Biology subjects

Kruse, A.

Publications and source records attributed to Kruse, A..

14 recordsLinked to original sources

bioRxiv2026

Reduced physiological reserve and a blunted response to acute exercise in adults with cerebral palsy

Cerebral palsy (CP) is an early-onset neurodevelopmental condition associated with metabolic impairment and an increased risk of non-communicable diseases across the lifespan. However, the basis of these changes remains largely unknown. This study provides a comprehensive cardiometabolic and physical function profile of 23 adults with CP relative to 33 typically developing (TD) adolescents and 61 TD adults. Compared to TD individuals, adults with CP exhibited reduced cardiorespiratory fitness, smaller cardiac dimensions, and lower muscle mass. Circulating metabolomic and proteomic profiling identified a distinct molecular signature in CP, including altered tricarboxylic acid (TCA) cycle metabolites, and elevated myostatin, matrix-related proteins and pro-inflammatory cytokines. We further tested the capacity for physiological and molecular adaptation using an acute bout of endurance exercise. In response to exercise, individuals with CP exhibited an attenuated response compared to TD groups, characterized by a blunted lactate response and lower venous oxygen levels. TD participants also increased canonical exercise-responsive factors, including NADK, IL-8, ANGPTL1 and GDF15, whereas these responses were attenuated in CP. These novel findings define a distinct cardiometabolic profile in adults with CP at rest and reveal an attenuated molecular response to exercise. These data carry implications for targeted interventions and prevention strategies across the lifespan.

physiology↗

bioRxiv2026

Structural Basis for Angiotensin II Type I Receptor G Protein-biased Signaling

Biased agonism at the angiotensin II type 1 receptor (AT1R) offers a promising strategy for developing safer cardiovascular therapeutics. While beta-arrestin-biased agonism has been extensively investigated, G protein-biased signaling remains poorly understood. Here, we report structures of AT1R coupled to G protein and either the endogenous agonist angiotensin II (AngII) or the G protein-biased agonist TRV055. The ligands adopt similar overall poses, with coordinated rearrangements extending from the orthosteric pocket to the intracellular surface. The structures provide a detailed view of a TM7-centered microswitch network linking ligand recognition to G protein coupling. Functional analyses of peptide analogs identify the ligand's amino terminus as a key determinant of G protein bias, while mutagenesis of the microswitch network shifts AngII toward beta-arrestin-biased signaling and converts the G protein-biased agonist TRV055 into a beta-arrestin-biased ligand. These findings establish a framework for G protein-biased AT1R activation and provide mechanistic insight for the rational design of pathway-selective GPCR therapeutics.

biochemistry↗

bioRxiv2026

Healthy-to-Stroke Translation of EEG-Based BMIs: EEG Characterization and Reinforcement Learning-Based Decoder Evaluation

PurposeEEG-based brain-machine interfaces (BMIs) may support assistive technologies for individuals with stroke-related motor impairment by translating neural activity into control commands for external devices. However, post-stroke neural reorganization and interindividual EEG variability challenge reliable decoding. This study characterized motor imagery EEG features in healthy and acute stroke participants and evaluated whether population-trained Q-learning Kernel Temporal Difference (Q-KTD) decoders could improve individual stroke decoding through transfer learning. These analyses assess the feasibility of healthy-to-stroke translation for EEG-based BMI neural decoding. Materials and MethodsPublicly available motor imagery EEG datasets from healthy participants (n = 109) and individuals with acute stroke (n = 50) were analyzed using left- and right-hand motor imagery trials. The datasets were selected because of their relatively large sample sizes and comparable motor imagery tasks. EEG characterization included baseline and motor imagery-period band power, ERD/ERS, hemispheric asymmetry, and time-frequency representations. For Q-learning Kernel Temporal Difference (Q-KTD) decoding, filtered time-domain EEG from 0- 0.5 s after motor imagery onset was used as the neural-state input. A Q-KTD model trained on the healthy population was transferred to individual stroke participants, and repeated Monte Carlo simulations compared decoding performance with and without transfer learning across multiple learning epochs. ResultsHealthy and acute stroke participants showed shared motor imagery-related EEG structure, including post-onset mu-band suppression, while the stroke group exhibited greater interparticipant variability, more diffuse time- frequency modulation, and altered hemispheric asymmetry. No channel-level healthy-stroke differences in windowed band power remained significant after false discovery rate correction. Healthy-source transfer learning improved first-epoch Q-KTD success rates in 29 of 50 stroke participants (58%). Across all participants, mean success rate increased from 49.46% without transfer learning to 51.82% with transfer learning. Among participants showing positive transfer, the mean gain was 7.34% and the maximum gain was 18.75%. However, 21 participants showed negative transfer, demonstrating substantial subject-level variability. ConclusionHealthy-source Q-KTD transfer learning improved first-epoch motor imagery BMI decoding for a majority of acute stroke participants, supporting the offline feasibility of population-informed Q-KTD decoding in stroke. These early performance gains may reduce subject-specific calibration burden, although substantial interparticipant variability and negative transfer indicate the need for individualized transfer-selection or adaptation strategies. Assistive Technology ImplicationsO_LIEEG-based brain-machine interfaces may support assistive technologies for individuals with stroke-related motor impairment by translating motor imagery-related neural activity into control commands for external devices. C_LIO_LIHealthy-to-stroke transfer learning may improve early BMI neural-decoder performance and potentially reduce the amount of subject-specific calibration required. C_LIO_LIThe findings support the offline feasibility of Q-KTD for motor imagery BMI neural decoding in individuals with acute stroke. C_LIO_LISubstantial interparticipant variability and negative transfer suggest that individualized source-model selection or adaptation strategies may be needed for reliable post-stroke BMI implementation. C_LIO_LIPhysiological EEG characteristics, including ERD/ERS and hemispheric asymmetry, may provide candidate markers for future transfer-selection strategies, although their predictive value requires direct validation. C_LI

