Biology subjects

Fromm, S.

Publications and source records attributed to Fromm, S..

5 recordsLinked to original sources

bioRxiv2025

Evaluating Deep Learning Based Structure Prediction Methods on Antibody-Antigen Complexes

MotivationAlphaFold2 significantly improved the prediction of protein complex structures. However, its accuracy is lower for interactions without coevolutionary signals, such as host-pathogen and antibody-antigen interactions. Two strategies have been developed to address this limitation: massive sampling and replacing the evoformer with the pairformer, which does not rely on coevolution, as introduced in AlphaFold3, thereby enabling more structural reasoning by the network. ResultsIn this study, we benchmark structure prediction methods on unseen antibody-antigen complexes. We found that increased sampling improves the chances of generating a correct protein model, roughly in a log-linear manner. However, the internal quality estimates by AlphaFold often cannot identify the best predicted structures for each target, resulting in a significant loss of performance for the top-ranked protein model compared with the best model. For all methods, a significant challenge remains the identification of the best model. We also show that AlphaFold3 outperforms AlphaFold2, Boltz-1, and Chai-1. Furthermore, AlphaFold3 performance declines significantly for complexes that lack structural similarity to the training set, indicating that it has to some extent learned to detect remote structural similarities. Availability and implementationAll code is available from github.com/samuelfromm/abag-benchmark-set/ and all data from DOI:10.5281/zenodo.17978681. The latter repository also contains the code. Supplementary informationSupplementary information is available online.

bioinformatics↗

bioRxiv2022

Multiplexed selectivity screening of anti-GPCR antibodies

G protein-coupled receptors (GPCRs) control critical cellular signaling pathways. Therapeutic agents, such as antibodies (Abs), are being developed to modulate GPCR signaling pathways. However, validating the selectivity of anti-GPCR Abs is challenging due to sequence similarities of individual receptors within GPCR subfamilies. To address this, we developed a multiplexed immunoassay to test >400 anti-GPCR Abs from the Human Protein Atlas targeting a customized library of 215 expressed and solubilized GPCRs representing all GPCR subfamilies. We found that ~61% of Abs were selective for their intended target, ~11% to bind off-target, and ~28% not to bind any GPCR. Antigens of on-target Abs were, on average, significantly longer, more disordered, and less likely to be buried in the interior of the GPCR protein than the other Abs. These results provide important insights into the immunogenicity of GPCR epitopes and form a basis for the design of therapeutic Abs and the detection of pathological auto-antibodies. TEASERA multiplexed library-to-library selectivity analysis of 400 anti-GPCR antibodies within subfamilies of 200 solubilized receptors.

biochemistry↗

bioRxiv2022

Structural plasticity of Atg18 oligomers: organization of assembled tubes and scaffolds at the isolation membrane

Autophagy-related protein 18 (Atg18) participates in the elongation of early autophagosomal structures in concert with Atg2 and Atg9 complexes. How Atg18 contributes to the structural coordination of Atg2 and Atg9 at the isolation membrane remains to be understood. Here, we determined the cryo-EM structures of Atg18 organized in helical tubes as well as soluble oligomers. The helical assembly is composed of Atg18 tetramers forming a lozenge cylindrical lattice with remarkable structural similarity to the COPII outer coat. When reconstituted with lipid membranes, using subtomogram averaging we determined tilted Atg18 dimer structures bridging two juxtaposed lipid membranes spaced apart by 80 [A]. Together with an AlphaFold Atg18-Atg2 model, we propose that Atg18 oligomers form a structural scaffold coordinating the Atg2 membrane bridge. The observed structural plasticity of Atg18s oligomeric organization and membrane binding provide a molecular framework for the positioning of downstream components of the autophagy machinery.

biophysics↗

bioRxiv2021

Fat and carbohydrate interact to potentiate food reward in healthy weight but not in overweight or obesity

Prior work suggests that actual, but not estimated, energy density drives the reinforcing value of food [1,2] and that energy from fat and carbohydrate can interact to potentiate reward [2]. Here we sought to replicate these findings in an American sample and to determine if the effects are influenced by body mass index (BMI). Thirty participants with healthy weight (HW; BMI 21.92 {+/-} 1.77; M {+/-} SD) and 30 participants with overweight/obesity (OW/OB; BMI 29.42 {+/-} 4.44) rated pictures of common American snacks in 120-kcal portions for liking, familiarity, frequency of consumption, expected satiety, healthiness, energy content, energy density, and price. Participants then completed an auction task where they bid for the opportunity to consume each food. Snacks contained either primarily carbohydrate, primarily fat, or roughly equal portions of fat and carbohydrate (combo). Replicating prior work, we found that participants with HW bid the most for combo foods in linear mixed model analyses. This effect was not observed among individuals with OW/OB. Additionally, in contrast with previous reports [1,2], our linear regression analyses revealed a negative relationship between the actual energy density of the snacks and bid amount that was mediated by food price. Our findings support altered macronutrient reinforcement in obesity and highlight potential influences of the food environment on the regulation of food reward.

neuroscience↗

bioRxiv2020

Structural mechanism for amino acid-dependent Rag GTPase switching by SLC38A9

The mechanistic target of rapamycin complex 1 (mTORC1) couples cell growth to nutrient, energy and growth factor availability (1-3). mTORC1 is activated at the lysosomal membrane when amino acids are replete via the Rag guanosine triphosphatases (GTPases) (4-6). Rags exist in two stable states, an inactive (RagA/BGDP:RagC/DGTP) and active (RagA/BGTP:RagC/DGDP) state, during low and high cellular amino acid levels (4, 5). The lysosomal folliculin (FLCN) complex (LFC) consists of the inactive Rag dimer, the pentameric scaffold Ragulator (7, 8), and the FLCN:FNIP (FLCN-interacting protein) GTPase activating protein (GAP) complex (9), and prevents activation of the Rag dimer during amino acid starvation (10, 11). How the LFC is released upon amino acid refeeding is a major outstanding question in amino-acid dependent Rag activation. Here we show that the cytoplasmic tail of the lysosomal solute carrier family 38 member 9 (SLC38A9), a known Rag activator (12-14), destabilizes the LFC. By breaking up the LFC, SLC38A9 triggers the GAP activity of FLCN:FNIP toward RagC. We present the cryo electron microscopy (cryo-EM) structures of Rags in complex with their lysosomal anchor complex Ragulator and the cytoplasmic tail of SLC38A9 in the pre and post GTP hydrolysis state of RagC, which explain how SLC38A9 destabilizes the LFC and so promotes Rag dimer activation.

biochemistry↗