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Jespersen N, Barbar E. Emerging Features of Linear Motif-Binding Hub Proteins. Trends Biochem Sci 2020; 45:375-384. [DOI: 10.1016/j.tibs.2020.01.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Revised: 01/05/2020] [Accepted: 01/21/2020] [Indexed: 01/15/2023]
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Dayebgadoh G, Sardiu ME, Florens L, Washburn MP. Biochemical Reduction of the Topology of the Diverse WDR76 Protein Interactome. J Proteome Res 2019; 18:3479-3491. [PMID: 31353912 DOI: 10.1021/acs.jproteome.9b00373] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
A hub protein in protein interaction networks will typically have a large number of diverse interactions. Determining the core interactions and the function of such a hub protein remains a significant challenge in the study of networks. Proteins with WD40 repeats represent a large class of proteins that can be hub proteins. WDR76 is a poorly characterized WD40 repeat protein with possible involvement in DNA damage repair, cell-cycle progression, apoptosis, gene expression regulation, and protein quality control. WDR76 has a large and diverse interaction network that has made its study challenging. Here we rigorously carry out a series of affinity purification coupled to mass spectrometry (AP-MS) analyses to map out the WDR76 interactome through different biochemical conditions. We apply AP-MS analysis coupled to size-exclusion chromatography to resolve WDR76-based protein complexes. Furthermore, we also show that WDR76 interacts with the CCT complex via its WD40 repeat domain and with DNA-PK-KU, PARP1, GAN, SIRT1, and histones outside of the WD40 domain. An evaluation of the stability of WDR76 interactions led to focused and streamlined reciprocal analyses that validate the interactions with GAN and SIRT1. Overall, the approaches used to study WDR76 would be valuable to study other proteins containing WD40 repeat domains, which are conserved in a large number of proteins in many organisms.
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Affiliation(s)
- Gerald Dayebgadoh
- Stowers Institute for Medical Research , Kansas City , Missouri 64110 , United States
| | - Mihaela E Sardiu
- Stowers Institute for Medical Research , Kansas City , Missouri 64110 , United States
| | - Laurence Florens
- Stowers Institute for Medical Research , Kansas City , Missouri 64110 , United States
| | - Michael P Washburn
- Stowers Institute for Medical Research , Kansas City , Missouri 64110 , United States.,Department of Pathology and Laboratory Medicine , The University of Kansas Medical Center , 3901 Rainbow Boulevard , Kansas City , Kansas 66160 , United States
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Jespersen N, Estelle A, Waugh N, Davey NE, Blikstad C, Ammon YC, Akhmanova A, Ivarsson Y, Hendrix DA, Barbar E. Systematic identification of recognition motifs for the hub protein LC8. Life Sci Alliance 2019; 2:2/4/e201900366. [PMID: 31266884 PMCID: PMC6607443 DOI: 10.26508/lsa.201900366] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Revised: 06/21/2019] [Accepted: 06/24/2019] [Indexed: 01/17/2023] Open
Abstract
LC8 is a eukaryotic hub protein that interacts with multifarious partners; analysis of more than 100 binding/nonbinding sequences led to an algorithm that predicts LC8 partners with 78% accuracy. Hub proteins participate in cellular regulation by dynamic binding of multiple proteins within interaction networks. The hub protein LC8 reversibly interacts with more than 100 partners through a flexible pocket at its dimer interface. To explore the diversity of the LC8 partner pool, we screened for LC8 binding partners using a proteomic phage display library composed of peptides from the human proteome, which had no bias toward a known LC8 motif. Of the identified hits, we validated binding of 29 peptides using isothermal titration calorimetry. Of the 29 peptides, 19 were entirely novel, and all had the canonical TQT motif anchor. A striking observation is that numerous peptides containing the TQT anchor do not bind LC8, indicating that residues outside of the anchor facilitate LC8 interactions. Using both LC8-binding and nonbinding peptides containing the motif anchor, we developed the “LC8Pred” algorithm that identifies critical residues flanking the anchor and parses random sequences to predict LC8-binding motifs with ∼78% accuracy. Our findings significantly expand the scope of the LC8 hub interactome.
