1
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Yarawsky AE, Gough ES, Zai-Rose V, Figueroa NI, Cunningham HM, Burgner JW, DeLion MT, Paul LN. BASIS: BioAnalysis SEDFIT integrated software for cGMP analysis of SV-AUC data. EUROPEAN BIOPHYSICS JOURNAL : EBJ 2024; 53:111-121. [PMID: 38329496 DOI: 10.1007/s00249-024-01700-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Revised: 01/08/2024] [Accepted: 01/10/2024] [Indexed: 02/09/2024]
Abstract
Sedimentation velocity analytical ultracentrifugation (SV-AUC) has long been an important method for characterization of antibody therapeutics. Recently, SV-AUC has experienced a wave of new interest and usage from the gene and cell therapy industry, where SV-AUC has proven itself to be the "gold standard" analytical approach for determining capsid loading ratios for adeno-associated virus (AAV) and other viral vectors. While other more common approaches have existed in the realm of cGMP-compliant techniques for years, SV-AUC has long been used strictly for characterization, but not for release testing. This manuscript describes the challenges faced in bringing SV-AUC to a cGMP environment and describes a new program, "BASIS", which allows for 21 CFR Part 11-compliant data handling and data analysis using the well-known and frequently cited SEDFIT analysis software.
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Affiliation(s)
| | - Erik S Gough
- BioAnalysis, LLC, 3401 I Street Suite 206, Philadelphia, PA, 19134, USA
| | - Valeria Zai-Rose
- BioAnalysis, LLC, 3401 I Street Suite 206, Philadelphia, PA, 19134, USA
| | | | | | - John W Burgner
- BioAnalysis, LLC, 3401 I Street Suite 206, Philadelphia, PA, 19134, USA
| | - Michael T DeLion
- BioAnalysis, LLC, 3401 I Street Suite 206, Philadelphia, PA, 19134, USA
| | - Lake N Paul
- BioAnalysis, LLC, 3401 I Street Suite 206, Philadelphia, PA, 19134, USA.
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2
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Demeler B. Methods for the Design and Analysis of Analytical Ultracentrifugation Experiments. Curr Protoc 2024; 4:e974. [PMID: 38319042 PMCID: PMC10857736 DOI: 10.1002/cpz1.974] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2024]
Abstract
Analytical ultracentrifugation experiments play an integral role in the solution-phase characterization of biological macromolecules and their interactions. This unit discusses the design of sedimentation velocity and sedimentation equilibrium experiments performed with a Beckman Proteomelab XL-A or XL-I analytical ultracentrifuge and with a Beckman Optima AUC. Instrument settings and experimental design considerations are explained, and strategies for the analysis of experimental data with the UltraScan data analysis software package are presented. Special attention is paid to the strengths and weaknesses of the available detectors, and guidance is provided on how to extract maximum information from analytical ultracentrifugation experiments. © 2024 The Authors. Current Protocols published by Wiley Periodicals LLC.
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Affiliation(s)
- Borries Demeler
- Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, Alberta, Canada
- Department of Chemistry and Biochemistry, University of Montana, Missoula, Montana
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3
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Singh S, Machida S, Tulsian NK, Choong YK, Ng J, Shankar S, Liu Y, Chandiramani KV, Shi J, Sivaraman J. Structural Basis for the Enzymatic Activity of the HACE1 HECT-Type E3 Ligase Through N-Terminal Helix Dimerization. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2207672. [PMID: 37537642 PMCID: PMC10520629 DOI: 10.1002/advs.202207672] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Revised: 06/15/2023] [Indexed: 08/05/2023]
Abstract
HACE1 is an ankyrin repeat (AKR) containing HECT-type E3 ubiquitin ligase that interacts with and ubiquitinates multiple substrates. While HACE1 is a well-known tumor suppressor, its structure and mode of ubiquitination are not understood. The authors present the cryo-EM structures of human HACE1 along with in vitro functional studies that provide insights into how the enzymatic activity of HACE1 is regulated. HACE1 comprises of an N-terminal AKR domain, a middle (MID) domain, and a C-terminal HECT domain. Its unique G-shaped architecture interacts as a homodimer, with monomers arranged in an antiparallel manner. In this dimeric arrangement, HACE1 ubiquitination activity is hampered, as the N-terminal helix of one monomer restricts access to the C-terminal domain of the other. The in vitro ubiquitination assays, hydrogen-deuterium exchange mass spectrometry (HDX-MS) analysis, mutagenesis, and in silico modeling suggest that the HACE1 MID domain plays a crucial role along with the AKRs in RAC1 substrate recognition.
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Affiliation(s)
- Sunil Singh
- Department of Biological SciencesNational University of Singapore14 Science Drive 4Singapore117558Singapore
| | - Satoru Machida
- Department of Biological SciencesNational University of Singapore14 Science Drive 4Singapore117558Singapore
| | - Nikhil Kumar Tulsian
- Department of Biological SciencesNational University of Singapore14 Science Drive 4Singapore117558Singapore
- Department of BiochemistryNational University of Singapore28 Medical DriveSingapore117546Singapore
| | - Yeu Khai Choong
- Department of Biological SciencesNational University of Singapore14 Science Drive 4Singapore117558Singapore
| | - Joel Ng
- Department of Biological SciencesNational University of Singapore14 Science Drive 4Singapore117558Singapore
| | - Srihari Shankar
- Department of Biological SciencesNational University of Singapore14 Science Drive 4Singapore117558Singapore
| | - Yaochen Liu
- Department of Biological SciencesNational University of Singapore14 Science Drive 4Singapore117558Singapore
| | | | - Jian Shi
- Department of Biological SciencesNational University of Singapore14 Science Drive 4Singapore117558Singapore
| | - J Sivaraman
- Department of Biological SciencesNational University of Singapore14 Science Drive 4Singapore117558Singapore
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4
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Henrickson A, Ding X, Seal AG, Qu Z, Tomlinson L, Forsey J, Gradinaru V, Oka K, Demeler B. Characterization and quantification of adeno-associated virus capsid-loading states by multi-wavelength analytical ultracentrifugation with UltraScan. Nanomedicine (Lond) 2023; 18:1519-1534. [PMID: 37877696 PMCID: PMC10652292 DOI: 10.2217/nnm-2023-0156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Accepted: 09/04/2023] [Indexed: 10/26/2023] Open
Abstract
Aim: We present multi-wavelength (MW) analytical ultracentrifugation (AUC) methods offering superior accuracy for adeno-associated virus characterization and quantification. Methods: Experimental design guidelines are presented for MW sedimentation velocity and analytical buoyant density equilibrium AUC. Results: Our results were compared with dual-wavelength AUC, transmission electron microscopy and mass photometry. In contrast to dual-wavelength AUC, MW-AUC correctly quantifies adeno-associated virus capsid ratios and identifies contaminants. In contrast to transmission electron microscopy, partially filled capsids can also be detected and quantified. In contrast to mass photometry, first-principle results are obtained. Conclusion: Our study demonstrates the improved information provided by MW-AUC, highlighting the utility of several recently integrated UltraScan programs, and reinforces AUC as the gold-standard analysis for viral vectors.
