Research

Our laboratory uses the tools of biomolecular engineering, synthetic biology, and systems biology to understand fundamental biological design principles and to design new molecular and cellular therapeutics for applications in cancer, diabetes, and infectious diseases. Current research areas of interest include:

Multivalent protein design

Multivalent workflow

Multivalency involves the binding of multiple domains within a given molecule to multiple domains on a given target, such as the binding of an antibody to two antigens on the surface of a cell or virus. Multivalent proteins can achieve binding dynamics and selectivities that are not possible with monovalent binding, making them attractive for therapeutic protein design. However, the multiplicity of binding states makes multivalency combinatorially complex and non-intuitive to engineer.

We have established a new computational framework that enables predictive modeling of multivalent protein-protein interactions by taking into account both the spatial presentation and combinatorics of binding configurations. Advances to this framework have enabled us to analyze protein logic gates, uncover hidden dynamics in the SARS-CoV-2 spike protein, and optimize the design of multivalent therapeutics. It has also underscored the importance of specific, low-affinity binders as building blocks for constructing selective multivalent proteins, and we have developed an experimental method for extracting such low-affinity binders using cell-free directed evolution.

Recent Publications:

  1. A. Ohoka and C.A. Sarkar. "Facile display of homomultivalent proteins for in vitro selections." ACS Synthetic Biology, 12:634-638 (2023).
  2. B. Bruncsics†, W.J. Errington†, and C.A. Sarkar. "MVsim is a toolset for quantifying and designing multivalent interactions." Nature Communications, 13:5029 (2022). †Contributed equally. | Link to MVsim
  3. W.J. Errington†, B. Bruncsics†, and C.A. Sarkar. "Mechanisms of non-canonical binding dynamics in multivalent protein-protein interactions." Proceedings of the National Academy of Sciences USA, 116:25659-25667 (2019). †Contributed equally.

Cellular therapeutics and diagnostics

The significant promise of cellular therapeutics that can be reprogrammed to sense and respond to their local environment has led to a proliferation of immunoengineering approaches to combat diseases such as cancer. We are interested in elucidating principles of therapeutic cell proliferation, differentiation, and engagement with target cells to better inform cell designs.

Furthermore, we are developing new classes of bacteria to be used as therapeutics and diagnostics. We have engineered Escherichia coli with the ability to sense and respond to cell-impermeable proteins in their environment. We have also evolved E. coli strains that are more resistant to acid and bile for oral drug delivery applications. In addition to their potential use as therapeutic agents, E. coli biosensors are inexpensive to manufacture and distribute, so they can be used as cheap diagnostics in low-resource settings.

We have also had a longstanding interest in rationally tuning cellular response dynamics. Recent research includes model-guided approaches to quantifying cell identity, understanding cell-fate decisions, and tuning DNA recombination rates for cell engineering.

Recent Publications:

  1. H. Venkatachalapathy, S. Dallon, Z. Yang, S.M. Azarin, C.A. Sarkar†, and E. Batchelor†. "Pulsed stimuli enable p53 phase resetting to synchronize single cells and modulate cell fate." Molecular Systems Biology, 21:390-412 (2025). †Co-corresponding authors.
  2. H. Venkatachalapathy, C. Brzakala, E. Batchelor, S.M. Azarin†, and C.A. Sarkar†. "Inertial effect of cell state velocity on the quiescence-proliferation fate decision." npj Systems Biology and Applications, 10:111 (2024). †Co-corresponding authors.
  3. Q. Zhang, S.M. Azarin, and C.A. Sarkar. "Model-guided engineering of DNA sequences with predictable site-specific recombination rates." Nature Communications, 13:4152 (2022).
  4. N.A. Shah and C.A. Sarkar. "Variable cellular decision-making behavior in a constant synthetic network topology." BMC Bioinformatics, 20:237 (2019).

Drug delivery across cellular barriers

We are building stem cell-based models of various cellular barriers in the body, including the intestinal epithelium, the blood-brain barrier, and the placenta. We use these in vitro models to study healthy barrier function as well as barrier dysregulation in the context of diseases such as diabetes and Alzheimer’s disease. We are particularly interested in developing new strategies for selective drug delivery across these physiological barriers.

Recent Publications:

  1. K.A. Lemke, C.A. Sarkar, and S.M. Azarin. "Rapid retinoic acid-induced trophoblast cell model from human induced pluripotent stem cells." Scientific Reports, 14:18204 (2024).

Improving food security

With the growing impacts of climate change, food insecurity and malnutrition will have increasingly adverse effects on human health. In parallel with our efforts to engineer therapeutic proteins and cells for human disease applications, we are also elucidating the molecular determinants of pathogen-plant interactions and using protein engineering methodologies to create more durable crops in the face of significant threats to the global food supply.

Recent Publications:

  1. G.C. Markou and C.A. Sarkar. "A cell-free approach to identify binding hotspots in plant immune receptors." Scientific Reports, 12:501 (2022).