bioengineering↗

bioRxiv2026

Divergent activation of the RXFP1 relaxin receptor by protein and small molecule agonists

RXFP1 is an unusual G protein-coupled receptor (GPCR) that mediates physiological adaptations to pregnancy and is a therapeutic target due to its benefits in treatment of fibrosis and heart failure. Protein and small-molecule agonists are currently in mid-stage clinical trials. Here, we present three cryo-electron microscopy structures of RXFP1: ligand-free, bound to the native agonist relaxin-2, and bound to the small-molecule drug candidate AZD5462. These structures show that relaxin-2 engages the receptors ectodomain while AZD5462 binds within transmembrane domain. Together with hydrogen-deuterium exchange mass spectrometry, we show that relaxin-2 induces conformational reorganization of the linker domain into a helical secondary structure. In contrast, AZD5462 stabilizes a unique active conformation capable of inducing {beta}-arrestin recruitment. Both mechanisms are distinctive from the "push-pull" mechanism of glycoprotein hormone receptors. Altogether, our findings define divergent activation mechanisms for protein and small-molecule agonists of RXFP1 and provide structural framework for next-generation drug discovery targeting relaxin receptors and their relatives.

biochemistry↗

bioRxiv2025

Decoding protein-peptide interactions using a large, target-agnostic yeast surface display library

Protein-peptide interactions underlie key biological processes and are commonly utilized in biomedical research and therapeutic discovery. It is often desirable to identify peptide sequence properties that confer high-affinity binding to a target protein. However, common approaches to such characterization are typically low throughput and only sample regions of sequence space near an initial hit. To overcome these challenges, we built a yeast surface displayed library representing [~]6.1 x 109 unique peptides. We then performed screens against diverse protein targets, including two antibodies, an E3 ubiquitin ligase, and an essential membrane-bound bacterial enzyme. In each case, we observed motifs that appear to drive peptide binding and we identified multiple novel, high-affinity clones. These results highlight the librarys utility as a robust and versatile tool for discovering peptide ligands and for characterizing protein-peptide binding interactions more generally. To enable further studies, we will make the library freely available upon request.

bioengineering↗

bioRxiv2024

An aberrant protamine ratio is associated with decreased H4ac levels in murine and human sperm