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Affiliation(s)
- Amy Henrickson
- Department of Chemistry & Biochemistry, University of Lethbridge, Lethbridge, AB, T1K 3M4, Canada
| | - Xiaozhe Ding
- Division of Biology & Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Austin G Seal
- Gene Vector Core, Advanced Technology Cores, Baylor College of Medicine Houston, TX 77030, USA
| | - Zhe Qu
- Division of Biology & Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | | | - John Forsey
- Pharmaron Biologics Ltd, Speke, Liverpool, L24 8RB, UK
| | - Viviana Gradinaru
- Division of Biology & Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Kazuhiro Oka
- Gene Vector Core, Advanced Technology Cores, Baylor College of Medicine Houston, TX 77030, USA
- Department of Molecular & Cellular Biology, Baylor College of Medicine, TX 77030, USA
| | - Borries Demeler
- Department of Chemistry & Biochemistry, University of Lethbridge, Lethbridge, AB, T1K 3M4, Canada
- Department of Chemistry & Biochemistry, University of Montana, Missoula, MT 59812, USA
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5
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Henrickson A, Montina T, Hazendonk P, Lomonte B, Neves-Ferreira AGC, Demeler B. SDS-induced hexameric oligomerization of myotoxin-II from Bothrops asper assessed by sedimentation velocity and nuclear magnetic resonance. EUROPEAN BIOPHYSICS JOURNAL : EBJ 2023; 52:445-457. [PMID: 37209172 PMCID: PMC10526984 DOI: 10.1007/s00249-023-01658-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Revised: 04/21/2023] [Accepted: 04/30/2023] [Indexed: 05/22/2023]
Abstract
We report the solution behavior, oligomerization state, and structural details of myotoxin-II purified from the venom of Bothrops asper in the presence and absence of sodium dodecyl sulfate (SDS) and multiple lipids, as examined by analytical ultracentrifugation and nuclear magnetic resonance. Molecular functional and structural details of the myotoxic mechanism of group II Lys-49 phospholipase A2 homologues have been only partially elucidated so far, and conflicting observations have been reported in the literature regarding the monomeric vs. oligomeric state of these toxins in solution. We observed the formation of a stable and discrete, hexameric form of myotoxin-II, but only in the presence of small amounts of SDS. In SDS-free medium, myotoxin-II was insensitive to mass action and remained monomeric at all concentrations examined (up to 3 mg/ml, 218.2 μM). At SDS concentrations above the critical micelle concentration, only dimers and trimers were observed, and at intermediate SDS concentrations, aggregates larger than hexamers were observed. We found that the amount of SDS required to form a stable hexamer varies with protein concentration, suggesting the need for a precise stoichiometry of free SDS molecules. The discovery of a stable hexameric species in the presence of a phospholipid mimetic suggests a possible physiological role for this oligomeric form, and may shed light on the poorly understood membrane-disrupting mechanism of this myotoxic protein class.
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Affiliation(s)
- Amy Henrickson
- Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, AB, Canada
| | - Tony Montina
- Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, AB, Canada
| | - Paul Hazendonk
- Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, AB, Canada
| | - Bruno Lomonte
- Instituto Clodomiro Picado, Facultad de Microbiología San José, Universidad de Costa Rica, San José, Costa Rica
| | | | - Borries Demeler
- Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, AB, Canada.
- Department of Chemistry and Biochemistry, University of Montana, Missoula, MT, USA.
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6
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Mortezazadeh S, Demeler B. Systematic noise removal from analytical ultracentrifugation data with UltraScan. EUROPEAN BIOPHYSICS JOURNAL : EBJ 2023; 52:203-213. [PMID: 36786920 PMCID: PMC10423743 DOI: 10.1007/s00249-023-01631-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Revised: 12/29/2022] [Accepted: 01/23/2023] [Indexed: 02/15/2023]
Abstract
A method for removing time- and radially invariant noise from sedimentation velocity and sedimentation equilibrium experiments performed in an analytical ultracentrifuge is presented. The method averages repeat radial incident light measurements as a function of the photomultiplier response at different wavelengths to remove the majority of the time-invariant noise contributions from intensity data measurements. The results of this method are compared to traditional absorbance data generated with a buffer reference and the Beckman Optima AUC data acquisition program, and with the standard UltraScan refinement workflow. The method avoids the amplification of stochastic noise inherent in the absorbance scan subtraction traditionally employed in sedimentation velocity and equilibrium data. In addition, the collection of intensity data frees up the reference channel for additional samples, doubling the capacity of the instrument. In comparison to absorbance data, the residual mean square deviation of a fitted sedimentation velocity experiment without additional noise correction by UltraScan was improved by a factor of 4.5 when using the new method. This improvement benefits sedimentation equilibrium experiments as well as analytical buoyant density equilibrium experiments where routine time-invariant noise correction calculations cannot be performed.
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Affiliation(s)
- Saeed Mortezazadeh
- Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, AB, T1K3M4, Canada
| | - Borries Demeler
- Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, AB, T1K3M4, Canada.
- Department of Chemistry and Biochemistry, University of Montana, Missoula, MT, 59812, United States.
