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In Situ Detection of Protein Interactions for Recombinant Therapeutic Enzymes
In situ detection of protein interactions for recombinant therapeutic enzymes Mojtaba Samoudi1, Chih-Chung Kuo1, Caressa Robinson1, Km Shams-Ud-Doha2, Song-Min Schinn1, Stefan Kol3, Linus Weiss4, Sara Petersen Bjørn5, Bjørn Voldborg5, Alexandre Rosa Campos2, and Nathan Lewis6 1University of California San Diego 2Sanford Burnham Prebys Medical Discovery Institute 3Technical University of Denmark 4Eberhard Karls University T¨ubingen 5DTU Biosustain 6University of California, San Diego May 15, 2020 Abstract Despite their therapeutic potential, many protein drugs remain inaccessible to patients since they are difficult to secrete. Each recombinant protein has unique physicochemical properties and requires different machinery for proper folding, assembly, and post-translational modifications (PTMs). Here we aimed to identify the machinery supporting recombinant protein secretion by measuring the protein-protein interaction (PPI) networks of four different recombinant proteins (SERPINA1, SERPINC1, SERPING1 and SeAP) with various PTMs and structural motifs using the proximity-dependent biotin identification (BioID) method. We identified PPIs associated with specific features of the secreted proteins using a Bayesian statistical model, and found proteins involved in protein folding, disulfide bond formation and N-glycosylation were positively correlated with the corresponding features of the four model proteins. Among others, oxidative folding enzymes showed the strongest association with disulfide bond formation, supporting their critical roles in proper folding and maintaining the ER stability. Knock down of ERP44, a measured interactor with the highest fold change, led to the decreased secretion of SERPINC1, which relies on its extensive disulfide bonds. Proximity-dependent labeling successfully identified the transient interactions supporting synthesis of secreted recombinant proteins and refined our understanding of key molecular mechanisms of the secretory pathway during recombinant protein production. -
In Situ Detection of Protein Interactions for Recombinant Therapeutic Enzymes
bioRxiv preprint doi: https://doi.org/10.1101/2020.05.06.081885; this version posted May 7, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. In situ detection of protein interactions for recombinant therapeutic enzymes Mojtaba Samoudi*,1,2, Chih-Chung Kuo*,2,3, Caressa M. Robinson*,2,3, Km Shams-Ud- Doha4, Song-Min Schinn1,2, Stefan Kol5, Linus Weiss6, Sara Petersen Bjorn5, Bjorn G. Voldborg5, Alexandre Rosa Campos4, Nathan E. Lewis1,2,3, 1 Dept of Pediatrics, University of California, San Diego 2 Novo Nordisk Foundation Center for Biosustainability at UC San Diego 3 Dept of Bioengineering, University of California, San Diego 4 Sanford Burnham Prebys Medical Discovery Institute 5 Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark 6 Dept of Biochemistry, Eberhard Karls University of Tübingen, Germany * Equal contribution Correspondence to Nathan E. Lewis, [email protected] Abstract Despite their therapeutic potential, many protein drugs remain inaccessible to patients since they are difficult to secrete. Each recombinant protein has unique physicochemical properties and requires different machinery for proper folding, assembly, and post-translational modifications (PTMs). Here we aimed to identify the machinery supporting recombinant protein secretion by measuring the protein-protein interaction (PPI) networks of four different recombinant proteins (SERPINA1, SERPINC1, SERPING1 and SeAP) with various PTMs and structural motifs using the proximity- dependent biotin identification (BioID) method. We identified PPIs associated with specific features of the secreted proteins using a Bayesian statistical model, and found proteins involved in protein folding, disulfide bond formation and N-glycosylation were positively correlated with the corresponding features of the four model proteins. -
Genetic Analysis of VCP and WASH Complex Genes in a German Cohort of Sporadic ALS-FTD Patients
Genetic analysis of VCP and WASH complex genes in a German cohort of sporadic ALS-FTD patients Author Tuerk, Matthias, Schroeder, Rolf, Khuller, Katharina, Hofmann, Andreas, Berwanger, Carolin, Ludolph, Albert C, Dekomien, Gabriele, Mueller, Kathrin, Weishaupt, Jochen H, Thiel, Christian T, Clemen, Christoph S Published 2017 Journal Title Neurobiology of Aging Version Accepted Manuscript (AM) DOI https://doi.org/10.1016/j.neurobiolaging.2017.04.023 Copyright Statement © 2017 Federation of European Biochemical Societies, published by Elsevier. Licensed under the Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (http:// creativecommons.org/licenses/by-nc-nd/4.0/) which permits unrestricted, non-commercial use, distribution and reproduction in any medium, providing that