Protamine 2 (Prm2/PRM2), together with Protamine 1 (Prm1/PRM1), constitute the two protamines found in both murine and human sperm. During spermiogenesis in haploid male germ cells, chromatin undergoes significant condensation, a phase in which most histones are replaced by a species-specific ratio of these two protamines. Altered PRM1/PRM2 ratios are associated with subfertility and infertility in both male mice and men. Notably, during histone-to-protamine exchange a small fraction of histones remains (ranging from 1% to 15%) bound to DNA. The regulatory roles of these residual histones, governed by post-translational modifications (PTMs), play a pivotal role in spermatogenesis, particularly in chromatin remodeling and epigenetic regulation of genes during sperm differentiation or even in early embryogenesis. In this study, utilizing a Prm2-deficient mouse model and conducting an analysis of sperm samples from men exhibiting either normozoospermia or atypical spermiograms, we observed alterations in the methylation and acetylation profiles of histones H3 and H4. Subsequent in-depth analysis revealed that discrepancies in protamine ratios do not significantly influence the post-translational modifications (PTMs) of histones in testicular sperm. In epididymal sperm these altered protamine ratios are associated with a reduction in the acetylation levels of histone H4 (H4ac), a phenomenon consistent across both murine and human samples. In particular, H4K5ac and H4K12ac were identified as the two modifications that appear to decrease as a result of reduced Prm2/PRM2 levels. Our findings reveal that Protamine 2 is necessary for the maintenance of specific histone PTMs, such as acetylation, which is essential for proper spermatogenesis and particularly for chromatin remodeling.

molecular biology↗

bioRxiv2023

AlphaFold2 structures template ligand discovery

AlphaFold2 (AF2) and RosettaFold have greatly expanded the number of structures available for structure-based ligand discovery, even though retrospective studies have cast doubt on their direct usefulness for that goal. Here, we tested unrefined AF2 models prospectively, comparing experimental hit-rates and affinities from large library docking against AF2 models vs the same screens targeting experimental structures of the same receptors. In retrospective docking screens against the {sigma}2 and the 5-HT2A receptors, the AF2 structures struggled to recapitulate ligands that we had previously found docking against the receptors experimental structures, consistent with published results. Prospective large library docking against the AF2 models, however, yielded similar hit rates for both receptors versus docking against experimentally-derived structures; hundreds of molecules were prioritized and tested against each model and each structure of each receptor. The success of the AF2 models was achieved despite differences in orthosteric pocket residue conformations for both targets versus the experimental structures. Intriguingly, against the 5-HT2A receptor the most potent, subtype-selective agonists were discovered via docking against the AF2 model, not the experimental structure. To understand this from a molecular perspective, a cryoEM structure was determined for one of the more potent and selective ligands to emerge from docking against the AF2 model of the 5-HT2A receptor. Our findings suggest that AF2 models may sample conformations that are relevant for ligand discovery, much extending the domain of applicability of structure-based ligand discovery.

pharmacology and toxicology↗

bioRxiv2023

Circulating immune cell populations at rest and in response to acute endurance exercise in young adults with cerebral palsy

AimLow physical activity alters immune function and increases the risk of developing chronic inflammation. This cross-sectional study aimed at determining the immune status and function in young adults with cerebral palsy (CP) in comparison to typically developing (TD) individuals. MethodBlood samples from 12 individuals with CP and 17 TD were collected before, immediately after, and one hour following 45 minutes of Frame Running or running, respectively. Independent t-tests were used to compare heart rate, level of exertion, and baseline cell proportions between groups. Mixed model ANOVA was utilized to investigate immune cell responses to exercise across groups. ResultsBaseline levels of TCR{gamma}{delta}+ T-cells were significantly higher in the individuals with CP. Several cell populations showed significant changes after exercise in both CP and TD groups. CD8+ T-cells were only significantly elevated immediately after exercise in the TD participants. Individuals with CP exhibited significantly lower heart rates, despite similar ratings of perceived exertion. InterpretationElevated baseline TCR{gamma}{delta}+ T-cells may indicate low-grade inflammation in adults with CP. Although most of the cell populations showed typical responses to endurance exercise, the absence of response in CD8+ T-cells in individuals with CP may indicate the need for higher intensity during exercise. What this paper addsO_LIThis is the first study addressing immune cells in adults with CP C_LIO_LITCR{gamma}{delta}+ T-cell baseline levels are elevated in adults with CP C_LIO_LIThe CD8+ T-cell response to exercise was blunted in adults with CP C_LIO_LIExercise intensity is decisive for CD8+ T-cell responses in individuals with CP C_LI

immunology↗

bioRxiv2022

An in silico method to assess antibody fragment polyreactivity

Antibodies are essential biological research tools and important therapeutic agents, but some exhibit non-specific binding to off-target proteins and other biomolecules. Such polyreactive antibodies compromise screening pipelines, lead to incorrect and irreproducible experimental results, and are generally intractable for clinical development. We designed a set of experiments using a diverse naive synthetic camelid antibody fragment ( nanobody) library to enable machine learning models to accurately assess polyreactivity from protein sequence (AUC > 0.8). Moreover, our models provide quantitative scoring metrics that predict the effect of amino acid substitutions on polyreactivity. We experimentally tested our models performance on three independent nanobody scaffolds, where over 90% of predicted substitutions successfully reduced polyreactivity. Importantly, the model allowed us to diminish the polyreactivity of an angiotensin II type I receptor antagonist nanobody, without compromising its pharmacological properties. We provide a companion web-server that offers a straightforward means of predicting polyreactivity and polyreactivity-reducing mutations for any given nanobody sequence.

