Biology subjects

Hemme, C.

Publications and source records attributed to Hemme, C..

4 recordsLinked to original sources

bioRxiv2026

A shark variable new antigen receptor recognizes an occluded epitope of fibroblast activation protein

Variable new antigen receptors (VNARs) are the smallest naturally occurring antibody binding domains. Their size allows VNARs to access sterically restricted epitopes that are inaccessible to conventional antibodies. We recently identified a suite of VNARs that target fibroblast activation protein (FAP), a stromal serine protease indicative of extracellular matrix remodeling. The presence of FAP on the surface of cancer-associated fibroblasts (CAFs) that promote immunosuppression has made FAP a compelling therapeutic target for cancer therapy. Although antibodies targeting FAP have been developed, there is a paucity of information on how biologics engage FAP. Here, we used single-particle cryogenic electron microscopy (cryo-EM) to compare FAP recognition of three antibody architectures: a shark-derived VNAR, variable heavy (VH) and light domains (VL) of a humanized Immunoglobulin G (IgG), and a camelid-derived VHH. The humanized VH-VL domains and camelid VHH both target a solvent-exposed {beta}-propeller domain, whereas the VNAR binds a highly conserved, topologically recessed epitope at the FAP dimer interface. Radical-footprinting mass spectrometry (MS) further mapped two additional immune-derived VNARs to distinct FAP surfaces outside the shared {beta}-propeller epitope. These findings demonstrate how unique VNAR architecture can expand access to underexplored FAP surfaces and establish a structural framework for rational multiepitope targeting strategies.

biochemistry↗

bioRxiv2025

NMR Spectral Alignment Utilizing a CryoEM Motion Correction Algorithm

With recent advances in magic-angle spinning (MAS) solid-state NMR (SSNMR) resolution, precise spectral alignment has become a critical bottleneck in data processing workflows. While solution NMR employs deuterium lock systems, most SSNMR probes still lack this capability; though a lock corrects for magnet drift and instabilities, it is not alone sufficient to account for field gradients, sample temperature differences, and pulse sequence effects that can contribute to referencing errors among several data sets. These offsets become particularly problematic in the lengthy multidimensional experiments that provide the foundation for resonance assignment and structure determination procedures. Currently, researchers rely on manual alignment through visual peak inspection--a qualitative approach that often overemphasizes prominent, outlying peaks while overlooking subtle, global patterns. This subjective process becomes increasingly impractical for use cases with lower sensitivity, such as large proteins with thousands of peaks. To address these challenges, here we present Automated NMR Spectral Alignment (ANSA), a program that adapts cryo-electron microscopy motion correction principles to NMR spectroscopy. ANSA treats NMR spectra as images and applies cross-correlation functions to determine optimal alignment, improving cross-correlation scores from 0.33 to 1.00 in controlled tests and achieving 0.96 correlation in real-world applications with previously misaligned spectra. The algorithm successfully aligns spectra across varying experimental conditions, corrects shifts in long-duration experiments, and works with 2D and 3D datasets, with approaches that can be readily extended to additional dimensions. By eliminating human bias and providing objective, consistent spectral alignment, ANSA enhances scientific rigor, improves reproducibility between experiments, and enables automation of critical data processing steps. The software is freely available as an open-source tool, ready for integration into existing NMR workflows.

biophysics↗

bioRxiv2025

A novel inducible mtDNA mutator mouse model to study mitochondrial dysfunction with temporal and spatial control

Mitochondrial dysfunction is a hallmark of aging and numerous age-related diseases. A wealth of studies supports the accumulation of mitochondrial DNA (mtDNA) mutations as a contributing factor to mitochondrial dysfunction in aging and disease. One of the best models to study the relationship between mtDNA mutations and mitochondrial dysfunction is the mtDNA mutator mouse, which expresses a proofreading-deficient version of mtDNA polymerase-{gamma} (PolgA). Despite its groundbreaking contributions to mitochondrial biology and aging research, this model is limited by the whole-body accumulation of mtDNA mutations, which prevents the investigation of tissue-specific differences in mitochondrial dysfunction. To overcome this limitation, we developed a novel inducible knock-in mtDNA mutator mouse model that allows spatial and temporal control of mtDNA mutations, enabling the precise study of mitochondrial dysfunction in a tissue- and time-specific manner. Here, we report the generation and validation of this novel model through whole-body induction via Cre recombinase. Our data demonstrate that, upon induction, this model recapitulates the phenotype of the original mtDNA mutator mouse manifesting the same behavioral and biochemical alterations. This work establishes the functionality of our model and highlights its value as a powerful tool for studying the impact of mtDNA mutations with enhanced specificity and control.

genetics↗

bioRxiv2023

Cryogenic Soft Landing Improves Structural Preservation of Protein Complexes

We describe an apparatus for the cryogenic landing of particles from the ion beam of a mass spectrometer onto transmission electron microscope grids for cryo-electron microscopy. This system also allows for the controlled formation of thin films of amorphous ice on the grid surface. We demonstrate that as compared to room temperature landings, use of this cryogenic landing device greatly improves the structural preservation of deposited protein-protein complexes. Further, landing under cryogenic conditions can increase the diversity of particle orientations, allowing for improved 3D structural interpretation. Finally, we conclude that this approach allows for the direct coupling of mass spectrometry with cryo-electron microscopy.

biochemistry↗