the work is properly cited. Downloaded from http://hdl.handle.net/10072/346255 Griffith Research Online https://research-repository.griffith.edu.au Genetic analysis of VCP and WASH-complex genes in a German cohort of sporadic ALS-FTD patients Matthias Türk, MD1,#; Christoph S. Clemen, MD2; Katharina Timmer, MD3; Andreas Hofmann, PhD4,5; Albert C. Ludolph, MD6; Gabriele Dekomien, PhD3; Kathrin Müller, PhD6; Jochen H. Weishaupt, MD6; Rolf Schröder, MD7; Christian T. Thiel, MD8 1Department of Neurology, Friedrich-Alexander University Erlangen-Nuremberg, Erlangen, Germany 2Center for Biochemistry, Institute of Biochemistry I, Medical Faculty, University of Cologne, Cologne, Germany 3Department for Human Genetics, Ruhr-University Bochum, Bochum, Germany -
Structures of Β-Klotho Reveal a ‘Zip Code’-Like Mechanism for Endocrine FGF Signalling Sangwon Lee1, Jungyuen Choi1, Jyotidarsini Mohanty1, Leiliane P
LETTER doi:10.1038/nature25010 Structures of β-klotho reveal a ‘zip code’-like mechanism for endocrine FGF signalling Sangwon Lee1, Jungyuen Choi1, Jyotidarsini Mohanty1, Leiliane P. Sousa1, Francisco Tome1, Els Pardon2, Jan Steyaert2, Mark A. Lemmon1, Irit Lax1 & Joseph Schlessinger1 Canonical fibroblast growth factors (FGFs) activate FGF receptors demonstrates the strong similarity of both D1 and D2 to glycoside (FGFRs) through paracrine or autocrine mechanisms in a process hydrolase family-1 (GH1) enzymes (Fig. 1d, e). GH1 enzymes hydrolyse that requires cooperation with heparan sulfate proteoglycans, glycosidic linkages between carbohydrate moieties (http://www.cazy. which function as co-receptors for FGFR activation1,2. By contrast, org/GH1.html) through a double-replacement mechanism mediated by endocrine FGFs (FGF19, FGF21 and FGF23) are circulating two conserved glutamate residues located in their active sites6. In each hormones that regulate critical metabolic processes in a variety of the sKLB domains, one of these two ‘catalytic’ glutamates is replaced of tissues3,4. FGF19 regulates bile acid synthesis and lipogenesis, by another amino acid (Fig. 1d–f): the first glutamate in D1 is replaced whereas FGF21 stimulates insulin sensitivity, energy expenditure by Asn241, and the second glutamate in D2 is replaced by Ala889. This and weight loss5. Endocrine FGFs signal through FGFRs in a indicates that neither glycoside hydrolase-like domain in β-klotho can manner that requires klothos, which are cell-surface proteins that function as an active glycoside- hydrolase enzyme. Structural alignment possess tandem glycosidase domains3,4. Here we describe the crystal using the Dali server7 indicates that GH1 and GH5 members exhibit structures of free and ligand-bound β-klotho extracellular regions high structural similarities to each of the glycoside hydrolase-like that reveal the molecular mechanism that underlies the specificity of domains of sKLB, suggesting a common evolutionary origin. -
Theses Digitisation: This Is a Digitised Version of the Original Print Thesis. Copyright and Moral
https://theses.gla.ac.uk/ Theses Digitisation: https://www.gla.ac.uk/myglasgow/research/enlighten/theses/digitisation/ This is a digitised version of the original print thesis. Copyright and moral rights for this work are retained by the author A copy can be downloaded for personal non-commercial research or study, without prior permission or charge This work cannot be reproduced or quoted extensively from without first obtaining permission in writing from the author The content must not be changed in any way or sold commercially in any format or medium without the formal permission of the author When referring to this work, full bibliographic details including the author, title, awarding institution and date of the thesis must be given Enlighten: Theses https://theses.gla.ac.uk/ [email protected] The Geometry of Hydrogen-Bonds and Carbonyl-Carbonyl Interactions Between Tra/is-Amides in Proteins and Small Molecules William John Buddy Submitted for the degree of Doctor of Philosophy Division of Biochemistry and Molecular Biology Faculty of Biomedical and Life Sciences UNIVERSITY o / GLASGOW April 2005 ProQuest Number: 10391071 All rights reserved INFORMATION TO ALL USERS The quality of this reproduction is dependent upon the quality of the copy submitted. In the unlikely event that the author did not send a com plete manuscript and there are missing pages, these will be noted. Also, if material had to be removed, a note will indicate the deletion. uest ProQuest 10391071 Published by ProQuest LLO (2017). Copyright of the Dissertation is held by the Author. All rights reserved. This work is protected against unauthorized copying under Title 17, United States C ode Microform Edition © ProQuest LLO. -
Msdmotif: Exploring Protein Sites and Motifs Adel Golovin and Kim Henrick*
