CoChat
Sign Up
Cited by 22Protein Structure and DynamicsEvolution and Genetic DynamicsRNA and protein synthesis mechanisms

The DOI matches its Crossref record; 6 of the 6 references it cites were found in a registry or an index.

The genetic architecture of protein interaction affinity and specificity

Open access
Bendel, Alexandra M., Faure, Andre J., Klein, Dominique, Shimada, Kenji, Lyautey, Romane, Schiffelholz, Nicole, Kempf, Georg, Cavadini, Simone, Lehner, Ben, Diss, Guillaume·2024·Nature Communications
DOI 10.1038/s41467-024-53195-4PMC PMC11479274

Published version of a preprint

Open this paper in CoChat — free accountOpen PDF

Abstract

Abstract Proteins function in crowded cellular environments in which they must bind to specific target proteins but also avoid binding to many other off-target proteins. In large protein families this task is particularly challenging because many off-target proteins have very similar structures. How this specificity of physical protein-protein interactions in cellular networks is encoded and evolves is not very well understood. Here we address the question of specificity-encoding by comprehensively quantifying the effects of all mutations in one protein, JUN, on its binding to all other members of a protein family, the 54 human basic leucine zipper transcription factors. Fitting a global thermodynamic model to the data reveals that most affinity changing mutations equally affect JUN’s propensity to bind to all its interaction partners. Mutations that alter the specificity of binding are much rarer. These specificity-altering mutations are, however, distributed throughout the JUN interaction interface. JUN’s interaction specificity is encoded by both positive determinants that promote on-target interactions and negative determinants that prevent off-target interactions. Indeed, about half of the specificity-defining residues in JUN have dual functions and both promote on-target binding and prevent off-target binding. Whereas nearly all mutations that alter specificity are pleiotropic and also alter the affinity of binding to all interaction partners, the converse is not true with mutations outside of the interface able to tune affinity without affecting specificity. Our results provide the first global view of how mutations in a protein affect binding to all its potential interaction partners and reveal the distributed encoding of specificity and affinity in an interaction interface. They also show how the modular architecture of coiled-coils provides an elegant solution to the challenge of optimising specificity and affinity in a large protein family.

Overview

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Integrity signals

Registry

Crossref · 10.1038/s41467-024-53195-4

Cites

6 of 6 references verified0 citation errors · 0 not checkable

Statistics

Verification

Claims the paper makes

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Self-check

Percentages, sums and reported differences re-computed from the paper’s own numbers.

The self-check needs the paper’s full text.

