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However, most available assays report only equilibrium binding strength and do not resolve the underlying association and dissociation kinetics. Here, we developed an optimized liposome-based bio-layer interferometry (BLI) assay for specificity profiling and comparative kinetic analysis of protein\u2013phosphoinositide interactions. Buffer optimization showed that 0.5% bovine serum albumin and 0.001% Tween-20 almost completely suppressed nonspecific protein adsorption to the biosensor surface while preserving the expected specific interactions between proteins and liposomes. Using representative PX and PH domain proteins and binding-altered mutants, we obtained phosphoinositide-binding profiles consistent with previous biochemical data. Concentration-dependent BLI analysis further resolved distinct kinetics contributing to affinity enhancement: for a PX-SnxA mutant series, stronger apparent binding was associated primarily with increased association rates, whereas for PH-AKT1 mutants, it was associated primarily with decreased dissociation rates. These results show that the platform can attribute differences in apparent affinity to specific changes in association and\/or dissociation rates, providing a level of mechanistic resolution useful for both characterizing and engineering lipid-binding probes.<\/jats:p>","DOI":"10.1021\/acs.biochem.6c00344","type":"journal-article","created":{"date-parts":[[2026,8,4]],"date-time":"2026-08-04T13:22:18Z","timestamp":1785849738000},"page":"2557-2565","source":"Crossref","is-referenced-by-count":0,"title":["Quantitative\nKinetic Analysis of Protein\u2013Phosphoinositide\nBinding by Optimized Liposome-Based Bio-Layer Interferometry"],"prefix":"10.1021","volume":"65","author":[{"given":"Pinshuo","family":"Yao","sequence":"first","affiliation":[{"name":"The University of Tokyo , , ,","place":["Tokyo, Japan, 113-8656"]},{"name":"The University of Tokyo , , Meguro-ku , ,","place":["Tokyo, Japan, 153-8505"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4019-5984","authenticated-orcid":true,"given":"Taki","family":"Nishimura","sequence":"additional","affiliation":[{"name":"The University of Osaka , , Suita , ,","place":["Osaka, Japan, 565-0871"]},{"name":"The University of Osaka , , ,","place":["Osaka, Japan, 565-0871"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9034-8179","authenticated-orcid":true,"given":"Kotaro","family":"Tsuboyama","sequence":"additional","affiliation":[{"name":"The University of Tokyo , , ,","place":["Tokyo, Japan, 113-8656"]},{"name":"The University of Tokyo , , Meguro-ku , ,","place":["Tokyo, Japan, 153-8505"]},{"name":"The University of Osaka , , Suita , ,","place":["Osaka, Japan, 565-0871"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"316","published-online":{"date-parts":[[2026,7,30]]},"reference":[{"key":"2026081808120761200_cit1","doi-asserted-by":"publisher","first-page":"746","DOI":"10.1016\/j.bbalip.2015.02.013","article-title":"Polyphosphoinositide binding domains: Key to inositol\nlipid biology","volume":"1851","author":"Hammond","year":"2015","journal-title":"Biochim. Biophys. Acta"},{"key":"2026081808120761200_cit2","doi-asserted-by":"publisher","first-page":"651","DOI":"10.1038\/nature05185","article-title":"Phosphoinositides in cell regulation\nand membrane dynamics","volume":"443","author":"Di Paolo","year":"2006","journal-title":"Nature"},{"key":"2026081808120761200_cit3","doi-asserted-by":"publisher","first-page":"439","DOI":"10.1038\/nature05933","article-title":"A transforming mutation in the pleckstrin homology\ndomain of AKT1 in cancer","volume":"448","author":"Carpten","year":"2007","journal-title":"Nature"},{"key":"2026081808120761200_cit4","doi-asserted-by":"publisher","first-page":"68","DOI":"10.1038\/nature05876","article-title":"Mutation\nof