Name: In kaart brengen van disfunctionele eiwit-eiwitinteracties bij ziekte (Video) | JoVE Journal
Uploaded: 2025-10-24T13:55:00.000+00:00
Duration: 9 min 39 s
Description: Leer hoe je disfunctionele eiwit-eiwitinteracties in kaart brengt uit native weefsels met behulp van chemische probes en massaspectrometrie. Deze methode onthult ziektegerelateerde netwerkveranderingen zonder genetische modificatie.

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<ol><li>Liu, Z., Miller, D., Li, F., Liu, X., Levy, S. F. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/pubmed?term=((A+large+accessory+protein+interactome+is+rewired+across+environments%5BTitle%5D)+AND+%22Elife%22%5BJournal%5D)">A large accessory protein interactome is rewired across environments.</a> Elife. 9, e62365(2020).</li>
<li>Omranian, S., Nikoloski, Z., Grimm, D. G. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/pubmed?term=((Computational+identification+of+protein+complexes+from+network+interactions%3A+Present+state%2C+challenges%2C+and+the+way+forward%5BTitle%5D)+AND+%22Comput+Struct+Biotechnol+J%22%5BJournal%5D)">Computational identification of protein complexes from network interactions: Present state, challenges, and the way forward.</a> Comput Struct Biotechnol J. 20, 2699-2712 (2022).</li>
<li>Ginsberg, S. D., Sharma, S., Norton, L., Chiosis, G. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/pubmed?term=((Targeting+stressor-induced+dysfunctions+in+protein-protein+interaction+networks+via+epichaperomes%5BTitle%5D)+AND+%22Trends+Pharmacol+Sci%22%5BJournal%5D)">Targeting stressor-induced dysfunctions in protein-protein interaction networks via epichaperomes.</a> Trends Pharmacol Sci. 44 (1), 20-33 (2023).</li>
<li>Nussinov, R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/pubmed?term=((Pioneer+in+molecular+biology%3A+Conformational+ensembles+in+molecular+recognition%2C+allostery%2C+and+cell+function%5BTitle%5D)+AND+%22J+Mol+Biol%22%5BJournal%5D)">Pioneer in molecular biology: Conformational ensembles in molecular recognition, allostery, and cell function.</a> J Mol Biol. 437 (11), 169044(2025).</li>
<li>Lacoste, J., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/pubmed?term=((Pervasive+mislocalization+of+pathogenic+coding+variants+underlying+human+disorders%5BTitle%5D)+AND+%22Cell%22%5BJournal%5D)">Pervasive mislocalization of pathogenic coding variants underlying human disorders.</a> Cell. 187 (23), 6725-6741.e13 (2024).</li>
<li>Liu, X., Abad, L., Chatterjee, L., Cristea, I. M., Varjosalo, M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/pubmed?term=((Mapping+protein-protein+interactions+by+mass+spectrometry%5BTitle%5D)+AND+%22Mass+Spectrom+Rev%22%5BJournal%5D)">Mapping protein-protein interactions by mass spectrometry.</a> Mass Spectrom Rev. , (2024).</li>
<li>Luck, K., Sheynkman, G. M., Zhang, I., Vidal, M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/pubmed?term=((Proteome-scale+human+interactomics%5BTitle%5D)+AND+%22Trends+Biochem+Sci%22%5BJournal%5D)">Proteome-scale human interactomics.</a> Trends Biochem Sci. 42 (5), 342-354 (2017).</li>
<li>Greenblatt, J. F., Alberts, B. M., Krogan, N. J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/pubmed?term=((Discovery+and+significance+of+protein-protein+interactions+in+health+and+disease%5BTitle%5D)+AND+%22Cell%22%5BJournal%5D)">Discovery and significance of protein-protein interactions in health and disease.</a> Cell. 187 (23), 6501-6517 (2024).</li>
<li>Gonzalez-Avendano, M., Lopez, J., Vergara-Jaque, A., Cerda, O. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/pubmed?term=((The+power+of+computational+proteomics+platforms+to+decipher+protein-protein+interactions%5BTitle%5D)+AND+%22Curr+Opin+Struct+Biol%22%5BJournal%5D)">The power of computational proteomics platforms to decipher protein-protein interactions.</a> Curr Opin Struct Biol. 88, 102882(2024).</li>