pharmacology and toxicology↗

bioRxiv2021

Loss of Prm1 leads to defective chromatin protamination, impaired PRM2 processing, reduced sperm motility and subfertility in male mice

One of the key events during spermiogenesis is the hypercondensation of chromatin by substitution of the majority of histones by protamines. In humans and mice, protamine 1 (PRM1/Prm1) and protamine 2 (PRM2/Prm2), are expressed in a species-specific ratio. Using CRISPR-Cas9-mediated gene editing we generated Prm1-deficient mice and demonstrate, that Prm1+/- mice are subfertile while Prm1-/- are infertile. Prm1-deficiency was associated with higher levels of 8-OHdG, an indicator for reactive oxygen mediated DNA-damage. While Prm1+/- males displayed moderate increased levels of 8-OHdG virtually all sperm of Prm1-/- males displayed ROS mediated DNA damage. Consequently, DNA integrity was slightly hampered in Prm1+/-, while DNA was completely fragmented in Prm1-/- animals. Interestingly CMA3 staining which indicates protamine-free DNA revealed, that Prm1+/- sperm displayed high levels (93%), compared to Prm2+/- (29%) and WT (2%) sperm. This is not due to increased histone retention as demonstrated by mass spectrometry (MassSpec) of nuclear proteins in Prm1+/- sperm. Further analysis of the MassSpec data from sperm nuclear proteome revealed, that only one protein (RPL31) is significantly higher abundant in Prm1+/- compared to WT sperm. Comparison of the proteome from Prm1-/- and Prm2-/- to WT suggested, that there are a small number of proteins which differ in abundance. However, their function was not linked mechanistically to primary defects seen in Prm1-/- mice and rather represent a general stress response. Interestingly, using acid urea gels we found that sperm from Prm1+/- and Prm1-/- mice contain a high level of unprocessed, full-length PRM2. Prm2 is transcribed as a precursor protein which, upon binding to DNA is successively processed. Further, the overall ratio of PRM1:PRM2 is skewed from 1:2 in WT to 1:5 in Prm1+/- animals. Our results reveal that Prm1 is required for proper processing of PRM2 to produce the mature PRM2 which, together with Prm1 is able to hypercondense DNA. Hence, the species specific PRM1:PRM2 ratio has to be precisely controlled in order to retain full fertility.

developmental biology↗

bioRxiv2021

Dormant spores sense amino acids through the B subunits of their germination receptors

Bacteria from the orders Bacillales and Clostridiales differentiate into stress-resistant spores that can remain dormant for years, yet rapidly germinate upon nutrient sensing. How spores monitor nutrients is poorly understood but in most cases requires putative membrane receptors. The prototypical receptor from Bacillus subtilis consists of three proteins (GerAA, GerAB, GerAC) required for germination in response to L-alanine. GerAB belongs to the Amino Acid-Polyamine-Organocation superfamily of transporters. Using evolutionary co-variation analysis, we provide evidence that GerAB adopts a structure similar to an L-alanine transporter from this superfamily. We show that mutations in gerAB predicted to disrupt the ligand-binding pocket impair germination, while mutations predicted to function in L-alanine recognition enable spores to respond to L-leucine or L-serine. Finally, substitutions of bulkier residues at these positions cause constitutive germination. These data suggest that GerAB is the L-alanine sensor and that B subunits in this broadly conserved family function in nutrient detection.

microbiology↗

bioRxiv2021

Phospholipidosis is a shared mechanism underlying the in vitro antiviral activity of many repurposed drugs against SARS-CoV-2