FIG4 causes neurodegeneration in the pale tremor mouse and patients\nwith CMT4J","volume":"448","author":"Chow","year":"2007","journal-title":"Nature"},{"key":"2026081808120761200_cit5","doi-asserted-by":"publisher","first-page":"92","DOI":"10.1038\/35051094","article-title":"The lipid\nphosphatase SHIP2 controls insulin sensitivity","volume":"409","author":"Cle\u0301ment","year":"2001","journal-title":"Nature"},{"key":"2026081808120761200_cit6","doi-asserted-by":"publisher","first-page":"99","DOI":"10.1038\/nrm2328","article-title":"Membrane\nrecognition by phospholipid-binding domains","volume":"9","author":"Lemmon","year":"2008","journal-title":"Nat. Rev. Mol. Cell Biol."},{"key":"2026081808120761200_cit7","doi-asserted-by":"publisher","first-page":"10472","DOI":"10.1073\/pnas.92.23.10472","article-title":"Specific and\nhigh-affinity binding of inositol phosphates to an isolated pleckstrin\nhomology domain","volume":"92","author":"Lemmon","year":"1995","journal-title":"Proc. Natl. Acad. Sci. U.S.A."},{"key":"2026081808120761200_cit8","doi-asserted-by":"publisher","first-page":"16228","DOI":"10.1021\/bi00049a039","article-title":"The pleckstrin homology domain of\nphospholipase C-delta\n1 binds with high affinity to phosphatidylinositol 4,5-bisphosphate\nin bilayer membranes","volume":"34","author":"Garcia","year":"1995","journal-title":"Biochemistry"},{"key":"2026081808120761200_cit9","doi-asserted-by":"publisher","first-page":"709","DOI":"10.1042\/bj3150709","article-title":"Specific binding\nof the Akt-1 protein kinase to phosphatidylinositol\n3,4,5-trisphosphate without subsequent activation","volume":"315","author":"James","year":"1996","journal-title":"Biochem. J."},{"key":"2026081808120761200_cit10","doi-asserted-by":"publisher","first-page":"8474","DOI":"10.1074\/jbc.272.13.8474","article-title":"High affinity\nbinding of inositol phosphates and phosphoinositides\nto the pleckstrin homology domain of RAC\/protein kinase B and their\ninfluence on kinase activity","volume":"272","author":"Frech","year":"1997","journal-title":"J. Biol. Chem."},{"key":"2026081808120761200_cit11","doi-asserted-by":"publisher","DOI":"10.1126\/scisignal.aad4337","article-title":"PLIF: A rapid, accurate method to\ndetect and quantitatively assess protein-lipid interactions","volume":"9","author":"Ceccato","year":"2016","journal-title":"Sci. Signaling"},{"key":"2026081808120761200_cit12","doi-asserted-by":"publisher","DOI":"10.1083\/jcb.202209077","article-title":"A PI(3,5)P2 reporter\nreveals PIKfyve activity and dynamics on macropinosomes and phagosomes","volume":"222","author":"Vines","year":"2023","journal-title":"J. Cell Biol."},{"key":"2026081808120761200_cit13","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-019-09355-y","article-title":"Classification of\nthe human phox homology (PX) domains based on their phosphoinositide\nbinding specificities","volume":"10","author":"Chandra","year":"2019","journal-title":"Nat. Commun."},{"key":"2026081808120761200_cit14","doi-asserted-by":"publisher","first-page":"1574","DOI":"10.1038\/s41556-026-01996-8","article-title":"Cell surface\nLiposome Binding (CLiB) allows lipid-binding probe engineering via\nhigh-throughput screening","volume":"28","author":"Nishimura","year":"2026","journal-title":"Nat. Cell Biol."},{"key":"2026081808120761200_cit15","doi-asserted-by":"publisher","first-page":"141","DOI":"10.1007\/978-1-4939-3170-5_12","article-title":"Using surface Plasmon Resonance to\nquantitatively assess lipid-protein interactions","volume":"1376","author":"Del Vecchio","year":"2016","journal-title":"Methods Mol. Biol."