<li>Komives, E. A., Chiosis, G. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/pubmed?term=((Editorial+overview%3A+Protein+networks+in+health+and+disease%5BTitle%5D)+AND+%22Curr+Opin+Struct+Biol%22%5BJournal%5D)">Editorial overview: Protein networks in health and disease.</a> Curr Opin Struct Biol. 90, 102953(2025).</li>
<li>Botticelli, L., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/pubmed?term=((Chemical+cross-linking+and+mass+spectrometry+enabled+systems-level+structural+biology%5BTitle%5D)+AND+%22Curr+Opin+Struct+Biol%22%5BJournal%5D)">Chemical cross-linking and mass spectrometry enabled systems-level structural biology.</a> Curr Opin Struct Biol. 87, 102872(2024).</li>
<li>Chakrabarty, S., Wang, S., Roychowdhury, T., Ginsberg, S. D., Chiosis, G. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/pubmed?term=((Introducing+dysfunctional+protein-protein+interactome+%28dfppi%29+-+a+platform+for+systems-level+protein-protein+interaction+%28ppi%29+dysfunction+investigation+in+disease%5BTitle%5D)+AND+%22Curr+Opin+Struct+Biol%22%5BJournal%5D)">Introducing dysfunctional protein-protein interactome (dfppi) - a platform for systems-level protein-protein interaction (ppi) dysfunction investigation in disease.</a> Curr Opin Struct Biol. 88, 102886(2024).</li>
<li>Pasala, C., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/pubmed?term=((Epichaperomes%3A+Redefining+chaperone+biology+and+therapeutic+strategies+in+complex+diseases%5BTitle%5D)+AND+%22RSC+Chem+Biol%22%5BJournal%5D)">Epichaperomes: Redefining chaperone biology and therapeutic strategies in complex diseases.</a> RSC Chem Biol. 6 (5), 678-698 (2025).</li>
<li>Chu, F., Sharma, S., Ginsberg, S. D., Chiosis, G. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/pubmed?term=((PTMs+as+molecular+encoders%3A+Reprogramming+chaperones+into+epichaperomes+for+network+control+in+disease%5BTitle%5D)+AND+%22Trends+Biochem+Sci%22%5BJournal%5D)">PTMs as molecular encoders: Reprogramming chaperones into epichaperomes for network control in disease.</a> Trends Biochem Sci. , (2025).</li>
<li>Chiosis, G., Digwal, C. S., Trepel, J. B., Neckers, L. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/pubmed?term=((Structural+and+functional+complexity+of+hsp90+in+cellular+homeostasis+and+disease%5BTitle%5D)+AND+%22Nat+Rev+Mol+Cell+Biol%22%5BJournal%5D)">Structural and functional complexity of hsp90 in cellular homeostasis and disease.</a> Nat Rev Mol Cell Biol. 24 (11), 797-815 (2023).</li>
<li>Rodina, A., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/pubmed?term=((The+epichaperome+is+an+integrated+chaperome+network+that+facilitates+tumour+survival%5BTitle%5D)+AND+%22Nature%22%5BJournal%5D)">The epichaperome is an integrated chaperome network that facilitates tumour survival.</a> Nature. 538 (7625), 397(2016).</li>
<li>Rodina, A., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/pubmed?term=((Systems-level+analyses+of+protein-protein+interaction+network+dysfunctions+via+epichaperomics+identify+cancer-specific+mechanisms+of+stress+adaptation%5BTitle%5D)+AND+%22Nat+Commun%22%5BJournal%5D)">Systems-level analyses of protein-protein interaction network dysfunctions via epichaperomics identify cancer-specific mechanisms of stress adaptation.</a> Nat Commun. 14 (1), 26(2023).</li>
<li>Inda, M. C., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/pubmed?term=((The+epichaperome+is+a+mediator+of+toxic+hippocampal+stress+and+leads+to+protein+connectivity-based+dysfunction%5BTitle%5D)+AND+%22Nat+Commun%22%5BJournal%5D)">The epichaperome is a mediator of toxic hippocampal stress and leads to protein connectivity-based dysfunction.</a> Nat Commun. 11 (1), 19(2020).</li>