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7
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Nandy S, Maranholkar VM, Crum M, Wasden K, Patil U, Goyal A, Vu B, Kourentzi K, Mo W, Henrickson A, Demeler B, Sen M, Willson RC. Expression and Characterization of Intein-Cyclized Trimer of Staphylococcus aureus Protein A Domain Z. Int J Mol Sci 2023; 24:1281. [PMID: 36674796 PMCID: PMC9865183 DOI: 10.3390/ijms24021281] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 12/22/2022] [Accepted: 12/27/2022] [Indexed: 01/11/2023] Open
Abstract
Staphylococcus aureus protein A (SpA) is an IgG Fc-binding virulence factor that is widely used in antibody purification and as a scaffold to develop affinity molecules. A cyclized SpA Z domain could offer exopeptidase resistance, reduced chromatographic ligand leaching after single-site endopeptidase cleavage, and enhanced IgG binding properties by preorganization, potentially reducing conformational entropy loss upon binding. In this work, a Z domain trimer (Z3) was cyclized using protein intein splicing. Interactions of cyclic and linear Z3 with human IgG1 were characterized by differential scanning fluorimetry (DSF), surface plasmon resonance (SPR), and isothermal titration calorimetry (ITC). DSF showed a 5 ℃ increase in IgG1 melting temperature when bound by each Z3 variant. SPR showed the dissociation constants of linear and cyclized Z3 with IgG1 to be 2.9 nM and 3.3 nM, respectively. ITC gave association enthalpies for linear and cyclic Z3 with IgG1 of -33.0 kcal/mol and -32.7 kcal/mol, and -T∆S of association 21.2 kcal/mol and 21.6 kcal/mol, respectively. The compact cyclic Z3 protein contains 2 functional binding sites and exhibits carboxypeptidase Y-resistance. The results suggest cyclization as a potential approach toward more stable SpA-based affinity ligands, and this analysis may advance our understanding of protein engineering for ligand and drug development.
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Affiliation(s)
- Suman Nandy
- William A. Brookshire Department of Chemical and Biomolecular Engineering, University of Houston, Houston, TX 77204, USA
| | - Vijay M. Maranholkar
- Department of Biology and Biochemistry, University of Houston, Houston, TX 77004, USA
| | - Mary Crum
- William A. Brookshire Department of Chemical and Biomolecular Engineering, University of Houston, Houston, TX 77204, USA
| | - Katherine Wasden
- William A. Brookshire Department of Chemical and Biomolecular Engineering, University of Houston, Houston, TX 77204, USA
| | - Ujwal Patil
- Department of Biology and Biochemistry, University of Houston, Houston, TX 77004, USA
| | - Atul Goyal
- William A. Brookshire Department of Chemical and Biomolecular Engineering, University of Houston, Houston, TX 77204, USA
| | - Binh Vu
- William A. Brookshire Department of Chemical and Biomolecular Engineering, University of Houston, Houston, TX 77204, USA
| | - Katerina Kourentzi
- William A. Brookshire Department of Chemical and Biomolecular Engineering, University of Houston, Houston, TX 77204, USA
| | - William Mo
- William A. Brookshire Department of Chemical and Biomolecular Engineering, University of Houston, Houston, TX 77204, USA
| | - Amy Henrickson
- Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, AB T1K 3M4, Canada
| | - Borries Demeler
- Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, AB T1K 3M4, Canada
- Department of Chemistry and Biochemistry, University of Montana, Missoula, MT 59812, USA
| | - Mehmet Sen
- Department of Biology and Biochemistry, University of Houston, Houston, TX 77004, USA
| | - Richard C. Willson
- William A. Brookshire Department of Chemical and Biomolecular Engineering, University of Houston, Houston, TX 77204, USA
- Department of Biology and Biochemistry, University of Houston, Houston, TX 77004, USA
- Escuela de Medicina y Ciencias de Salud, Tecnológico de Monterrey, Monterrey 64849, Nuevo León, Mexico
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8
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Waszkiewicz R, Ranasinghe M, Fogg JM, Catanese DJ, Ekiel-Jeżewska ML, Lisicki M, Demeler B, Zechiedrich L, Szymczak P. DNA supercoiling-induced shapes alter minicircle hydrodynamic properties. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.04.522747. [PMID: 36711572 PMCID: PMC9881935 DOI: 10.1101/2023.01.04.522747] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
DNA in cells is organized in negatively supercoiled loops. The resulting torsional and bending strain allows DNA to adopt a surprisingly wide variety of 3-D shapes. This interplay between negative supercoiling, looping, and shape influences how DNA is stored, replicated, transcribed, repaired, and likely every other aspect of DNA activity. To understand the consequences of negative supercoiling and curvature on the hydrodynamic properties of DNA, we submitted 336 bp and 672 bp DNA minicircles to analytical ultracentrifugation (AUC). We found that the diffusion coefficient, sedimentation coefficient, and the DNA hydrodynamic radius strongly depended on circularity, loop length, and degree of negative supercoiling. Because AUC cannot ascertain shape beyond degree of non-globularity, we applied linear elasticity theory to predict DNA shapes, and combined these with hydrodynamic calculations to interpret the AUC data, with reasonable agreement between theory and experiment. These complementary approaches, together with earlier electron cryotomography data, provide a framework for understanding and predicting the effects of supercoiling on the shape and hydrodynamic properties of DNA.
