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2. Macromolecular condensation buffers intracellular water potential

Author

Watson, Joseph L., Seinkmane, Estere, Styles, Christine T., Mihut, Andrei, Krüger, Lara K., McNally, Kerrie E., Planelles-Herrero, Vicente Jose, Dudek, Michal, McCall, Patrick M., Barbiero, Silvia, Vanden Oever, Michael, Peak-Chew, Sew Yeu, Porebski, Benjamin T., Zeng, Aiwei, Rzechorzek, Nina M., Wong, David C. S., Beale, Andrew D., Stangherlin, Alessandra, Riggi, Margot, Iwasa, Janet, Morf, Jörg, Miliotis, Christos, Guna, Alina, Inglis, Alison J., Brugués, Jan, Voorhees, Rebecca M., Chambers, Joseph E., Meng, Qing-Jun, O’Neill, John S., Edgar, Rachel S., and Derivery, Emmanuel

Published
2023
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3. Author Correction: Macromolecular condensation buffers intracellular water potential

Author

Watson, Joseph L., Seinkmane, Estere, Styles, Christine T., Mihut, Andrei, Krüger, Lara K., McNally, Kerrie E., Planelles-Herrero, Vicente Jose, Dudek, Michal, McCall, Patrick M., Barbiero, Silvia, Vanden Oever, Michael, Peak-Chew, Sew Yeu, Porebski, Benjamin T., Zeng, Aiwei, Rzechorzek, Nina M., Wong, David C. S., Beale, Andrew D., Stangherlin, Alessandra, Riggi, Margot, Iwasa, Janet, Morf, Jörg, Miliotis, Christos, Guna, Alina, Inglis, Alison J., Brugués, Jan, Voorhees, Rebecca M., Chambers, Joseph E., Meng, Qing-Jun, O’Neill, John S., Edgar, Rachel S., and Derivery, Emmanuel

Published
2024
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4. De novo design of modular peptide-binding proteins by superhelical matching

Author

Wu, Kejia, Bai, Hua, Chang, Ya-Ting, Redler, Rachel, McNally, Kerrie E., Sheffler, William, Brunette, T. J., Hicks, Derrick R., Morgan, Tomos E., Stevens, Tim J., Broerman, Adam, Goreshnik, Inna, DeWitt, Michelle, Chow, Cameron M., Shen, Yihang, Stewart, Lance, Derivery, Emmanuel, Silva, Daniel Adriano, Bhabha, Gira, Ekiert, Damian C., and Baker, David

Published
2023
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5. Structure of the endosomal Commander complex linked to Ritscher-Schinzel syndrome

Author

Healy, Michael D., McNally, Kerrie E., Butkovič, Rebeka, Chilton, Molly, Kato, Kohji, Sacharz, Joanna, McConville, Calum, Moody, Edmund R.R., Shaw, Shrestha, Planelles-Herrero, Vicente J., Yadav, Sathish K.N., Ross, Jennifer, Borucu, Ufuk, Palmer, Catherine S., Chen, Kai-En, Croll, Tristan I., Hall, Ryan J., Caruana, Nikeisha J., Ghai, Rajesh, Nguyen, Thi H.D., Heesom, Kate J., Saitoh, Shinji, Berger, Imre, Schaffitzel, Christiane, Williams, Tom A., Stroud, David A., Derivery, Emmanuel, Collins, Brett M., and Cullen, Peter J.

