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Zhang L, Duan HC, Paduch M, Hu J, Zhang C, Mu Y, Lin H, He C, Kossiakoff AA, Jia G, Zhang L. The Molecular Basis of Human ALKBH3 Mediated RNA N 1 -methyladenosine (m 1 A) Demethylation. Angew Chem Int Ed Engl 2024; 63:e202313900. [PMID: 38158383 DOI: 10.1002/anie.202313900] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 12/17/2023] [Accepted: 12/27/2023] [Indexed: 01/03/2024]
Abstract
N1 -methyladenosine (m1 A) is a prevalent post-transcriptional RNA modification, and the distribution and dynamics of the modification play key epitranscriptomic roles in cell development. At present, the human AlkB Fe(II)/α-ketoglutarate-dependent dioxygenase family member ALKBH3 is the only known mRNA m1 A demethylase, but its catalytic mechanism remains unclear. Here, we present the structures of ALKBH3-oligo crosslinked complexes obtained with the assistance of a synthetic antibody crystallization chaperone. Structural and biochemical results showed that ALKBH3 utilized two β-hairpins (β4-loop-β5 and β'-loop-β'') and the α2 helix to facilitate single-stranded substrate binding. Moreover, a bubble-like region around Asp194 and a key residue inside the active pocket (Thr133) enabled specific recognition and demethylation of m1 A- and 3-methylcytidine (m3 C)-modified substrates. Mutation of Thr133 to the corresponding residue in the AlkB Fe(II)/α-ketoglutarate-dependent dioxygenase family members FTO or ALKBH5 converted ALKBH3 substrate selectivity from m1 A to N6 -methyladenosine (m6 A), as did Asp194 deletion. Our findings provide a molecular basis for understanding the mechanisms of substrate recognition and m1 A demethylation by ALKBH3. This study is expected to aid structure-guided design of chemical probes for further functional studies and therapeutic applications.
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Affiliation(s)
- Lin Zhang
- Department of Pharmacology and Chemical Biology, State Key Laboratory of Systems Medicine for Cancer, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Hong-Chao Duan
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China
| | - Marcin Paduch
- Institute for Biophysical Dynamics, University of Chicago, Chicago, IL, USA
| | - Jingyan Hu
- Department of Pharmacology and Chemical Biology, State Key Laboratory of Systems Medicine for Cancer, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Chi Zhang
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China
| | - Yajuan Mu
- Department of Pharmacology and Chemical Biology, State Key Laboratory of Systems Medicine for Cancer, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Houwen Lin
- Research Centre for Marine Drugs, State Key Laboratory of Oncogene and Related Genes, Department of Pharmacy, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
- Institute of Marine Biomedicine, Shenzhen Polytechnic, Shenzhen, 518055, China
| | - Chuan He
- Department of Chemistry and Institute for Biophysical Dynamics, University of Chicago, Chicago, IL, USA
- Howard Hughes Medical Institute, University of Chicago, Chicago, IL, USA
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, USA
| | - Anthony A Kossiakoff
- Institute for Biophysical Dynamics, University of Chicago, Chicago, IL, USA
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, USA
| | - Guifang Jia
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China
- Peking-Tsinghua Center for Life Sciences, Beijing, 100871, China
| | - Liang Zhang
- Department of Pharmacology and Chemical Biology, State Key Laboratory of Systems Medicine for Cancer, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
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Ding S, Marie PK, Zhang R, Bohn A, Moseley RM, Baro N, Brown D, Pittman K, Paduch M, Hsu D, Kopetz S, Shen X. Abstract 183: Evaluating targeted therapy combination for refractory colorectal cancer using MicroOrganoSpheres (MOS). Cancer Res 2023. [DOI: 10.1158/1538-7445.am2023-183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/07/2023]
Abstract
Abstract
Metastatic colorectal cancer (CRC) patients who have become resistant to standard-of-care (SOC) treatments are often put on targeted therapies, including experimental drugs still in clinical trials. However, patients with targeted mutations still often do not respond to the targeted therapies alone, hence it remains a critically unmet need to explore potential combinatorial regimens that will enhance the efficacy. We performed a high-throughput screen using MicroOrganoSpheres (MOS) derived from metastatic refractory patients to correlate with clinical outcomes and explore alternative combinations that might benefit the patients. Biopsies from metastatic CRC patients who became resistant to SOC and were about to receive targeted therapies in clinical trials were molecularly profiled and implanted into immunodeficient mice to generate patient-derived xenografts (PDX). MOS were derived and established from PDX using droplet-based microfluidics for high-throughput 3D screening. These MOS-based refractory patient avatars contain either targetable mutations including KRAS G12C and BRAF 600E or no such mutations. Response of the MOS to dose-titrated single and combination drug treatments including the available targeted therapies were measured by a fully automated robotic dispensing and imaging pipeline and quantified by AI-based live imaging analytical algorithm to generate robust drug response curves, which were used to derive IC50 and EC50. We tested both FDA-approved and experimental targeted therapies as single agent or in combination in 5-dose titrations. Longitudinal tracking of each MOS with Live/dead fluorescence dye signals was obtained for 5 days. MOS drug response curves and IC50s show correlation with clinical outcomes. Furthermore, this comprehensive dataset enabled us to assess the potential benefit of different combinations, help deconvolute the efficacy and synergy of individual drugs, and provide insight into patients who fail to response to targeted therapies despite possessing the targeted mutations. As the MOS diagnostic assay can be completed from a patient biopsy within 10 days and is currently in a registered, multi-site clinical trial (ClinicalTrials.gov # NCT05189171), this study provides proof-of-principle for a potential clinical MOS-based assay to guide refractory patients to the optimal combination regimen containing targeted therapy.
Citation Format: Shengli Ding, Preeti Kanikarla Marie, Ray Zhang, Alan Bohn, Robert Moseley Moseley, Nicholas Baro, Dan Brown, Kelly Pittman, Marcin Paduch, David Hsu, Scott Kopetz, Xiling Shen. Evaluating targeted therapy combination for refractory colorectal cancer using MicroOrganoSpheres (MOS) [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 183.