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Affiliation(s)
- Radost Waszkiewicz
- Institute of Theoretical Physics, Faculty of Physics, University of Warsaw, Pasteura 5, 02-093 Warsaw, Poland
| | - Maduni Ranasinghe
- University of Lethbridge, Dept. of Chemistry and Biochemistry, Alberta, T1K3M4, Canada
| | - Jonathan M. Fogg
- Department of Molecular Virology and Microbiology, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Department of Pharmacology and Chemical Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
| | - Daniel J. Catanese
- Department of Biosciences, Rice University, 6100 Main St., Houston, TX 77005-1827, USA
| | - Maria L. Ekiel-Jeżewska
- Institute of Fundamental Technological Research, Polish Academy of Sciences, A. Pawińskiego 5B, 02-106 Warsaw, Poland,Co-contributing authors: MLE-J: , ML: , BD: , LZ: , PS:
| | - Maciej Lisicki
- Institute of Theoretical Physics, Faculty of Physics, University of Warsaw, Pasteura 5, 02-093 Warsaw, Poland,Co-contributing authors: MLE-J: , ML: , BD: , LZ: , PS:
| | - Borries Demeler
- University of Lethbridge, Dept. of Chemistry and Biochemistry, Alberta, T1K3M4, Canada,University of Montana, Dept. of Chemistry and Biochemistry, Missoula, MT 59812, USA,Co-contributing authors: MLE-J: , ML: , BD: , LZ: , PS:
| | - Lynn Zechiedrich
- Department of Molecular Virology and Microbiology, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Department of Pharmacology and Chemical Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA,Co-contributing authors: MLE-J: , ML: , BD: , LZ: , PS:
| | - Piotr Szymczak
- Institute of Theoretical Physics, Faculty of Physics, University of Warsaw, Pasteura 5, 02-093 Warsaw, Poland,Co-contributing authors: MLE-J: , ML: , BD: , LZ: , PS:
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9
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Henrickson A, Gorbet GE, Savelyev A, Kim M, Hargreaves J, Schultz SK, Kothe U, Demeler B. Multi-wavelength analytical ultracentrifugation of biopolymer mixtures and interactions. Anal Biochem 2022; 652:114728. [PMID: 35609686 PMCID: PMC10276540 DOI: 10.1016/j.ab.2022.114728] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2022] [Revised: 05/07/2022] [Accepted: 05/11/2022] [Indexed: 11/01/2022]
Abstract
Multi-wavelength analytical ultracentrifugation (MW-AUC) is a recent development made possible by new analytical ultracentrifuge optical systems. MW-AUC extends the basic hydrodynamic information content of AUC and provides access to a wide range of new applications for biopolymer characterization, and is poised to become an essential analytical tool to study macromolecular interactions. It adds an orthogonal spectral dimension to the traditional hydrodynamic characterization by exploiting unique chromophores in analyte mixtures that may or may not interact. Here we illustrate the utility of MW-AUC for experimental investigations where the benefit of the added spectral dimension provides critical information that is not accessible, and impossible to resolve with traditional AUC methods. We demonstrate the improvements in resolution and information content obtained by this technique compared to traditional single- or dual-wavelength approaches, and discuss experimental design considerations and limitations of the method. We further address the advantages and disadvantages of the two MW optical systems available today, and the differences in data analysis strategies between the two systems.
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Affiliation(s)
- Amy Henrickson
- University of Lethbridge, Dept. of Chemistry and Biochemistry, Lethbridge, Alberta, Canada
| | | | - Alexey Savelyev
- University of Montana, Dept. of Chemistry, Missoula, MT, USA
| | - Minji Kim
- Carnegie Mellon University, Dept. of Computer Science, Pittsburgh, PA, USA
| | | | - Sarah K Schultz
- University of Lethbridge, Dept. of Chemistry and Biochemistry, Lethbridge, Alberta, Canada
| | - Ute Kothe
- University of Lethbridge, Dept. of Chemistry and Biochemistry, Lethbridge, Alberta, Canada; University of Manitoba, Department of Chemistry, Winnipeg, Manitoba, Canada
| | - Borries Demeler
- University of Lethbridge, Dept. of Chemistry and Biochemistry, Lethbridge, Alberta, Canada; AUC Solutions, LLC, Houston, TX, USA; University of Montana, Dept. of Chemistry, Missoula, MT, USA.
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10
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Structure of Reelin repeat 8 and the adjacent C-terminal region. Biophys J 2022; 121:2526-2537. [DOI: 10.1016/j.bpj.2022.06.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Revised: 05/15/2022] [Accepted: 05/31/2022] [Indexed: 11/02/2022] Open
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11
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Tenorio CA, Parker JB, Blaber M. Functionalization of a symmetric protein scaffold: Redundant folding nuclei and alternative oligomeric folding pathways. Protein Sci 2022; 31:e4301. [PMID: 35481645 PMCID: PMC8996475 DOI: 10.1002/pro.4301] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 03/12/2022] [Accepted: 03/15/2022] [Indexed: 02/02/2023]
Abstract
Successful de novo protein design ideally targets specific folding kinetics, stability thermodynamics, and biochemical functionality, and the simultaneous achievement of all these criteria in a single step design is challenging. Protein design is potentially simplified by separating the problem into two steps: (a) an initial design of a protein "scaffold" having appropriate folding kinetics and stability thermodynamics, followed by (b) appropriate functional mutation-possibly involving insertion of a peptide functional "cassette." This stepwise approach can also separate the orthogonal effects of the "stability/function" and "foldability/function" tradeoffs commonly observed in protein design. If the scaffold is a protein architecture having an exact rotational symmetry, then there is the potential for redundant folding nuclei and multiple equivalent sites of functionalization; thereby enabling broader functional adaptation. We describe such a "scaffold" and functional "cassette" design strategy applied to a β-trefoil threefold symmetric architecture and a heparin ligand functionality. The results support the availability of redundant folding nuclei within this symmetric architecture, and also identify a minimal peptide cassette conferring heparin affinity. The results also identify an energy barrier of destabilization that switches the protein folding pathway from monomeric to trimeric, thereby identifying another potential advantage of symmetric protein architecture in de novo design.
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Affiliation(s)
- Connie A. Tenorio
- Department of Biomedical Sciences Florida State University Tallahassee Florida USA
| | - Joseph B. Parker
- Department of Biomedical Sciences Florida State University Tallahassee Florida USA
| | - Michael Blaber
- Department of Biomedical Sciences Florida State University Tallahassee Florida USA
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12
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Soares BS, Rocha SLG, Bastos VA, Lima DB, Carvalho PC, Gozzo FC, Demeler B, Williams TL, Arnold J, Henrickson A, Jørgensen TJD, Souza TACB, Perales J, Valente RH, Lomonte B, Gomes-Neto F, Neves-Ferreira AGC. Molecular Architecture of the Antiophidic Protein DM64 and its Binding Specificity to Myotoxin II From Bothrops asper Venom. Front Mol Biosci 2022; 8:787368. [PMID: 35155563 PMCID: PMC8830425 DOI: 10.3389/fmolb.2021.787368] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 12/07/2021] [Indexed: 01/11/2023] Open
Abstract
DM64 is a toxin-neutralizing serum glycoprotein isolated from Didelphis aurita, an ophiophagous marsupial naturally resistant to snake envenomation. This 64 kDa antitoxin targets myotoxic phospholipases A2, which account for most local tissue damage of viperid snakebites. We investigated the noncovalent complex formed between native DM64 and myotoxin II, a myotoxic phospholipase-like protein from Bothrops asper venom. Analytical ultracentrifugation (AUC) and size exclusion chromatography indicated that DM64 is monomeric in solution and binds equimolar amounts of the toxin. Attempts to crystallize native DM64 for X-ray diffraction were unsuccessful. Obtaining recombinant protein to pursue structural studies was also challenging. Classical molecular modeling techniques were impaired by the lack of templates with more than 25% sequence identity with DM64. An integrative structural biology approach was then applied to generate a three-dimensional model of the inhibitor bound to myotoxin II. I-TASSER individually modeled the five immunoglobulin-like domains of DM64. Distance constraints generated by cross-linking mass spectrometry of the complex guided the docking of DM64 domains to the crystal structure of myotoxin II, using Rosetta. AUC, small-angle X-ray scattering (SAXS), molecular modeling, and molecular dynamics simulations indicated that the DM64-myotoxin II complex is structured, shows flexibility, and has an anisotropic shape. Inter-protein cross-links and limited hydrolysis analyses shed light on the inhibitor's regions involved with toxin interaction, revealing the critical participation of the first, third, and fifth domains of DM64. Our data showed that the fifth domain of DM64 binds to myotoxin II amino-terminal and beta-wing regions. The third domain of the inhibitor acts in a complementary way to the fifth domain. Their binding to these toxin regions presumably precludes dimerization, thus interfering with toxicity, which is related to the quaternary structure of the toxin. The first domain of DM64 interacts with the functional site of the toxin putatively associated with membrane anchorage. We propose that both mechanisms concur to inhibit myotoxin II toxicity by DM64 binding. The present topological characterization of this toxin-antitoxin complex constitutes an essential step toward the rational design of novel peptide-based antivenom therapies targeting snake venom myotoxins.
