Engineered biological systems, ranging from molecules with new functions to entire organisms, have tremendous practical importance; they can also fundamentally change how we ask questions about the biological principles of function and fitness. Our research aims to invent approaches to engineer new molecules that operate as predicted in biological contexts, and to utilize prediction and engineering to address fundamental questions on the relationship of molecular characteristics, cellular function and organismal fitness. To address the many current challenges in the field – from developing more predictive computational design methods to determining the requirements for function in cells – we combine concepts from computer science, physics, chemistry, mathematics, engineering and biology.
Latest Preprints
- Engineered ACE2 receptor traps potently neutralize SARS-CoV-2. Anum Glasgow, Jeff Glasgow, Daniel Limonta, Paige Solomon, Irene Lui, Yang Zhang, Matthew A. Nix, Nicholas J. Rettko, Shion A. Lim, Shoshana Zha, Rachel Yamin, Kevin Kao, Oren S. Rosenberg, Jeffrey V. Ravetch, Arun P. Wiita, Kevin K. Leung, Xin X. Zhou, Tom C. Hobman, Tanja Kortemme, James A. Wells doi: https://doi.org/10.1101/2020.07.31.231746
- Biophysical basis of cellular multi-specificity encoded in a model molecular switch. Tina Perica, Christopher J. P. Mathy, Jiewei Xu, Gwendolyn M. Jang, Yang Zhang, Robyn Kaake, Noah Ollikainen, Hannes Braberg, Danielle L. Swaney, Mark J. S. Kelly, Nevan J. Krogan, Tanja Kortemme doi: https://doi.org/10.1101/2020.01.04.893909
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Selected Publications
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Pan X, Thompson M, Zhang Y, Liu L, Fraser JS, Kelly MJS & Kortemme T (2020). Expanding the space of protein geometries by computational design of de novo fold families. Science 369(6507):1132-1136.
Thompson S, Zhang Y, Ingle C, Reynolds KA, Kortemme T. Altered expression of a quality control protease in E. coli reshapes the in vivo mutational landscape of a model enzyme. Elife. 2020 Jul 23;9:e53476.
Glasgow AA, Huang YM, Mandell DJ, Thompson M, Ritterson R, Loshbaugh AL, Pellegrino J, Krivacic C, Pache RA, Barlow KA, Ollikainen N, Jeon D, Kelly MJS, Fraser JS, Kortemme T. (2019) Computational design of a modular protein sense-response system. Science. 22;366(6468):1024-1028.
Kundert K, Lucas JE, Watters KE, Fellmann C, Ng AH, Heineike BM, Fitzsimmons CM, Oakes BL, Qu J, Prasad N, Rosenberg OS, Savage DF, El-Samad H, Doudna JA, Kortemme T. (2019) Controlling CRISPR-Cas9 with ligand-activated and ligand-deactivated sgRNAs. Nat Commun. 9;10(1):2127.
Hoersch D, Roh SH, Chiu W, Kortemme T. (2013) Reprogramming an ATP-driven protein machine into a light-gated nanocage. Nat Nanotechnol. 8(12):928-32.
Eames M, Kortemme, T. (2012). Cost-benefit tradeoffs in engineered lac operons. Science 336(6083): 911-915.
Kapp GT, Liu S, Stein A, Wong DT, Reményi A, Yeh BJ, Fraser JS, Taunton J, Lim WA, Kortemme T. (2012). Control of protein signaling using a computationally designed GTPase/GEF orthogonal pair. Proc Natl Acad Sci U S A. 109(14): 5277-82.
Mandell DJ, Coutsias EA, Kortemme T. (2009). Sub-angstrom accuracy in protein loop reconstruction by robotics-inspired conformational sampling. Nat Methods 6:551–552.
Smith CA, Kortemme T. (2008). Backrub-like backbone simulation recapitulates natural protein conformational variability and improves mutant side-chain prediction. J Mol Biol. 380(4):742-56.
Thompson S, Zhang Y, Ingle C, Reynolds KA, Kortemme T. Altered expression of a quality control protease in E. coli reshapes the in vivo mutational landscape of a model enzyme. Elife. 2020 Jul 23;9:e53476.
Glasgow AA, Huang YM, Mandell DJ, Thompson M, Ritterson R, Loshbaugh AL, Pellegrino J, Krivacic C, Pache RA, Barlow KA, Ollikainen N, Jeon D, Kelly MJS, Fraser JS, Kortemme T. (2019) Computational design of a modular protein sense-response system. Science. 22;366(6468):1024-1028.
Kundert K, Lucas JE, Watters KE, Fellmann C, Ng AH, Heineike BM, Fitzsimmons CM, Oakes BL, Qu J, Prasad N, Rosenberg OS, Savage DF, El-Samad H, Doudna JA, Kortemme T. (2019) Controlling CRISPR-Cas9 with ligand-activated and ligand-deactivated sgRNAs. Nat Commun. 9;10(1):2127.
Hoersch D, Roh SH, Chiu W, Kortemme T. (2013) Reprogramming an ATP-driven protein machine into a light-gated nanocage. Nat Nanotechnol. 8(12):928-32.
Eames M, Kortemme, T. (2012). Cost-benefit tradeoffs in engineered lac operons. Science 336(6083): 911-915.
Kapp GT, Liu S, Stein A, Wong DT, Reményi A, Yeh BJ, Fraser JS, Taunton J, Lim WA, Kortemme T. (2012). Control of protein signaling using a computationally designed GTPase/GEF orthogonal pair. Proc Natl Acad Sci U S A. 109(14): 5277-82.
Mandell DJ, Coutsias EA, Kortemme T. (2009). Sub-angstrom accuracy in protein loop reconstruction by robotics-inspired conformational sampling. Nat Methods 6:551–552.
Smith CA, Kortemme T. (2008). Backrub-like backbone simulation recapitulates natural protein conformational variability and improves mutant side-chain prediction. J Mol Biol. 380(4):742-56.
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Highlights from the Lab
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Samuel's QBI interview for the 2017 Dr. Herbert Landahl Mathematical Biophysics Student Excellence Award.
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Amanda's 90-second video, "A generalized strategy for engineering biological sense/response pairs," wins 3rd place in the 2014 Synberc Perfect Pitch Contest!
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Our biosensor project wins first prize in Gen9's inaugural G-Prize contest
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