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Ding S, Kanikarla Marie P, Zhang R, Baro N, Brown DW, Bohn A, Pittman K, Paduch M, Hsu SD, Kopetz S, Shen X. Identifying targeted therapy combination for refractory colorectal cancer using micro-organospheres. J Clin Oncol 2023. [DOI: 10.1200/jco.2023.41.4_suppl.27] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
27 Background: Metastatic colorectal cancer (CRC) patients who have become resistant to standard-of-care (SOC) treatments are often put on targeted therapies. However, patients with targeted mutations still often do not respond to the targeted therapies alone, hence it remains a critically unmet need to explore potential combinatorial regimens that will enhance the efficacy. Using micro-organospheres (MOS) derived from metastatic refractory patients who received targeted therapies, we performed a high-throughput combo screen and compared the response of these patient tumor avatars with their clinical responses. Methods: Biopsies from metastatic CRC patients who became resistant to SOC and were about to receive targeted therapies in clinical trials were molecularly profiled and implanted into immunodeficient mice to generate patient-derived xenografts (PDX). MOS were derived and established from PDX using droplet-based microfluidics for high-throughput 3D screening. Response of the MOS patient avatars to dose-titrated single and combination drug treatments including the available targeted therapies were measured by a fully automated robotic dispensing and imaging pipeline and quantified by AI-based live imaging analytical algorithm to generate drug response curves with IC50 and EC50. Results: MOS were successfully established in all PDX derived from refractory patients with targetable mutations including KRAS G12C and BRAF 600E as well as patients without targetable mutations. We tested both FDA-approved and experimental targeted therapies as single agent or in combination in 5-dose titrations. Longitudinal tracking of each MOS with Live/dead fluorescence dye signals was obtained for 5 days. MOS drug response curves and IC50s show correlation with clinical outcomes. Furthermore, this comprehensive dataset enabled us to assess the potential benefit of different combinations, help deconvolute the efficacy and synergy of individual drugs, and provide insight into patients who fail to response to targeted therapies despite possessing the targeted mutations. As the MOSdiagnostic assay can be completed from a patient biopsy within 10 days and is currently in a registered, multi-site clinical trial (ClinicalTrials.gov # NCT05189171), this study provides proof-of-principle for a potential clinical MOS-based assay to guide refractory patients to the optimal combination regimen. Conclusions: Refractory patients may benefit from a MOS-based high-throughput screen assay to select the optimal combination regimen containing targeted therapy.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Scott Kopetz
- The University of Texas MD Anderson Cancer Center, Houston, TX
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Enderle L, Shalaby KH, Gorelik M, Weiss A, Blazer LL, Paduch M, Cardarelli L, Kossiakoff A, Adams JJ, Sidhu SS. A T cell redirection platform for co-targeting dual antigens on solid tumors. MAbs 2021; 13:1933690. [PMID: 34190031 PMCID: PMC8253144 DOI: 10.1080/19420862.2021.1933690] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
In order to direct T cells to specific features of solid cancer cells, we engineered a bispecific antibody format, named Dual Antigen T cell Engager (DATE), by fusing a single-chain variable fragment targeting CD3 to a tumor-targeting antigen-binding fragment. In this format, multiple novel paratopes against different tumor antigens were able to recruit T-cell cytotoxicity to tumor cells in vitro and in an in vivo pancreatic ductal adenocarcinoma xenograft model. Since unique surface antigens in solid tumors are limited, in order to enhance selectivity, we further engineered “double-DATEs” targeting two tumor antigens simultaneously. The double-DATE contains an additional autonomous variable heavy-chain domain, which binds a second tumor antigen without itself eliciting a cytotoxic response. This novel modality provides a strategy to enhance the selectivity of immune redirection through binary targeting of native tumor antigens. The modularity and use of a common, stable human framework for all components enables a pipeline approach to rapidly develop a broad repertoire of tailored DATEs and double-DATEs with favorable biophysical properties and high potencies and selectivities.
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Affiliation(s)
- Leonie Enderle
- Donnelly Centre, University of Toronto, Toronto, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - Karim H Shalaby
- Donnelly Centre, University of Toronto, Toronto, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - Maryna Gorelik
- Donnelly Centre, University of Toronto, Toronto, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - Alexander Weiss
- Donnelly Centre, University of Toronto, Toronto, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - Levi L Blazer
- Donnelly Centre, University of Toronto, Toronto, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - Marcin Paduch
- Institute for Biophysical Dynamics, Gordon Center for Integrative Science, Chicago, USA
| | - Lia Cardarelli
- Donnelly Centre, University of Toronto, Toronto, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - Anthony Kossiakoff
- Institute for Biophysical Dynamics, Gordon Center for Integrative Science, Chicago, USA.,Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, USA
| | - Jarrett J Adams
- Donnelly Centre, University of Toronto, Toronto, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - Sachdev S Sidhu
- Donnelly Centre, University of Toronto, Toronto, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Canada
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Lokareddy RK, Ko YH, Hong N, Doll SG, Paduch M, Niederweis M, Kossiakoff AA, Cingolani G. Recognition of an α-helical hairpin in P22 large terminase by a synthetic antibody fragment. Acta Crystallogr D Struct Biol 2020; 76:876-888. [PMID: 32876063 PMCID: PMC7466751 DOI: 10.1107/s2059798320009912] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2020] [Accepted: 07/20/2020] [Indexed: 11/10/2022] Open
Abstract
The genome-packaging motor of tailed bacteriophages and herpesviruses is a multisubunit protein complex formed by several copies of a large (TerL) and a small (TerS) terminase subunit. The motor assembles transiently at the portal protein vertex of an empty precursor capsid to power the energy-dependent packaging of viral DNA. Both the ATPase and nuclease activities associated with genome packaging reside in TerL. Structural studies of TerL from bacteriophage P22 have been hindered by the conformational flexibility of this enzyme and its susceptibility to proteolysis. Here, an unbiased, synthetic phage-display Fab library was screened and a panel of high-affinity Fabs against P22 TerL were identified. This led to the discovery of a recombinant antibody fragment, Fab4, that binds a 33-amino-acid α-helical hairpin at the N-terminus of TerL with an equilibrium dissociation constant Kd of 71.5 nM. A 1.51 Å resolution crystal structure of Fab4 bound to the TerL epitope (TLE) together with a 1.15 Å resolution crystal structure of the unliganded Fab4, which is the highest resolution ever achieved for a Fab, elucidate the principles governing the recognition of this novel helical epitope. TLE adopts two different conformations in the asymmetric unit and buries as much as 1250 Å2 of solvent-accessible surface in Fab4. TLE recognition is primarily mediated by conformational changes in the third complementarity-determining region of the Fab4 heavy chain (CDR H3) that take place upon epitope binding. It is demonstrated that TLE can be introduced genetically at the N-terminus of a target protein, where it retains high-affinity binding to Fab4.
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Affiliation(s)
- Ravi K. Lokareddy
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, 1020 Locust Street, JAH-4E, Philadelphia, PA 19107, USA
| | - Ying-Hui Ko
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, 1020 Locust Street, JAH-4E, Philadelphia, PA 19107, USA
| | - Nathaniel Hong
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, 1020 Locust Street, JAH-4E, Philadelphia, PA 19107, USA
| | - Steven G. Doll
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, 1020 Locust Street, JAH-4E, Philadelphia, PA 19107, USA
| | - Marcin Paduch
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL 60637, USA
| | - Michael Niederweis
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Anthony A. Kossiakoff
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL 60637, USA
- Institute for Biophysical Dynamics, University of Chicago, Chicago, IL 60637, USA
| | - Gino Cingolani
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, 1020 Locust Street, JAH-4E, Philadelphia, PA 19107, USA
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Laas T, Laas K, Paju J, Priimets J, Tõkke S, Väli B, Shirokova V, Antonov M, Gribkov V, Demina E, Pimenov V, Paduch M, Matulka R, Akel M. Behaviour of tungsten alloy with iron and nickel under repeated high temperature plasma pulses. Fusion Engineering and Design 2020. [DOI: 10.1016/j.fusengdes.2019.111408] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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Gribkov V, Paduch M, Zielinska E, Demin A, Demina E, Kazilin E, Latyshev S, Maslyaev S, Morozov E, Pimenov V. Comparative analysis of damageability produced by powerful pulsed ion/plasma streams and laser radiation on the plasma-facing W samples. Radiat Phys Chem Oxf Engl 1993 2018. [DOI: 10.1016/j.radphyschem.2018.03.020] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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Gribkov V, Bienkowska B, Paduch M. Examination of a chamber of a large fusion facility by means of neutron activation techique with nanosecond neutron pulse generated by dense plasma focus device PF-6. Fusion Engineering and Design 2017. [DOI: 10.1016/j.fusengdes.2017.10.023] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Chernyshova M, Gribkov V, Kowalska-Strzeciwilk E, Kubkowska M, Miklaszewski R, Paduch M, Pisarczyk T, Zielinska E, Demina E, Pimenov V, Maslyaev S, Bondarenko G, Vilemova M, Matejicek J. Interaction of powerful hot plasma and fast ion streams with materials in dense plasma focus devices. Fusion Engineering and Design 2016. [DOI: 10.1016/j.fusengdes.2016.11.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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Szydłowski A, Malinowska A, Szewczak K, Jaskóła M, Korman A, Paduch M, Kuk M. Influence of intense soft X-ray radiation on the parameters of tracks induced in CR-39 and PM-355 solid state nuclear track detectors. RADIAT MEAS 2015. [DOI: 10.1016/j.radmeas.2015.06.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Zhong N, Loppnau P, Seitova A, Ravichandran M, Fenner M, Jain H, Bhattacharya A, Hutchinson A, Paduch M, Lu V, Olszewski M, Kossiakoff AA, Dowdell E, Koide A, Koide S, Huang H, Nadeem V, Sidhu SS, Greenblatt JF, Marcon E, Arrowsmith CH, Edwards AM, Gräslund S. Optimizing Production of Antigens and Fabs in the Context of Generating Recombinant Antibodies to Human Proteins. PLoS One 2015; 10:e0139695. [PMID: 26437229 PMCID: PMC4593582 DOI: 10.1371/journal.pone.0139695] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2015] [Accepted: 09/16/2015] [Indexed: 01/18/2023] Open
Abstract
We developed and optimized a high-throughput project workflow to generate renewable recombinant antibodies to human proteins involved in epigenetic signalling. Three different strategies to produce phage display compatible protein antigens in bacterial systems were compared, and we found that in vivo biotinylation through the use of an Avi tag was the most productive method. Phage display selections were performed on 265 in vivo biotinylated antigen domains. High-affinity Fabs (<20nM) were obtained for 196. We constructed and optimized a new expression vector to produce in vivo biotinylated Fabs in E. coli. This increased average yields up to 10-fold, with an average yield of 4 mg/L. For 118 antigens, we identified Fabs that could immunoprecipitate their full-length endogenous targets from mammalian cell lysates. One Fab for each antigen was converted to a recombinant IgG and produced in mammalian cells, with an average yield of 15 mg/L. In summary, we have optimized each step of the pipeline to produce recombinant antibodies, significantly increasing both efficiency and yield, and also showed that these Fabs and IgGs can be generally useful for chromatin immunoprecipitation (ChIP) protocols.
