-
Prof. Volker Zickermann (Goethe University Medical School)
Cardiolipin (CL) is the signature phospholipid of mitochondria. CL is essential for cristae formation and the functionality of the enzyme complexes involved in biological energy conversion. The mitochondrial transacylase Tafazzin catalyses the obligatory remodeling of CL, a process in which the composition of the four CL acyl chains is altered. Tafazzin dysfunction causes Barth syndrome, a...
Go to contribution page -
Mr Harsh Oza (Max Planck Institute of Biophysics / Goethe University Frankfurt)
Harsh Vinodkumar Oza, Marius Wegener, Timur Makarov*, Jonas Busam, Kathi Zarnack# & Michaela Müller-McNicoll# A critical quality control step in gene expression is the coupling of pre-mRNA splicing to nuclear export, ensuring that only fully processed transcripts reach the cytoplasm. How splicing fidelity is monitored and translated into export competence, however, remains poorly understood....
Go to contribution page -
Dr Jürgen Köfinger (Max Planck Institute of Biophysics)
We combine experiments with molecular simulations to learn more about a biomolecular system than we could from the individual methods alone. Ensemble and force-field refinement provide consistent, reproducible, and robust ways to do so. Biophysical experiments like SAXS, FRET, NMR, PELDOR/DEER provide ensemble averaged information. Although valuable by themselves, such information can be of...
Go to contribution page -
Balázs Fábián (Max Planck Institute of Biophysics)
Membrane buckling simulations are routinely analysed using Fourier fits to estimate protein intrinsic curvature. We show that such fits introduce systematic artifacts, despite accurate height profiles. Fitting the analytical Helfrich buckle shape yields consistent curvature distributions and intrinsic curvatures. Applying this approach to Martini 3 simulations, we extract the intrinsic...
Go to contribution page -
Lucia Baltz (JGU Mainz)
Molecular dynamics (MD) simulations have been proven essential for elucidating the hierarchical interplay of molecular interaction patterns on different time and length scales. To study the material properties of biomolecular condensates and ultimately their biological function, simulations of large systems require a vast amount of computational resources. Gaining insight into minute details...
Go to contribution page -
Dr Caterina Merla (ENEA BIOTEC-RED)
Accurate evaluation of the delivered electric dose is a key challenge in therapeutic brain stimulation based on physical stimulation, as clinical effects depend on the spatial distribution of brain induced electric fields. Numerical simulations were developed to describe electric field distributions in the heads of patients using two modelling approaches: one simulating transcranial magnetic...
Go to contribution page -
Horacio V. Guzman (ICMAB-Consejo Superior de Inv. Científicas)
We are standing at a unique crossroads in the fabrication of nanoparticles in-house [1-6] and AI algorithms. A decade from now, we have seen computational power explode, giving us the tools to dream up new biocompatible materials as novel drugs and treatments, designed faster than ever before. However, in the high-stakes world of nanomedicine, simply having a 'black-box answer' from AI isn't...
Go to contribution page -
Mr Magnus Petersen (Frankfurt Institute for Advanced Studies)
Characterizing conformational transitions in physical systems remains a fundamental challenge, as traditional sampling methods struggle with the high-dimensional nature of molecular systems and high-energy barriers between stable states. These rare events often represent the most biologically significant processes, yet may require months of continuous simulation to observe. One way to...
Go to contribution page -
Anika Dolata (Goethe University Frankfurt)
In plant biology, functional imaging enables the visualization and quantitative analysis of molecular activities in living cells with high spatiotemporal resolution. It involves fluorescent protein (FP) tagging combined with advanced fluorescence microscopy techniques, such as laser-scanning confocal imaging, super-resolution Airyscan detection, Förster Resonance Energy Transfer (FRET) and...
Go to contribution page -
Dr Ali Eljebbawi (Goethe University Frankfurt)
In plant biology, functional imaging enables the visualization and quantitative analysis of molecular activities in living cells with high spatiotemporal resolution. It involves fluorescent protein (FP) tagging combined with advanced fluorescence microscopy techniques, such as laser-scanning confocal imaging, super-resolution Airyscan detection, Förster Resonance Energy Transfer (FRET) and...
Go to contribution page -
Dr Sergio Alejandro Alejandro Poveda (Goethe University)
We developed an integrative pipeline that combines multi-omics data, structural screening, AlphaFold2 modeling, and all-atom molecular dynamics to identify and characterize selective autophagy receptors (SARs). The framework enables rapid screening of canonical LIR-LDS interactions by scoring motif-based residue contacts and pocket occlusion across experimental structures, AF2 models, and MD...
Go to contribution page -
Dr Vladimir Despic (Goethe University Frankfurt)
UV-C crosslinking and immunoprecipitation (CLIP)–based methods are the gold standard for identifying direct RNA binding protein (RBP) interaction sites on cellular RNA in vivo. Here, we describe individual nucleotide resolution CLIP version 3 (iCLIP3), an optimized protocol for generating transcriptome-wide maps of RBP-RNA interaction sites at single-nucleotide resolution from low-input...
Go to contribution page -
Ms Rachita Sharma (Max Planck Institute for Biophysics)
Here, we investigate Caenorhabditis elegans gap junctions (GJs) using an integrative approach combining electron cryo-tomography and molecular dynamics (MD) simulations. Cryo-tomographic analysis of primary embryonic cells revealed hexagonally packed arrays of GJs at cell–cell junctions. Notably, we identified a previously uncharacterized cap-like cytosolic density occluding the channel pore....