<li>Joshi, S., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/pubmed?term=((Pharmacologically+controlling+protein-protein+interactions+through+epichaperomes+for+therapeutic+vulnerability+in+cancer%5BTitle%5D)+AND+%22Commun+Biol%22%5BJournal%5D)">Pharmacologically controlling protein-protein interactions through epichaperomes for therapeutic vulnerability in cancer.</a> Commun Biol. 4 (1), 20(2021).</li>
<li>Bay, S., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/pubmed?term=((Systems-level+interactome+mapping+reveals+actionable+protein+network+dysregulation+across+the+alzheimer%27s+disease+spectrum%5BTitle%5D)+AND+%22Res+Sq%22%5BJournal%5D)">Systems-level interactome mapping reveals actionable protein network dysregulation across the alzheimer's disease spectrum.</a> Res Sq. , (2025).</li>
<li>Moulick, K., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/pubmed?term=((Affinity-based+proteomics+reveal+cancer-specific+networks+coordinated+by+HSP90%5BTitle%5D)+AND+%22Nat+Chem+Biol%22%5BJournal%5D)">Affinity-based proteomics reveal cancer-specific networks coordinated by HSP90.</a> Nat Chem Biol. 7 (11), 818-826 (2011).</li>
<li>Kishinevsky, S., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/pubmed?term=((Hsp90-incorporating+chaperome+networks+as+biosensor+for+disease-related+pathways+in+patient-specific+midbrain+dopamine+neurons%5BTitle%5D)+AND+%22Nat+Commun%22%5BJournal%5D)">Hsp90-incorporating chaperome networks as biosensor for disease-related pathways in patient-specific midbrain dopamine neurons.</a> Nat Commun. 9, 15(2018).</li>
<li>Roychowdhury, T., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/pubmed?term=((Phosphorylation-driven+epichaperome+assembly+is+a+regulator+of+cellular+adaptability+and+proliferation%5BTitle%5D)+AND+%22Nat+Commun%22%5BJournal%5D)">Phosphorylation-driven epichaperome assembly is a regulator of cellular adaptability and proliferation.</a> Nat Commun. 15 (1), 8912(2024).</li>
<li>Roychowdhury, T., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/pubmed?term=((Use+of+native-page+for+the+identification+of+epichaperomes+in+cell+lines%5BTitle%5D)+AND+%22Methods+Mol+Biol%22%5BJournal%5D)">Use of native-page for the identification of epichaperomes in cell lines.</a> Methods Mol Biol. 2693, 175-191 (2023).</li>
<li>Taldone, T., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/pubmed?term=((synthesis%2C+and+evaluation+of+small+molecule+HSP90+probes%5BTitle%5D)+AND+%22Bioorg+Med+Chem%22%5BJournal%5D)">synthesis, and evaluation of small molecule HSP90 probes.</a> Bioorg Med Chem. 19 (8), 2603-2614 (2011).</li>
<li>Meier, F., Park, M. A., Mann, M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/pubmed?term=((Trapped+ion+mobility+spectrometry+and+parallel+accumulation-serial+fragmentation+in+proteomics%5BTitle%5D)+AND+%22Mol+Cell+Proteomics%22%5BJournal%5D)">Trapped ion mobility spectrometry and parallel accumulation-serial fragmentation in proteomics.</a> Mol Cell Proteomics. 20, 100138(2021).</li>
<li>Rappsilber, J., Mann, M., Ishihama, Y. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/pubmed?term=((Protocol+for+micro-purification%2C+enrichment%2C+pre-fractionation+and+storage+of+peptides+for+proteomics+using+stagetips%5BTitle%5D)+AND+%22Nat+Protoc%22%5BJournal%5D)">Protocol for micro-purification, enrichment, pre-fractionation and storage of peptides for proteomics using stagetips.</a> Nat Protoc. 2 (8), 1896-1906 (2007).</li>