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Affiliation(s)
- Nan Zhong
- Structural Genomics Consortium, University of Toronto, MaRS South tower, 101 College street, Toronto, ON M5G 1L7, Canada
| | - Peter Loppnau
- Structural Genomics Consortium, University of Toronto, MaRS South tower, 101 College street, Toronto, ON M5G 1L7, Canada
| | - Alma Seitova
- Structural Genomics Consortium, University of Toronto, MaRS South tower, 101 College street, Toronto, ON M5G 1L7, Canada
| | - Mani Ravichandran
- Structural Genomics Consortium, University of Toronto, MaRS South tower, 101 College street, Toronto, ON M5G 1L7, Canada
| | - Maria Fenner
- Structural Genomics Consortium, University of Toronto, MaRS South tower, 101 College street, Toronto, ON M5G 1L7, Canada
| | - Harshika Jain
- Structural Genomics Consortium, University of Toronto, MaRS South tower, 101 College street, Toronto, ON M5G 1L7, Canada
| | - Anandi Bhattacharya
- Structural Genomics Consortium, University of Toronto, MaRS South tower, 101 College street, Toronto, ON M5G 1L7, Canada
| | - Ashley Hutchinson
- Structural Genomics Consortium, University of Toronto, MaRS South tower, 101 College street, Toronto, ON M5G 1L7, Canada
| | - Marcin Paduch
- Department of Biochemistry and Molecular Biology, Knapp Center for Biomedical Discovery, University of Chicago, 900 East 57th St., Chicago, IL 60637, United States of America
| | - Vincent Lu
- Department of Biochemistry and Molecular Biology, Knapp Center for Biomedical Discovery, University of Chicago, 900 East 57th St., Chicago, IL 60637, United States of America
| | - Michal Olszewski
- Department of Biochemistry and Molecular Biology, Knapp Center for Biomedical Discovery, University of Chicago, 900 East 57th St., Chicago, IL 60637, United States of America
| | - Anthony A. Kossiakoff
- Department of Biochemistry and Molecular Biology, Knapp Center for Biomedical Discovery, University of Chicago, 900 East 57th St., Chicago, IL 60637, United States of America
| | - Evan Dowdell
- Department of Biochemistry and Molecular Biology, Knapp Center for Biomedical Discovery, University of Chicago, 900 East 57th St., Chicago, IL 60637, United States of America
| | - Akiko Koide
- Department of Biochemistry and Molecular Biology, Knapp Center for Biomedical Discovery, University of Chicago, 900 East 57th St., Chicago, IL 60637, United States of America
| | - Shohei Koide
- Department of Biochemistry and Molecular Biology, Knapp Center for Biomedical Discovery, University of Chicago, 900 East 57th St., Chicago, IL 60637, United States of America
| | - Haiming Huang
- Terrence Donnelly Center for Cellular & Biomolecular Research, University of Toronto, 160 College Street, Toronto, ON M5S 3E1, Canada
| | - Vincent Nadeem
- Terrence Donnelly Center for Cellular & Biomolecular Research, University of Toronto, 160 College Street, Toronto, ON M5S 3E1, Canada
| | - Sachdev S. Sidhu
- Terrence Donnelly Center for Cellular & Biomolecular Research, University of Toronto, 160 College Street, Toronto, ON M5S 3E1, Canada
| | - Jack F. Greenblatt
- Terrence Donnelly Center for Cellular & Biomolecular Research, University of Toronto, 160 College Street, Toronto, ON M5S 3E1, Canada
- Department of Molecular Genetics, University of Toronto, 1 Kings College Circle, MSB-4180, Toronto, ON M5S 1A8, Canada
| | - Edyta Marcon
- Terrence Donnelly Center for Cellular & Biomolecular Research, University of Toronto, 160 College Street, Toronto, ON M5S 3E1, Canada
| | - Cheryl H. Arrowsmith
- Structural Genomics Consortium, University of Toronto, MaRS South tower, 101 College street, Toronto, ON M5G 1L7, Canada
| | - Aled M. Edwards
- Structural Genomics Consortium, University of Toronto, MaRS South tower, 101 College street, Toronto, ON M5G 1L7, Canada
| | - Susanne Gräslund
- Structural Genomics Consortium, University of Toronto, MaRS South tower, 101 College street, Toronto, ON M5G 1L7, Canada
- * E-mail:
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Stuwe T, Bley CJ, Thierbach K, Petrovic S, Schilbach S, Mayo DJ, Perriches T, Rundlet EJ, Jeon YE, Collins LN, Huber FM, Lin DH, Paduch M, Koide A, Lu V, Fischer J, Hurt E, Koide S, Kossiakoff AA, Hoelz A. Architecture of the fungal nuclear pore inner ring complex. Science 2015; 350:56-64. [PMID: 26316600 DOI: 10.1126/science.aac9176] [Citation(s) in RCA: 94] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Accepted: 08/12/2015] [Indexed: 12/20/2022]
Abstract
The nuclear pore complex (NPC) constitutes the sole gateway for bidirectional nucleocytoplasmic transport. We present the reconstitution and interdisciplinary analyses of the ~425-kilodalton inner ring complex (IRC), which forms the central transport channel and diffusion barrier of the NPC, revealing its interaction network and equimolar stoichiometry. The Nsp1•Nup49•Nup57 channel nucleoporin heterotrimer (CNT) attaches to the IRC solely through the adaptor nucleoporin Nic96. The CNT•Nic96 structure reveals that Nic96 functions as an assembly sensor that recognizes the three-dimensional architecture of the CNT, thereby mediating the incorporation of a defined CNT state into the NPC. We propose that the IRC adopts a relatively rigid scaffold that recruits the CNT to primarily form the diffusion barrier of the NPC, rather than enabling channel dilation.
