The genetic architecture of protein interaction affinity and specificity.
Journal
Nature communications
ISSN: 2041-1723
Titre abrégé: Nat Commun
Pays: England
ID NLM: 101528555
Informations de publication
Date de publication:
14 Oct 2024
14 Oct 2024
Historique:
received:
17
10
2023
accepted:
04
10
2024
medline:
15
10
2024
pubmed:
15
10
2024
entrez:
14
10
2024
Statut:
epublish
Résumé
The encoding and evolution of specificity and affinity in protein-protein interactions is poorly understood. Here, we address this question by quantifying how all mutations in one protein, JUN, alter binding to all other members of a protein family, the 54 human basic leucine zipper transcription factors. We fit a global thermodynamic model to the data to reveal that most affinity changing mutations equally affect JUN's affinity to all its interaction partners. Mutations that alter binding specificity are relatively rare but distributed throughout the interaction interface. Specificity is determined both by features that promote on-target interactions and by those that prevent off-target interactions. Approximately half of the specificity-defining residues in JUN contribute both to promoting on-target binding and preventing off-target binding. Nearly all specificity-altering mutations in the interaction interface are pleiotropic, also altering affinity to all partners. In contrast, mutations outside the interface can tune global affinity without affecting specificity. Our results reveal the distributed encoding of specificity and affinity in an interaction interface and how coiled-coils provide an elegant solution to the challenge of optimizing both specificity and affinity in a large protein family.
Identifiants
pubmed: 39402041
doi: 10.1038/s41467-024-53195-4
pii: 10.1038/s41467-024-53195-4
doi:
Substances chimiques
Basic-Leucine Zipper Transcription Factors
0
Proto-Oncogene Proteins c-jun
0
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
8868Subventions
Organisme : Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (Swiss National Science Foundation)
ID : 197593
Organisme : EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)
ID : 883742
Informations de copyright
© 2024. The Author(s).
Références
Crick, F. H. C. The packing of α-helices: simple coiled-coils. Acta Crystallogr. 6, 689–697 (1953).
doi: 10.1107/S0365110X53001964
O’Neil, K. T. & DeGrado, W. F. A thermodynamic scale for the helix-forming tendencies of the commonly occurring amino acids. Science 250, 646–651 (1990).
pubmed: 2237415
doi: 10.1126/science.2237415
O’Shea, E. K., Rutkowski, R. & Kim, P. S. Evidence that the leucine zipper is a coiled coil. Science 243, 538–542 (1989).
pubmed: 2911757
doi: 10.1126/science.2911757
Landschulz, W. H., Johnson, P. F. & McKnight, S. L. The leucine zipper: a hypothetical structure common to a new class of DNA binding proteins. Science 240, 1759–1764 (1988).
pubmed: 3289117
doi: 10.1126/science.3289117
Thompson, K. S., Freire, E. & Vinson, C. R. Thermodynamic characterization of the structural stability of the coiled-coil region of the bZIP transcription factor GCN4. Biochemistry 32, 5491–5496 (1993).
pubmed: 8504069
doi: 10.1021/bi00072a001
Vinson, C. R., Hai, T. & Boyd, S. M. Dimerization specificity of the leucine zipper-containing bZIP motif on DNA binding: prediction and rational design. Genes Dev. 7, 1047–1058 (1993).
pubmed: 8504929
doi: 10.1101/gad.7.6.1047
Newman, J. R. S. & Keating, A. E. Comprehensive identification of human bZIP interactions with coiled-coil arrays. Science 300, 2097–2101 (2003).
pubmed: 12805554
doi: 10.1126/science.1084648
Hai, T. & Curran, T. Cross-family dimerization of transcription factors Fos/Jun and ATF/CREB alters DNA binding specificity. PNAS 88, 3720–3724 (1991).