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Affiliation(s)
- Barbara S. Soares
- Laboratory of Toxinology, Oswaldo Cruz Institute, Rio de Janeiro, Brazil
| | | | - Viviane A. Bastos
- Laboratory of Toxinology, Oswaldo Cruz Institute, Rio de Janeiro, Brazil
| | - Diogo B. Lima
- Department of Chemical Biology, Leibniz Forschungsinstitut für Molekulare Pharmakologie (FMP), Berlin, Germany
| | - Paulo C. Carvalho
- Laboratory for Structural and Computational Proteomics, Carlos Chagas Institute, Curitiba, Brazil
| | - Fabio C. Gozzo
- Dalton Mass Spectrometry Laboratory, University of Campinas, Campinas, Brazil
| | - Borries Demeler
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX, United States
- Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, AB, Canada
- Department of Chemistry and Biochemistry, University of Montana, Missoula, MT, United States
| | - Tayler L. Williams
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX, United States
| | - Janelle Arnold
- Department of Environmental Science, Princeton University, Princeton, NJ, United States
| | - Amy Henrickson
- Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, AB, Canada
| | - Thomas J. D. Jørgensen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Tatiana A. C. B. Souza
- Laboratory for Structural and Computational Proteomics, Carlos Chagas Institute, Curitiba, Brazil
| | - Jonas Perales
- Laboratory of Toxinology, Oswaldo Cruz Institute, Rio de Janeiro, Brazil
| | - Richard H. Valente
- Laboratory of Toxinology, Oswaldo Cruz Institute, Rio de Janeiro, Brazil
| | - Bruno Lomonte
- Clodomiro Picado Institute, University of Costa Rica, San José, Costa Rica
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13
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Evans CM, Phillips M, Malone KL, Tonelli M, Cornilescu G, Cornilescu C, Holton SJ, Gorjánácz M, Wang L, Carlson S, Gay JC, Nix JC, Demeler B, Markley JL, Glass KC. Coordination of Di-Acetylated Histone Ligands by the ATAD2 Bromodomain. Int J Mol Sci 2021; 22:9128. [PMID: 34502039 PMCID: PMC8430952 DOI: 10.3390/ijms22179128] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 08/13/2021] [Accepted: 08/17/2021] [Indexed: 12/15/2022] Open
Abstract
The ATPase Family, AAA domain-containing protein 2 (ATAD2) bromodomain (BRD) has a canonical bromodomain structure consisting of four α-helices. ATAD2 functions as a co-activator of the androgen and estrogen receptors as well as the MYC and E2F transcription factors. ATAD2 also functions during DNA replication, recognizing newly synthesized histones. In addition, ATAD2 is shown to be up-regulated in multiple forms of cancer including breast, lung, gastric, endometrial, renal, and prostate. Furthermore, up-regulation of ATAD2 is strongly correlated with poor prognosis in many types of cancer, making the ATAD2 bromodomain an innovative target for cancer therapeutics. In this study, we describe the recognition of histone acetyllysine modifications by the ATAD2 bromodomain. Residue-specific information on the complex formed between the histone tail and the ATAD2 bromodomain, obtained through nuclear magnetic resonance spectroscopy (NMR) and X-ray crystallography, illustrates key residues lining the binding pocket, which are involved in coordination of di-acetylated histone tails. Analytical ultracentrifugation, NMR relaxation data, and isothermal titration calorimetry further confirm the monomeric state of the functionally active ATAD2 bromodomain in complex with di-acetylated histone ligands. Overall, we describe histone tail recognition by ATAD2 BRD and illustrate that one acetyllysine group is primarily engaged by the conserved asparagine (N1064), the "RVF" shelf residues, and the flexible ZA loop. Coordination of a second acetyllysine group also occurs within the same binding pocket but is essentially governed by unique hydrophobic and electrostatic interactions making the di-acetyllysine histone coordination more specific than previously presumed.
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Affiliation(s)
- Chiara M. Evans
- Department of Pharmaceutical Sciences, Albany College of Pharmacy and Health Sciences, Colchester, VT 05446, USA; (C.M.E.); (M.P.); (K.L.M.); (S.C.); (J.C.G.)
| | - Margaret Phillips
- Department of Pharmaceutical Sciences, Albany College of Pharmacy and Health Sciences, Colchester, VT 05446, USA; (C.M.E.); (M.P.); (K.L.M.); (S.C.); (J.C.G.)
- Department of Pharmacology, Larner College of Medicine, University of Vermont, Burlington, VT 05405, USA
| | - Kiera L. Malone
- Department of Pharmaceutical Sciences, Albany College of Pharmacy and Health Sciences, Colchester, VT 05446, USA; (C.M.E.); (M.P.); (K.L.M.); (S.C.); (J.C.G.)
