Dr. Katherine Alfieri joined Stanford ChEM-H in 2016. As Scientific Program Manager, she develops and manages ChEM-H programs that advance research and training at the interface of chemistry, engineering, and medicine. Before coming to Stanford, Dr. Alfieri completed her Ph.D. in Chemistry at the University of California, Berkeley.

Honors & Awards

  • Graduate Research Fellowship, National Science Foundation (2010-2013)

Education & Certifications

  • Certification, Stanford University, Research Administration (2017)
  • Ph.D., University of California, Berkeley, Chemistry (2015)
  • B.S., Haverford College, Chemistry (2010)

Professional Affiliations and Activities

  • Member, National Organization of Research Development Professionals (2017 - Present)

All Publications

  • Mapping the stochastic sequence of individual ligand-receptor binding events to cellular activation: T cells act on the rare events. Science signaling Lin, J. J., Low-Nam, S. T., Alfieri, K. N., McAffee, D. B., Fay, N. C., Groves, J. T. 2019; 12 (564)


    T cell receptor (TCR) binding to agonist peptide major histocompatibility complex (pMHC) triggers signaling events that initiate T cell responses. This system is remarkably sensitive, requiring only a few binding events to successfully activate a cellular response. On average, activating pMHC ligands exhibit mean dwell times of at least a few seconds when bound to the TCR. However, a T cell accumulates pMHC-TCR interactions as a stochastic series of discrete, single-molecule binding events whose individual dwell times are broadly distributed. With activation occurring in response to only a handful of such binding events, individual cells are unlikely to experience the average binding time. Here, we mapped the ensemble of pMHC-TCR binding events in space and time while simultaneously monitoring cellular activation. Our findings revealed that T cell activation hinges on rare, long-dwell time binding events that are an order of magnitude longer than the average agonist pMHC-TCR dwell time. Furthermore, we observed that short pMHC-TCR binding events that were spatially correlated and temporally sequential led to cellular activation. These observations indicate that T cell antigen discrimination likely occurs by sensing the tail end of the pMHC-TCR binding dwell time distribution rather than its average properties.

    View details for DOI 10.1126/scisignal.aat8715

    View details for PubMedID 30647147

  • Early T cell receptor signals globally modulate ligand:receptor affinities during antigen discrimination. Proceedings of the National Academy of Sciences of the United States of America Pielak, R. M., O'Donoghue, G. P., Lin, J. J., Alfieri, K. N., Fay, N. C., Low-Nam, S. T., Groves, J. T. 2017


    Antigen discrimination by T cells occurs at the junction between a T cell and an antigen-presenting cell. Juxtacrine binding between numerous adhesion, signaling, and costimulatory molecules defines both the topographical and lateral geometry of this cell-cell interface, within which T cell receptor (TCR) and peptide major histocompatibility complex (pMHC) interact. These physical constraints on receptor and ligand movement have significant potential to modulate their molecular binding properties. Here, we monitor individual ligand:receptor binding and unbinding events in space and time by single-molecule imaging in live primary T cells for a range of different pMHC ligands and surface densities. Direct observations of pMHC:TCR and CD80:CD28 binding events reveal that the in situ affinity of both pMHC and CD80 ligands for their respective receptors is modulated by the steady-state number of agonist pMHC:TCR interactions experienced by the cell. By resolving every single pMHC:TCR interaction it is evident that this cooperativity is accomplished by increasing the kinetic on-rate without altering the off-rate and has a component that is not spatially localized. Furthermore, positive cooperativity is observed under conditions where the T cell activation probability is low. This TCR-mediated feedback is a global effect on the intercellular junction. It is triggered by the first few individual pMHC:TCR binding events and effectively increases the efficiency of TCR scanning for antigen before the T cell is committed to activation.

