Biology subjects

Overgaard, M. T.

Publications and source records attributed to Overgaard, M. T..

9 recordsLinked to original sources

bioRxiv2025

Whats left from the brew? Investigating residual barley proteins in spent grains for downstream valorization opportunities

Brewers spent grain (BSG) is the major side-stream from beer production but remains highly underutilized. While the direct use of BSG as a food ingredient is limited due to subpar techno- functionality, the vast amounts and fairly high protein content of up to 30% makes it a high potential source for production of protein-based ingredient by valorization through e.g. enzymatic hydrolysis. However, little attention has been put towards the protein-level composition of BSG, which is essential for developing hydrolysis strategies for improving functionality in a targeted manner. Here, we present an in-depth characterization of the BSG proteome and investigate dynamic proteome changes from malting and mashing in the initial phases of beer production. We show dynamic and selective changes in the proteome across the different process steps, where 29% of reproducibly identified proteins display differential abundance. BSG represents a significantly higher proportion of intracellular protein compared to both barley and malt and has a nutritionally favorable amino acid composition. The major constituent of the BSG proteome is B3-Hordein, constituting more than 30% of the BSG protein. Moreover, we find that a large proportion (> 45%) of the BSG protein is associated with potential food safety concerns, being classified as potential allergens and antinutritional factors. Our analysis emphasizes the need for downstream processing of BSG to produce safe and functional food ingredients, while also providing protein-level insights for development of targeted hydrolysis strategies to achieve this. HighlightsO_LIAn optimized sample preparation for proteomics analysis has been developed C_LIO_LI29% of barley proteins are differentially abundant across malting and mashing C_LIO_LIB3-Hordein is the major protein in BSG with an abundance over 30% C_LIO_LIBSG contains a high content of potential allergenic and antinutritional proteins C_LIO_LIA protein-level basis for targeted downstream processing of BSG is presented C_LI

plant biology↗

bioRxiv2024

Brown Bears activates a Satiety Hormone Cholecystokinin (CCK) pathway in adipose tissue during hibernation

The brown bear (Ursus arctos) hibernates to survive cold winters without access to food. It builds enormous subcutaneous fat stores during summer and relies on it for energy during winter. Remarkably, the weight loss during winter occurs without muscle loss despite inactivity. Studying brown bear biology can therefore provide insights for improving human health in obesity and weight loss treatments. We here investigate subcutaneous adipose tissue biopsies obtained during summer and winter from free-living brown bears. During winter, a signature of genes involved in food intake and digestion is upregulated. Among these are several regulators of satiety, substrate transport and lipid metabolism. Interestingly, in humans these genes are enriched in distinct metabolic organs including, brain, intestine, stomach, liver and even salivary glands. We focused on the satiety brain/intestinal hormone cholecystokinin (CCK), which we demonstrate is produced in adipocytes, accompanied by an upregulation of the CCK receptor CCKBR. Importantly, CCK was undetectable in the circulation during winter and presence of sensory neurons suggest a neuronal feedback mechanism within the adipose tissue. Using RNA sequencing, we predict additionally 537 secreted proteins to be seasonally regulated, 37 of which could be confirmed with plasma proteomics. In conclusion, we propose that brown bears have developed a strategy of healthy fat burning and satiety regulation through an adipose tissue-contained mechanism which includes digestion factors and satiety mediators to provide safe energy turnover during hibernation-dependent weight loss.

molecular biology↗

bioRxiv2024

Voltage Gated Calcium Channel Dysregulation May Contribute to Neurological Symptoms in Calmodulinopathies

Calmodulinopathies are caused by mutations in calmodulin (CaM), and result in debilitating cardiac arrythmias such as long-QT syndrome (LQTS) and catecholaminergic polymorphic ventricular tachycardia (CPVT). In addition, many patients exhibit neurological comorbidities, including developmental delay and autism spectrum disorder. Until now, most work into these mutations has focused on cardiac effects, identifying impairment of Ca2+/CaM-dependent inactivation (CDI) of CaV1.2 channels as a major pathogenic mechanism. However, the impact of these mutations on neurological function has yet to be fully explored. CaM regulation of voltage-gated calcium channels (VGCCs) is a critical element of neuronal function, implicating multiple VGCC subtypes in the neurological pathogenesis of calmodulinopathies. Here, we explore the potential for pathological CaM variants to impair the Ca2+/CaM-dependent regulation of CaV1.3 and CaV2.1, both essential for neuronal function. We find that mutations in CaM can impair the CDI of CaV1.3 and reduce the Ca2+-dependent facilitation (CDF) of CaV2.1 channels. We find that mutations associated with significant neurological symptoms exhibit marked effects on CaV1.3 CDI, with overlapping but distinct impacts on CaV2.1 CDF. Moreover, while the majority of CaM variants demonstrated the ability to bind the IQ region of each channel, distinct differences were noted between CaV1.3 and CaV2.1, demonstrating distinct CaM interactions across the two channel subtypes. Further, C-domain CaM variants display a reduced ability to sense Ca2+ when in complex with the CaV IQ domains, explaining the Ca2+/CaM regulation deficits. Overall, these results support the possibility that disrupted Ca2+/CaM regulation of VGCCs may contribute to neurological pathogenesis of calmodulinopathies.