},{"key":"2026081808120761200_cit16","doi-asserted-by":"publisher","first-page":"150","DOI":"10.1016\/j.jpba.2012.10.008","article-title":"Application\nof Bio-Layer Interferometry for the analysis of protein\/liposome interactions","volume":"72","author":"Wallner","year":"2013","journal-title":"J. Pharm. Biomed. Anal."},{"key":"2026081808120761200_cit17","doi-asserted-by":"publisher","first-page":"883","DOI":"10.1091\/mbc.e12-10-0713","article-title":"Surface\nplasmon resonance: a useful technique for cell biologists to characterize\nbiomolecular interactions","volume":"24","author":"Stahelin","year":"2013","journal-title":"Mol. Biol. Cell"},{"key":"2026081808120761200_cit18","doi-asserted-by":"publisher","first-page":"3191","DOI":"10.1016\/j.bbamem.2014.09.003","article-title":"Two homologous\nneutrophil serine proteases bind to POPC vesicles with different affinities:\nWhen aromatic amino acids matter","volume":"1838","author":"Schillinger","year":"2014","journal-title":"Biochim. Biophys.\nActa"},{"key":"2026081808120761200_cit19","doi-asserted-by":"publisher","first-page":"1502","DOI":"10.1016\/j.bbamem.2019.06.009","article-title":"Peptidomimetic inhibitors targeting\nthe membrane-binding site of the neutrophil proteinase 3","volume":"1861","author":"Maximova","year":"2019","journal-title":"Biochim. Biophys. Acta Biomembr."},{"key":"2026081808120761200_cit20","doi-asserted-by":"publisher","first-page":"5341","DOI":"10.1021\/acs.jpclett.2c00704","article-title":"Tween-20 induces\nthe structural remodeling of single lipid vesicles","volume":"13","author":"Dresser","year":"2022","journal-title":"J. Phys. Chem. Lett."},{"key":"2026081808120761200_cit21","doi-asserted-by":"publisher","first-page":"493","DOI":"10.1038\/s41586-024-07487-w","article-title":"Accurate structure\nprediction of\nbiomolecular interactions with AlphaFold 3","volume":"630","author":"Abramson","year":"2024","journal-title":"Nature"},{"key":"2026081808120761200_cit22","doi-asserted-by":"publisher","DOI":"10.1083\/jcb.202308004","article-title":"Molding a PI(3,5)P2 biosensor","volume":"222","author":"Weckerly","year":"2023","journal-title":"J. Cell Biol."},{"key":"2026081808120761200_cit23","doi-asserted-by":"publisher","first-page":"19","DOI":"10.1002\/0471140864.ps1925s79","article-title":"Measuring protein-protein and protein-nucleic acid\ninteractions by biolayer interferometry","volume":"79","author":"Sultana","year":"2015","journal-title":"Curr.\nProtoc. Protein Sci."},{"key":"2026081808120761200_cit24","doi-asserted-by":"publisher","first-page":"9206","DOI":"10.1021\/acsomega.1c05659","article-title":"Suppressing nonspecific\nbinding in biolayer interferometry experiments for weak ligand-analyte\ninteractions","volume":"7","author":"Dubrow","year":"2022","journal-title":"ACS Omega"},{"key":"2026081808120761200_cit25","doi-asserted-by":"publisher","first-page":"1019","DOI":"10.1152\/physrev.00028.2012","article-title":"Phosphoinositides:\ntiny lipids with giant impact on cell regulation","volume":"93","author":"Balla","year":"2013","journal-title":"Physiol. Rev."},{"key":"2026081808120761200_cit26","unstructured":"Swayhoover, T.; Weckerly, C. C.; Hammond, G. R. V.\n          Quantitative comparison of PI(3,5)P2 biosensors reveals SnxA is the\nmost sensitive and unbiased\n          bioRxiv\n          2025\n          10.1101\/2025.11.10.687688."},{"key":"2026081808120761200_cit27","doi-asserted-by":"publisher","first-page":"1256","DOI":"10.1016\/S0960-9822(02)00972-7","article-title":"High-resolution\nstructure of the pleckstrin homology domain of protein kinase b\/akt\nbound to phosphatidylinositol (3,4,5)-trisphosphate","volume":"12","author":"Thomas","year":"2002","journal-title":"Curr. Biol."