Repurposing drugs as treatments for COVID-19 has drawn much attention. A common strategy has been to screen for established drugs, typically developed for other indications, that are antiviral in cells or organisms. Intriguingly, most of the drugs that have emerged from these campaigns, though diverse in structure, share a common physical property: cationic amphiphilicity. Provoked by the similarity of these repurposed drugs to those inducing phospholipidosis, a well-known drug side effect, we investigated phospholipidosis as a mechanism for antiviral activity. We tested 23 cationic amphiphilic drugs--including those from phenotypic screens and others that we ourselves had found--for induction of phospholipidosis in cell culture. We found that most of the repurposed drugs, which included hydroxychloroquine, azithromycin, amiodarone, and four others that have already progressed to clinical trials, induced phospholipidosis in the same concentration range as their antiviral activity; indeed, there was a strong monotonic correlation between antiviral efficacy and the magnitude of the phospholipidosis. Conversely, drugs active against the same targets that did not induce phospholipidosis were not antiviral. Phospholipidosis depends on the gross physical properties of drugs, and does not reflect specific target-based activities, rather it may be considered a confound in early drug discovery. Understanding its role in infection, and detecting its effects rapidly, will allow the community to better distinguish between drugs and lead compounds that more directly impact COVID-19 from the large proportion of molecules that manifest this confounding effect, saving much time, effort and cost. One Sentence SummaryDrug-induced phospholipidosis is a single mechanism that may explain the in vitro efficacy of a wide-variety of therapeutics repurposed for COVID-19.

pharmacology and toxicology↗

bioRxiv2020

Prm2 deficiency triggers a Reactive Oxygen Species (ROS)-mediated destruction cascade during epididymal sperm maturation in mice

Protamines are the safeguards of the paternal sperm genome. They replace most of the histones during spermiogenesis, resulting in DNA hypercondensation, thereby protecting its genome from environmental noxa. Impaired protamination has been linked to male infertility in mice and humans in many studies. Apart from impaired DNA integrity, protamine-deficient human and murine sperm show multiple secondary effects, including decreased motility and aberrant head morphology. In this study, we use a Prm2-deficient mouse model in combination with label-free quantitative proteomics to decipher the underlying molecular processes of these effects. We show that loss of the sperms antioxidant capacity, indicated by downregulation of key proteins like SOD1 and PRDX5, ultimately initiates an oxidative stress-mediated destruction cascade during epididymal sperm maturation. This is confirmed by an increased level of 8-OHdG in epididymal sperm, a biomarker for oxidative stress-mediated DNA damage. Prm2-deficient testicular sperm are not affected and initiate the proper development of blastocyst stage preimplantation embryos in vitro upon intracytoplasmic sperm injection (ICSI) into oocytes. Our results provide new insight into the role of Prm2 and its downstream molecular effects on sperm function and present an important contribution to the investigation of new treatment regimens for infertile men with impaired protamination. Significance statementSexual reproduction requires the successful fertilization of female eggs by male sperm. The generation of functional sperm is a complex, multi-step differentiation process known as spermatogenesis that takes places in the male testis. One important step for physiological sperm function is the incorporation of small proteins, known as protamines into the DNA. Defects within this process are common causes of male infertility. However, the underlying molecular mechanisms still remain largely unknown, thus preventing targeted therapies. Here, we identify the molecular cascade being initiated in protamine-deficient murine sperm that ultimately impedes fertilization. Our findings have broad implications for the development of new treatment options for infertile men with faulty protamination that seek medical advice.

molecular biology↗

bioRxiv2019

A dynamic interaction between CD19 and the tetraspanin CD81 controls B cell co-receptor trafficking

CD81 and its binding partner CD19 are core subunits of the B cell co-receptor complex. While CD19 is a single-pass transmembrane protein belonging to the extensively studied Ig superfamily, CD81 belongs to a conserved but poorly understood family of four-pass transmembrane proteins called tetraspanins. These functionally diverse proteins play important roles in a wide variety of different organ systems by controlling protein trafficking and other cellular processes. Here, we show that CD81 relies on its ectodomain to control trafficking of CD19 to the cell surface. Moreover, the anti-CD81 antibody 5A6, which binds selectively to activated B cells, recognizes a conformational epitope on CD81 that is masked when CD81 is in complex with CD19. Mutations of CD81 in this contact interface suppress its CD19 surface-export activity. Taken together, these data indicate that the CD81 - CD19 interaction is dynamically regulated upon B cell activation, suggesting that this dynamism can be exploited to regulate B cell function. These results are not only important for understanding B cell biology, but also have important implications for understanding tetraspanin function more generally.

immunology↗