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Affiliation(s)
- Nathan Jespersen
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR, USA
| | - Aidan Estelle
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR, USA
| | - Nathan Waugh
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR, USA
| | - Norman E Davey
- Conway Institute of Biomolecular and Biomedical Sciences, University College Dublin, Ireland
| | - Cecilia Blikstad
- Department of Chemistry - Biomedical Centre, Uppsala University, Uppsala, Sweden
| | | | - Anna Akhmanova
- Department of Biology, Utrecht University, Utrecht, The Netherlands
| | - Ylva Ivarsson
- Department of Chemistry - Biomedical Centre, Uppsala University, Uppsala, Sweden
| | - David A Hendrix
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR, USA.,School of Electrical Engineering and Computer Science, Oregon State University, Corvallis, OR, USA
| | - Elisar Barbar
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR, USA
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Wheeler LC, Anderson JA, Morrison AJ, Wong CE, Harms MJ. Conservation of Specificity in Two Low-Specificity Proteins. Biochemistry 2017; 57:684-695. [PMID: 29240404 DOI: 10.1021/acs.biochem.7b01086] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Many regulatory proteins bind peptide regions of target proteins and modulate their activity. Such regulatory proteins can often interact with highly diverse target peptides. In many instances, it is not known if the peptide-binding interface discriminates targets in a biological context, or whether biological specificity is achieved exclusively through external factors such as subcellular localization. We used an evolutionary biochemical approach to distinguish these possibilities for two such low-specificity proteins: S100A5 and S100A6. We used isothermal titration calorimetry to study the binding of peptides with diverse sequence and biochemistry to human S100A5 and S100A6. These proteins bound distinct, but overlapping, sets of peptide targets. We then studied the peptide binding properties of orthologs sampled from across five amniote species. Binding specificity was conserved along all lineages, for the last 320 million years, despite the low specificity of each protein. We used ancestral sequence reconstruction to determine the binding specificity of the last common ancestor of the paralogs. The ancestor bound the entire set of peptides bound by modern S100A5 and S100A6 proteins, suggesting that paralog specificity evolved via subfunctionalization. To rule out the possibility that specificity is conserved because it is difficult to modify, we identified a single historical mutation that, when reverted in human S100A5, gave it the ability to bind an S100A6-specific peptide. These results reveal strong evolutionary constraints on peptide binding specificity. Despite being able to bind a large number of targets, the specificity of S100 peptide interfaces is likely important for the biology of these proteins.
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Affiliation(s)
- Lucas C Wheeler
- Department of Chemistry and Biochemistry, University of Oregon , Eugene, Oregon 97403, United States.,Institute of Molecular Biology, University of Oregon , Eugene, Oregon 97403, United States
| | - Jeremy A Anderson
- Department of Chemistry and Biochemistry, University of Oregon , Eugene, Oregon 97403, United States.,Institute of Molecular Biology, University of Oregon , Eugene, Oregon 97403, United States
| | - Anneliese J Morrison
- Department of Chemistry and Biochemistry, University of Oregon , Eugene, Oregon 97403, United States.,Institute of Molecular Biology, University of Oregon , Eugene, Oregon 97403, United States
| | - Caitlyn E Wong
- Department of Chemistry and Biochemistry, University of Oregon , Eugene, Oregon 97403, United States.,Institute of Molecular Biology, University of Oregon , Eugene, Oregon 97403, United States
| | - Michael J Harms
- Department of Chemistry and Biochemistry, University of Oregon , Eugene, Oregon 97403, United States.,Institute of Molecular Biology, University of Oregon , Eugene, Oregon 97403, United States
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Yura K. Preface of Special Issue "Protein-Ligand Interactions". Biophys Physicobiol 2016; 13:85-86. [PMID: 27924261 PMCID: PMC5042156 DOI: 10.2142/biophysico.13.0_85] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Affiliation(s)
- Kei Yura
- Graduate School of Humanities and Sciences, Ochanomizu University, 2-1-1 Otsuka, Bunkyo, Tokyo 112-8610, Japan; Center for Informational Biology, Ochanomizu University, 2-1-1 Otsuka, Bunkyo, Tokyo 112-8610, Japan; National Institute of Genetics, 1111 Yata, Mishima, Shizuoka 411-8540, Japan
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