- Department of Pharmacology, Larner College of Medicine, University of Vermont, Burlington, VT 05405, USA
| | - Marco Tonelli
- National Magnetic Resonance Facility at Madison, University of Wisconsin-Madison, Madison, WI 53706, USA; (M.T.); (G.C.); (C.C.); (J.L.M.)
| | - Gabriel Cornilescu
- National Magnetic Resonance Facility at Madison, University of Wisconsin-Madison, Madison, WI 53706, USA; (M.T.); (G.C.); (C.C.); (J.L.M.)
| | - Claudia Cornilescu
- National Magnetic Resonance Facility at Madison, University of Wisconsin-Madison, Madison, WI 53706, USA; (M.T.); (G.C.); (C.C.); (J.L.M.)
| | - Simon J. Holton
- Bayer AG, Pharmaceuticals, Research & Early Development Oncology, 13353 Berlin, Germany; (S.J.H.); (M.G.)
| | - Mátyás Gorjánácz
- Bayer AG, Pharmaceuticals, Research & Early Development Oncology, 13353 Berlin, Germany; (S.J.H.); (M.G.)
| | - Liping Wang
- Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, TX 78229, USA; (L.W.); (B.D.)
| | - Samuel Carlson
- Department of Pharmaceutical Sciences, Albany College of Pharmacy and Health Sciences, Colchester, VT 05446, USA; (C.M.E.); (M.P.); (K.L.M.); (S.C.); (J.C.G.)
| | - Jamie C. Gay
- Department of Pharmaceutical Sciences, Albany College of Pharmacy and Health Sciences, Colchester, VT 05446, USA; (C.M.E.); (M.P.); (K.L.M.); (S.C.); (J.C.G.)
| | - Jay C. Nix
- Molecular Biology Consortium, Advanced Light Source, Berkeley, CA 94720, USA;
| | - Borries Demeler
- Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, TX 78229, USA; (L.W.); (B.D.)
- Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, AB T1K 3M4, Canada
| | - John L. Markley
- National Magnetic Resonance Facility at Madison, University of Wisconsin-Madison, Madison, WI 53706, USA; (M.T.); (G.C.); (C.C.); (J.L.M.)
| | - Karen C. Glass
- Department of Pharmaceutical Sciences, Albany College of Pharmacy and Health Sciences, Colchester, VT 05446, USA; (C.M.E.); (M.P.); (K.L.M.); (S.C.); (J.C.G.)
- Department of Pharmacology, Larner College of Medicine, University of Vermont, Burlington, VT 05405, USA
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14
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Kodera N, Abe H, Nguyen PDN, Ono S. Native cyclase-associated protein and actin from Xenopus laevis oocytes form a unique 4:4 complex with a tripartite structure. J Biol Chem 2021; 296:100649. [PMID: 33839148 PMCID: PMC8113726 DOI: 10.1016/j.jbc.2021.100649] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Revised: 04/01/2021] [Accepted: 04/07/2021] [Indexed: 11/26/2022] Open
Abstract
Cyclase-associated protein (CAP) is a conserved actin-binding protein that regulates multiple aspects of actin dynamics, including polymerization, depolymerization, filament severing, and nucleotide exchange. CAP has been isolated from different cells and tissues in an equimolar complex with actin, and previous studies have shown that a CAP–actin complex contains six molecules each of CAP and actin. Intriguingly, here, we successfully isolated a complex of Xenopus cyclase-associated protein 1 (XCAP1) with actin from oocyte extracts, which contained only four molecules each of XCAP1 and actin. This XCAP1–actin complex remained stable as a single population of 340 kDa species during hydrodynamic analyses using gel filtration or analytical ultracentrifugation. Examination of the XCAP1–actin complex by high-speed atomic force microscopy revealed a tripartite structure: one middle globular domain and two globular arms. The two arms were observed in high and low states. The arms at the high state were spontaneously converted to the low state by dissociation of actin from the complex. However, when extra G-actin was added, the arms at the low state were converted to the high state. Based on the known structures of the N-terminal helical-folded domain and C-terminal CARP domain, we hypothesize that the middle globular domain corresponds to a tetramer of the N-terminal helical-folded domain of XCAP1 and that each arm in the high state corresponds to a heterotetramer containing a dimer of the C-terminal CARP domain of XCAP1 and two G-actin molecules. This novel configuration of a CAP–actin complex should help to understand how CAP promotes actin filament disassembly.
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Affiliation(s)
- Noriyuki Kodera
- WPI-Nano Life Science Institute, Kanazawa University, Kanazawa, Ishikawa, Japan
| | - Hiroshi Abe
- Department of Biology, Graduate School of Science, Chiba University, Chiba, Japan
| | | | - Shoichiro Ono
- Departments of Pathology and Cell Biology, Emory University School of Medicine, Atlanta, Georgia, USA; Winship Cancer Institute, Emory University School of Medicine, Atlanta, Georgia, USA.
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15
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Horne CR, Venugopal H, Panjikar S, Wood DM, Henrickson A, Brookes E, North RA, Murphy JM, Friemann R, Griffin MDW, Ramm G, Demeler B, Dobson RCJ. Mechanism of NanR gene repression and allosteric induction of bacterial sialic acid metabolism. Nat Commun 2021; 12:1988. [PMID: 33790291 PMCID: PMC8012715 DOI: 10.1038/s41467-021-22253-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Accepted: 03/03/2021] [Indexed: 12/20/2022] Open
Abstract
Bacteria respond to environmental changes by inducing transcription of some genes and repressing others. Sialic acids, which coat human cell surfaces, are a nutrient source for pathogenic and commensal bacteria. The Escherichia coli GntR-type transcriptional repressor, NanR, regulates sialic acid metabolism, but the mechanism is unclear. Here, we demonstrate that three NanR dimers bind a (GGTATA)3-repeat operator cooperatively and with high affinity. Single-particle cryo-electron microscopy structures reveal the DNA-binding domain is reorganized to engage DNA, while three dimers assemble in close proximity across the (GGTATA)3-repeat operator. Such an interaction allows cooperative protein-protein interactions between NanR dimers via their N-terminal extensions. The effector, N-acetylneuraminate, binds NanR and attenuates the NanR-DNA interaction. The crystal structure of NanR in complex with N-acetylneuraminate reveals a domain rearrangement upon N-acetylneuraminate binding to lock NanR in a conformation that weakens DNA binding. Our data provide a molecular basis for the regulation of bacterial sialic acid metabolism. The GntR superfamily is one of the largest families of transcription factors in prokaryotes. Here the authors combine biophysical analysis and structural biology to dissect the mechanism by which NanR — a GntR-family regulator — binds to its promoter to repress the transcription of genes necessary for sialic acid metabolism.