pubmed: 1827203
pmcid: 51524
doi: 10.1073/pnas.88.9.3720
O’Shea, E. K., Klemm, J. D., Kim, P. S. & Alber, T. X-ray structure of the GCN4 leucine zipper, a two-stranded, parallel coiled coil. Science 254, 539–544 (1991).
pubmed: 1948029
doi: 10.1126/science.1948029
O’Shea, E. K., Rutkowski, R. & Kim, P. S. Mechanism of specificity in the Fos-Jun oncoprotein heterodimer. Cell 68, 699–708 (1992).
pubmed: 1739975
doi: 10.1016/0092-8674(92)90145-3
O’Shea, E. K., Lumb, K. J. & Kim, P. S. Peptide ‘Velcro’: design of a heterodimeric coiled coil. Curr. Biol. 3, 658–667 (1993).
pubmed: 15335856
doi: 10.1016/0960-9822(93)90063-T
Moitra, J., Szilák, L., Krylov, D. & Vinson, C. Leucine is the most stabilizing aliphatic amino acid in the d position of a dimeric leucine zipper coiled coil. Biochemistry 36, 12567–12573 (1997).
pubmed: 9376362
doi: 10.1021/bi971424h
Vinson, C. et al. Classification of human B-ZIP proteins based on dimerization properties. Mol. Cell. Biol. 22, 6321–6335 (2002).
pubmed: 12192032
pmcid: 135624
doi: 10.1128/MCB.22.18.6321-6335.2002
Oakley, M. G. & Kim, P. S. A buried polar interaction can direct the relative orientation of helices in a coiled coil. Biochemistry 37, 12603–12610 (1998).
pubmed: 9730833
doi: 10.1021/bi981269m
Acharya, A., Ruvinov, S. B., Gal, J., Moll, J. R. & Vinson, C. A heterodimerizing leucine zipper coiled coil system for examining the specificity of a position interactions: amino acids I, V, L, N, A, and K. Biochemistry 41, 14122–14131 (2002).
pubmed: 12450375
doi: 10.1021/bi020486r
Horovitz, A., Serrano, L., Avron, B., Bycroft, M. & Fersht, A. R. Strength and co-operativity of contributions of surface salt bridges to protein stability. J. Mol. Biol. 216, 1031–1044 (1990).
pubmed: 2266554
doi: 10.1016/S0022-2836(99)80018-7
Serrano, L., Horovitz, A., Avron, B., Bycroft, M. & Fersht, A. R. Estimating the contribution of engineered surface electrostatic interactions to protein stability by using double-mutant cycles. Biochemistry 29, 9343–9352 (1990).
pubmed: 2248951
doi: 10.1021/bi00492a006
Arndt, K. M. et al. A heterodimeric coiled-coil peptide pair selected in vivo from a designed library-versus-library ensemble. J. Mol. Biol. 295, 627–639 (2000).
pubmed: 10623552
doi: 10.1006/jmbi.1999.3352
Arndt, K. M., Pelletier, J. N., Müller, K. M., Plückthun, A. & Alber, T. Comparison of in vivo selection and rational design of heterodimeric coiled coils. Structure 10, 1235–1248 (2002).
pubmed: 12220495
doi: 10.1016/S0969-2126(02)00838-9
Kaplan, J. B., Reinke, A. W. & Keating, A. E. Increasing the affinity of selective bZIPbinding peptides through surface residue redesign. Protein Sci. 23, 940–953 (2014).
pubmed: 24729132
pmcid: 4088978
doi: 10.1002/pro.2477
Dahiyat, B. I., Gordon, D. B. & Mayo, S. L. Automated design of the surface positions of protein helices. Protein Sci. 6, 1333–1337 (1997).
pubmed: 9194194
pmcid: 2143725
doi: 10.1002/pro.5560060622
Drobnak, I., Gradišar, H., Ljubetič, A., Merljak, E. & Jerala, R. Modulation of coiled-coil dimer stability through surface residues while preserving pairing specificity. J. Am. Chem. Soc. 139, 8229–8236 (2017).
