Computational design of dynamic biosensors for emerging synthetic opioids

An automated protocol for the TREMD conformer generation protocol is available on GitHub https://github.com/ajfriedman22/SM_ConfGen. PyRosetta scripts for biosensor design by structural replacement are available at https://github.com/alisoncleonard/Structural-Replacement-Biosensor-Design. Scripts used to generate Supplementary Figs. 1 and 10 and to process raw deep sequencing data are available at https://github.com/WhiteheadGroup/Leonard_ComputationalDesign_Supplemental⁶⁹.

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Author notes

1. These authors contributed equally: Alison C. Leonard, Chase Lenert-Mondou, Rachel Chayer, Samuel Swift.

Authors and Affiliations

1. Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, CO, USA

   Alison C. Leonard, Rachel Chayer, Samuel Swift, Zachary T. Baumer, Ryan Delaney, Anika J. Friedman, Jordan Wells, Lindsey M. Whitmore, Michael R. Shirts & Timothy A. Whitehead

2. Department of Biochemistry and Molecular Biology, University of California, Riverside, CA, USA

   Chase Lenert-Mondou

3. Department of Bioengineering, University of California, Riverside, CA, USA

   Nicholas R. Robertson & Norman Seder

4. Department of Botany and Plant Sciences, University of California, Riverside, CA, USA

   Sean R. Cutler

5. Department of Chemical and Environmental Engineering, University of California, Riverside, CA, USA

   Ian Wheeldon

6. Center for Industrial Biotechnology, University of California, Riverside, CA, USA

   Ian Wheeldon

Contributions

Non co-1st author trainees are listed in alphabetical order. Conceptualization: A.C.L., C.L.M., N.R.R., I.W., and T.A.W. Methodology: A.C.L., C.L.M., R.C., S.S., R.D., A.J.F., M.R.S., I.W., and T.A.W. Investigation: A.C.L., C.L.M., R.C., S.S., Z.T.B., R.D., A.J.F., N.R.R., N.S., J.W., and L.M.W. Visualization: A.C.L., C.L.M., R.C., S.S., I.W., and A.W. Funding acquisition: A.C.L., Z.T.B., S.C., M.R.S., I.W., and T.A.W. Project administration: I.W. and T.A.W. Supervision: S.C., M.R.S., I.W., and T.A.W. Writing – original draft: A.C.L., C.L.M., R.C., S.S., I.W., and T.A.W. Writing – review & editing: S.C., M.R.S., I.W., and T.A.W.

Corresponding authors

Correspondence to Ian Wheeldon or Timothy A. Whitehead.

Competing interests

T.A.W., S.R.C., and I.W. have filed a provisional patent entitled REAGENTS AND SYSTEMS FOR GENERATING BIOSENSORS (US9738902B2; WO2011139798A2) covering some research in the present work. T.A.W. is a consultant for Inari Ag and serves on the scientific advisory board for Metaphore Biotechnologies and Alta Tech. S.R.C. and I.W. are cofounders of Living Sensors Inc., which has interests in sensing technologies. The remaining authors declare no competing interests.

Peer review information

Nature Communications thanks Christophe Stove, who co-reviewed with Marthe M. Vandeputte, and the other, anonymous, reviewer(s) for their contribution to the peer review of this work. A peer review file is available.

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