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Affiliation(s)
- Christopher R Horne
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Hariprasad Venugopal
- Clive and Vera Ramaciotti Centre for Cryo-Electron Microscopy, Monash University, Clayton, VIC, Australia
| | - Santosh Panjikar
- Australian Synchrotron, ANSTO, Clayton, VIC, Australia.,Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC, Australia
| | - David M Wood
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Amy Henrickson
- Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, AB, Canada
| | - Emre Brookes
- Department of Chemistry, University of Montana, Missoula, MT, USA
| | - Rachel A North
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - James M Murphy
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia.,Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | - Rosmarie Friemann
- Department of Clinical Microbiology, Sahlgrenska University Hospital, Gothenburg, Sweden.,Centre for Antibiotic Resistance Research (CARe), University of Gothenburg, Gothenburg, Sweden
| | - Michael D W Griffin
- Bio21 Molecular Science and Biotechnology Institute, Department of Biochemistry and Pharmacology, University of Melbourne, Parkville, VIC, Australia
| | - Georg Ramm
- Clive and Vera Ramaciotti Centre for Cryo-Electron Microscopy, Monash University, Clayton, VIC, Australia.,Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC, Australia
| | - Borries Demeler
- Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, AB, Canada.,Department of Chemistry, University of Montana, Missoula, MT, USA
| | - Renwick C J Dobson
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, Christchurch, New Zealand. .,Bio21 Molecular Science and Biotechnology Institute, Department of Biochemistry and Pharmacology, University of Melbourne, Parkville, VIC, Australia.
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16
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Henrickson A, Kulkarni JA, Zaifman J, Gorbet GE, Cullis PR, Demeler B. Density Matching Multi-wavelength Analytical Ultracentrifugation to Measure Drug Loading of Lipid Nanoparticle Formulations. ACS NANO 2021; 15:5068-5076. [PMID: 33617224 DOI: 10.1021/acsnano.0c10069] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Previous work suggested that lipid nanoparticle (LNP) formulations, encapsulating nucleic acids, display electron-dense morphology when examined by cryogenic-transmission electron microscopy (cryo-TEM). Critically, the employed cryo-TEM method cannot differentiate between loaded and empty LNP formulations. Clinically relevant formulations contain high lipid-to-nucleic acid ratios (10-25 (w/w)), and for systems that contain mRNA or DNA, it is anticipated that a substantial fraction of the LNP population does not contain a payload. Here, we present a method based on the global analysis of multi-wavelength sedimentation velocity analytical ultracentrifugation, using density matching with heavy water, that not only measures the standard sedimentation and diffusion coefficient distributions of LNP mixtures, but also reports the corresponding partial specific volume distributions and optically separates signal contributions from nucleic acid cargo and lipid shell. This makes it possible to reliably predict molar mass and anisotropy distributions, in particular, for systems that are heterogeneous in partial specific volume and have low to intermediate densities. Our method makes it possible to unambiguously measure the density of nanoparticles and is motivated by the need to characterize the extent to which lipid nanoparticles are loaded with nucleic acid cargoes. Since the densities of nucleic acids and lipids substantially differ, the measured density is directly proportional to the loading of nanoparticles. Hence, different loading levels will produce particles with variable density and partial specific volume. An UltraScan software module was developed to implement this approach for routine analysis.
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Affiliation(s)
- Amy Henrickson
- Department of Chemistry and Biochemistry, The University of Lethbridge, Lethbridge, Alberta, Canada T1K 3M4
| | - Jayesh A Kulkarni
- Department of Biochemistry and Molecular Biology, Faculty of MedicineUniversity of British Columbia, Vancouver, British Columbia, Canada V6T 1Z3
| | - Josh Zaifman
- Department of Biochemistry and Molecular Biology, Faculty of MedicineUniversity of British Columbia, Vancouver, British Columbia, Canada V6T 1Z3
| | | | - Pieter R Cullis
- Department of Biochemistry and Molecular Biology, Faculty of MedicineUniversity of British Columbia, Vancouver, British Columbia, Canada V6T 1Z3
| | - Borries Demeler
- Department of Chemistry and Biochemistry, The University of Lethbridge, Lethbridge, Alberta, Canada T1K 3M4
- AUC Solutions, Houston, Texas 77494, United States
- Department of Chemistry, University of Montana, Missoula, Montana 59812, United States
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17
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Yu CH, Bhattacharya A, Persaud M, Taylor AB, Wang Z, Bulnes-Ramos A, Xu J, Selyutina A, Martinez-Lopez A, Cano K, Demeler B, Kim B, Hardies SC, Diaz-Griffero F, Ivanov DN. Nucleic acid binding by SAMHD1 contributes to the antiretroviral activity and is enhanced by the GpsN modification. Nat Commun 2021; 12:731. [PMID: 33531504 PMCID: PMC7854603 DOI: 10.1038/s41467-021-21023-8] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Accepted: 01/08/2021] [Indexed: 12/26/2022] Open
Abstract
SAMHD1 impedes infection of myeloid cells and resting T lymphocytes by retroviruses, and the enzymatic activity of the protein-dephosphorylation of deoxynucleotide triphosphates (dNTPs)-implicates enzymatic dNTP depletion in innate antiviral immunity. Here we show that the allosteric binding sites of the enzyme are plastic and can accommodate oligonucleotides in place of the allosteric activators, GTP and dNTP. SAMHD1 displays a preference for oligonucleotides containing phosphorothioate bonds in the Rp configuration located 3' to G nucleotides (GpsN), the modification pattern that occurs in a mechanism of antiviral defense in prokaryotes. In the presence of GTP and dNTPs, binding of GpsN-containing oligonucleotides promotes formation of a distinct tetramer with mixed occupancy of the allosteric sites. Mutations that impair formation of the mixed-occupancy complex abolish the antiretroviral activity of SAMHD1, but not its ability to deplete dNTPs. The findings link nucleic acid binding to the antiretroviral activity of SAMHD1, shed light on the immunomodulatory effects of synthetic phosphorothioated oligonucleotides and raise questions about the role of nucleic acid phosphorothioation in human innate immunity.