<li>Kovalchuk, S. I., Jensen, O. N., Rogowska-Wrzesinska, A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/pubmed?term=((Flashpack%3A+Fast+and+simple+preparation+of+ultrahigh-performance+capillary+columns+for+LC-MS%5BTitle%5D)+AND+%22Mol+Cell+Proteomics%22%5BJournal%5D)">Flashpack: Fast and simple preparation of ultrahigh-performance capillary columns for LC-MS.</a> Mol Cell Proteomics. 18 (2), 383-390 (2019).</li>
<li>Sinitcyn, P., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/pubmed?term=((Maxdia+enables+library-based+and+library-free+data-independent+acquisition+proteomics%5BTitle%5D)+AND+%22Nat+Biotechnol%22%5BJournal%5D)">Maxdia enables library-based and library-free data-independent acquisition proteomics.</a> Nat Biotechnol. 39 (12), 1563-1573 (2021).</li>
<li>DiscoveryLibraries. , The Max Planck Institute of Biochemistry. Available from: 
 <a target="_blank" href="https://datashare.biochem.mpg.de/s/qe1IqcKbz2j2Ruf?dir=/DiscoveryLibraries">https://datashare.biochem.mpg.de/s/qe1IqcKbz2j2Ruf?dir=/DiscoveryLibraries</a> (2025).</li>
<li>Rappsilber, J., Ishihama, Y., Mann, M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/pubmed?term=((Stop+and+go+extraction+tips+for+matrix-assisted+laser+desorption%2Fionization%2C+nanoelectrospray%2C+and+LC%2FMS+sample+pretreatment+in+proteomics%5BTitle%5D)+AND+%22Anal+Chem%22%5BJournal%5D)">Stop and go extraction tips for matrix-assisted laser desorption/ionization, nanoelectrospray, and LC/MS sample pretreatment in proteomics.</a> Anal Chem. 75 (3), 663-670 (2003).</li>
<li>Meier, F., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/pubmed?term=((Diapasef%3A+Parallel+accumulation-serial+fragmentation+combined+with+data-independent+acquisition%5BTitle%5D)+AND+%22Nat+Methods%22%5BJournal%5D)">Diapasef: Parallel accumulation-serial fragmentation combined with data-independent acquisition.</a> Nat Methods. 17 (12), 1229-1236 (2020).</li>
<li>Lou, R., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/pubmed?term=((Benchmarking+commonly+used+software+suites+and+analysis+workflows+for+dia+proteomics+and+phosphoproteomics%5BTitle%5D)+AND+%22Nat+Commun%22%5BJournal%5D)">Benchmarking commonly used software suites and analysis workflows for dia proteomics and phosphoproteomics.</a> Nat Commun. 14 (1), 94(2023).</li>
<li>Demichev, V., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/pubmed?term=((Dia-pasef+data+analysis+using+fragpipe+and+dia-nn+for+deep+proteomics+of+low+sample+amounts%5BTitle%5D)+AND+%22Nat+Commun%22%5BJournal%5D)">Dia-pasef data analysis using fragpipe and dia-nn for deep proteomics of low sample amounts.</a> Nat Commun. 13 (1), 3944(2022).</li>
<li>Wen, C., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/pubmed?term=((Evaluation+of+DDA+library-free+strategies+for+phosphoproteomics+and+ubiquitinomics+data-independent+acquisition+data%5BTitle%5D)+AND+%22J+Proteome+Res%22%5BJournal%5D)">Evaluation of DDA library-free strategies for phosphoproteomics and ubiquitinomics data-independent acquisition data.</a> J Proteome Res. 22 (7), 2232-2245 (2023).</li>
<li>Bowler-Barnett, E. H., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/pubmed?term=((Uniprot+and+mass+spectrometry-based+proteomics-A+2-way+working+relationship%5BTitle%5D)+AND+%22Mol+Cell+Proteomics%22%5BJournal%5D)">Uniprot and mass spectrometry-based proteomics-A 2-way working relationship.</a> Mol Cell Proteomics. 22 (8), 100591(2023).</li>
<li>Demichev, V., Messner, C. B., Vernardis, S. I., Lilley, K. S., Ralser, M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/pubmed?term=((Dia-nn%3A+Neural+networks+and+interference+correction+enable+deep+proteome+coverage+in+high+throughput%5BTitle%5D)+AND+%22Nat+Methods%22%5BJournal%5D)">Dia-nn: Neural networks and interference correction enable deep proteome coverage in high throughput.</a> Nat Methods. 17 (1), 41-44 (2020).</li>