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Affiliation(s)
- Tobias Stuwe
- California Institute of Technology, Division of Chemistry and Chemical Engineering, 1200 East California Boulevard, Pasadena, CA 91125, USA
| | - Christopher J Bley
- California Institute of Technology, Division of Chemistry and Chemical Engineering, 1200 East California Boulevard, Pasadena, CA 91125, USA
| | - Karsten Thierbach
- California Institute of Technology, Division of Chemistry and Chemical Engineering, 1200 East California Boulevard, Pasadena, CA 91125, USA
| | - Stefan Petrovic
- California Institute of Technology, Division of Chemistry and Chemical Engineering, 1200 East California Boulevard, Pasadena, CA 91125, USA
| | - Sandra Schilbach
- California Institute of Technology, Division of Chemistry and Chemical Engineering, 1200 East California Boulevard, Pasadena, CA 91125, USA
| | - Daniel J Mayo
- California Institute of Technology, Division of Chemistry and Chemical Engineering, 1200 East California Boulevard, Pasadena, CA 91125, USA
| | - Thibaud Perriches
- California Institute of Technology, Division of Chemistry and Chemical Engineering, 1200 East California Boulevard, Pasadena, CA 91125, USA
| | - Emily J Rundlet
- California Institute of Technology, Division of Chemistry and Chemical Engineering, 1200 East California Boulevard, Pasadena, CA 91125, USA
| | - Young E Jeon
- California Institute of Technology, Division of Chemistry and Chemical Engineering, 1200 East California Boulevard, Pasadena, CA 91125, USA
| | - Leslie N Collins
- California Institute of Technology, Division of Chemistry and Chemical Engineering, 1200 East California Boulevard, Pasadena, CA 91125, USA
| | - Ferdinand M Huber
- California Institute of Technology, Division of Chemistry and Chemical Engineering, 1200 East California Boulevard, Pasadena, CA 91125, USA
| | - Daniel H Lin
- California Institute of Technology, Division of Chemistry and Chemical Engineering, 1200 East California Boulevard, Pasadena, CA 91125, USA
| | - Marcin Paduch
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60637, USA
| | - Akiko Koide
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60637, USA
| | - Vincent Lu
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60637, USA
| | - Jessica Fischer
- Biochemistry Center of Heidelberg University, 69120 Heidelberg, Germany
| | - Ed Hurt
- Biochemistry Center of Heidelberg University, 69120 Heidelberg, Germany
| | - Shohei Koide
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60637, USA
| | - Anthony A Kossiakoff
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60637, USA
| | - André Hoelz
- California Institute of Technology, Division of Chemistry and Chemical Engineering, 1200 East California Boulevard, Pasadena, CA 91125, USA.
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Hornsby M, Paduch M, Miersch S, Sääf A, Matsuguchi T, Lee B, Wypisniak K, Doak A, King D, Usatyuk S, Perry K, Lu V, Thomas W, Luke J, Goodman J, Hoey RJ, Lai D, Griffin C, Li Z, Vizeacoumar FJ, Dong D, Campbell E, Anderson S, Zhong N, Gräslund S, Koide S, Moffat J, Sidhu S, Kossiakoff A, Wells J. A High Through-put Platform for Recombinant Antibodies to Folded Proteins. Mol Cell Proteomics 2015; 14:2833-47. [PMID: 26290498 PMCID: PMC4597156 DOI: 10.1074/mcp.o115.052209] [Citation(s) in RCA: 85] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2015] [Indexed: 01/09/2023] Open
Abstract
Antibodies are key reagents in biology and medicine, but commercial sources are rarely recombinant and thus do not provide a permanent and renewable resource. Here, we describe an industrialized platform to generate antigens and validated recombinant antibodies for 346 transcription factors (TFs) and 211 epigenetic antigens. We describe an optimized automated phage display and antigen expression pipeline that in aggregate produced about 3000 sequenced Fragment antigen-binding domain that had high affinity (typically EC50<20 nm), high stability (Tm∼80 °C), good expression in E. coli (∼5 mg/L), and ability to bind antigen in complex cell lysates. We evaluated a subset of Fabs generated to homologous SCAN domains for binding specificities. These Fragment antigen-binding domains were monospecific to their target SCAN antigen except in rare cases where they cross-reacted with a few highly related antigens. Remarkably, immunofluorescence experiments in six cell lines for 270 of the TF antigens, each having multiple antibodies, show that ∼70% stain predominantly in the cytosol and ∼20% stain in the nucleus which reinforces the dominant role that translocation plays in TF biology. These cloned antibody reagents are being made available to the academic community through our web site recombinant-antibodies.org to allow a more system-wide analysis of TF and chromatin biology. We believe these platforms, infrastructure, and automated approaches will facilitate the next generation of renewable antibody reagents to the human proteome in the coming decade.
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Affiliation(s)
- Michael Hornsby
- From the ‡Department of Pharmaceutical Chemistry University of California, San Francisco, California 94158
| | - Marcin Paduch
- §Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois 60637
| | - Shane Miersch
- ¶Donnelly Center for Cellular and Biomolecular Research, Department of Molecular Genetics, University of Toronto, Toronto, MG5 1L6, Canada
| | - Annika Sääf
- §Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois 60637
| | - Tet Matsuguchi
- From the ‡Department of Pharmaceutical Chemistry University of California, San Francisco, California 94158
| | - Brian Lee
- From the ‡Department of Pharmaceutical Chemistry University of California, San Francisco, California 94158
| | - Karolina Wypisniak
- From the ‡Department of Pharmaceutical Chemistry University of California, San Francisco, California 94158
| | - Allison Doak
- From the ‡Department of Pharmaceutical Chemistry University of California, San Francisco, California 94158
| | - Daniel King
- §Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois 60637
| | - Svitlana Usatyuk
- §Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois 60637
| | - Kimberly Perry
- §Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois 60637
| | - Vince Lu
- §Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois 60637
| | - William Thomas
- §Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois 60637
| | - Judy Luke
- §Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois 60637
| | - Jay Goodman
- §Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois 60637
| | - Robert J Hoey
- §Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois 60637
| | - Darson Lai
- §Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois 60637
| | - Carly Griffin
- ¶Donnelly Center for Cellular and Biomolecular Research, Department of Molecular Genetics, University of Toronto, Toronto, MG5 1L6, Canada
| | - Zhijian Li
- ¶Donnelly Center for Cellular and Biomolecular Research, Department of Molecular Genetics, University of Toronto, Toronto, MG5 1L6, Canada
| | - Franco J Vizeacoumar
- **Saskatchewan Cancer Agency, University of Saskatchewan, Saskatoon, S7N 4H4, Canada
| | - Debbie Dong
- ¶Donnelly Center for Cellular and Biomolecular Research, Department of Molecular Genetics, University of Toronto, Toronto, MG5 1L6, Canada
| | - Elliot Campbell
- ‖Center for Advanced Biotechnology and Medicine, Department of Molecular Biology and Biochemistry, Rutgers University, Piscataway, New Jersey 08854
| | - Stephen Anderson
- ‖Center for Advanced Biotechnology and Medicine, Department of Molecular Biology and Biochemistry, Rutgers University, Piscataway, New Jersey 08854
| | - Nan Zhong
- ‡‡Structural Genomics Consortium, Toronto, M5G Il7, Canada
| | | | - Shohei Koide
- §Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois 60637
| | - Jason Moffat
- ¶Donnelly Center for Cellular and Biomolecular Research, Department of Molecular Genetics, University of Toronto, Toronto, MG5 1L6, Canada
| | - Sachdev Sidhu
- ¶Donnelly Center for Cellular and Biomolecular Research, Department of Molecular Genetics, University of Toronto, Toronto, MG5 1L6, Canada;
| | - Anthony Kossiakoff
- §Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois 60637;
| | - James Wells
- From the ‡Department of Pharmaceutical Chemistry University of California, San Francisco, California 94158;
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Griffin C, Miersch S, Marcon E, Banerjee S, Wells J, Hornsby M, Kossiakoff A, Koide S, Paduch M, Sidhu S, Moffat J. Validation of Recombinant Antibodies Against Human Transcription Factors. FASEB J 2015. [DOI: 10.1096/fasebj.29.1_supplement.571.13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Carly Griffin
- Donnelly Centre University of TorontoTorontoOntarioCanada
| | - Shane Miersch
- Donnelly Centre University of TorontoTorontoOntarioCanada
| | - Edyta Marcon
- Donnelly Centre University of TorontoTorontoOntarioCanada
| | | | - Jim Wells
- Pharmaceutical Chemistry University of California San FranciscoSan FranciscoCaliforniaUnited States
| | - Michael Hornsby
- Pharmaceutical Chemistry University of California San FranciscoSan FranciscoCaliforniaUnited States
| | - Anthony Kossiakoff
- Biochemistry and Molecular BiologyUniversity of ChicagoChicagoIllinoisUnited States
| | - Shohei Koide
- Biochemistry and Molecular BiologyUniversity of ChicagoChicagoIllinoisUnited States
| | - Marcin Paduch
- Biochemistry and Molecular BiologyUniversity of ChicagoChicagoIllinoisUnited States
| | - Sachdev Sidhu
- Donnelly Centre University of TorontoTorontoOntarioCanada
| | - Jason Moffat
- Donnelly Centre University of TorontoTorontoOntarioCanada
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15
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Mateja A, Paduch M, Chang HY, Szydlowska A, Kossiakoff AA, Hegde RS, Keenan RJ. Protein targeting. Structure of the Get3 targeting factor in complex with its membrane protein cargo. Science 2015; 347:1152-5. [PMID: 25745174 PMCID: PMC4413028 DOI: 10.1126/science.1261671] [Citation(s) in RCA: 87] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Tail-anchored (TA) proteins are a physiologically important class of membrane proteins targeted to the endoplasmic reticulum by the conserved guided-entry of TA proteins (GET) pathway. During transit, their hydrophobic transmembrane domains (TMDs) are chaperoned by the cytosolic targeting factor Get3, but the molecular nature of the functional Get3-TA protein targeting complex remains unknown. We reconstituted the physiologic assembly pathway for a functional targeting complex and showed that it comprises a TA protein bound to a Get3 homodimer. Crystal structures of Get3 bound to different TA proteins showed an α-helical TMD occupying a hydrophobic groove that spans the Get3 homodimer. Our data elucidate the mechanism of TA protein recognition and shielding by Get3 and suggest general principles of hydrophobic domain chaperoning by cellular targeting factors.