},{"key":"2026081808120761200_cit28","doi-asserted-by":"publisher","first-page":"501","DOI":"10.1083\/jcb.143.2.501","article-title":"Visualization of phosphoinositides\nthat bind pleckstrin homology\ndomains: calcium- and agonist-induced dynamic changes and relationship\nto myo-[3H]inositol-labeled phosphoinositide pools","volume":"143","author":"Va\u0301rnai","year":"1998","journal-title":"J. Cell Biol."},{"key":"2026081808120761200_cit29","doi-asserted-by":"publisher","first-page":"417","DOI":"10.1074\/jbc.273.1.417","article-title":"Replacements of single basic amino acids in the pleckstrin homology\ndomain of phospholipase C-delta1 alter the ligand binding, phospholipase\nactivity, and interaction with the plasma membrane","volume":"273","author":"Yagisawa","year":"1998","journal-title":"J. Biol. Chem."},{"key":"2026081808120761200_cit30","doi-asserted-by":"publisher","first-page":"12260","DOI":"10.1021\/bi801683k","article-title":"Molecular mechanism of an oncogenic\nmutation that alters membrane targeting: Glu17Lys modifies the PIP\nlipid specificity of the AKT1 PH domain","volume":"47","author":"Landgraf","year":"2008","journal-title":"Biochemistry"},{"key":"2026081808120761200_cit31","doi-asserted-by":"publisher","first-page":"30497","DOI":"10.1074\/jbc.273.46.30497","article-title":"Specificity\nand promiscuity in phosphoinositide\nbinding by pleckstrin homology domains","volume":"273","author":"Kavran","year":"1998","journal-title":"J. Biol.\nChem."},{"key":"2026081808120761200_cit32","doi-asserted-by":"publisher","first-page":"122","DOI":"10.1016\/j.ymeth.2006.05.006","article-title":"Determining selectivity of phosphoinositide-binding\ndomains","volume":"39","author":"Narayan","year":"2006","journal-title":"Methods"},{"key":"2026081808120761200_cit33","doi-asserted-by":"publisher","DOI":"10.1091\/mbc.E21-07-0363","article-title":"An update on genetically\nencoded lipid biosensors","volume":"33","author":"Hammond","year":"2022","journal-title":"Mol. Biol. Cell"},{"key":"2026081808120761200_cit34","doi-asserted-by":"publisher","first-page":"186","DOI":"10.1016\/j.colsurfb.2017.03.015","article-title":"An approach\nfor liposome immobilization using sterically stabilized micelles (SSMs)\nas a precursor for bio-layer interferometry-based interaction studies","volume":"154","author":"Wallner","year":"2017","journal-title":"Colloids Surf., B"},{"key":"2026081808120761200_cit35","doi-asserted-by":"publisher","DOI":"10.1016\/j.ijbiomac.2024.134889","article-title":"Methods for monitoring protein-membrane\nbinding. Comparison based on the interactions between amyloidogenic\nprotein human cystatin C and phospholipid liposomes","volume":"278","author":"Orlikowska","year":"2024","journal-title":"Int. J. Biol. Macromol."}],"container-title":["Biochemistry"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/pubs.acs.org\/doi\/pdf\/10.1021\/acs.biochem.6c00344","content-type":"application\/pdf","content-version":"vor","intended-application":"unspecified"},{"URL":"https:\/\/pubs.acs.org\/bichaw\/article-pdf\/65\/16\/2557\/66340138\/acs.biochem.6c00344.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/pubs.acs.org\/bichaw\/article-pdf\/65\/16\/2557\/66340138\/acs.biochem.6c00344.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,8,18]],"date-time":"2026-08-18T12:35:46Z","timestamp":1787056546000},"score":1,"resource":{"primary":{"URL":"https:\/\/pubs.acs.org\/bichaw\/article\/65\/16\/2557\/5237309\/Quantitative-Kinetic-Analysis-of-Protein"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,7,30]]},"references-count":35,"journal-issue":{"issue":"16","published-online":{"date-parts":[[2026,7,30]]},"published-print":{"date-parts":[[2026,8,18]]}},"URL":"https:\/\/doi.org\/10.1021\/acs.biochem.6c00344","relation":{},"ISSN":["0006-2960","1520-4995"],"issn-type":[{"value":"0006-2960","type":"print"},{"value":"1520-4995","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,7,30]]}}}