<li>Wang, T., Digwal, C. S., Alam, A., Chiosis, G. R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/pubmed?term=((script+epichaperomics+-+systems-level+analyses+of+protein-protein+interaction+network+dysfunctions+via+epichaperomics+identify+cancer-specific+mechanisms+of+stress+adaptation%5BTitle%5D)+AND+%22Zenodo%22%5BJournal%5D)">script epichaperomics - systems-level analyses of protein-protein interaction network dysfunctions via epichaperomics identify cancer-specific mechanisms of stress adaptation.</a> Zenodo. , https://doi.org/10.5281/zenodo.7416220 (2022).</li>
<li>Chaperomics_ad_2019. , Chiosislab. 
 <a target="_blank" href="https://github.com/chiosislab/Chaperomics_AD_2019">https://github.com/chiosislab/Chaperomics_AD_2019</a> (2019).</li>
<li>Chaperomics_controllability_2020. , Chiosislab. 
 <a target="_blank" href="https://github.com/chiosislab/Chaperomics_controllability_2020">https://github.com/chiosislab/Chaperomics_controllability_2020</a> (2019).</li>
<li>Alam, A., Wang, T., Chiosis, G. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/pubmed?term=((Cytoscape+files+-+systems-level+analyses+of+protein-protein+interaction+network+dysfunctions+via+epichaperomics+identify+cancer-specific+mechanisms+of+stress+adaptation+%5Bdata+set%5D%5BTitle%5D)+AND+%22Zenodo%22%5BJournal%5D)">Cytoscape files - systems-level analyses of protein-protein interaction network dysfunctions via epichaperomics identify cancer-specific mechanisms of stress adaptation [data set].</a> Zenodo. , https://doi.org/10.5281/zenodo.7433980 (2022).</li>
<li>Kolberg, L., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/pubmed?term=((G%3AProfiler-interoperable+web+service+for+functional+enrichment+analysis+and+gene+identifier+mapping+%282023+update%29%5BTitle%5D)+AND+%22Nucleic+Acids+Res%22%5BJournal%5D)">G:Profiler-interoperable web service for functional enrichment analysis and gene identifier mapping (2023 update).</a> Nucleic Acids Res. 51 (W1), W207-W212 (2023).</li>
<li>Yan, P. R., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/pubmed?term=((Molecular+stressors+engender+protein+connectivity+dysfunction+through+aberrant+n-glycosylation+of+a+chaperone%5BTitle%5D)+AND+%22Cell+Reports%22%5BJournal%5D)">Molecular stressors engender protein connectivity dysfunction through aberrant n-glycosylation of a chaperone.</a> Cell Reports. 31 (13), 27(2020).</li>
<li>Castelli, M., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/pubmed?term=((How+aberrant+n-glycosylation+can+alter+protein+functionality+and+ligand+binding%3A+An+atomistic+view%5BTitle%5D)+AND+%22Structure%22%5BJournal%5D)">How aberrant n-glycosylation can alter protein functionality and ligand binding: An atomistic view.</a> Structure. 31 (8), 987-1004.e8 (2023).</li>
<li>Sharma, S., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/pubmed?term=((Unraveling+the+mechanism+of+epichaperome+modulation+by+zelavespib%3A+Biochemical+insights+on+target+occupancy+and+extended+residence+time+at+the+site+of+action%5BTitle%5D)+AND+%22Biomedicines%22%5BJournal%5D)">Unraveling the mechanism of epichaperome modulation by zelavespib: Biochemical insights on target occupancy and extended residence time at the site of action.</a> Biomedicines. 11 (10), 2599(2023).</li>
<li>Guzman, U. H., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/pubmed?term=((Ultra-fast+label-free+quantification+and+comprehensive+proteome+coverage+with+narrow-window+data-independent+acquisition%5BTitle%5D)+AND+%22Nat+Biotechnol%22%5BJournal%5D)">Ultra-fast label-free quantification and comprehensive proteome coverage with narrow-window data-independent acquisition.</a> Nat Biotechnol. 42 (12), 1855-1866 (2024).</li>
</ol>