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Affiliation(s)
- Agnieszka Mateja
- Department of Biochemistry and Molecular Biology, The University of Chicago, 929 East 57th Street, Chicago, IL 60637, USA
| | - Marcin Paduch
- Department of Biochemistry and Molecular Biology, The University of Chicago, 929 East 57th Street, Chicago, IL 60637, USA
| | - Hsin-Yang Chang
- Department of Biochemistry and Molecular Biology, The University of Chicago, 929 East 57th Street, Chicago, IL 60637, USA
| | - Anna Szydlowska
- Department of Biochemistry and Molecular Biology, The University of Chicago, 929 East 57th Street, Chicago, IL 60637, USA
| | - Anthony A Kossiakoff
- Department of Biochemistry and Molecular Biology, The University of Chicago, 929 East 57th Street, Chicago, IL 60637, USA
| | - Ramanujan S Hegde
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK.
| | - Robert J Keenan
- Department of Biochemistry and Molecular Biology, The University of Chicago, 929 East 57th Street, Chicago, IL 60637, USA.
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Abstract
The nuclear pore complex (NPC) constitutes the sole gateway for bidirectional nucleocytoplasmic transport. Despite half a century of structural characterization, the architecture of the NPC remains unknown. Here we present the crystal structure of a reconstituted ~400-kilodalton coat nucleoporin complex (CNC) from Saccharomyces cerevisiae at a 7.4 angstrom resolution. The crystal structure revealed a curved Y-shaped architecture and the molecular details of the coat nucleoporin interactions forming the central "triskelion" of the Y. A structural comparison of the yeast CNC with an electron microscopy reconstruction of its human counterpart suggested the evolutionary conservation of the elucidated architecture. Moreover, 32 copies of the CNC crystal structure docked readily into a cryoelectron tomographic reconstruction of the fully assembled human NPC, thereby accounting for ~16 megadalton of its mass.
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Affiliation(s)
- Tobias Stuwe
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA 91125, USA. These authors contributed equally to this work
| | - Ana R Correia
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA 91125, USA. These authors contributed equally to this work
| | - Daniel H Lin
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA 91125, USA
| | - Marcin Paduch
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL 60637, USA
| | - Vincent T Lu
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL 60637, USA
| | - Anthony A Kossiakoff
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL 60637, USA
| | - André Hoelz
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA 91125, USA.
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Miersch S, Li Z, Hanna R, McLaughlin ME, Hornsby M, Matsuguchi T, Paduch M, Sääf A, Wells J, Koide S, Kossiakoff A, Sidhu SS. Scalable high throughput selection from phage-displayed synthetic antibody libraries. J Vis Exp 2015:51492. [PMID: 25651360 DOI: 10.3791/51492] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
The demand for antibodies that fulfill the needs of both basic and clinical research applications is high and will dramatically increase in the future. However, it is apparent that traditional monoclonal technologies are not alone up to this task. This has led to the development of alternate methods to satisfy the demand for high quality and renewable affinity reagents to all accessible elements of the proteome. Toward this end, high throughput methods for conducting selections from phage-displayed synthetic antibody libraries have been devised for applications involving diverse antigens and optimized for rapid throughput and success. Herein, a protocol is described in detail that illustrates with video demonstration the parallel selection of Fab-phage clones from high diversity libraries against hundreds of targets using either a manual 96 channel liquid handler or automated robotics system. Using this protocol, a single user can generate hundreds of antigens, select antibodies to them in parallel and validate antibody binding within 6-8 weeks. Highlighted are: i) a viable antigen format, ii) pre-selection antigen characterization, iii) critical steps that influence the selection of specific and high affinity clones, and iv) ways of monitoring selection effectiveness and early stage antibody clone characterization. With this approach, we have obtained synthetic antibody fragments (Fabs) to many target classes including single-pass membrane receptors, secreted protein hormones, and multi-domain intracellular proteins. These fragments are readily converted to full-length antibodies and have been validated to exhibit high affinity and specificity. Further, they have been demonstrated to be functional in a variety of standard immunoassays including Western blotting, ELISA, cellular immunofluorescence, immunoprecipitation and related assays. This methodology will accelerate antibody discovery and ultimately bring us closer to realizing the goal of generating renewable, high quality antibodies to the proteome.
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Affiliation(s)
- Shane Miersch
- The Recombinant Antibody Network; The Banting and Best Department of Medical Research, University of Toronto;
| | - Zhijian Li
- The Recombinant Antibody Network; The Banting and Best Department of Medical Research, University of Toronto
| | - Rachel Hanna
- The Recombinant Antibody Network; The Banting and Best Department of Medical Research, University of Toronto
| | - Megan E McLaughlin
- The Recombinant Antibody Network; The Banting and Best Department of Medical Research, University of Toronto
| | - Michael Hornsby
- The Recombinant Antibody Network; Antibiome Center, University of California, San Francisco at Mission Bay
| | - Tet Matsuguchi
- The Recombinant Antibody Network; Antibiome Center, University of California, San Francisco at Mission Bay
| | - Marcin Paduch
- The Recombinant Antibody Network; Department of Biochemistry and Molecular Biology, The University of Chicago
| | - Annika Sääf
- The Recombinant Antibody Network; Department of Biochemistry and Molecular Biology, The University of Chicago
| | - Jim Wells
- The Recombinant Antibody Network; Antibiome Center, University of California, San Francisco at Mission Bay
| | - Shohei Koide
- The Recombinant Antibody Network; Department of Biochemistry and Molecular Biology, The University of Chicago
| | - Anthony Kossiakoff
- The Recombinant Antibody Network; Department of Biochemistry and Molecular Biology, The University of Chicago
| | - Sachdev S Sidhu
- The Recombinant Antibody Network; The Banting and Best Department of Medical Research, University of Toronto
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18
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Malinowski K, Skladnik-Sadowska E, Sadowski MJ, Szydlowski A, Czaus K, Kwiatkowski R, Zaloga D, Paduch M, Zielinska E. Research on anisotropy of fusion-produced protons and neutrons emission from high-current plasma-focus discharges. Rev Sci Instrum 2015; 86:013502. [PMID: 25638081 DOI: 10.1063/1.4905181] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The paper concerns fast protons and neutrons from D-D fusion reactions in a Plasma-Focus-1000U facility. Measurements were performed with nuclear-track detectors arranged in "sandwiches" of an Al-foil and two PM-355 detectors separated by a polyethylene-plate. The Al-foil eliminated all primary deuterons, but was penetrable for fast fusion protons. The foil and first PM-355 detector were penetrable for fast neutrons, which were converted into recoil-protons in the polyethylene and recorded in the second PM-355 detector. The "sandwiches" were irradiated by discharges of comparable neutron-yields. Analyses of etched tracks and computer simulations of the fusion-products behavior in the detectors were performed.
