Dynamic 3D proteomes reveal protein functional alterations at high resolution in situ.
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ABSTRACT:
SUBMITTER: Cappelletti V
PROVIDER: S-EPMC7836100 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:Many biological processes are regulated via molecular events, such as intermolecular interactions and chemical modifications, which do not affect protein levels and escape detection in classical proteomic screens. Reasoning that these events affect protein structure, we propose here that a global protein structural readout could detect many functional alterations simultaneously and in situ. We test this idea using limited proteolysis-mass spectrometry (LiP-MS), which monitors structural changes in thousands of proteins within a native-like environment. In bacteria undergoing nutrient adaptation and in yeast responding to acute stress, this global structural readout captures enzyme activity changes, allosteric regulation, phosphorylation, protein aggregation and protein complex formation, with sufficiently high resolution to identify alterations of single functional sites such as active site occupancy and binding interfaces. Comparison with prior knowledge, including flux, phosphoproteomics and metabolomics data, shows that LiP-MS captures most known enzyme functional alterations and suggests novel metabolite-protein binding events, enabling identification of a fructose-1,6-bisphosphate-based regulatory mechanism of glucose uptake in E. coli. The structural readout dramatically increases classical proteomics screen coverage and generates mechanistic hypotheses, thus better linking holistic and reductionist approaches and paving the way for a new in situ structural systems biology.
2020-11-02 | PXD022297 | Pride
Project description:BackgroundChildren of aged fathers are at a higher risk of developing mental disorders. Alterations in sperm DNA methylation have been implicated as a potential cause. However, age-dependent modifications of the germ cells' epigenome remain poorly understood. Our objective was to assess the DNA methylation profile of human spermatozoa during aging.ResultsWe used a high throughput, customized methylC-capture sequencing (MCC-seq) approach to characterize the dynamic DNA methylation in spermatozoa from 94 fertile and infertile men, who were categorized as young, 48 men between 18-38 years or old 46 men between 46-71 years. We identified more than 150,000 age-related CpG sites that are significantly differentially methylated among 2.65 million CpG sites covered. We conducted machine learning using our dataset to predict the methylation age of subjects; the age prediction accuracy based on our assay provided a more accurate prediction than that using the 450 K chip approach. In addition, we found that there are more hypermethylated (62%) than hypomethylated (38%) CpG sites in sperm of aged men, corresponding to 798 of total differential methylated regions (DMRs), of which 483 are hypermethylated regions (HyperDMR), and 315 hypomethylated regions (HypoDMR). Moreover, the distribution of age-related hyper- and hypomethylated CpGs in sperm is not random; the CpG sites that were hypermethylated with advanced age were frequently located in the distal region to genes, whereas hypomethylated sites were near to gene transcription start sites (TSS). We identified a high density of age-associated CpG changes in chromosomes 4 and 16, particularly HyperDMRs with localized clusters, the chr4 DMR cluster overlaps PGC1α locus, a protein involved in metabolic aging and the chr16 DMR cluster overlaps RBFOX1 locus, a gene implicated in neurodevelopmental disease. Gene ontology analysis revealed that the most affected genes by age were associated with development, neuron projection, differentiation and recognition, and behaviour, suggesting a potential link to the higher risk of neurodevelopmental disorders in children of aged fathers.ConclusionWe identified thousands of age-related and sperm-specific epigenetic alterations. These findings provide novel insight in understanding human sperm DNA methylation dynamics during paternal aging, and the subsequently affected genes potentially related to diseases in offspring.
