Biology subjects

Tsaban, T.

Publications and source records attributed to Tsaban, T..

4 recordsLinked to original sources

bioRxiv2021

Tandem WW/PPxY motif interactions in WWOX: the multifaceted role of the second WW domain

Class I WW domains mediate protein interactions by binding short linear PPxY motifs. They occur predominantly as tandem repeats, and their target proteins often contain multiple PPxY motifs, but the interplay of WW/peptide interactions is not always intuitive. WW domain-containing oxidoreductase (WWOX) protein harbors two WW domains: unstable WW1 capable of PPxY binding, and well-folded but mutated WW2 that cannot bind such motifs. WW2 is considered to act as a WW1 chaperone, but the underlying mechanism remains to be revealed. Here we combine NMR, ITC and structural modeling to elucidate the role of both WW domains in WWOX binding to single and double motif peptides derived from its substrate ErbB4. Using NMR we identified an interaction surface between the two domains that supports a WWOX conformation that is compatible with peptide substrate binding. ITC and NMR measurements reveal that while binding affinity to a single motif is marginally increased in the presence of WW2, affinity to a dual motif peptide increases tenfold, and that WW2 can directly bind double motif-peptides using its canonical binding site. Finally, differential binding of peptides in a mutagenesis study is consistent with a parallel orientation binding to the WW1-WW2 tandem domain, agreeing with structural models of the interaction. Our results reveal the complex nature of tandem WW domain organization and substrate binding, highlighting the contribution of WWOX WW2 to both stability and binding. This opens the way to assess how evolution can utilize the multivariate nature of binding to fine-tune interactions for specific biological functions.

biophysics↗

bioRxiv2021

PatchMAN docking: Modeling peptide-protein interactions in the context of the receptor surface

Peptide docking can be perceived as a subproblem of protein-protein docking. However, due to the short length and flexible nature of peptides, many do not adopt one defined conformation prior to binding. Therefore, to tackle a peptide docking problem, not only the relative orientation between the two partners, but also the bound conformation of the peptide needs to be modeled. Traditional peptide-centered approaches use information about the peptide sequence to generate a representative conformer ensemble, which can then be rigid body docked to the receptor. Alternatively, one may look at this problem from the viewpoint of the receptor, namely that the protein surface defines the peptide bound conformation.We present PatchMAN (Patch-Motif AligNments), a novel peptide docking approach which uses structural motifs to map the receptor surface with backbone scaffolds extracted from protein structures. On a non-redundant set of protein-peptide complexes, starting from free receptor structures, PatchMAN successfully models and identifies near-native peptide-protein complexes in 62% / 81% within 2.5[A] / 5[A] RMSD, with corresponding sampling in 81% / 100% of the cases, outperforming other approaches. PatchMAN leverages the observation that structural units of peptides with their binding pocket can be found not only within interfaces, but also within monomers. We show that the conformation of the bound peptide is sampled based on the structural context of the receptor only, without taking into account any sequence information. Beyond peptide docking, this approach opens exciting new avenues to study principles of peptide-protein association, and to the design of new peptide binders.

bioinformatics↗

bioRxiv2021

Harnessing protein folding neural networks for peptide-protein docking

Highly accurate protein structure predictions by the recently published deep neural networks such as AlphaFold2 and RoseTTAFold are truly impressive achievements, and will have a tremendous impact far beyond structural biology. If peptide-protein binding can be seen as a final complementing step in the folding of a protein monomer, we reasoned that these approaches might be applicable to the modeling of such interactions. We present a simple implementation of AlphaFold2 to model the structure of peptide-protein interactions, enabled by linking the peptide sequence to the protein c-terminus via a poly glycine linker. We show on a large non-redundant set of 162 peptide-protein complexes that peptide-protein interactions can indeed be modeled accurately. Importantly, prediction is fast and works without multiple sequence alignment information for the peptide partner. We compare performance on a smaller, representative set to the state-of-the-art peptide docking protocol PIPER-FlexPepDock, and describe in detail specific examples that highlight advantages of the two approaches, pointing to possible further improvements and insights in the modeling of peptide-protein interactions. Peptide-mediated interactions play important regulatory roles in functional cells. Thus the present advance holds much promise for significant impact, by bringing into reach a wide range of peptide-protein complexes, and providing important starting points for detailed study and manipulation of many specific interactions.

bioinformatics↗

bioRxiv2021

Uncovering the modified immunopeptidome reveals insights into principles of PTM-driven antigenicity

Antigen processing and presentation are critical for modulating tumor-host interactions. While post-translational modifications (PTMs) can alter the binding and recognition of antigens, their identification remains challenging. Here we uncover the role PTMs may play in antigen presentation and recognition in human cancers by profiling 29 different PTM combinations in immunopeptidomics data from multiple clinical samples and cell lines. We established and validated an antigen discovery pipeline and showed that newly identified modified antigens from a murine cancer model are cancer-specific and can elicit T cell killing. Systematic analysis of PTMs across multiple cohorts defined new haplotype preferences and binding motifs in association with specific PTM types. By expanding the antigenic landscape with modifications, we uncover disease-specific targets, including thousands of novel cancer-specific antigens and reveal insight into PTM-driven antigenicity. Collectively, our findings highlight an immunomodulatory role for modified peptides presented on HLA I, which may have broad implications for T-cell mediated therapies in cancer and beyond. SignificanceMajor efforts are underway to identify cancer-specific antigens for personalized immunotherapy. Here, we enrich the immunopeptidome landscape by uncovering thousands of novel putative antigens that are post-translationally modified. We define unique preferences for PTM-driven alterations affecting HLA binding and TCR recognition, which in turn alter tumor-immune interactions. Conflict of interest statementAuthors declare no conflicts of interest.

cancer biology↗