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Affiliation(s)
- K Malinowski
- National Centre for Nuclear Research (NCBJ), 05-400 Otwock, Poland
| | | | - M J Sadowski
- National Centre for Nuclear Research (NCBJ), 05-400 Otwock, Poland
| | - A Szydlowski
- National Centre for Nuclear Research (NCBJ), 05-400 Otwock, Poland
| | - K Czaus
- National Centre for Nuclear Research (NCBJ), 05-400 Otwock, Poland
| | - R Kwiatkowski
- National Centre for Nuclear Research (NCBJ), 05-400 Otwock, Poland
| | - D Zaloga
- National Centre for Nuclear Research (NCBJ), 05-400 Otwock, Poland
| | - M Paduch
- Institute of Plasma Physics and Laser Microfusion (IFPiLM), 01-497 Warsaw, Poland
| | - E Zielinska
- Institute of Plasma Physics and Laser Microfusion (IFPiLM), 01-497 Warsaw, Poland
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19
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Zhang X, Hoey R, Koide A, Dolios G, Paduch M, Nguyen P, Wu X, Li Y, Wagner SL, Wang R, Koide S, Sisodia SS. A synthetic antibody fragment targeting nicastrin affects assembly and trafficking of γ-secretase. J Biol Chem 2014; 289:34851-61. [PMID: 25352592 DOI: 10.1074/jbc.m114.609636] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The γ-secretase complex, composed of presenilin, nicastrin (NCT), anterior pharynx-defective 1 (APH-1), and presenilin enhancer 2 (PEN-2), is assembled in a highly regulated manner and catalyzes the intramembranous proteolysis of many type I membrane proteins, including Notch and amyloid precursor protein. The Notch family of receptors plays important roles in cell fate specification during development and in adult tissues, and aberrant hyperactive Notch signaling causes some forms of cancer. γ-Secretase-mediated processing of Notch at the cell surface results in the generation of the Notch intracellular domain, which associates with several transcriptional coactivators involved in nuclear signaling events. On the other hand, γ-secretase-mediated processing of amyloid precursor protein leads to the production of amyloid β (Aβ) peptides that play an important role in the pathogenesis of Alzheimer disease. We used a phage display approach to identify synthetic antibodies that specifically target NCT and expressed them in the single-chain variable fragment (scFv) format in mammalian cells. We show that expression of a NCT-specific scFv clone, G9, in HEK293 cells decreased the production of the Notch intracellular domain but not the production of amyloid β peptides that occurs in endosomal and recycling compartments. Biochemical studies revealed that scFvG9 impairs the maturation of NCT by associating with immature forms of NCT and, consequently, prevents its association with the other components of the γ-secretase complex, leading to degradation of these molecules. The reduced cell surface levels of mature γ-secretase complexes, in turn, compromise the intramembranous processing of Notch.
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Affiliation(s)
| | - Robert Hoey
- Biochemistry and Molecular Biology, The University of Chicago, Chicago, Illinois 60637
| | - Akiko Koide
- Biochemistry and Molecular Biology, The University of Chicago, Chicago, Illinois 60637
| | - Georgia Dolios
- the Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York 10029
| | - Marcin Paduch
- Biochemistry and Molecular Biology, The University of Chicago, Chicago, Illinois 60637
| | - Phuong Nguyen
- the Department of Neurosciences, University of California, San Diego School of Medicine, La Jolla, California 92093, and
| | - Xianzhong Wu
- Molecular Pharmacology and Chemistry, Memorial Sloan-Kettering Cancer Center, New York, New York 10065
| | - Yueming Li
- Molecular Pharmacology and Chemistry, Memorial Sloan-Kettering Cancer Center, New York, New York 10065
| | - Steven L Wagner
- the Department of Neurosciences, University of California, San Diego School of Medicine, La Jolla, California 92093, and
| | - Rong Wang
- the Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York 10029
| | - Shohei Koide
- Biochemistry and Molecular Biology, The University of Chicago, Chicago, Illinois 60637
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20
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Li Q, Wanderling S, Paduch M, Medovoy D, Singharoy A, McGreevy R, Villalba-Galea CA, Hulse RE, Roux B, Schulten K, Kossiakoff A, Perozo E. Structural mechanism of voltage-dependent gating in an isolated voltage-sensing domain. Nat Struct Mol Biol 2014; 21:244-52. [PMID: 24487958 DOI: 10.1038/nsmb.2768] [Citation(s) in RCA: 188] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2013] [Accepted: 01/10/2014] [Indexed: 01/26/2023]
Abstract
The transduction of transmembrane electric fields into protein motion has an essential role in the generation and propagation of cellular signals. Voltage-sensing domains (VSDs) carry out these functions through reorientations of positive charges in the S4 helix. Here, we determined crystal structures of the Ciona intestinalis VSD (Ci-VSD) in putatively active and resting conformations. S4 undergoes an ~5-Å displacement along its main axis, accompanied by an ~60° rotation. This movement is stabilized by an exchange in countercharge partners in helices S1 and S3 that generates an estimated net charge transfer of ~1 eo. Gating charges move relative to a ''hydrophobic gasket' that electrically divides intra- and extracellular compartments. EPR spectroscopy confirms the limited nature of S4 movement in a membrane environment. These results provide an explicit mechanism for voltage sensing and set the basis for electromechanical coupling in voltage-dependent enzymes and ion channels.
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Affiliation(s)
- Qufei Li
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois, USA
| | - Sherry Wanderling
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois, USA
| | - Marcin Paduch
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois, USA
| | - David Medovoy
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois, USA
| | - Abhishek Singharoy
- Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Ryan McGreevy
- Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Carlos A Villalba-Galea
- Department of Physiology and Biophysics, Virginia Commonwealth University School of Medicine, Richmond, Virginia, USA
| | - Raymond E Hulse
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois, USA
| | - Benoît Roux
- 1] Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois, USA. [2] Institute of Biophysical Dynamics, University of Chicago, Chicago, Illinois, USA
| | - Klaus Schulten
- 1] Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA. [2] Department of Physics, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Anthony Kossiakoff
- 1] Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois, USA. [2] Institute of Biophysical Dynamics, University of Chicago, Chicago, Illinois, USA
| | - Eduardo Perozo
- 1] Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois, USA. [2] Institute of Biophysical Dynamics, University of Chicago, Chicago, Illinois, USA
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21
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Li Q, Wanderling S, Paduch M, Medovoy D, Villalba-Galea C, Hulse R, Roux B, Kossiakoff A, Perozo E. Structural Mechanism of Voltage-Dependent Gating in an Isolated Voltage-Sensing Domain. Biophys J 2013. [DOI: 10.1016/j.bpj.2012.11.1108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
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22
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Paduch M, Koide A, Uysal S, Rizk SS, Koide S, Kossiakoff AA. Generating conformation-specific synthetic antibodies to trap proteins in selected functional states. Methods 2012; 60:3-14. [PMID: 23280336 DOI: 10.1016/j.ymeth.2012.12.010] [Citation(s) in RCA: 80] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2012] [Revised: 12/17/2012] [Accepted: 12/19/2012] [Indexed: 11/17/2022] Open
Abstract
A set of phage display sorting strategies and validation methodologies are presented that are capable of producing high performance synthetic antibodies (sABs) with customized properties. Exquisite control of antigen and conditions during the phage display selection process can yield sABs that: (1) recognize conformational states, (2) target specific regions of the surface of a protein, (3) induce conformational changes, and (4) capture and stabilize multi-protein complexes. These unique capabilities open myriad opportunities to study complex macromolecular processes inaccessible to traditional affinity reagent technology. We present detailed protocols for de novo isolation of binders, as well as examples of downstream biophysical characterization. The methods described are generalizable and can be adapted to other in vitro direct evolution approaches based on yeast or mRNA display.