Published
2023
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6. Structure of the endosomal Commander complex mutated in Ritscher-Schinzel syndrome: combining crystallography, cryo-EM and AlphaFold2

Author

Healy, Michael D., primary, McNally, Kerrie E., additional, Butkovic, Rebeka, additional, Chilton, Molly, additional, Kato, Kohji, additional, Sacharz, Joanna, additional, McConville, Calum, additional, Moody, Edmund R. R., additional, Shaw, Shrestha, additional, Planelles-Herrero, Vicente J., additional, and Sathish, K. N., additional

Published
2023
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8. Structure of the Commander endosomal trafficking complex linked to X-linked intellectual disability/Ritscher-Schinzel syndrome

Author

Healy, Michael D., primary, McNally, Kerrie E., additional, Butkovic, Rebeka, additional, Chilton, Molly, additional, Kato, Kohji, additional, Sacharz, Joanna, additional, McConville, Calum, additional, Moody, Edmund R.R., additional, Shaw, Shrestha, additional, Planelles-Herrero, Vicente J., additional, Yadav, Sathish K.N., additional, Ross, Jennifer, additional, Borucu, Ufuk, additional, Palmer, Catherine S., additional, Chen, Kai-En, additional, Croll, Tristan I., additional, Hall, Ryan J., additional, Caruana, Nikeisha J., additional, Ghai, Rajesh, additional, Nguyen, Thi H.D., additional, Heesom, Kate J., additional, Saitoh, Shinji, additional, Berger, Imre, additional, Schaffitzel, Christiane, additional, Williams, Tom A., additional, Stroud, David A., additional, Derivery, Emmanuel, additional, Collins, Brett M., additional, and Cullen, Peter J., additional

Published
2023
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9. Proteomic identification and structural basis for the interaction between sorting nexin SNX17 and PDLIM family proteins

Author

Healy, Michael D., primary, Sacharz, Joanna, additional, McNally, Kerrie E., additional, McConville, Calum, additional, Tillu, Vikas A., additional, Hall, Ryan J., additional, Chilton, Molly, additional, Cullen, Peter J., additional, Mobli, Mehdi, additional, Ghai, Rajesh, additional, Stroud, David A., additional, and Collins, Brett M., additional

Published
2022
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10. De novodesign of modular peptide binding proteins by superhelical matching

Author

Wu, Kejia, primary, Bai, Hua, additional, Chang, Ya-Ting, additional, Redler, Rachel, additional, McNally, Kerrie E., additional, Sheffler, William, additional, Brunette, TJ, additional, Hicks, Derrick R., additional, Morgan, Tomos E, additional, Stevens, Tim J, additional, Broerman, Adam, additional, Goreshnik, Inna, additional, DeWitt, Michelle, additional, Chow, Cameron M., additional, Shen, Yihang, additional, Stewart, Lance, additional, Derivery, Emmanuel, additional, Silva, Daniel Adriano, additional, Bhabha, Gira, additional, Ekiert, Damian, additional, and Baker, David, additional

Published
2022
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11. Proteomic identification and structural basis for the interaction between sorting nexin SNX17 and PDLIM family proteins

Author

Healy, Michael D., primary, Sacharz, Joanna, additional, McNally, Kerrie E., additional, McConville, Calum, additional, Tillu, Vikas A., additional, Hall, Ryan J., additional, Chilton, Molly, additional, Cullen, Peter J., additional, Mobli, Mehdi, additional, Ghai, Rajesh, additional, Stroud, David A., additional, and Collins, Brett M., additional

Published
2021
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13. Retriever is a multiprotein complex for retromer-independent endosomal cargo recycling

Author

McNally, Kerrie E., primary, Faulkner, Rebecca, additional, Steinberg, Florian, additional, Gallon, Matthew, additional, Ghai, Rajesh, additional, Pim, David, additional, Langton, Paul, additional, Pearson, Neil, additional, Danson, Chris M., additional, Nägele, Heike, additional, Morris, Lindsey L., additional, Singla, Amika, additional, Overlee, Brittany L., additional, Heesom, Kate J., additional, Sessions, Richard, additional, Banks, Lawrence, additional, Collins, Brett M., additional, Berger, Imre, additional, Billadeau, Daniel D., additional, Burstein, Ezra, additional, and Cullen, Peter J., additional

Published
2017
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14. PKCθ links proximal T cell and Notch signaling through localized regulation of the actin cytoskeleton