biophysics↗

bioRxiv2024

To fly, or not to fly, that is the question: A deep learning model for peptide detectability prediction in mass spectrometry

Identifying detectable peptides, known as flyers, is key in mass spectrometry-based proteomics. Peptide detectability is strongly related with the peptide sequence and its resulting physicochemical properties. Moreover, the high variability in MS data, particularly in peptide detectability and intensity across multiple analyses and samples, makes the development of a generic model for detectability prediction unfeasible. This underlines the need for tools that can be refined for specific experimental conditions. To address this need, we present Pfly, a deep learning model developed to predicts peptide detectability based solely on peptide sequence. Pfly distinguishes itself as a versatile and reliable state-of-the-art tool, offering high performance, accessibility, and easy customizability for end-users. This adaptability allows researchers to tailor the model to their specific experimental conditions, facilitating the creation of lab-specific models. This, in turn, can lead to more accurate results and expand the models applicability across various research fields. The models architecture is an encoder-decoder with an attention mechanism. This tool classifies peptides as either flyers or non-flyers, providing both binary probabilities and detailed categorical probabilities for four distinct classes defined in this study: non-flyer, weak flyer, intermediate flyer, and strong flyer. The model was initially trained on a synthetic peptide library and subsequently fine-tuned with a biological dataset to mitigate bias towards synthesizability, improving the predictive capacity and outperforming state-of-the-art predictors in a benchmark comparison. The study further investigates the influence of protein abundance and the search engine, illustrating the negative impact on peptide identification due to misclassification. Pfly has been integrated in the DLOmix framework and it is accessible on GitHub at https://github.com/wilhelm-lab/dlomix.

bioinformatics↗

bioRxiv2024

Decoding the Impact of Neighboring Amino Acid on MS Intensity Output through Deep Learning

Peptide-level quantification using mass spectrometry (MS) is no trivial task as the physicochemical properties affect both response and detectability. The specific amino acid (AA) sequence affects these properties, however the link from sequence to intensity output remains poorly understood. In this work, we explore combinations of amino acid pairs (i.e., dimer motifs) to determine a potential relationship between the local amino acid environment and MS1 intensity. For this purpose, a deep learning (DL) model, consisting of an encoder-decoder with an attention mechanism, was built. The attention mechanism allowed to identify the most relevant motifs. Specific patterns were consistently observed where a bulky/aromatic and hydrophobic AA followed by a cationic AA as well as consecutive bulky/aromatic and hydrophobic AAs were found important for the MS1 intensity. Correlating attention weights to mean MS1 intensities revealed that some important motifs, particularly containing Trp, His, and Cys, were linked with low responding peptides whereas motifs containing Lys and most bulky hydrophobic AAs were often associated with high responding peptides. Moreover, Asn-Gly was associated with low MS1 response. The model could predict MS1 response with a mean average percentage error of [~]11% and a Pearson correlation coefficient of [~]0.68.

bioinformatics↗

bioRxiv2023

Insight on physicochemical properties governing peptide MS1 response in HPLC-ESI-MS/MS proteomics: A deep learning approach

Accurate and absolute quantification of individual peptides in complex mixtures is a challenge not easily overcome. A potential solution is the use of quantitative mass spectrometry (MS) based methods, however, current state of the art requires foreground knowledge and isotopically labeled standards for each peptide to be accurately quantified. This increases analytical expenses, time consumption, and labor, limiting the number of peptides that can be quantified. A key step in developing less restrictive label-free quantitative peptidomics methods is understanding of the physicochemical properties of peptides that influence the MS response. In this work, a deep learning model was developed to identify the most relevant physicochemical properties based on repository MS data from equimolar peptide pools. Using an autoencoder with attention mechanism and correlating attention weights with corresponding physicochemical property indices from AAindex1, we were able to obtain insight on the properties governing the peptide-level MS1 response. These properties can be grouped in three main categories related to peptide hydrophobicity, charge, and structural propensities. Moreover, we present a model for predicting the MS1 intensity output based solely on peptide sequence input. Using a refined training dataset, the model predicted log-transformed peptide MS1 intensities with an average error of 11%.