pubmed: 28553984
doi: 10.1021/jacs.7b01690
Mason, J. M., Schmitz, M. A., Müller, K. M. & Arndt, K. M. Semirational design of Jun-Fos coiled coils with increased affinity: Universal implications for leucine zipper prediction and design. PNAS 103, 8989–8994 (2006).
pubmed: 16754880
pmcid: 1482553
doi: 10.1073/pnas.0509880103
Mason, J. M., Müller, K. M. & Arndt, K. M. Positive aspects of negative design: simultaneous selection of specificity and interaction stability †. Biochemistry 46, 4804–4814 (2007).
pubmed: 17402748
doi: 10.1021/bi602506p
Grigoryan, G. & Keating, A. E. Structure-based prediction of bZIP partnering specificity. J. Mol. Biol. 355, 1125–1142 (2006).
pubmed: 16359704
doi: 10.1016/j.jmb.2005.11.036
Potapov, V., Kaplan, J. B. & Keating, A. E. Data-driven prediction and design of bZIP coiled-coil interactions. PLoS Comput. Biol. 11, 1–28 (2015).
doi: 10.1371/journal.pcbi.1004046
Fong, J. H., Keating, A. E. & Singh, M. Predicting specificity in bZIP coiled-coil protein interactions. Genome Biol. 5, R11 (2004).
pubmed: 14759261
pmcid: 395749
doi: 10.1186/gb-2004-5-2-r11
Grigoryan, G., Reinke, A. W. & Keating, A. E. Design of protein-interaction specificity affords selective bZIP- binding peptides. Nature 458, 859–864 (2009).
pubmed: 19370028
pmcid: 2748673
doi: 10.1038/nature07885
Reinke, A. W., Baek, J., Ashenberg, O. & Keating Networks of bZIP protein-protein interactions diversified over a billion years of evolution. Science 340, 730–735 (2013).
pubmed: 23661758
pmcid: 4115154
doi: 10.1126/science.1233465
Pelletier, J. N., Campbell-Valois, F.-X. & Michnick, S. W. Oligomerization domain-directed reassembly of active dihydrofolate reductase from rationally designed fragments. PNAS 95, 12141–12146 (1998).
pubmed: 9770453
pmcid: 22798
doi: 10.1073/pnas.95.21.12141
Freschi, L., Torres-Quiroz, F., Dubé, A. K. & Landry, C. R. qPCA: a scalable assay to measure the perturbation of protein-protein interactions in living cells. Mol. Biosyst. 9, 36–43 (2013).
pubmed: 23099892
doi: 10.1039/C2MB25265A
Levy, E. D., Kowarzyk, J. & Michnick, S. W. High-resolution mapping of protein concentration reveals principles of proteome architecture and adaptation. Cell Rep. 7, 1333–1340 (2014).
pubmed: 24813894
doi: 10.1016/j.celrep.2014.04.009
Diss, G. & Lehner, B. The genetic landscape of a physical interaction. eLife 7, 1–31 (2018).
doi: 10.7554/eLife.32472
Faure, A. J. et al. Mapping the energetic and allosteric landscapes of protein binding domains. Nature 604, 175–183 (2022).
pubmed: 35388192
doi: 10.1038/s41586-022-04586-4
Weng, C., Faure, A. J. & Lehner, B. The energetic and allosteric landscape for KRAS inhibition. bioRxiv 2022.12.06.519122 https://doi.org/10.1101/2022.12.06.519122 (2022).