BMC Bioinformatics BioMed Central Software Open Access MSDmotif: exploring protein sites and motifs Adel Golovin and Kim Henrick* Address: EMBL Outstation, The European Bioinformatics Institute, Welcome Trust Genome Campus, Hinxton, Cambridge, UK Email: Adel Golovin - [email protected]; Kim Henrick* - [email protected] * Corresponding author Published: 17 July 2008 Received: 7 May 2008 Accepted: 17 July 2008 BMC Bioinformatics 2008, 9:312 doi:10.1186/1471-2105-9-312 This article is available from: http://www.biomedcentral.com/1471-2105/9/312 © 2008 Golovin and Henrick; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Abstract Background: Protein structures have conserved features – motifs, which have a sufficient influence on the protein function. These motifs can be found in sequence as well as in 3D space. Understanding of these fragments is essential for 3D structure prediction, modelling and drug- design. The Protein Data Bank (PDB) is the source of this information however present search tools have limited 3D options to integrate protein sequence with its 3D structure. Results: We describe here a web application for querying the PDB for ligands, binding sites, small 3D structural and sequence motifs and the underlying database. Novel algorithms for chemical fragments, 3D motifs, ϕ/ψ sequences, super-secondary structure motifs and for small 3D structural motif associations searches are incorporated. The interface provides functionality for visualization, search criteria creation, sequence and 3D multiple alignment options. -
UCLA UCLA Electronic Theses and Dissertations
UCLA UCLA Electronic Theses and Dissertations Title Synthesis and Assembly of Pt-based Nanocrystals and the Mechanism Study Permalink https://escholarship.org/uc/item/3fm6p1bx Author Zhu, Enbo Publication Date 2017 Peer reviewed|Thesis/dissertation eScholarship.org Powered by the California Digital Library University of California UNIVERSITY OF CALIFORNIA Los Angeles Synthesis and Assembly of Pt-based Nanocrystals and the Mechanism Study A dissertation submitted in partial satisfaction of the requirements for the degree Doctor of Philosophy in Materials Science and Engineering by Enbo Zhu 2017 © Copyright by Enbo Zhu 2017 ABSTRACT OF THE DISSERTATION Synthesis and Assembly of Pt-based Nanocrystals and the Mechanism Study by Enbo Zhu Doctor of Philosophy in Materials Science and Engineering University of California, Los Angeles, 2017 Professor Yu Huang, Chair The design and synthesis of multicomponent Pt-based nanomaterials with highly controlled structures have attracted extensive research attention, mainly due to their highly active catalytic properties. The performance enhancement of these catalytic systems largely requires the precise control over the structure with the lowest Pt amount yet high activity to mitigate the high cost of Pt-based nanomaterials. Specific surfactant molecules have been widely employed to manipulate the morphologies and assemblies of nanostructures. Thus rational designs of the surfactants become very significant. In nature, a lot of biomaterials evolved well-developed nanostructures with unique properties through long-time natural selection using biomolecules as the surfactant. Compared with traditional trial-and-error design, biomimetic design ii provides more rational controls leading to new synthetic design for nanostructures. In this thesis, synthesis and assembly of Pt-based nanocrystals and the mechanisms were studied. -
In Situ Detection of Protein Interactions for Recombinant Therapeutic Enzymes
bioRxiv preprint doi: https://doi.org/10.1101/2020.05.06.081885; this version posted October 26, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. In situ detection of protein interactions for recombinant therapeutic enzymes Mojtaba Samoudi*,1,2, Chih-Chung Kuo*,2,3, Caressa M. Robinson*,2,3, Km Shams-Ud-Doha4, Song-Min Schinn1,2, Stefan Kol5, Linus Weiss6, Sara Petersen Bjorn5, Bjorn G. Voldborg5, Alexandre Rosa Campos4, Nathan E. Lewis1,2,3,§ 1 Dept of Pediatrics, University of California, San Diego 2 Novo Nordisk Foundation Center for Biosustainability at UC San Diego 3 Dept of Bioengineering, University of California, San Diego 4 Sanford Burnham Prebys Medical Discovery Institute 5 Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark 6 Dept of Biochemistry, Eberhard Karls University of Tübingen, Germany § Corresponding author: Nathan E. Lewis 9500 Gilman Dr. MC 0760, Building BRF2, Room 4a16, La Jolla, CA 92093 Email: [email protected], Tel: (858) 997 – 5844 Short title: In situ detection of protein interactions. bioRxiv preprint doi: https://doi.org/10.1101/2020.05.06.081885; this version posted October 26, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. Abstract Despite their therapeutic potential, many protein drugs remain inaccessible to patients since they are difficult to secrete. Each recombinant protein has unique physicochemical properties and requires different machinery for proper folding, assembly, and post-translational modifications (PTMs).