Citations

Cites

Flagged first, then by citations

Research works printed but not linked: 62

  1. Crick, F. H. C. The packing of α-helices: simple coiled-coils. Acta Crystallogr. 6, 689–697 (1953). · DOI · Paper page
  2. 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). · DOI
  3. O’Shea, E. K., Rutkowski, R. & Kim, P. S. Evidence that the leucine zipper is a coiled coil. Science 243, 538–542 (1989). · DOI
  4. 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). · DOI · Paper page
  5. 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). · DOI
  6. Newman, J. R. S. & Keating, A. E. Comprehensive identification of human bZIP interactions with coiled-coil arrays. Science 300, 2097–2101 (2003). · DOI · Paper page
  7. Hai, T. & Curran, T. Cross-family dimerization of transcription factors Fos/Jun and ATF/CREB alters DNA binding specificity. PNAS 88, 3720–3724 (1991). · DOI
  8. 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). · DOI
  9. O’Shea, E. K., Lumb, K. J. & Kim, P. S. Peptide ‘Velcro’: design of a heterodimeric coiled coil. Curr. Biol. 3, 658–667 (1993). · DOI
  10. 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). · DOI
  11. Vinson, C. et al. Classification of human B-ZIP proteins based on dimerization properties. Mol. Cell. Biol. 22, 6321–6335 (2002). · DOI
  12. 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). · DOI
  13. 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). · DOI
  14. 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). · DOI
  15. 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). · DOI
  16. 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). · DOI
  17. 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). · DOI
  18. 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). · DOI
  19. Dahiyat, B. I., Gordon, D. B. & Mayo, S. L. Automated design of the surface positions of protein helices. Protein Sci. 6, 1333–1337 (1997). · DOI
  20. 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). · DOI
  21. 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). · DOI
  22. 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). · DOI
  23. Grigoryan, G. & Keating, A. E. Structure-based prediction of bZIP partnering specificity. J. Mol. Biol. 355, 1125–1142 (2006). · DOI
  24. 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
  25. Fong, J. H., Keating, A. E. & Singh, M. Predicting specificity in bZIP coiled-coil protein interactions. Genome Biol. 5, R11 (2004). · DOI
  26. Grigoryan, G., Reinke, A. W. & Keating, A. E. Design of protein-interaction specificity affords selective bZIP- binding peptides. Nature 458, 859–864 (2009). · DOI
  27. 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). · DOI
  28. 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). · DOI
  29. 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). · DOI
  30. 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). · DOI
  31. Diss, G. & Lehner, B. The genetic landscape of a physical interaction. eLife 7, 1–31 (2018). · DOI · Paper page
  32. Faure, A. J. et al. Mapping the energetic and allosteric landscapes of protein binding domains. Nature 604, 175–183 (2022). · DOI
  33. 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). · DOI
  34. 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
  35. Oughtred, R. et al. The BioGRID database: a comprehensive biomedical resource of curated protein, genetic, and chemical interactions. Protein Sci. 30, 187–200 (2021). · DOI · Paper page
  36. Tebo, A. G. & Gautier, A. A split fluorescent reporter with rapid and reversible complementation. Nat. Commun. 10, 2822 (2019). · DOI
  37. 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). · DOI
  38. Chen, S. et al. The emerging role of XBP1 in cancer. Biomed. Pharmacother. Biomed. Pharmacother. 127, 110069 (2020). · DOI
  39. 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). · DOI
  40. 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). · DOI
  41. 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). · DOI
  42. 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). · DOI
  43. Kawashima, S. et al. AAindex: amino acid index database, progress report 2008. Nucleic Acids Res. 36, D202–D205 (2008). · DOI
  44. Qian, N. & Sejnowski, T. J. Predicting the secondary structure of globular proteins using neural network models. J. Mol. Biol. 202, 865–884 (1988). · DOI
  45. Roseman, M. A. Hydrophobicity of the peptide C=O…H-N hydrogen-bonded group. J. Mol. Biol. 201, 621–623 (1988). · DOI
  46. 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
  47. Bastolla, U., Porto, M., Roman, H. E. & Vendruscolo, M. Principal eigenvector of contact matrices and hydrophobicity profiles in proteins. Proteins 58, 22–30 (2005). · DOI
  48. Bigelow, C. C. On the average hydrophobicity of proteins and the relation between it and protein structure. J. Theor. Biol. 16, 187–211 (1967). · DOI
  49. 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). · DOI
  50. 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
  51. 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). · DOI
  52. Podgornaia, A. I. & Laub, M. T. Determinants of specificity in two-component signal transduction. Curr. Opin. Microbiol. 16, 156–162 (2013). · DOI
  53. Schreiber, G. & Keating, A. E. Protein binding specificity versus promiscuity. Curr. Opin. Struct. Biol. 21, 50–61 (2011). · DOI
  54. 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
  55. 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). · DOI
  56. Aakre, C. D. et al. Evolving new protein-protein interaction specificity through promiscuous intermediates. Cell 163, 594–606 (2015). · DOI
  57. 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).
  58. 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). · DOI
  59. Martin, M. CUTADAPT removes adapter sequences from high-throughput sequencing reads. EMBnet. J. 17, 10–12 (2011). · DOI · Paper page
  60. Zhang, J., Kobert, K., Flouri, T. & Stamatakis, A. PEAR: a fast and accurate Illumina Paired-End reAd mergeR. Bioinformatics 30, 614–620 (2014). · DOI · Paper page
  61. Kempf, G. & Cavadini, S. GUIFold - a graphical user interface for local AlphaFold2. bioRxiv https://doi.org/10.1101/2023.01.19.521406 (2023). · DOI
  62. 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). · DOI