| S-EPMC7735420 | biostudies-literature
Project description:PurposeTo achieve motion robust high resolution 3D free-breathing pulmonary MRI utilizing a novel dynamic 3D image navigator derived directly from imaging data.MethodsFive-minute free-breathing scans were acquired with a 3D ultrashort echo time (UTE) sequence with 1.25 mm isotropic resolution. From this data, dynamic 3D self-navigating images were reconstructed under locally low rank (LLR) constraints and used for motion compensation with one of two methods: a soft-gating technique to penalize the respiratory motion induced data inconsistency, and a respiratory motion-resolved technique to provide images of all respiratory motion states.ResultsRespiratory motion estimation derived from the proposed dynamic 3D self-navigator of 7.5 mm isotropic reconstruction resolution and a temporal resolution of 300 ms was successful for estimating complex respiratory motion patterns. This estimation improved image quality compared to respiratory belt and DC-based navigators. Respiratory motion compensation with soft-gating and respiratory motion-resolved techniques provided good image quality from highly undersampled data in volunteers and clinical patients.ConclusionAn optimized 3D UTE sequence combined with the proposed reconstruction methods can provide high-resolution motion robust pulmonary MRI. Feasibility was shown in patients who had irregular breathing patterns in which our approach could depict clinically relevant pulmonary pathologies. Magn Reson Med 79:2954-2967, 2018. © 2017 International Society for Magnetic Resonance in Medicine.
| S-EPMC6474413 | biostudies-literature
Project description:Heterosis plays a significant role in enhancing variety, boosting yield, and raising economic value in crops, but the molecular mechanism is still unclear. We analyzed the transcriptomes and 3D genomes of a hybrid (F1) and its parents (w30 and 082). The analysis of the expression revealed a total of 485 specially expressed genes (SEGs), 173 differentially expressed genes (DEGs) above the parental expression level, more actively expressed genes, and up-regulated DEGs in the F1. Further study revealed that the DEGs detected in the F1 and its parents were mainly involved in the response to auxin, plant hormone signal transduction, DNA metabolic process, purine metabolism, starch, and sucrose metabolism, which suggested that these biological processes may play a crucial role in the heterosis of Brassica rapa. The analysis of 3D genome data revealed that hybrid F1 plants tend to contain more transcriptionally active A chromatin compartments after hybridization. Supplementaryly, the F1 had a smaller TAD (topologically associated domain) genome length, but the number was the highest, and the expression change in activated TAD was higher than that of repressed TAD. More specific TAD boundaries were detected between the parents and F1. Subsequently, 140 DEGs with genomic structural variants were selected as potential candidate genes. We found two DEGs with consistent expression changes in A/B compartments and TADs. Our findings suggested that genomic structural variants, such as TADs and A/B chromatin compartments, may affect gene expression and contribute to heterosis in Brassica rapa. This study provides further insight into the molecular mechanism of heterosis in Brassica rapa.
| S-EPMC10931744 | biostudies-literature
Project description:High-resolution three-dimensional models of Caulobacter crescentus nucleoid structures were generated via a multi-scale modeling protocol. Models were built as a plectonemically supercoiled circular DNA and by incorporating chromosome conformation capture based data to generate an ensemble of base pair resolution models consistent with the experimental data. Significant structural variability was found with different degrees of bending and twisting but with overall similar topologies and shapes that are consistent with C. crescentus cell dimensions. The models allowed a direct mapping of the genomic sequence onto the three-dimensional nucleoid structures. Distinct spatial distributions were found for several genomic elements such as AT-rich sequence elements where nucleoid associated proteins (NAPs) are likely to bind, promoter sites, and some genes with common cellular functions. These findings shed light on the correlation between the spatial organization of the genome and biological functions.
| S-EPMC5934669 | biostudies-literature
Project description:PurposeTo develop a method for fast pediatric 3D free-breathing abdominal dynamic contrast enhanced (DCE) magnetic resonance imaging (MRI) and investigate its clinical feasibility.Materials and methodsA combined locally low rank parallel imaging method with soft gating is proposed for free-breathing DCE MRI acquisition. With Institutional Review Board (IRB) approval and informed consent/assent, 23 consecutive pediatric patients were recruited for this study. Free-breathing DCE MRI with ∼1 mm(3) spatial resolution and a 6.5-sec frame rate was acquired on a 3T scanner. Undersampled data were reconstructed with a compressed sensing method without motion correction (FB-CS) and the proposed method (FB-LR). A follow-up respiratory-triggered acquisition (RT-CS) was performed as a reference standard. The reconstructed images were evaluated independently by two radiologists. Wilcoxon tests were performed to test the hypothesis that there was no significant difference between different reconstructions. Quantitative evaluation of contrast dynamics was also performed.ResultsThe mean score of overall image quality of FB-LR was 4.0 on a 5-point scale, significantly better (P < 0.05) than FB-CS reconstruction (mean score 2.9), and similar to RT-CS (mean score 4.1). FB-LR also matched the temporal fidelity of contrast dynamics with a root mean square error less than 5%.ConclusionFast 3D free-breathing DCE MRI with high scan efficiency and image quality similar to respiratory-triggered acquisition is feasible in a pediatric clinical setting.
