulation approach was undertaken. Approximately 150,000 secondary structures of EPI-X4 were subjected to simulations to identify thermodynamically stable candidates. This simulation process harnessed a self-developed reactive force field operating within the ReaxFF framework. The application of the Two-Phase Thermodynamic methodology to ReaxFF facilitated the derivation of crucial thermodynamic attributes of the EPI-X4 conformers. To deepen insights, an ab initio density functional theory calculation method was employed to assess the electrostatic potentials of the most relevant (i.e., stable) EPI-X4 structures. This analytical endeavor aimed to enhance comprehension of the inhibitor’s structural characteristics. As a result of these investigations, predictions were made regarding how EPI-X4 interacts with CXCR4. Two pivotal requirements emerged. Firstly, the spatial conformation of EPI-X4 must align effectively with the CXCR4 receptor protein. Secondly, the functional groups present on the surface of the inhibitor’s structure must complement the corresponding features of CXCR4 to induce attraction between the two entities. These predictive outcomes were based on a meticulous analysis of the conformers, conducted in a gaseous environment. Ultimately, this rigorous exploration yielded a suitable EPI-X4 structure that fulfills the spatial and functional prerequisites for interacting with CXCR4, thus potentially shedding light on new avenues for therapeutic development

Taylor line swimming in microchannels and cubic lattices of obstacles

Microorganisms naturally move in microstructured fluids. Using the simulation method of multi-particle collision dynamics, we study in two dimensions an undulatory Taylor line swimming in a microchannel and in a cubic lattice of obstacles, which represent simple forms of a microstructured environment. In the microchannel the Taylor line swims at an acute angle along a channel wall with a clearly enhanced swimming speed due to hydrodynamic interactions with the bounding wall. While in a dilute obstacle lattice swimming speed is also enhanced, a dense obstacle lattice gives rise to geometric swimming. This new type of swimming is characterized by a drastically increased swimming speed. Since the Taylor line has to fit into the free space of the obstacle lattice, the swimming speed is close to the phase velocity of the bending wave traveling along the Taylor line. While adjusting its swimming motion within the lattice, the Taylor line chooses a specific swimming direction, which we classify by a lattice vector. When plotting the swimming velocity versus the magnitude of the lattice vector, all our data collapse on a single master curve. Finally, we also report more complex trajectories within the obstacle lattice.DFG, GRK 1558, Kollektive Dynamik im Nichtgleichgewicht: in kondensierter Materie und biologischen SystemenDFG, SPP 1726, Mikroschwimmer - Von Einzelpartikelbewegung zu kollektivem Verhalte

Development of a New Procedure for Nail Penetration of Lithium-Ion Cells to Obtain Meaningful and Reproducible Results

Internal short circuit tests of Lithium-Ion Batteries (LIBs) are used to test battery safety behavior in a custom made battery cell stressing chamber. However, systematic investigations regarding the test setup and test procedure are rare. In our research commercially available pouch cells (5 Ah) are employed for the method development and validation of nail penetration tests including measurement of gaseous reaction products. The effects of the thermal insulation material, the nail material (conductive and non-conductive), the influence of the penetration depth and the nail velocity were examined. It was observed that low penetration velocities (1 mm s−1) in combination with a conductive nail and a nail motion control, which is based on monitoring the temporal evaluation of the cell voltage change, provide the most promising results in terms of reproducibility at low standard deviation. By applying this method, only the energy required for a Thermal Runaway (TR) is released, which makes it possible to determine a novel key value for the assessment of battery safety. Based on this, a proposal has been made for a nail penetration test method which would allow the results to be compared between different test facilities