Author

Britton, Graham J, primary, Ambler, Rachel, additional, Clark, Danielle J, additional, Hill, Elaine V, additional, Tunbridge, Helen M, additional, McNally, Kerrie E, additional, Burton, Bronwen R, additional, Butterweck, Philomena, additional, Sabatos-Peyton, Catherine, additional, Hampton-O’Neil, Lea A, additional, Verkade, Paul, additional, Wülfing, Christoph, additional, and Wraith, David Cameron, additional

Published
2017
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15. Author response: PKCθ links proximal T cell and Notch signaling through localized regulation of the actin cytoskeleton

Author

Britton, Graham J, primary, Ambler, Rachel, additional, Clark, Danielle J, additional, Hill, Elaine V, additional, Tunbridge, Helen M, additional, McNally, Kerrie E, additional, Burton, Bronwen R, additional, Butterweck, Philomena, additional, Sabatos-Peyton, Catherine, additional, Hampton-O’Neil, Lea A, additional, Verkade, Paul, additional, Wülfing, Christoph, additional, and Wraith, David Cameron, additional

Published
2016
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16. De novo design of modular peptide-binding proteins by superhelical matching

Author

Kejia Wu, Hua Bai, Ya-Ting Chang, Rachel Redler, Kerrie E. McNally, William Sheffler, T. J. Brunette, Derrick R. Hicks, Tomos E. Morgan, Tim J. Stevens, Adam Broerman, Inna Goreshnik, Michelle DeWitt, Cameron M. Chow, Yihang Shen, Lance Stewart, Emmanuel Derivery, Daniel Adriano Silva, Gira Bhabha, Damian C. Ekiert, David Baker, Bai, Hua [0000-0002-0448-4052], Chang, Ya-Ting [0000-0003-2580-4622], McNally, Kerrie E [0000-0003-2376-3003], Brunette, TJ [0000-0003-0748-8224], Hicks, Derrick R [0000-0003-2950-1848], Broerman, Adam [0000-0002-6878-1769], Stewart, Lance [0000-0003-4264-5125], Derivery, Emmanuel [0000-0003-3927-5944], Silva, Daniel Adriano [0000-0002-3195-9009], Bhabha, Gira [0000-0003-0624-6178], Ekiert, Damian C [0000-0002-2570-0404], Baker, David [0000-0001-7896-6217], and Apollo - University of Cambridge Repository

Subjects
Models, Molecular, Protein Folding, Multidisciplinary, Protein Conformation, Proteins, Hydrogen Bonding, Amino Acid Sequence, Peptides, Protein Engineering, Protein Binding
Abstract

General approaches for designing sequence-specific peptide-binding proteins would have wide utility in proteomics and synthetic biology. However, designing peptide-binding proteins is challenging, as most peptides do not have defined structures in isolation, and hydrogen bonds must be made to the buried polar groups in the peptide backbone1–3. Here, inspired by natural and re-engineered protein–peptide systems4–11, we set out to design proteins made out of repeating units that bind peptides with repeating sequences, with a one-to-one correspondence between the repeat units of the protein and those of the peptide. We use geometric hashing to identify protein backbones and peptide-docking arrangements that are compatible with bidentate hydrogen bonds between the side chains of the protein and the peptide backbone12. The remainder of the protein sequence is then optimized for folding and peptide binding. We design repeat proteins to bind to six different tripeptide-repeat sequences in polyproline II conformations. The proteins are hyperstable and bind to four to six tandem repeats of their tripeptide targets with nanomolar to picomolar affinities in vitro and in living cells. Crystal structures reveal repeating interactions between protein and peptide interactions as designed, including ladders of hydrogen bonds from protein side chains to peptide backbones. By redesigning the binding interfaces of individual repeat units, specificity can be achieved for non-repeating peptide sequences and for disordered regions of native proteins.

Published
2023

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