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Affiliation(s)
- Marcin Paduch
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60637, USA
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23
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Rizk SS, Misiura A, Paduch M, Kossiakoff AA. Substance P derivatives as versatile tools for specific delivery of various types of biomolecular cargo. Bioconjug Chem 2011; 23:42-6. [PMID: 22175275 DOI: 10.1021/bc200496e] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The use of proteins or nucleic acids as therapeutic agents has been severely hampered by their intrinsic inability to cross the cell membrane. Moreover, common techniques for driving the delivery of macromolecules lack the ability to distinguish between healthy and diseased tissue, precluding their clinical use. Recently, receptor-mediated delivery (RMD) has emerged as a technology with the potential to circumvent the obstacles associated with the delivery of drug targets by utilizing the natural endocytosis of a ligand upon binding to its receptor. Here, we describe the synthesis of variants of substance P (SP), an eleven amino acid neuropeptide ligand of the neurokinin type 1 receptor (NK1R), for the delivery of various types of cargo. The variants of SP were synthesized with an N-terminal maleimide moiety that allows conjugation to surface thiols, resulting in a nonreducible thioether. Cargos lacking an available thiol are conjugated to SP using commercially available cross-linkers. In addition to the delivery of proteins, we expand the use of SP to include nuclear delivery of DNA fragments that are actively expressed in the target cells. We also show that SP can be used to deliver whole bacteriophage particles as well as polystyrene beads up to 1 μm in diameter. The results show the ability of SP to deliver cargo of various sizes and chemical properties that retain their function within the cell. Furthermore, the overexpression of the NK1R in many tumors provides the potential for developing targeted delivery reagents that are specific toward diseased tissue.
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Affiliation(s)
- Shahir S Rizk
- Department of Biochemistry and Molecular Biology, The University of Chicago, 900 East 57th Street, Chicago, IL 60637, United States
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24
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Klir D, Kravarik J, Kubes P, Rezac K, Litseva E, Tomaszewski K, Karpinski L, Paduch M, Scholz M. Fusion neutron detector for time-of-flight measurements in z-pinch and plasma focus experiments. Rev Sci Instrum 2011; 82:033505. [PMID: 21456735 DOI: 10.1063/1.3559548] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
We have developed and tested sensitive neutron detectors for neutron time-of-flight measurements in z-pinch and plasma focus experiments with neutron emission times in tens of nanoseconds and with neutron yields between 10(6) and 10(12) per one shot. The neutron detectors are composed of a BC-408 fast plastic scintillator and Hamamatsu H1949-51 photomultiplier tube (PMT). During the calibration procedure, a PMT delay was determined for various operating voltages. The temporal resolution of the neutron detector was measured for the most commonly used PMT voltage of 1.4 kV. At the PF-1000 plasma focus, a novel method of the acquisition of a pulse height distribution has been used. This pulse height analysis enabled to determine the single neutron sensitivity for various neutron energies and to calibrate the neutron detector for absolute neutron yields at about 2.45 MeV.
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Affiliation(s)
- D Klir
- Faculty of Electrical Engineering, Czech Technical University in Prague, Technicka 2, 16627 Prague 6, Czech Republic.
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Zając S, Rzadkiewicz J, Rosmej O, Scholz M, Yongtao Z, Gójska A, Paduch M, Zielińska E. Spatially resolved high-resolution x-ray spectroscopy of high-current plasma-focus discharges. Rev Sci Instrum 2010; 81:10E312. [PMID: 21034011 DOI: 10.1063/1.3483190] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Soft x-ray emission from a Mather-type plasma-focus device (PF-1000) operated at ∼400 kJ was measured. The high density and temperature plasma were generated by the discharge in the deuterium-argon gas mixture in the modified (high-current) plasma-focus configuration. A spherically bent mica crystal spectrograph viewing the axial output of the pinch region was used to measure the x-ray spectra. Spatially resolved spectra including the characteristic x-ray lines of highly ionized Ar and continua were recorded by means of an x-ray film. The x-ray emission of PF-1000 device was studied at different areas of the pinch.
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Affiliation(s)
- S Zając
- Institute of Plasma Physics and Laser Microfusion, Hery 23, 01-497 Warsaw, Poland.
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Malinowska A, Szydlowski A, Malinowski K, Sadowski M, Zebrowski J, Scholz M, Paduch M, Zielinska E, Jaskóła M, Korman A. Application of SSNTDs for measurements of fusion reaction products in high-temperature plasma experiments. RADIAT MEAS 2009. [DOI: 10.1016/j.radmeas.2009.10.021] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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Affiliation(s)
- M. Hangartner
- a Institute for Hygiene and Ergonomics , Swiss Federal Institute of Technology , Clausiusstrasse 21, 8092, Zurich, Switzerland
| | - J. Hartung
- b Institute for Animal Hygiene and Animal Protection , Hannover School of Veterinary Medicine , Bünteweg 17p, 3000, Hannover 71, F.R. of Germany
| | - M. Paduch
- c Verein Deutscher Ingenieure , Graf‐Recke‐Strasse 84, 4000, Düsseldorf 1, F.R. of Germany
| | - B. F. Pain
- d AFRC Institute for Grassland and Animal Production , Hurley, Maidenhead, Berkshire, SL6 5LR, UK
| | - J. H. Voorburg
- e Institute of Agricultural Engineering (IMAG) , Mansholtlaan 10–12, Wageningen, The Netherlands
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Smietana K, Kasztura M, Paduch M, Derewenda U, Derewenda ZS, Otlewski J. Degenerate specificity of PDZ domains from RhoA-specific nucleotide exchange factors PDZRhoGEF and LARG. Acta Biochim Pol 2008. [DOI: 10.18388/abp.2008_3074] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
PDZ domains are ubiquitous protein-protein interaction modules which bind short, usually carboxyterminal fragments of receptors, other integral or membrane-associated proteins, and occasionally cytosolic proteins. Their role in organizing multiprotein complexes at the cellular membrane is crucial for many signaling pathways, but the rules defining their binding specificity are still poorly understood and do not readily explain the observed diversity of their known binding partners. Two homologous RhoA-specific, multidomain nucleotide exchange factors PDZRhoGEF and LARG contain PDZ domains which show a particularly broad recognition profile, as suggested by the identification of five diverse biological targets. To investigate the molecular roots of this phenomenon, we constructed a phage display library of random carboxyterminal hexapeptides. Peptide variants corresponding to the sequences identified in library selection were synthesized and their affinities for both PDZ domains were measured and compared with those of peptides derived from sequences of natural partners. Based on the analysis of the binding sequences identified for PDZRhoGEF, we propose a sequence for an 'optimal' binding partner. Our results support the hypothesis that PDZ-peptide interactions may be best understood when one considers the sum of entropic and dynamic effects for each peptide as a whole entity, rather than preferences for specific residues at a given position.