Faure, A. J., Schmiedel, J. M., Baeza-Centurion, P. & Lehner, B. DiMSum: an error model and pipeline for analyzing deep mutational scanning data and diagnosing common experimental pathologies. Genome Biol. 21, 1–23 (2020).
doi: 10.1186/s13059-020-02091-3
Oughtred, R. et al. The BIOGRID database: a comprehensive biomedical resource of curated protein, genetic, and chemical interactions. Protein Sci. 30, 187–200 (2021).
pubmed: 33070389
doi: 10.1002/pro.3978
Tebo, A. G. & Gautier, A. A split fluorescent reporter with rapid and reversible complementation. Nat. Commun. 10, 2822 (2019).
pubmed: 31249300
pmcid: 6597557
doi: 10.1038/s41467-019-10855-0
Aronheim, A., Zandi, E., Hennemann, H., Elledge, S. J. & Karin, M. Isolation of an AP-1 repressor by a novel method for detecting protein-protein interactions. Mol. Cell. Biol. 17, 3094–3102 (1997).
pubmed: 9154808
pmcid: 232162
doi: 10.1128/MCB.17.6.3094
Chen, S. et al. The emerging role of XBP1 in cancer. Biomed. Pharmacother. Biomed. Pharmacother. 127, 110069 (2020).
pubmed: 32294597
doi: 10.1016/j.biopha.2020.110069
Patel, L. R., Curran, T. & Kerppola, T. K. Energy transfer analysis of Fos-Jun dimerization and DNA binding. Proc. Natl. Acad. Sci. USA 91, 7360–7364 (1994).
pubmed: 8041795
pmcid: 44399
doi: 10.1073/pnas.91.15.7360
Bentley, E. P., Scholl, D., Wright, P. E. & Deniz, A. A. Coupling of binding and differential subdomain folding of the intrinsically disordered transcription factor CREB. FEBS Lett. 597, 917–932 (2023).
pubmed: 36480418
doi: 10.1002/1873-3468.14554
Deng, T. & Karin, M. JunB differs from c-Jun in its DNA-binding and dimerization domains, and represses c-Jun by formation of inactive heterodimers. Genes Dev. 7, 479–490 (1993).
pubmed: 8383624
doi: 10.1101/gad.7.3.479
Halazonetis, T. D., Georgopoulos, K., Greenberg, M. E. & Leder, P. c-Jun dimerizes with itself and with c-Fos, forming complexes of different DNA binding affinities. Cell 55, 917–924 (1988).
pubmed: 3142692
doi: 10.1016/0092-8674(88)90147-X
Kawashima, S. et al. AAindex: amino acid index database, progress report 2008. Nucleic Acids Res. 36, D202–D205 (2008).
pubmed: 17998252
doi: 10.1093/nar/gkm998
Qian, N. & Sejnowski, T. J. Predicting the secondary structure of globular proteins using neural network models. J. Mol. Biol. 202, 865–884 (1988).
pubmed: 3172241
doi: 10.1016/0022-2836(88)90564-5
Roseman, M. A. Hydrophobicity of the peptide C=O…H-N hydrogen-bonded group. J. Mol. Biol. 201, 621–623 (1988).
pubmed: 3418713
doi: 10.1016/0022-2836(88)90642-0
Hutchens, J. O. in Handbook of Biochemistry B60–B61 (Chemical Rubber Co., 1970).
DeGrado, W. F. & Lear, J. D. Induction of peptide conformation at apolar water interfaces. 1. A study with model peptides of defined hydrophobic periodicity. J. Am. Chem. Soc. 107, 7684–7689 (1985).
doi: 10.1021/ja00311a076
Bastolla, U., Porto, M., Roman, H. E. & Vendruscolo, M. Principal eigenvector of contact matrices and hydrophobicity profiles in proteins. Proteins 58, 22–30 (2005).
pubmed: 15523667
doi: 10.1002/prot.20240
Bigelow, C. C. On the average hydrophobicity of proteins and the relation between it and protein structure. J. Theor. Biol. 16, 187–211 (1967).
pubmed: 6048539
doi: 10.1016/0022-5193(67)90004-5
Nakashima, H. & Nishikawa, K. The amino acid composition is different between the cytoplasmic and extracellular sides in membrane proteins. FEBS Lett. 303, 141–146 (1992).
