Falk’s scientific breakthrough began with a deceptively simple question: what exactly occupies the molecular groove of an MHC class I protein? By the late 1980s, researchers had determined the crystal structure of MHC class I molecules and observed that each protein contained a cleft apparently filled with material that was not part of the MHC molecule itself. Scientists suspected that the material consisted of short fragments of proteins, known as peptides, continually generated inside healthy cells and loaded onto MHC molecules. Yet the identity of those peptides remained uncertain. Falk and Rötzschke set out to isolate these naturally occurring cellular antigens directly from living cells, an ambitious goal requiring a combination of cell biology, protein chemistry and painstaking biochemical separation.

Falk had begun studying biochemistry at the University of Hannover before continuing her education at the University of Tübingen with Rötzschke. During a laboratory rotation in 1988, she joined a newly established junior research group at the Max Planck Institute for Biology’s Department of Immunogenetics, directed by Hans-Georg Rammensee. A previous rotation in a peptide chemistry laboratory had given her practical expertise in extracting and separating small protein fragments. She applied those techniques to material derived from cells, solubilizing the antigens and passing them through high-performance liquid chromatography, or HPLC. This method separates compounds according to their chemical properties as they move through a column, allowing complex biological mixtures to be divided into fractions that can be tested individually.

The resulting fractions were exposed to T cells, the immune system’s precision detectors. Some T cells responded specifically to particular fractions, demonstrating that the isolated molecules were not random cellular debris but biologically meaningful antigens. The experiments showed that minor histocompatibility antigens could be peptides derived from polymorphic proteins, whose sequences differ between individuals, or from sex-specific proteins. Crucially, the work also proved that MHC-restricted peptides could be isolated from cells and functionally characterized. “MHC-restricted” means that a T cell recognizes an antigen only when it is bound to a particular MHC molecule; the same peptide can provoke recognition in one molecular context but not another. This finding helped explain how the immune system distinguishes molecular evidence of cellular identity and infection.

The next test was whether virus-infected cells displayed viral peptides through the same pathway. Falk and her collaborators successfully isolated virus-derived peptides from infected cells, showing that MHC molecules could present fragments of invading pathogens to T cells. The result established a direct biochemical link between infection and immune surveillance: proteins made during viral replication are broken down into peptides, selected fragments are loaded into MHC class I molecules, and the resulting complexes move to the cell surface. There, cytotoxic T cells can inspect them through their T-cell receptors. In the same issue of Nature, Grada van Bleek and Stan Nathenson independently reported that similar peptides could be recovered from purified MHC molecules obtained from infected cells, reinforcing the conclusion that antigen presentation was a general cellular process rather than an experimental anomaly.

Comparing the sequences of naturally processed viral peptides led Falk, Rötzschke and their colleagues to a further insight: MHC molecules do not bind every peptide equally. Instead, each MHC variant, or allele, favors peptides with particular chemical patterns at defined positions. These patterns are called binding motifs. MHC molecules are extraordinarily polymorphic, meaning that the genes encoding them exist in many versions across the human population. Their peptide-binding grooves differ subtly in shape and charge, so a peptide that fits securely into one allele may bind weakly or not at all to another. Falk and Rötzschke tested this principle by purifying MHC molecules, extracting the bound peptides and analyzing the resulting mixture directly through classical Edman degradation, a method that identifies amino-acid sequences by progressively removing residues from the end of a peptide.

The approach was unconventional because the researchers analyzed a complex pool rather than a single purified peptide. Organic chemist Günther Jung was initially reluctant to endorse what was described as a “dirty” experiment, but his doctoral student Stefan Stevanović carried out the pool sequencing. The data clearly revealed recurring amino-acid preferences among the peptides associated with a given MHC molecule. Those results demonstrated that stable presentation depends on allele-specific motifs. The discovery was later recognized as a landmark contribution because it made it possible to predict which peptides would naturally associate with particular MHC variants. That predictive capability eventually helped launch immunoinformatics, a field that combines immunology, molecular biology and computation to map the enormous universe of possible antigen–MHC interactions. Databases such as the Immune Epitope Database now contain vast collections of experimentally measured and predicted immune epitopes.

The scale of Falk’s achievement was especially striking because she performed much of the foundational work as an undergraduate. According to the memorial, she was known for intense concentration on experimental design and execution, often arriving late at the laboratory and working deep into the night. She was less interested in conventional academic visibility than in conducting experiments, and Rötzschke frequently presented their results. Her early record nevertheless earned major recognition, including the Otto Westphal doctoral award from the German Society for Immunology in 1993 and the Walter and Christine Richtzenhain Prize in 1995. She completed her PhD in less than six months, an extraordinary pace made possible by the strength of her publications and experimental accomplishments.

Falk later joined Jack Strominger’s laboratory at Harvard University as a postdoctoral researcher, continuing to study interactions between MHC molecules and peptides while expanding into T-cell biology and autoimmune reactions. She and Rötzschke subsequently led a research group at the Max Delbrück Center for Molecular Medicine in Berlin, where she investigated both antigen presentation and regulatory T cells, immune cells that help suppress excessive or misdirected immune responses. In 2008, she accepted a position at the Singapore Immunology Network, part of Singapore’s Agency for Science, Technology and Research, but an accident during a scientific visit to West Africa caused a severe cervical-spine injury before she could move. The injury left her completely paralyzed. She spent the final 16 years of her life in Berlin with the support of a nursing team, remaining deeply interested in science despite profound physical limitations. Her work continues to shape how researchers understand the molecular conversation between infected cells and the immune system.