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Smietana K, Kasztura M, Paduch M, Derewenda U, Derewenda ZS, Otlewski J. Degenerate specificity of PDZ domains from RhoA-specific nucleotide exchange factors PDZRhoGEF and LARG. Acta Biochim Pol 2008; 55:269-280. [PMID: 18542831] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2008] [Revised: 05/20/2008] [Accepted: 05/29/2008] [Indexed: 05/26/2023]
Abstract
PDZ domains are ubiquitous protein-protein interaction modules which bind short, usually carboxyterminal fragments of receptors, other integral or membrane-associated proteins, and occasionally cytosolic proteins. Their role in organizing multiprotein complexes at the cellular membrane is crucial for many signaling pathways, but the rules defining their binding specificity are still poorly understood and do not readily explain the observed diversity of their known binding partners. Two homologous RhoA-specific, multidomain nucleotide exchange factors PDZRhoGEF and LARG contain PDZ domains which show a particularly broad recognition profile, as suggested by the identification of five diverse biological targets. To investigate the molecular roots of this phenomenon, we constructed a phage display library of random carboxyterminal hexapeptides. Peptide variants corresponding to the sequences identified in library selection were synthesized and their affinities for both PDZ domains were measured and compared with those of peptides derived from sequences of natural partners. Based on the analysis of the binding sequences identified for PDZRhoGEF, we propose a sequence for an 'optimal' binding partner. Our results support the hypothesis that PDZ-peptide interactions may be best understood when one considers the sum of entropic and dynamic effects for each peptide as a whole entity, rather than preferences for specific residues at a given position.
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Affiliation(s)
- Katarzyna Smietana
- Faculty of Biotechnology, Laboratory of Protein Engineering, University of Wrocław, Wrocław, Poland
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Abstract
PDZ domains are among the most common modules in eukaryotic, including human, genomes. They are found exclusively in large, multidomain cytosolic proteins--often with other domains that belong to a variety of families--and are involved in a plethora of physiological and pathophysiological events. PDZ domains mediate protein-protein interactions by binding to solvent-exposed and extended C-terminal short fragments of membrane-associated proteins, such as receptors and ion channels. Most of what is known about the mechanisms of target binding by PDZ domains is inferred from studies that involve isolated recombinant PDZ domains and short synthetic peptides that represent the targets. These binary systems constitute an obvious oversimplification and disregard factors such as noncanonical modes of binding and enhanced affinity due to multimeric interactions mediated by clusters and oligomers of PDZ-domain-containing proteins. We have tested whether the interaction between a dimeric form of PDZ domain that mimics a functional dimeric guanine nucleotide exchange factor, PDZ-RhoGEF (PDZ-containing RhoA-specific guanine nucleotide exchange factor) or LARG (leukemia-associated RhoA specific guanine nucleotide exchange factor), and a bivalent peptide that mimics the dimer of the plexin B receptor, could enhance the interaction between the two moieties. Peptide dimerization was achieved by cross-linking the N-terminal ends of peptides attached to Wang resin with poly(ethylene glycol) spacers (30-45 Angstroms in length). The interaction of dimeric PDZ domains with dimeric peptides resulted in an up to 20-fold increase in affinity compared to the simple binary system. This is consistent with the notion that multimerization of both receptors and PDZ-containing proteins might constitute an important regulatory mechanism.
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Affiliation(s)
- Marcin Paduch
- Faculty of Biotechnology, Department of Protein Engineering, University of Wrocław, Tamka 2, 54-137 Wrocław, Poland
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Scholz M, Bieńkowska B, Ivanova-Stanik IM, Karpiński L, Paduch M, Zielińska E, Kravárik J, Kubeš P, Sadowski MJ, Szydłowski A, Schmidt H. General characteristics of fusion-neutron emission from megajoule plasma-focus facility. ACTA ACUST UNITED AC 2006. [DOI: 10.1007/s10582-006-0206-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Mateja A, Cierpicki T, Paduch M, Derewenda ZS, Otlewski J. The dimerization mechanism of LIS1 and its implication for proteins containing the LisH motif. J Mol Biol 2006; 357:621-31. [PMID: 16445939 DOI: 10.1016/j.jmb.2006.01.002] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2005] [Revised: 12/02/2005] [Accepted: 01/03/2006] [Indexed: 10/25/2022]
Abstract
Miller-Dieker lissencephaly, or "smooth-brain" is a debilitating genetic developmental syndrome of the cerebral cortex, and is linked to mutations in the Lis1 gene. The LIS1 protein contains a so-called LisH motif at the N terminus, followed by a coiled-coil region and a seven WD-40 repeat forming beta-propeller structure. In vivo and in vitro, LIS1 is a dimer, and the dimerization is mediated by the N-terminal fragment and is essential for the protein's biological function. The recently determined crystal structure of the murine LIS1 N-terminal fragment encompassing residues 1-86 (N-LIS1) revealed that the LisH motif forms a tightly associated homodimer with a four-helix antiparallel bundle core, while the parallel coiled-coil situated downstream is stabilized by three canonical heptad repeats. This homodimer is uniquely asymmetric because of a distinct kink in one of the helices. Because the LisH motif is widespread among many proteins, some of which are implicated in human diseases, we investigated in detail the mechanism of N-LIS1 dimerization. We found that dimerization is dependent on both the LisH motif and the residues downstream of it, including the first few turns of the helix. We also have found that the coiled-coil does not contribute to dimerization, but instead is very labile and can adopt both supercoiled and helical conformations. These observations suggest that the presence of the LisH motif alone is not sufficient for high-affinity homodimerization and that other structural elements are likely to play an important role in this large family of proteins. The observed lability of the coiled-coil fragment in LIS1 is most likely of functional importance.
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Affiliation(s)
- Agnieszka Mateja
- Laboratory of Protein Engineering, Institute of Biochemistry and Molecular Biology, University of Wroclaw, Tamka 2, 50-137 Wroclaw, Poland
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Banaszak A, Szydlowski A, Sadowski MJ, Paduch M, Schmidt H, Scholz M, Wolowski J, Bonheure G, Van Wassenhove G. Application of PM-355 Solid-State Nulear Track Detectors for ion diagnostics in high-temperature plasma experiments. ACTA ACUST UNITED AC 2004. [DOI: 10.1007/bf03166404] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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Paduch M, Jeleń F, Otlewski J. Structure of small G proteins and their regulators. Acta Biochim Pol 2002; 48:829-50. [PMID: 11995995] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/24/2023]
Abstract
In recent years small G proteins have become an intensively studied group of regulatory GTP hydrolases involved in cell signaling. More than 100 small G proteins have been identified in eucaryotes from protozoan to human. The small G protein superfamily includes Ras, Rho Rab, Rac, Sarl/Arf and Ran homologs, which take part in numerous and diverse cellular processes, such as gene expression, cytoskeleton reorganization, microtubule organization, and vesicular and nuclear transport. These proteins share a common structural core, described as the G domain, and significant sequence similarity. In this paper we review the available data on G domain structure, together with a detailed analysis of the mechanism of action. We also present small G protein regulators: GTPase activating proteins that bind to a catalytic G domain and increase its low intrinsic hydrolase activity, GTPase dissociation inhibitors that stabilize the GDP-bound, inactive state of G proteins, and guanine nucleotide exchange factors that accelerate nucleotide exchange in response to cellular signals. Additionally, in this paper we describe some aspects of small G protein interactions with down-stream effectors.
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Affiliation(s)
- M Paduch
- Institute of Biochemistry and Molecular Biology, University of Wrocław, Poland
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Abstract
In recent years small G proteins have become an intensively studied group of regulatory GTP hydrolases involved in cell signaling. More than 100 small G proteins have been identified in eucaryotes from protozoan to human. The small G protein superfamily includes Ras, Rho Rab, Rac, Sarl/Arf and Ran homologs, which take part in numerous and diverse cellular processes, such as gene expression, cytoskeleton reorganization, microtubule organization, and vesicular and nuclear transport. These proteins share a common structural core, described as the G domain, and significant sequence similarity. In this paper we review the available data on G domain structure, together with a detailed analysis of the mechanism of action. We also present small G protein regulators: GTPase activating proteins that bind to a catalytic G domain and increase its low intrinsic hydrolase activity, GTPase dissociation inhibitors that stabilize the GDP-bound, inactive state of G proteins, and guanine nucleotide exchange factors that accelerate nucleotide exchange in response to cellular signals. Additionally, in this paper we describe some aspects of small G protein interactions with down-stream effectors.
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