<table><tbody><tr><td>2-mercaptoethanol</td><td>Sigma-Aldrich</td><td>M6250</td><td>Giftig, Ontvlambaar</td></tr><tr><td>Acetonitrile (ACN) Optima&nbsp;</td><td>Fisher Scientific&nbsp;</td><td>A955-1</td><td>LC/MS grade (Ontvlambaar)</td></tr><tr><td>Affi-Gel 10 activated affinity chromatography media</td><td>Bio-Rad</td><td>1536099</td><td>Wordt gebruikt om PU-beads en controlebeads te maken (Ontvlambaar)</td></tr><tr><td>Ammonium Bicarbonate (ABC)</td><td>Sigma-Aldrich</td><td>09830-500G</td><td></td></tr><tr><td>Aurora Ultimate 25x75 C18 UHPLC column</td><td>IonOpticks</td><td>AUR3-25075C18-CSI</td><td></td></tr><tr><td>Autoradiographic film</td><td>EWEN-PARKER X-RAY CORP</td><td>EBA45</td><td>Alternatief voor chemiluminescente signaaldetectie na Western blot</td></tr><tr><td>Biomasher micro tissue homogenizer</td><td>DWK Life Sciences Kimble</td><td>7496250010</td><td>Wordt gebruikt voor het homogeniseren van bevroren hersenweefsel voor eiwitextractie</td></tr><tr><td>Bromophenol blue</td><td>Fisher Bioreagent</td><td>BP115-25</td><td></td></tr><tr><td>Centrifuge for 1.5 mL tubes</td><td>Eppendorf</td><td>5424</td><td></td></tr><tr><td>Centrifuge for 1.5 mL tubes&nbsp;</td><td>Eppendorf</td><td>5417R</td><td>Met temperatuurregeling</td></tr><tr><td>Centrifuge for 15-50 mL tubes</td><td>Eppendorf</td><td>5810R</td><td>Wordt gebruikt voor conische buisjes</td></tr><tr><td>ChemiDoc MP imaging system</td><td>Bio-Rad</td><td>17001402</td><td>Wordt gebruikt voor gel/blot densitometrie</td></tr><tr><td>Column oven</td><td>Sonation GmBH, Germany</td><td>ES071/ES072</td><td>Houdt de nanoLC kolom op 50 &deg;C voor consistente retentie</td></tr><tr><td>Conical tubes (15 mL)</td><td>Fisher Scientific</td><td>352096</td><td></td></tr><tr><td>Control-beads</td><td>Chiosis Lab</td><td>N/A</td><td>Taldone et al. (PMID:&nbsp;21459002)</td></tr><tr><td>Coomassie G-250 stain (Bio-safe)</td><td>Bio-Rad</td><td>1610786</td><td></td></tr><tr><td>Dark Eppendorf tubes (1.5 mL)</td><td>USA Scientific</td><td>1415-2507</td><td></td></tr><tr><td>Dithiothreitol (DTT)</td><td>Roche</td><td>10197777001</td><td>Prikkend</td></tr><tr><td>Easy nLC 1000</td><td>Thermo Fisher Scientific</td><td>Easy nLC 1000</td><td>LC systeem gebruikt met Q Exactive HF</td></tr><tr><td>Empore Solid Phase Extraction Disks</td><td>3M Company</td><td>2215-C18 (Octadecyl)</td><td>Wordt gebruikt om StageTips voor peptide desalting voor te bereiden; Geactiveerd met 100% Methanol</td></tr><tr><td>Enhanced chemiluminescence (ECL) kit</td><td>Thermo Fisher Scientific</td><td>32209</td><td></td></tr><tr><td>Eppendorf tubes (1.5 mL)</td><td>Fisher Scientific</td><td>05-408-129</td><td></td></tr><tr><td>Formic Acid (FA) Optima&nbsp;</td><td>Fisher Scientific</td><td>A117-10X1AMP</td><td>LC/MS-grade</td></tr><tr><td>g:Profiler (e111_eg58_p18_f463989d)</td><td>BIIT Group-Tartu &Uuml;likool</td><td>https://biit.cs.ut.ee/gprofiler/gost</td><td>Pathway verrijking</td></tr><tr><td>Glycerol</td><td>Fisher Bioreagent</td><td>BP229-1</td><td>Moleculaire biologie