Metadata

Authors
Bendel, A. M., Faure, A. J., Klein, D., Shimada, K., Lyautey, R., Schiffelholz, N., Kempf, G., Cavadini, S., Lehner, B., & Diss, G.
Affiliations
  • University of Basel (CH)
  • Friedrich Miescher Institute (CH)
  • Institució Catalana de Recerca i Estudis Avançats (ES)
Corresponding author
  • Lehner, Ben
  • Diss, Guillaume
ORCID
Venue
Nature Communications
Publisher
Springer Science and Business Media LLC
Published
2024-10-14
Volume
15
Issue
1
Pages
8868-8868
ISSN
2041-1723 (ISSN-L)
DOI
10.1038/s41467-024-53195-4
PMC
PMC11479274
OpenAlex
W4403382069
Cited by
22
References
6
Citations by year
2026: 5 · 2025: 14 · 2024: 3
FWCI
2.99
Type
journal article
Language
en
Open access
Licence
Locations
  • Nature Communications (publishedVersion, cc-by-nc-nd)
  • bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc-nd)
  • PubMed Central (publishedVersion, cc-by-nc-nd)
  • PubMed (publishedVersion)
  • Repositori digital de la UPF (Universitat Pompeu Fabra) (submittedVersion, cc-by-nc-nd)
  • Infoscience (Ecole Polytechnique Fédérale de Lausanne) (submittedVersion, cc-by-nc-nd)
  • RePEc: Research Papers in Economics (submittedVersion)
  • DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
Funders
  • Centres de Recerca de Catalunya (501100011033, MCIN/AEI/10.13039/501100011033)
  • European Commission (RYC2021-033375-I, MCIN /AEI/ 10.13039/501100011033, 10.13039/501100011033, 13039/501100011033, 501100011033, /AEI/10.13039/501100011033)
  • Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (197593, 11033)
  • AXA Research Fund
  • Generalitat de Catalunya (10.13039/501100011033, 13039/501100011033, 501100011033, 2017-SGR, AEI/10.13039/501100011033, MCIN /AEI/10.13039/501100011033)
  • Ministerio de Ciencia e Innovación (MCIN/AEI/10, .13039/501100011033, 10.13039, / AEI/10, MCIN/AEI/10.13039/501100011033,, 13039, 10.13039/501100011033/, RYC2021-033375-I, 501100011033, LCF/PR/HR21/52410004, RYC2021, MCIN /AEI /10.13039, /AEI/10.13039/ 501100011033)
  • Fondation Bettencourt Schueller (MCIN/AEI/10.13039/501100011033)
  • Agència de Gestió d'Ajuts Universitaris i de Recerca (2017 SGR 1322, AEI/10.13039/501100011033, MCIN/AEI/10.13039/501100011033/, 10.13039/501100011033, 2017SGR, 13039/501100011033, SGR 1322)
  • Agencia Estatal de Investigación (AEI//10.13039/501100011033/, 501100011033, 10.13039/501100011033, MCIN/AEI/10.13039/501 100 011 033, 13039, .13039/501100011033, 10.13039, AEI/10)
  • H2020 European Research Council (883742)
  • NextGenerationEU
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Evolution and Genetic Dynamics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA and protein synthesis mechanisms
Keywords
protein-protein interaction, binding affinity, binding specificity, c-Jun, bZIP transcription factors, coiled coil, interaction interfaces, pleiotropic mutations, thermodynamic modeling, off-target binding, protein family evolution
MeSH terms
Binding Sites, Humans, Models, Molecular, Mutation, Protein Binding, Thermodynamics, Proto-Oncogene Proteins c-jun, Basic-Leucine Zipper Transcription Factors

About these checks

Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

What counts as a claim ›How we measure confidence ›How we check this ›

Are you an author, or do you see a problem with this page? Request a review