    View details for DOI 10.1073/pnas.1613140114

    View details for PubMedID 29087297

  • Using Infrared Spectroscopy of Cyanylated Cysteine To Map the Membrane Binding Structure and Orientation of the Hybrid Antimicrobial Peptide CM15 BIOCHEMISTRY Alfieri, K. N., Vienneau, A. R., Londergan, C. H. 2011; 50 (51): 11097-11108


    The synthetic antimicrobial peptide CM15, a hybrid of N-terminal sequences from cecropin and melittin peptides, has been shown to be extremely potent. Its mechanism of action has been thought to involve pore formation based on prior site-directed spin labeling studies. This study examines four single-site β-thiocyanatoalanine variants of CM15 in which the artificial amino acid side chain acts as a vibrational reporter of its local environment through the frequency and line shape of the unique CN stretching band in the infrared spectrum. Circular dichroism experiments indicate that the placements of the artificial side chain have only small perturbative effects on the membrane-bound secondary structure of the CM15 peptide. All variant peptides were placed in buffer solution, in contact with dodecylphosphatidylcholine micelles, and in contact with vesicles formed from Escherichia coli polar lipid extract. At each site, the CN stretching band reports a different behavior. Time-dependent attenuated total reflectance infrared spectra were also collected for each variant as it was allowed to remodel the E. coli lipid vesicles. The results of these experiments agree with the previously proposed formation of toroidal pores, in which each peptide finds itself in an increasingly homogeneous and curved local environment without apparent peptide-peptide interactions. This work also demonstrates the excellent sensitivity of the SCN stretching vibration to small changes in the peptide-lipid interfacial structure.

    View details for DOI 10.1021/bi200903p

    View details for Web of Science ID 000298198400012

    View details for PubMedID 22103476

    View details for PubMedCentralID PMC3246368

  • Polyglutamine fibrils are formed using a simple designed beta-hairpin model PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS Smith, M. H., Miles, T. F., Sheehan, M., Alfieri, K. N., Kokona, B., Fairman, R. 2010; 78 (8): 1971-1979


    Polyglutamine repeats are found in proteins associated with many neurodegenerative diseases. These repeats are responsible for intracellular protein aggregation that resemble amyloid plaques and contain the hallmarks of cross-beta fibrillar structures. Recent work has suggested that the glutamines are involved in aggregation through two possible mechanisms: one involving only side-chain hydrogen bonding and a second involving interdigitation of the glutamines with tight van der Waal's packing (steric zipper model). We are interested in determining which interactions are particularly involved in early assembly processes and have developed a beta-hairpin model system to address this problem. Our model system is designed to stabilize a putative high-energy nucleating structure to provide a window to view early assembly processes. We have applied spectroscopy tools (circular dichroism, infrared, and dynamic light scattering) to probe the self-assembly of beta-sheet fibrils. These experiments established the conditions to study fibrillar morphology using atomic force microscopy. We show that fibrils are short with minimal lateral growth, suggesting that this may be a good model system for studying early assembly steps.

    View details for DOI 10.1002/prot.22713

    View details for Web of Science ID 000277767700014

    View details for PubMedID 20408173

  • Cyanylated Cysteine: A Covalently Attached Vibrational Probe of Protein-Lipid Contacts JOURNAL OF PHYSICAL CHEMISTRY LETTERS McMahon, H. A., Alfieri, K. N., Clark, C. A., Londergan, C. H. 2010; 1 (5): 850-855


    Cyanylated cysteine, or beta-thiocyanatoalanine, is an artificial amino acid that can be introduced into peptides and proteins by post-translational chemical modification of solvent-exposed cysteine side chains, and thus it can be used in any protein with a suitable expression and mutagenesis system. In this study, cyanylated cysteine is introduced at selected sites in two model peptides that have been shown to bind to membrane interfaces: a membrane-binding sequence of the human myelin basic protein and the antimicrobial peptide CM15. Far-UV circular dichroism indicates that the secondary structures of the bound peptides are not influenced by introduction of the artificial side chain. Infrared spectra of both systems in buffer and exposed to dodecylphosphocholine micelles indicate that the CN stretching absorption band of cyanylated cysteine can clearly distinguish between membrane burial and solvent exposure of the artificial side chain. Since infrared spectroscopy can be applied in a wide variety of lipid systems, and since cyanylated cysteine can be introduced into proteins of arbitrary size via mutagenesis and post-translational modification, this new probe could see wide use in characterizing the protein-lipid interactions of membrane proteins.

    View details for DOI 10.1021/jz1000177

    View details for Web of Science ID 000277041000010

    View details for PubMedID 20228945

    View details for PubMedCentralID PMC2836368