kwaliteit</td></tr><tr><td>Glycine</td><td>Fisher Bioreagent</td><td>BP381-5</td><td>Kristalline poeder</td></tr><tr><td>Goat anti-mouse HRP-conjugated secondary antibody (RRID: AB_2619742)</td><td>Sothern Biotech</td><td>1030-05</td><td>Secundair voor de H90-10 antistof</td></tr><tr><td>Goat anti-rabbit HRP-conjugated secondary antibody (RRID: AB_2632593)</td><td>Sothern Biotech</td><td>4010-05</td><td>Secundair voor de HSP90&alpha; en HOP antistoffen</td></tr><tr><td>Goat anti-rat HRP-conjugated secondary antibody (RRID: AB_2716837)</td><td>Sothern Biotech</td><td>3030-05</td><td>Secundair voor de HSC70 antistof</td></tr><tr><td>Heated orbital shaker</td><td>Eppendorf</td><td>ThermoMixer C (2231001127)</td><td></td></tr><tr><td>HeLa protein digest standard-Pierce</td><td>Thermo Fisher Scientific</td><td>88329</td><td>Wordt gebruikt voor LC-MS QC beoordeling</td></tr><tr><td>HOP antibody (RRID: AB_10828378)</td><td>Cell Signaling</td><td>5670</td><td>Voor PU-beads QC</td></tr><tr><td>HSC70 antibody (RRID: AB_10617277)</td><td>Enzo</td><td>SPA-815</td><td>Voor PU-beads QC</td></tr><tr><td>HSP90 (H90-10) antibody (RRID: AB_854214)</td><td>StressMarq</td><td>SMC-107</td><td>Voor PU-beads QC</td></tr><tr><td>HSP90 alpha antibody (RRID: AB_303423)</td><td>Abcam</td><td>Ab2928</td><td>Voor normalisatie zoals in sectie 1.2</td></tr><tr><td>Human cell line: ASPC1 (RRID:CVCL_0152)</td><td>ATCC</td><td>CRL-1682</td><td>Controle cel lijn, epichaperome laag/chaperone hoog</td></tr><tr><td>Human cell line: MDA-MB-468 (RRID: CVCL_0419)</td><td>ATCC</td><td>HTB-132</td><td>Controle cel lijn, epichaperome hoog/chaperone hoog</td></tr><tr><td>ImageJ (v1.54p)</td><td>Wayne Rasband</td><td>https://imagej.net/ij/</td><td>Densitometrie</td></tr><tr><td>Iodoacetamide (IAA)</td><td>Sigma-Aldrich</td><td>I1149-5G</td><td>Giftig</td></tr><tr><td>Low-protein binding microcentrifuge tubes</td><td>Sarstedt</td><td>72.706.600</td><td></td></tr><tr><td>Lys-C protease</td><td>Promega&nbsp;</td><td>VA1170</td><td>LC/MS-grade</td></tr><tr><td>Magnesium Chloride</td><td>Sigma-Aldrich</td><td>63068</td><td>Moleculaire biologie kwaliteit</td></tr><tr><td>MaxQuant (v2.1.1.0)</td><td>Max-Planck-Institute of Biochemistry</td><td>https://www.maxquant.org/</td><td>MaxDIA workflow voor peptide/eiwit identificatie en label-free intensiteit-gebaseerde kwantificering</td></tr><tr><td>Methanol</td><td>Fisher Chemical</td><td>A454-4</td><td>HPLC grade, ontvlambaar, giftig</td></tr><tr><td>Mini Protease Inhibitor Cocktail tablet (Complete)</td><td>Roche</td><td>4693124001</td><td></td></tr><tr><td>Mini Trans Blot Electrophoretic Transfer Cell</td><td>Bio-Rad</td><td>1703930</td><td></td></tr><tr><td>Mini-gel electrophoresis tank&nbsp;</td><td>Thermo Fisher Scientific</td><td>A25977</td><td>Wordt gebruikt voor Novex precast gels</td></tr><tr><td>Mini-PROTEAN Tetra Vertical Electrophoresis Cell&nbsp;</td><td>Bio-Rad</td><td>1658004</td><td>Wordt gebruikt voor Mini-PROTEAN Precast Protein Gels of hand gegoten gels</td></tr><tr><td>Mini-PROTEAN&nbsp;TGX Precast Protein Gels (4&