bioinformatics↗

bioRxiv2022

Bioinformatically predicted emulsifying peptides and potato protein hydrolysate improves the oxidative stability of microencapsulated fish oil

The aim of this study was to investigate the potential of potato proteins and peptides as emulsifiers in the microencapsulation of fish oil by spray-drying. Microcapsules were produced using a potato protein extract, and fractions enriched in patatin and protease inhibitors. Furthermore, bioinformatically predicted emulsifier peptides from abundant potato proteins and a hydrolysate, obtained through targeted proteolysis of the extract, were investigated. During 28 days of storage at 25{degrees}C, peptides and hydrolysate exhibited better emulsifying properties and higher encapsulation efficiencies compared to native proteins and sodium caseinate. Significant differences (p < 0.05) were observed in the peroxide value (PV) and secondary volatile oxidation products between the microcapsules produced with peptides and native proteins. Microcapsules produced with peptides and hydrolysate showed the highest oxidative stability, not exceeding a PV of 10 meq/kg oil, and with concentrations of volatiles below the odor threshold in oil for five of the six studied compounds. These results show the emulsifying potential of potato peptides and hydrolysate for use in microencapsulation of hydrophobic bioactive ingredients such as fish oil.

bioengineering↗

bioRxiv2022

Targeted hydrolysis of native potato protein: A novel route for obtaining hydrolysates with improved interfacial properties

Peptides and protein hydrolysates are promising alternatives to substitute chemical additives as functional food ingredients. In this study, we present a novel approach for producing a potato protein hydrolysate with improved emulsifying and foaming properties by data-driven, targeted hydrolysis. Based on previous studies, we selected 15 emulsifier peptides derived from abundant potato proteins, which were clustered based on sequence identity. Through in silico analysis, we determined that from a range of industrial proteases (Neutrase (Neut), Alcalase (Alc), Flavorzyme (Flav) and Trypsin (Tryp)), Tryp was found more likely to release peptides resembling the target peptides. After applying all proteases individually, hydrolysates were assayed for in vitro emulsifying and foaming properties. No direct correlation between degree of hydrolysis and interfacial properties was found. Tryp produced a hydrolysate (DH=5.4%) with the highest (P<0.05) emulsifying and foaming abilities, good stabilities, and high aqueous solubility. Using LC-MS/MS, we identified >10,000 peptides in each hydrolysate. Through peptide mapping, we show that random overlapping with known peptide emulsifiers is not sufficient to quantitatively describe hydrolysate functionality. While Neut hydrolysates had the highest proportion of peptides with target overlap, they showed inferior interfacial activity. In contrast, Tryp was able to release specifically targeted peptides, explaining the high surface activity observed. While modest yields and residual unhydrolyzed protein indicate room for process improvement, this work shows that data-driven, targeted hydrolysis is a viable, interdisciplinary approach to facilitate hydrolysis design for production of functional hydrolysates from alternative protein sources.

biochemistry↗

bioRxiv2020

Proteomic characterization of pilot scale hot-water extracts from the industrial carrageenan red seaweed Eucheuma denticulatum

Seaweeds have a long history as a resource for polysaccharides/hydrocolloids extraction for use in the food industry due to their functionality as stabilizing agents. In addition to the carbohydrate content, seaweeds also contains a significant amount of protein, which may find application in food and feed. Here, we present a novel combination of transcriptomics, proteomics, and bioinformatics to determine the protein composition in two pilot-scale extracts from Eucheuma denticilatum (Spinosum) obtained via hot-water extraction. The extracts were characterized by qualitative and quantitative proteomics using LC-MS/MS and a de-novo transcriptome assembly for construction of a novel proteome. Using label-free, relative quantification, we were able to identify the most abundant proteins in the extracts and determined that the majority of quantified protein in the extracts (>75%) is constituted by merely three previously uncharacterized proteins. Putative subcellular localization for the quantified proteins was determined by bioinformatic prediction, and by correlating with the expected copy number from the transcriptome analysis, we determined that the extracts were highly enriched in extracellular proteins. This implies that the method predominantly extracts extracellular proteins, and thus appear ineffective for cellular disruption and subsequent release of intracellular proteins. Ultimately, this study highlight the power of quantitative proteomics as a novel tool for characterization of alternative protein sources intended for use in foods. Additionally, the study showcases the potential of proteomics for evaluation of protein extraction methods and as powerful tool in the development of an efficient extraction process.

biochemistry↗