Challenging Disease Ontology by Instances of Atypical PKHD1 and PKD1 Genetics

Background: Autosomal polycystic kidney disease is distinguished into dominant (ADPKD) and recessive (ARPKD) inheritance usually caused by either monoallelic (PKD1/PKD2) or biallelic (PKHD1) germline variation. Clinical presentations are genotype-dependent ranging from fetal demise to mild chronic kidney disease (CKD) in adults. Additionally, exemptions from dominant and recessive inheritance have been reported in both disorders resulting in respective phenocopies. Here, we comparatively report three young adults with microcystic-hyperechogenic kidney morphology based on unexpected genetic alterations beyond typical inheritance. Methods: Next-generation sequencing (NGS)-based gene panel analysis and multiplex ligation-dependent probe amplification (MLPA) of PKD-associated genes, familial segregation analysis, and reverse phenotyping. Results: Three unrelated individuals presented in late adolescence for differential diagnosis of incidental microcystic-hyperechogenic kidneys with preserved kidney and liver function. Upon genetic analysis, we identified a homozygous hypomorphic PKHD1 missense variant causing pseudodominant inheritance in a family, a large monoallelic PKDH1-deletion with atypical transmission, and biallelic PKD1 missense hypomorphs with recessive inheritance. Conclusion: By this report, we illustrate clinical presentations associated with atypical PKD-gene alterations beyond traditional modes of inheritance. Large monoallelic PKHD1-alterations as well as biallelic hypomorphs of both PKD1 and PKHD1 may lead to mild CKD in the absence of prominent macrocyst formation and functional liver impairment. The long-term renal prognosis throughout life, however, remains undetermined. Increased detection of atypical inheritance challenges our current thinking of disease ontology not only in PKD but also in Mendelian disorders in general

The alerting effect of the wake maintenance zone during 40 hours of sleep deprivation

Under entrained conditions, the accumulation of homeostatic sleep pressure in the evening is opposed by a strong circadian arousal signal prior to the dim light melatonin onset, called the Wake Maintenance Zone (WMZ). This study aimed at investigating the impact of the WMZ on different cognitive performance tests, as well as on subjective and objective sleepiness. Twelve young male participants completed a constant routine protocol with 40 h of extended wakefulness that included two WMZs. Cognitive tests and saliva samples were assessed hourly, while the electroencephalogram (EEG) was recorded continuously. Participants improved in cognitive response inhibition during WMZ1 (13.5 h awake) and sustained attention during WMZ2 (37.5 h awake), but not in higher executive function tests. There were significant EEG power density reductions in the delta/theta frequency range during WMZ1 and in delta/theta, alpha, and sigma/beta ranges during WMZ2, with a greater change in the sigma/beta range during WMZ2 compared toWMZ1. EEG power reductions coincided during WMZ1 with stable subjective sleepiness and sustained attention. During WMZ2, EEG power reductions were more pronounced and coincided with improved sustained attention. Our results suggest the circadian arousal signal in the evening differently modulates cognitive functions and EEG power depending on the duration of prior wakefulness

A Peptoid Delivers CoQ-derivative to Plant Mitochondria via Endocytosis

Controlled delivery of molecules interfering specifically with target activities in a cell of interest can be a powerful tool for experimental manipulation, because it can be administered at a defined time point and does not require genetic transformation, which in some systems is difficult and time consuming. Peptides as versatile tools that can be tailored for binding numerous binding partners, are of special interest. However, their passage through membranes, their intracellular targeting, and their sensitivity to proteases is limiting. The use of peptoids, where cationic amino-acid side chains are linked to nitrogen (rather than to carbon) of the peptide bond, can circumvent these limitations, because they are not cleavable by proteases. In the current work, we provide a proof-of-concept that such Trojan Peptoids, the plant PeptoQ, can be used to target a functional cargo (i.e. a rhodamine-labelled peptoid and a coenzyme Q10 derivative) into mitochondria of tobacco BY-2 cells as experimental model. We show that the uptake is specific for mitochondria, rapid, dose-dependent, and requires clathrin-mediated endocytosis, as well as actin filaments, while microtubules seem to be dispensable. Viability of the treated cells is not affected, and they show better survival under salt stress, a condition that perturbs oxidative homeostasis in mitochondria. In congruence with improved homeostasis, we observe that the salt induced accumulation of superoxide is mitigated and even inverted by pretreatment with PeptoQ. Using double labelling with appropriate fluorescent markers, we show that targeting of this Trojan Peptoid to the mitochondria is not based on a passage through the plasma membrane (as thought hitherto), but on import via endocytotic vesicles and subsequent accumulation in the mitochondrial intermembrane space, from where it can enter the matrix, e.g. when the permeability of the inner membrane is increased under salt stress