in kaart brengen van disfunctionele eiwit-eiwitinteracties bij ziekte

Mapping Dysfunctional Protein-Protein Interactions in Disease

In kaart brengen van disfunctionele eiwit-eiwitinteracties bij ziekte

Protein-protein interaction (PPI) networks are dynamically remodeled in disease, yet most systems biology approaches focus on changes in protein ...

mapping-dysfunctional-protein-protein-interactions-in-disease

Research

JoVE Journal

Neuroscience

Neurowetenschap

Synthetische eiwitsequenties gebaseerd op consensusmotieven negeren doorgaans co-evolerende residuen, die interpositionele afhankelijkheden (IPD's) impliceren. IPD's kunnen essentieel zijn voor activiteit, en ontwerpen die ze negeren, kunnen resulteren in suboptimale resultaten. Dit protocol gebruikt StickWRLD om IPD's te identificeren en helpt bij het informeren van rationeel eiwitdesign, wat resulteert in efficiëntere resultaten.

Optimalisatie van synthetische eiwitten: Identificatie van interpositioneel afhankelijkheden Indicating structureel en / of functioneel verbonden Residuen

Het regelen van eiwitexpressie is niet alleen essentieel voor elk levend organisme, maar ook een belangrijke strategie om eiwitfuncties in cellulaire modellen te onderzoeken. Het gepresenteerde protocol toont de toepassing van antilichaaminterferentie in zoogdiercellen, inclusief primaire hippocampale neuronen, en demonstreert het gebruik van driedimensionale reconstructies bij het bestuderen van eiwitfuncties.

Studeren Eiwit functie en de rol van veranderde eiwitexpressie door Antibody Interferentie en driedimensionale Reconstructies

Dit rapport beschrijft protocollen voor het meten van degradatiesnelheden van verkeerd gevouwen eiwitten door middel van western blot of fluorescentie-gebaseerde assays. De methoden kunnen worden toegepast op de analyse van andere verkeerd gevouwen eiwitten en voor high-throughput screening.

Assays voor de afbraak van Misfolded Eiwitten in Cellen

Dit protocol beschrijft experimentele procedures karakteriseren van genoom-brede veranderingen in de niveaus van Histon posttranslationele modificaties (PTM) die zich voordoen in verband met de overexpressie van eiwitten ALS en Parkinson in zijn gekoppeld Saccharomyces cerevisiae modellen. Na SDS-pagina de scheiding, worden individuele Histon PTM niveaus gedetecteerd met wijziging-specifieke antilichamen via het westelijke bevlekken.

Karakterisering van Histone posttranslationele wijziging wijzigingen in gist neurodegeneratieve Proteinopathy modellen

Het doel van dit protocol is om het ontwerp en de prestaties van in vivo experimenten in Drosophila melanogaster te schetsen om de functionele gevolgen van zeldzame genvarianten in verband met menselijke ziekten te beoordelen.

In vivo functionele studie van ziekten-geassocieerde zeldzame menselijke varianten met behulp van Drosophila

Proteostatische achteruitgang is een kenmerk van veroudering en vergemakkelijkt het begin van neurodegeneratieve ziekten. We schetsen een protocol om proteostase kwantificeerbaar te meten in twee verschillende Caenorhabditis elegans-weefsels door heterologe expressie van polyglutamine-herhalingen gefuseerd met een fluorescerende verslaggever. Dit model maakt een snelle in vivo genetische analyse van proteostase mogelijk.

Kwantificering van weefselspecifieke proteostatische achteruitgang van Caenorhabditis elegans

Om chaperonne-chaperonne- en chaperonne-substraatinteracties te bestuderen, voeren we synthetische interactiescreenings uit in Caenorhabditis elegans met behulp van RNA-interferentie in combinatie met milde mutaties of overexpressie van chaperonnes en monitoren we weefselspecifieke eiwitdisfunctie op organismaal niveau.

Caenorhabditis elegans gebruiken om te screenen op weefselspecifieke chaperonne-interacties

Een computationeel protocol, CaseOLAP LIFT, en een use case worden gepresenteerd voor het onderzoeken van mitochondriale eiwitten en hun associaties met hart- en vaatziekten zoals beschreven in biomedische rapporten. Dit protocol kan eenvoudig worden aangepast om door de gebruiker geselecteerde cellulaire componenten en ziekten te bestuderen.

Een kennisgrafiekbenadering om de rol van organellaire routes bij ziekten op te helderen via biomedische rapporten

We maken gebruik van magneto (MEG) en elektro-encefalogram (EEG) tot hersengebieden die betrokken zijn bij het verwerken van eenvoudige zintuiglijke prikkels kaart.

Functionele Mapping met gelijktijdige MEG en EEG

Een van de pathologische kenmerken van AD is de vorming van amyloïde eiwit β positief neuritische plaques. In dit protocol beschrijven we twee methoden om seniele plaques op te sporen in transgene muizen die model AD: immunohistochemische detectie met behulp van de ABC-en DAB-methode en fluorescerende detectie met behulp van thioflavin S kleuringsmethode.

Detectie van neuritische plaques in de ziekte van Alzheimer Mouse Model

Leer hoe je disfunctionele eiwit-eiwitinteracties in kaart brengt uit native weefsels met behulp van chemische probes en massaspectrometrie. Deze methode onthult ziektegerelateerde netwerkveranderingen zonder genetische modificatie.

In kaart brengen van disfunctionele eiwit-eiwitinteracties bij ziekte

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