pubmed: 1607012
doi: 10.1016/0014-5793(92)80506-C
Meirovitch, H., Rackovsky, S. & Scheraga, H. A. Empirical studies of hydrophobicity. 1. effect of protein size on the hydrophobic behavior of amino acids. Macromolecules 13, 1398–1405 (1980).
doi: 10.1021/ma60078a013
Ponnuswamy, P. K., Prabhakaran, M. & Manavalan, P. Hydrophobic packing and spatial arrangement of amino acid residues in globular proteins. Biochim. Biophys. Acta 623, 301–316 (1980).
pubmed: 7397216
doi: 10.1016/0005-2795(80)90258-5
Podgornaia, A. I. & Laub, M. T. Determinants of specificity in two-component signal transduction. Curr. Opin. Microbiol. 16, 156–162 (2013).
pubmed: 23352354
doi: 10.1016/j.mib.2013.01.004
Schreiber, G. & Keating, A. E. Protein binding specificity versus promiscuity. Curr. Opin. Struct. Biol. 21, 50–61 (2011).
pubmed: 21071205
doi: 10.1016/j.sbi.2010.10.002
Lite, T. L. V. et al. Uncovering the basis of protein-protein interaction specificity with a combinatorially complete library. eLife 9, 1–57 (2020).
doi: 10.7554/eLife.60924
McClune, C. J., Alvarez-Buylla, A., Voigt, C. A. & Laub, M. T. Engineering orthogonal signalling pathways reveals the sparse occupancy of sequence space. Nature 574, 702–706 (2019).
pubmed: 31645757
pmcid: 6858568
doi: 10.1038/s41586-019-1639-8
Aakre, C. D. et al. Evolving new protein-protein interaction specificity through promiscuous intermediates. Cell 163, 594–606 (2015).
pubmed: 26478181
pmcid: 4623991
doi: 10.1016/j.cell.2015.09.055
Ghosea, D. A., Przydziala, K. E., Mahoneya, E. M., Keating, A. E. & Laub, M. T. Marginal specificity in protein interactions constrains evolution of a paralogous family. PNAS 120, 1–10 (2023).
Sikorski, R. S. & Hieter, P. A system of shuttle vectors and yeast host strains designed for efficient manipulation of DNA in Saccharomyces cerevisiae. Genetics 122, 19–27 (1989).
pubmed: 2659436
pmcid: 1203683
doi: 10.1093/genetics/122.1.19
Martin, M. CUTADAPT removes adapter sequences from high-throughput sequencing reads. EMBnet. J. 17, 10–12 (2011).
doi: 10.14806/ej.17.1.200
Zhang, J., Kobert, K., Flouri, T. & Stamatakis, A. PEAR: a fast and accurate Illumina Paired-End reAd mergeR. Bioinformatics 30, 614–620 (2014).
pubmed: 24142950
doi: 10.1093/bioinformatics/btt593
Jumper, J. et al. Highly accurate protein structure prediction with AlphaFold. Nature 596, 583–589 (2021).
pubmed: 34265844
pmcid: 8371605
doi: 10.1038/s41586-021-03819-2
Evans, R. et al. Protein complex prediction with AlphaFold-Multimer. bioRxiv, (2022).
Kempf, G. & Cavadini, S. GUIFold - a graphical user interface for local AlphaFold2. bioRxiv https://doi.org/10.1101/2023.01.19.521406 (2023).
Diss, G. Code used for the analysis of data presented in this manuscript. https://doi.org/10.5281/zenodo.13324992 (2024).
Glover, J. N. & Harrison, S. C. Crystal structure of the heterodimeric bZIP transcription factor c-Fos-c-Jun bound to DNA. Nature 373, 257–261 (1995).
pubmed: 7816143
doi: 10.1038/373257a0