Go to contribution page -
Ms Alina Leiss (Max Planck Institute for Human Cognitive and Brain Sciences)
Our sham-controlled TMS study causally investigated the Angular Gyrus (AG) and DLPFC's roles in language comprehension and particularly examines how their contributions change under varying cognitive loads via dual-task reading/n-back. This detailed empirical data could serve as a valuable foundation for cognitive Digital Twins in the future, enabling simulation of individual responses and...
Go to contribution page -
Ainara Claveras (Max Planck Institute of Biophysics)
Autophagy requires lipid transfer from the ER to growing phagophores. Using structural predictions, molecular dynamics simulations, and in vitro lipid transfer assays, we investigated how the lipid transfer protein ATG2A mediates this process. We identified a novel gating mechanism driven by conformational rearrangements of N-terminal amphipathic helices. Guided by this insight, we designed an...
Go to contribution page -
Ms Sirgrid Trägenap (Franfkurt Institute of Advanced Studies)
The highly recurrent networks of the cerebral cortex are thought to profoundly shape neural responses, amplifying certain patterns of activity over others. However, whether such selective amplification organizes network activity at the level of the millimeter-scale networks which underlie perception and behavior remains unknown. Here, we combine patterned optogenetic stimulation informed by a...
Go to contribution page -
Mr Julian von Ehr (Goethe University Frankfurt)
The human serine-arginine rich splicing factor 6 (SRSF6) is part of the SR-protein family consisting of 12 members and as such is involved in (alternative-) splicing regulation. It is composed of an N-terminal RRM domain, followed by a pseudo RRM and a C-terminal serine-arginine rich disordered domain. With SRSF6 being an integral part of the splicing machinery, all three domains have been...
Go to contribution page -
Mr Alberto Cristiani (Goethe University Frankfurt)
E3 ubiquitin ligases define the ubiquitin code, regulating protein degradation and non-degradative processes such as DNA repair, signaling, and immunity. We present a comprehensive classification of the human E3 ligome by integrating sequence, structural, functional, and expression data using a weakly supervised metric-learning framework. This approach captures relationships across E3...
Go to contribution page -
Dr Anusha Chaudhuri (Goethe University Frankfurt)
-
Dr Josep BIayna (Goethe University Frankfurt)
Intron retention (IR) is an important regulator of RNA fate, yet its spatial and temporal organization in human cells remains poorly understood. Here, we investigate the dynamics, localization, and regulation of intron-retained RNAs in pluripotent stem cells using compartment-resolved transcriptional shutdown, sequence-based modeling, and advanced RNA imaging. We focus on the relationship...
Go to contribution page -
Dr Gabrijela Dumbovic (Goethe University Frankfurt)
Intron retention (IR) is an important regulator of RNA fate, yet its spatial and temporal organization in human cells remains poorly understood. Here, we investigate the dynamics, localization, and regulation of intron-retained RNAs in pluripotent stem cells using compartment-resolved transcriptional shutdown, sequence-based modeling, and advanced RNA imaging. We focus on the relationship...
Go to contribution page -
Mr Plamen Kondev (Goethe University Frankfurt)
Membrane remodeling underlies many eukaryotic processes and is presumed to have co-evolved with the ER. We characterize six protein families that contain the Reticulon and Reticulon-like domains across all sequenced genomes. We present a new sequence-based subfamily classification. Despite poor sequence conservation across various phyla, this classification correlates with distinct changes in...
Go to contribution page -
Dr Naresh Yandrapalli (Saarland University)
Synthetic cells are vital for modeling cellular complexity. We present a progressive inverted emulsion method that transitions from robust on-chip vesicle production to engineering complex bilayers with ~95% asymmetry. By integrating lateral phase-separation ($L_o$/$L_d$ domains) and domain-specific protein binding , we induce spontaneous curvature leading to autonomous budding and fission....
Go to contribution page -
Dr Kateryna Lohachova (IBCii)
Large-scale membrane remodeling events, such as budding, fusion, fission, and pore formation, help maintain cellular homeostasis. Integral and peripheral membrane proteins play crucial roles in these remodeling events. By using coarse-grained molecular dynamics simulations, we quantify the protein-induced membrane perturbation fields. By employing the continuum Helfrich model and incorporating...
Go to contribution page -
Ms Deyue Kong (Frankfurt Institute for Advanced Studies)
Cortical circuits are proposed to amplify weak sensory inputs but transition to feature competition during strong drive. However, the evidence for this is scarce in cortices with a functional, modular organization, such as in primates and carnivores, where neighboring excitatory and inhibitory cells share feature selectivity. Here, we demonstrate that networks in ferret primary visual cortex...
Go to contribution page -
Nora Blümel (Goethe University Frankfurt)
After completion of processing in the nucleus eukaryotic mRNAs are bound by the nuclear export factor NXF1 and are exported to the cytoplasm. For binding to mRNAs, NXF1 requires adapter proteins that recruit NXF1 to newly transcribed pre-mRNAs in a non-sequence-specific manner. To identify novel NXF1 adapter proteins for the selective export of specific transcript classes we developed a...
Go to contribution page -
Dr Hendrik Jung (Goethe University Frankfurt)
We used the AI for Molecular Mechanism Discovery to simulate and understand the activation cascade of the Ca(2+)-sensing stromal interaction molecule 1 (STIM1) dimer. The detailed atomistic insight into the dimerization pathways enabled us to shed light on the experimentally observed changes in dimerization propensities for four different mutants and to reconcile previous experimental results....
Go to contribution page
Choose timezone
Your profile timezone: