The King Lab (some assembly required)

Dept. of Biochemistry Institute for Protein Design University of Washington

King Lab | Lab Members

» Group Picture!

PI

neil@ipd.uw.edu

Neil King, PhD

Neil studied Biomedical Engineering as an undergraduate at Northwestern University, followed by graduate studies in Biochemistry in the lab of Todd Yeates at UCLA. During his postdoc in the group of David Baker at UW, he pioneered the development of general computational methods for the design of self-assembling proteins with atomic-level accuracy. He joined UW’s Department of Biochemistry and Institute for Protein Design as a Translational Investigator in 2014 before transitioning to Assistant Professor in July 2017. His group uses and extends computational methods to design functional protein nanomaterials for applications in structure-based vaccine design and targeted delivery of biologics.
Commercial Science Activities

Postdoctoral Fellows

bakerste@uw.edu

Stefanie Baker, PhD

Stefanie is investigating the assembly/disassembly kinetics and long-term stability of protein nanocages. The goal is to correlate nanocage in vitro stability to in vivo stability, which can provide important information on how these particles degrade in the body. Future studies will center on developing long-lasting nanocage formulations as well as optimizing nanocage designs for delivery of various types of therapeutic molecules.

 
 

Alena Khmelinskaia, PhD

Alena is generally intrigued by lipid membranes and their complex interactions with proteins. Her research is focused in how can a protein cage be singularly enveloped by a lipid membrane. In order to achieve a more malleable interface with the lipid membranes, she is introducing protein structural flexibility as a cage design principle. Her free time is passed in the company of her cat and piano.

Jake Kraft, PhD

How do pathogens avoid the immune systems of their mammalian hosts? Could these avoidance mechanisms be designed into novel protein nanomaterials to manipulate the immune response? These questions are at the heart of Jake’s research. His work aims to understand the immune-avoidance mechanisms that have evolved in pathogens in nature, and then translate these mechanisms into the design of novel protein nanoparticle vaccines and therapeutics to control/reduce their immunogenicity. He’s also employing covalent modification strategies the biopharmaceutical industry has used to shield immunogenic epitopes and reduce the clearance of protein therapeutics. Overall, his goal is to establish principles for evading and focusing the immune response to protein nanomaterials.

Sanela Rankovic, PhD

Sanela is a postdoctoral fellow with a background in Viral and Cellular Mechanobiology, Molecular Biology and Biophysics. She is generally interested in adapting virus properties and mechanisms for an application in Synthetic Biology. Her research in the King lab focuses on co-opting human immunodeficiency virus type 1 (HIV-1) capsid disassembly mechanism for programmed disassembly of designed protein nanomaterials upon encountering specific environmental cues.

Aaron Sciore, PhD

Aaron is developing next-generation self-assembling vaccines for respiratory diseases. He is also developing general methods for optimizing the secretion of self-assembling vaccines from mammalian cells.


Graduate Students

Chloe Adams

Chloe is a Biochemistry PhD student. She is broadly interested in vaccine design and drug development. Specifically, she aims to design proteins to activate aspects of the innate immune system.

Jung-Ho Chun

Jung-Ho is a BPSD graduate student in the King Lab and the Baker Lab. He is interested in B cell engineering and vaccine design. He is currently working on designing de novo proteins that can direct B cells to specific cell stages, activation, and are useful in vaccine development.

Annie Dosey

Annie is a BPSD graduate student with a background in structural biology. She is pursuing the creation of a nanoparticle-based universal influenza vaccine, as well as a deeper understanding of how to control the immune response induced by the vaccine. Annie is also using both structural and computational methods as a means to probe nanoparticle formation and improve upon the accuracy and breadth of their design.

Quinton Dowling

Quinton works to increase the functionality and translational applications of protein nanoparticles by developing particles that interact with new materials, biological functions, and signals. His work can be broken down into computational design and assay development. Design goals include i) extending the types of protein nanomaterials accessible to design by generating quasi-equivalent and pseudosymmetric interfaces and ii) producing molecules of value both as basic research tools and as potential translational candidates by altering enzyme function. To facilitate evaluation of these designed proteins, Quinton develops biophysical assays and library-based or high-throughput methods for measuring function.

Dan Humphrys

The activity of biological membranes is determined largely by transmembrane proteins. Dan is working to develop general methods for functionalizing the group’s EPN platform by recruiting specific membrane proteins to EPN membranes. This fundamental capability will enable a wide variety of applications in delivery, diagnostics, and structural biology.

Mark Langowski

Mark is a graduate student in the Molecular and Cellular Biology program. He is interested in developing malaria vaccines and other epitope-based vaccines. His long term goal is working on developing methods for the design of nanoparticle vaccines that optimally bind B-cells.

Audrey Olshefsky

Audrey is a Bioengineering PhD student working in the King Lab and the Pun Lab. She is interested in targeted delivery of designed proteins with applications in immunotherapy. To that end, Audrey is developing new methods for in vivo and in vitro library selection based on synthetic protein nanocages.

Marti Tooley

Marti is a Molecular Engineering student in the King Lab and Baker Lab. She is interested in elucidating how to fine tune the immune system in generating long lasting responses to vaccine platforms. Marti aims to achieve this through designing new protein nanocages and testing immune modulators in a high throughput pipeline.

Erin Yang

Erin is a BPSD graduate student in the King Lab and Baker Lab. She is interested in improving the functional and structural complexity of protein nanoparticles. To that end, she is improving protein nanoparticle function by designing particles that can simultaneously target cellular receptors and react to environmental stimuli, such as pH, and addressing structural complexity by exploring the possible icosahedral architectures available with pseudosymmetric components.

John Wang

John is a student in the Molecular and Cellular Biology PhD program. With a background in chemical biology and biophysical chemistry, he looks to augment protein design methods by informing them with existing empirical results. These methods can then be applied to the development of novel protein technologies, from research platforms to potential therapeutics. John has a particular interest in the precision with which proteins are able to assemble, and seeks to understand the fundamental driving forces of protein folding and assembly through computation-guided experiments.

Dane Zambrano

Dane is a Biochemistry PhD student. She is interested in developing a platform of nanocages that can display patches of lipid membranes using her previous knowledge in nanodiscs. Her long term goal would be to be able to display de novo and native membrane proteins on the surface of nanocages for antigen display.

Research Scientists

Dan Ellis, PhD

Dan obtained his PhD in the group and is now a Research Scientist. His research involves various strategies for designing improved influenza vaccines with the ultimate goal of a universally-protective vaccine. One project involves co-display of full-length hemagglutinin (HA) trimers on designed two-component nanoparticles, which have shown potential to protect against diverse viruses across the influenza family tree. Other projects involve structure-based design of various influenza antigens using Rosetta, and studying how precise structural properties of nanoparticle vaccines correlate with the strength and specificities of immune responses. In his free time, he enjoys playing lacrosse and taming stray cats.

 

Neil Gerstenmaier

Neil works with Quinton to produce and characterize novel classes of self-assembling protein nanomaterials.

 

Isaac Sappington

Isaac’s projects focus on the dynamics of nucleic acid packaging using engineered, self-assembling proteins capable of in vitro assembly and nucleic acid binding. These nanomaterial variants have been optimized for these functions through a combination of several engineering methods, including computational modeling, directed evolution, and rational design. The research explores which features in proteins are necessary to exhibit high yields of nucleic acid encapsulation and protection from nucleic acid-degrading environments. These synthetic, virion-like nanomaterials may eventually be applied therapeutically to increase biological half-life and cellular uptake.

Adam Wargacki

Protein cages are a promising platform for display and delivery of therapeutic molecules. However, their biophysical properties must be mapped and optimized to enable predictability, uniformity, and stability throughout manufacturing and deployment. To this end, Adam is investigating the stoichiometry of cage assembly products, the stability of protein cages and their components, the dynamics and kinetics of assembly/disassembly, and the affinities of computationally designed nanomaterial interfaces. We have found that remarkably efficient assembly leads to protein nanomaterials exhibiting enhanced stability compared to their unassembled building blocks. These features present a promising profile for use as vaccine and drug delivery platforms, and may also hint that the emergence of such properties in designed nanomaterials is an intrinsic feature of higher-order protein complexes. Adam is an exceedingly private person, often hiding in his 1000-tree apple and pear orchard, a complex biological assembly he tends together with his wife and son.

Undergraduate Researchers

 

Gargi Kher

Gargi has worked on a number of projects in the King lab, including nanoparticle vaccine platforms for inducing mucosal immunity, optimizing the in vitro assembly of several designed nanoparticle components, and analyzing library sequencing data related to nanoparticle evolution studies.

Lab Alumni

Postdocs 

2020–2021 Andrew Borst, PhD (EM Core Lead, IPD Core Laboratories)
2015–2021 Karla-Luise Herpoldt, PhD (Scientist, SeaGen
2018–2020 Thad Huber, PhD (Founder, Colorado Biofactory)
2016–2019 Carl Walkey, PhD (VP, Corporate Development at Neoleukin Therapeutics)

 

Graduate Students

2016–2021 Dan Ellis, PhD (Research Scientist, King Lab)

 

Research Scientists

2014–2020 Cassie Ogohara (Research Scientist, IPD Core Laboratories)
2014–2019 Brooke Fiala (Nanoparticle Core Lead, IPD Core Laboratories)
2015–2018 Kate DaPron (Graduate Program, CU Boulder, CO)
2015–2017 Julia Burrows (MSTP program, UCLA, Los Angeles, CA) 
2014–2016  Dan Ellis (Graduate Program in MCB, University of Washington, Seattle, WA)
2014–2015  Sueyeon Yi (MSTP program, University of Wisconsin, Madison, WI) 

Undergraduate Researchers

2016–2020 Rose Fields (Research Scientist, University of Washington)
2017–2020  Chelsea Shu (Undergraduate Research Assistant, University of Washington)
2018–2020  Margaux Randolph (Undergraduate Research Assistant, University of Washington)
2019–2019  Conlan Olson (summer student) 
2018–2019  Annamika Kannan (transferred to University of Michigan) 
2018–2018  Ariel Stiber (Caltech SURF program) 
2016–2018  Phong Ong 
2014–2018  Hyung Chan (Brian) Kim (Medical School, Washington State University) 
2014–2015 Rachel Park (Ph.D. program in Biochemistry, Stanford University)