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Design of protein-interaction specificity gives selective bZIP-binding peptides.

Grigoryan G, Reinke AW, Keating AE - Nature (2009)

Bottom Line: Nevertheless, many of the designs, including examples that bind the oncoproteins c-Jun, c-Fos and c-Maf (also called JUN, FOS and MAF, respectively), were selective for their targets over all 19 other families.Collectively, the designs exhibit a wide range of interaction profiles and demonstrate that human bZIPs have only sparsely sampled the possible interaction space accessible to them.Our computational method provides a way to systematically analyse trade-offs between stability and specificity and is suitable for use with many types of structure-scoring functions; thus, it may prove broadly useful as a tool for protein design.

View Article: PubMed Central - PubMed

Affiliation: MIT Department of Biology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, USA.

ABSTRACT
Interaction specificity is a required feature of biological networks and a necessary characteristic of protein or small-molecule reagents and therapeutics. The ability to alter or inhibit protein interactions selectively would advance basic and applied molecular science. Assessing or modelling interaction specificity requires treating multiple competing complexes, which presents computational and experimental challenges. Here we present a computational framework for designing protein-interaction specificity and use it to identify specific peptide partners for human basic-region leucine zipper (bZIP) transcription factors. Protein microarrays were used to characterize designed, synthetic ligands for all but one of 20 bZIP families. The bZIP proteins share strong sequence and structural similarities and thus are challenging targets to bind specifically. Nevertheless, many of the designs, including examples that bind the oncoproteins c-Jun, c-Fos and c-Maf (also called JUN, FOS and MAF, respectively), were selective for their targets over all 19 other families. Collectively, the designs exhibit a wide range of interaction profiles and demonstrate that human bZIPs have only sparsely sampled the possible interaction space accessible to them. Our computational method provides a way to systematically analyse trade-offs between stability and specificity and is suitable for use with many types of structure-scoring functions; thus, it may prove broadly useful as a tool for protein design.

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Properties of designed peptides compared to human bZIP leucine-zippers. A) Hierarchical clustering of interaction profiles for 33 human peptides and 48 designs; an interaction profile consists of the array signals for interactions with 33 surface-bound human peptides. Proteins on the surface are in columns and those in solution are in rows, with designed proteins and their interaction profiles in blue and human bZIP interaction profiles in yellow. B), C) Sequence logos for a, d, e, and g positions from the first 5 heptads of the 33 human bZIP leucine zippers in B) and the 48 designed peptides in C) (http://weblogo.berkeley.edu).
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Figure 3: Properties of designed peptides compared to human bZIP leucine-zippers. A) Hierarchical clustering of interaction profiles for 33 human peptides and 48 designs; an interaction profile consists of the array signals for interactions with 33 surface-bound human peptides. Proteins on the surface are in columns and those in solution are in rows, with designed proteins and their interaction profiles in blue and human bZIP interaction profiles in yellow. B), C) Sequence logos for a, d, e, and g positions from the first 5 heptads of the 33 human bZIP leucine zippers in B) and the 48 designed peptides in C) (http://weblogo.berkeley.edu).

Mentions: Fig. 3A shows the interaction profiles of native bZIP leucine zippers and the designed anti-bZIP peptides. The native proteins exhibit diverse interaction properties, despite their limited sequence variability (Fig. 3B)4. The designed peptides are even more limited in sequence diversity, yet they encode many additional, novel specificity profiles, suggesting that bZIP-like coiled-coil interaction space is only sparsely sampled by the human proteins (Fig. 3C). Based on the frequency of success of our interaction prediction model, and results from CLASSY analysis, we conservatively estimate that >1,900 very distinct interaction profiles can be encoded using the restricted sequence space employed in our designs. This may prove useful for applications in synthetic biology (see Supplementary Information).


Design of protein-interaction specificity gives selective bZIP-binding peptides.

Grigoryan G, Reinke AW, Keating AE - Nature (2009)

Properties of designed peptides compared to human bZIP leucine-zippers. A) Hierarchical clustering of interaction profiles for 33 human peptides and 48 designs; an interaction profile consists of the array signals for interactions with 33 surface-bound human peptides. Proteins on the surface are in columns and those in solution are in rows, with designed proteins and their interaction profiles in blue and human bZIP interaction profiles in yellow. B), C) Sequence logos for a, d, e, and g positions from the first 5 heptads of the 33 human bZIP leucine zippers in B) and the 48 designed peptides in C) (http://weblogo.berkeley.edu).
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC2748673&req=5

Figure 3: Properties of designed peptides compared to human bZIP leucine-zippers. A) Hierarchical clustering of interaction profiles for 33 human peptides and 48 designs; an interaction profile consists of the array signals for interactions with 33 surface-bound human peptides. Proteins on the surface are in columns and those in solution are in rows, with designed proteins and their interaction profiles in blue and human bZIP interaction profiles in yellow. B), C) Sequence logos for a, d, e, and g positions from the first 5 heptads of the 33 human bZIP leucine zippers in B) and the 48 designed peptides in C) (http://weblogo.berkeley.edu).
Mentions: Fig. 3A shows the interaction profiles of native bZIP leucine zippers and the designed anti-bZIP peptides. The native proteins exhibit diverse interaction properties, despite their limited sequence variability (Fig. 3B)4. The designed peptides are even more limited in sequence diversity, yet they encode many additional, novel specificity profiles, suggesting that bZIP-like coiled-coil interaction space is only sparsely sampled by the human proteins (Fig. 3C). Based on the frequency of success of our interaction prediction model, and results from CLASSY analysis, we conservatively estimate that >1,900 very distinct interaction profiles can be encoded using the restricted sequence space employed in our designs. This may prove useful for applications in synthetic biology (see Supplementary Information).

Bottom Line: Nevertheless, many of the designs, including examples that bind the oncoproteins c-Jun, c-Fos and c-Maf (also called JUN, FOS and MAF, respectively), were selective for their targets over all 19 other families.Collectively, the designs exhibit a wide range of interaction profiles and demonstrate that human bZIPs have only sparsely sampled the possible interaction space accessible to them.Our computational method provides a way to systematically analyse trade-offs between stability and specificity and is suitable for use with many types of structure-scoring functions; thus, it may prove broadly useful as a tool for protein design.

View Article: PubMed Central - PubMed

Affiliation: MIT Department of Biology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, USA.

ABSTRACT
Interaction specificity is a required feature of biological networks and a necessary characteristic of protein or small-molecule reagents and therapeutics. The ability to alter or inhibit protein interactions selectively would advance basic and applied molecular science. Assessing or modelling interaction specificity requires treating multiple competing complexes, which presents computational and experimental challenges. Here we present a computational framework for designing protein-interaction specificity and use it to identify specific peptide partners for human basic-region leucine zipper (bZIP) transcription factors. Protein microarrays were used to characterize designed, synthetic ligands for all but one of 20 bZIP families. The bZIP proteins share strong sequence and structural similarities and thus are challenging targets to bind specifically. Nevertheless, many of the designs, including examples that bind the oncoproteins c-Jun, c-Fos and c-Maf (also called JUN, FOS and MAF, respectively), were selective for their targets over all 19 other families. Collectively, the designs exhibit a wide range of interaction profiles and demonstrate that human bZIPs have only sparsely sampled the possible interaction space accessible to them. Our computational method provides a way to systematically analyse trade-offs between stability and specificity and is suitable for use with many types of structure-scoring functions; thus, it may prove broadly useful as a tool for protein design.

Show MeSH