| S-EPMC4065644 | biostudies-literature
Project description:Regulation of gene expression underlies the establishment and maintenance of cell identity. Chromatin structure and gene activity are linked at long-range via positioning of loci to transcriptionally permissive (euchromatin) or repressive (heterochromatin) environments and at short-range by connecting cis regulatory elements such as promoters and enhancers. However, the dynamics of these processes during cell differentiation still remains unclear. We used Tethered Chromatin Conformation Capture (TCC) to compare the three dimensional chromatin structure of mouse embryonic stem cells (ESC) and neural stem cells (NSC) which we directly derived from the ESC.
2019-08-27 | E-MTAB-2063 | biostudies-arrayexpress
Project description:Aging is a complex physiological process that poses considerable conundrums to rapidly aging societies. For example, the risk of dying from cardiovascular diseases and/or cancer steadily declines for people after their 60s, and other causes of death predominate for seniors older than 80 years of age. Thus, physiological aging presents numerous unanswered questions, particularly with regard to changing metabolic patterns. Urine proteomics analysis is becoming a non-invasive and reproducible diagnostic method. We investigated the urine proteomes in healthy elderly people to determine which metabolic processes were weakened or strengthened in aging humans. Urine samples from 37 healthy volunteers aged 19-90 years (19 men, 18 women) were analyzed for protein expression by liquid chromatography-tandem mass spectrometry. This generated a list of 19 proteins that were differentially expressed in different age groups (young, intermediate, and old age). In particular, the oldest group showed protein changes reflective of altered extracellular matrix turnover and declining immune function, in which changes corresponded to reported changes in cardiovascular tissue remodeling and immune disorders in the elderly. Thus, urinary proteome changes in the elderly appear to reflect the physiological processes of aging and are particularly clearly represented in the circulatory and immune systems. Detailed identification of "protein trails" creates a more global picture of metabolic changes that occur in the elderly.
| S-EPMC3889913 | biostudies-literature
Project description:The purpose of this quick guide is to help new modelers who have little or no background in comparative modeling yet are keen to produce high-resolution protein 3D structures for their study by following systematic good modeling practices, using affordable personal computers or online computational resources. Through the available experimental 3D-structure repositories, the modeler should be able to access and use the atomic coordinates for building homology models. We also aim to provide the modeler with a rationale behind making a simple list of atomic coordinates suitable for computational analysis abiding to principles of physics (e.g., molecular mechanics). Keeping that objective in mind, these quick tips cover the process of homology modeling and some postmodeling computations such as molecular docking and molecular dynamics (MD). A brief section was left for modeling nonprotein molecules, and a short case study of homology modeling is discussed.
| S-EPMC7117658 | biostudies-literature
Project description:SignificanceHigh-speed 3D imaging methods have been playing crucial roles in many biological discoveries.AimWe present a hybrid light-field imaging system and image processing algorithm that can visualize high-speed biological events.ApproachThe hybrid light-field imaging system uses the selective plane optical illumination, which simultaneously records a high-resolution 2D image and a low-resolution 4D light-field image. The high-resolution 4D light-field image is obtained by applying the hybrid algorithm derived from the deconvolution and phase retrieval methods.ResultsHigh-resolution 3D imaging at a speed of 100-s volumes per second over an imaging field of 250 × 250 × 80 μm3 in the x, y, and z axis, respectively, is achieved with a 2.5 times enhancement in lateral resolution over the entire imaging field compared with standard light-field systems. In comparison to the deconvolution algorithm, the hybrid algorithm addresses the artifact issue at the focal plane and reduces the computation time by a factor of 4.ConclusionsThe new hybrid light-field imaging method realizes high-resolution and ultrafast 3D imaging with a compact setup and simple algorithm, which may help discover important applications in biophotonics to visualize high-speed biological events.
| S-EPMC7548856 | biostudies-literature