Publications of the Perica Group

Mathy, CJP., Mishra, P., Flynn, JM., Perica, T., Mavor, D., Bolon, DNA. & Kortemme, T. A complete allosteric map of a GTPase switch in its native cellular network. Cell Syst 14, 237-246.e7 (2023). PMID: 36801015.

Perica, T., Mathy, CJP., Xu, J., Jang, GΜ., Zhang, Y., Kaake, R., Ollikainen, N., Braberg, H., Swaney, DL., Lambright, DG., Kelly, MJS., Krogan, NJ. & Kortemme, T. Systems-level effects of allosteric perturbations to a model molecular switch. Nature 599, 152-157 (2021). PMID: 34646016.

Gordon, DE., Jang, GM., Bouhaddou, M., Xu, J., Obernier, K., White, KM., O'Meara, MJ., Rezelj, VV., Guo, JZ., Swaney, DL., Tummino, TA., Hüttenhain, R., Kaake, RM., Richards, AL., Tutuncuoglu, B., Foussard, H., Batra, J., Haas, K., Modak, M., Kim, M., Haas, P., Polacco, BJ., Braberg, H., Fabius, JM., Eckhardt, M., Soucheray, M., Bennett, MJ., Cakir, M., McGregor, MJ., Li, Q., Meyer, B., Roesch, F., Vallet, T., Mac Kain, A., Miorin, L., Moreno, E., Naing, ZZC., Zhou, Y., Peng, S., Shi, Y., Zhang, Z., Shen, W., Kirby, IT., Melnyk, JE., Chorba, JS., Lou, K., Dai, SA., Barrio-Hernandez, I., Memon, D., Hernandez-Armenta, C., Lyu, J., Mathy, CJP., Perica, T., Pilla, KB., Ganesan, SJ., Saltzberg, DJ., Rakesh, R., Liu, X., Rosenthal, SB., Calviello, L., Venkataramanan, S., Liboy-Lugo, J., Lin, Y., Huang, XP., Liu, Y., Wankowicz, SA., Bohn, M., Safari, M., Ugur, FS., Koh, C., Savar, NS., Tran, QD., Shengjuler, D., Fletcher, SJ., O'Neal, MC., Cai, Y., Chang, JCJ., Broadhurst, DJ., Klippsten, S., Sharp, PP., Wenzell, NA., Kuzuoglu-Ozturk, D., Wang, HY., Trenker, R., Young, JM., Cavero, DA., Hiatt, J., Roth, TL., Rathore, U., Subramanian, A., Noack, J., Hubert, M., Stroud, RM., Frankel, AD., Rosenberg, OS., Verba, KA., Agard, DA., Ott, M., Emerman, M., Jura, N., von Zastrow, M., Verdin, E., Ashworth, A., Schwartz, O., d'Enfert, C., Mukherjee, S., Jacobson, M., Malik, HS., Fujimori, DG., Ideker, T., Craik, CS., Floor, SN., Fraser, JS., Gross, JD., Sali, A., Roth, BL., Ruggero, D., Taunton, J., Kortemme, T., Beltrao, P., Vignuzzi, M., García-Sastre, A., Shokat, KM., Shoichet, BK. & Krogan, NJ. A SARS-CoV-2 protein interaction map reveals targets for drug repurposing. Nature 583, 459-468 (2020). PMID: 32353859.

Perica, T., Kondo, Y., Tiwari, SP., McLaughlin, SH., Kemplen, KR., Zhang, X., Steward, A., Reuter, N., Clarke, J. & Teichmann, SA. Evolution of oligomeric state through allosteric pathways that mimic ligand binding. Science 346, 1254346 (2014). PMID: 25525255.

Roller, M., Lucić, V., Nagy, I., Perica, T. & Vlahovicek, K. Environmental shaping of codon usage and functional adaptation across microbial communities. Nucleic Acids Res 41, 8842-52 (2013). PMID: 23921637.

Zhang, X., Perica, T. & Teichmann, SA. Evolution of protein structures and interactions from the perspective of residue contact networks. Curr Opin Struct Biol 23, 954-63 (2013). PMID: 23890840.

Marsh, JA., Hernández, H., Hall, Z., Ahnert, SE., Perica, T., Robinson, CV. & Teichmann, SA. Protein complexes are under evolutionary selection to assemble via ordered pathways. Cell 153, 461-70 (2013). PMID: 23582331.

Perica, T., Marsh, JA., Sousa, FL., Natan, E., Colwell, LJ., Ahnert, SE. & Teichmann, SA. The emergence of protein complexes: quaternary structure, dynamics and allostery. Colworth Medal Lecture. Biochem Soc Trans 40, 475-91 (2012). PMID: 22616857.

Perica, T., Chothia, C. & Teichmann, SA. Evolution of oligomeric state through geometric coupling of protein interfaces. Proc Natl Acad Sci U S A 109, 8127-32 (2012). PMID: 22566652.

Liberles, DA., Teichmann, SA., Bahar, I., Bastolla, U., Bloom, J., Bornberg-Bauer, E., Colwell, LJ., de Koning, AP., Dokholyan, NV., Echave, J., Elofsson, A., Gerloff, DL., Goldstein, RA., Grahnen, JA., Holder, MT., Lakner, C., Lartillot, N., Lovell, SC., Naylor, G., Perica, T., Pollock, DD., Pupko, T., Regan, L., Roger, A., Rubinstein, N., Shakhnovich, E., Sjölander, K., Sunyaev, S., Teufel, AI., Thorne, JL., Thornton, JW., Weinreich, DM. & Whelan, S. The interface of protein structure, protein biophysics, and molecular evolution. Protein Sci 21, 769-85 (2012). PMID: 22528593.

Perica, T. & Chothia, C. Ubiquitin--molecular mechanisms for recognition of different structures. Curr Opin Struct Biol 20, 367-76 (2010). PMID: 20456943.

Crosetto, N., Bienko, M., Hibbert, RG., Perica, T., Ambrogio, C., Kensche, T., Hofmann, K., Sixma, TK. & Dikic, I. Human Wrnip1 is localized in replication factories in a ubiquitin-binding zinc finger-dependent manner. J Biol Chem 283, 35173-85 (2008). PMID: 18842586.