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Affiliation(s)
- Corey H Yu
- Department of Biochemistry and Structural Biology, UT Health San Antonio, San Antonio, TX, USA
| | - Akash Bhattacharya
- Department of Biochemistry and Structural Biology, UT Health San Antonio, San Antonio, TX, USA
| | - Mirjana Persaud
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Alexander B Taylor
- Department of Biochemistry and Structural Biology, UT Health San Antonio, San Antonio, TX, USA
| | - Zhonghua Wang
- Department of Biochemistry and Structural Biology, UT Health San Antonio, San Antonio, TX, USA
| | - Angel Bulnes-Ramos
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Joella Xu
- Department of Pediatrics, Emory School of Medicine, Atlanta, GA, USA
| | - Anastasia Selyutina
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Alicia Martinez-Lopez
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Kristin Cano
- Department of Biochemistry and Structural Biology, UT Health San Antonio, San Antonio, TX, USA
| | - Borries Demeler
- Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, AB, Canada.,Department of Chemistry and Biochemistry, University of Montana, Missoula, MT, USA
| | - Baek Kim
- Department of Pediatrics, Emory School of Medicine, Atlanta, GA, USA
| | - Stephen C Hardies
- Department of Biochemistry and Structural Biology, UT Health San Antonio, San Antonio, TX, USA
| | - Felipe Diaz-Griffero
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY, USA.
| | - Dmitri N Ivanov
- Department of Biochemistry and Structural Biology, UT Health San Antonio, San Antonio, TX, USA.
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18
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Krueger S, Curtis JE, Scott DR, Grishaev A, Glenn G, Smith G, Ellingsworth L, Borisov O, Maynard EL. Structural Characterization and Modeling of a Respiratory Syncytial Virus Fusion Glycoprotein Nanoparticle Vaccine in Solution. Mol Pharm 2021; 18:359-376. [PMID: 33322901 PMCID: PMC10467610 DOI: 10.1021/acs.molpharmaceut.0c00986] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
The respiratory syncytial virus (RSV) fusion (F) protein/polysorbate 80 (PS80) nanoparticle vaccine is the most clinically advanced vaccine for maternal immunization and protection of newborns against RSV infection. It is composed of a near-full-length RSV F glycoprotein, with an intact membrane domain, formulated into a stable nanoparticle with PS80 detergent. To understand the structural basis for the efficacy of the vaccine, a comprehensive study of its structure and hydrodynamic properties in solution was performed. Small-angle neutron scattering experiments indicate that the nanoparticle contains an average of 350 PS80 molecules, which form a cylindrical micellar core structure and five RSV F trimers that are arranged around the long axis of the PS80 core. All-atom models of full-length RSV F trimers were built from crystal structures of the soluble ectodomain and arranged around the long axis of the PS80 core, allowing for the generation of an ensemble of conformations that agree with small-angle neutron and X-ray scattering data as well as transmission electron microscopy (TEM) images. Furthermore, the hydrodynamic size of the RSV F nanoparticle was found to be modulated by the molar ratio of PS80 to protein, suggesting a mechanism for nanoparticle assembly involving addition of RSV F trimers to and growth along the long axis of the PS80 core. This study provides structural details of antigen presentation and conformation in the RSV F nanoparticle vaccine, helping to explain the induction of broad immunity and observed clinical efficacy. Small-angle scattering methods provide a general strategy to visualize surface glycoproteins from other pathogens and to structurally characterize nanoparticle vaccines.
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Affiliation(s)
- Susan Krueger
- NIST Center for Neutron Research, National Institute of Standards and Technology, 100 Bureau Drive, Gaithersburg, Maryland 20899, United States
| | - Joseph E Curtis
- NIST Center for Neutron Research, National Institute of Standards and Technology, 100 Bureau Drive, Gaithersburg, Maryland 20899, United States
| | - Daniel R Scott
- Novavax, Inc., 21 Firstfield Road, Gaithersburg, Maryland 20878, United States
| | - Alexander Grishaev
- Institute for Bioscience and Biotechnology Research, National Institute of Standards and Technology, 9600 Gudelsky Drive, Rockville, Maryland 20850, United States
| | - Greg Glenn
- Novavax, Inc., 21 Firstfield Road, Gaithersburg, Maryland 20878, United States
| | - Gale Smith
- Novavax, Inc., 21 Firstfield Road, Gaithersburg, Maryland 20878, United States
| | - Larry Ellingsworth
- Novavax, Inc., 21 Firstfield Road, Gaithersburg, Maryland 20878, United States
| | - Oleg Borisov
- Novavax, Inc., 21 Firstfield Road, Gaithersburg, Maryland 20878, United States
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19
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Mullen P, Abbott JA, Wellman T, Aktar M, Fjeld C, Demeler B, Ebert AM, Francklyn CS. Neuropathy-associated histidyl-tRNA synthetase variants attenuate protein synthesis in vitro and disrupt axon outgrowth in developing zebrafish. FEBS J 2021; 288:142-159. [PMID: 32543048 PMCID: PMC7736457 DOI: 10.1111/febs.15449] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Revised: 05/11/2020] [Accepted: 06/09/2020] [Indexed: 12/13/2022]
Abstract
Charcot-Marie-Tooth disease (CMT) encompasses a set of genetically and clinically heterogeneous neuropathies characterized by length-dependent dysfunction of the peripheral nervous system. Mutations in over 80 diverse genes are associated with CMT, and aminoacyl-tRNA synthetases (ARS) constitute a large gene family implicated in the disease. Despite considerable efforts to elucidate the mechanistic link between ARS mutations and the CMT phenotype, the molecular basis of the pathology is unknown. In this work, we investigated the impact of three CMT-associated substitutions (V155G, Y330C, and R137Q) in the cytoplasmic histidyl-tRNA synthetase (HARS1) on neurite outgrowth and peripheral nervous system development. The model systems for this work included a nerve growth factor-stimulated neurite outgrowth model in rat pheochromocytoma cells (PC12), and a zebrafish line with GFP/red fluorescent protein reporters of sensory and motor neuron development. The expression of CMT-HARS1 mutations led to attenuation of protein synthesis and increased phosphorylation of eIF2α in PC12 cells and was accompanied by impaired neurite and axon outgrowth in both models. Notably, these effects were phenocopied by histidinol, a HARS1 inhibitor, and cycloheximide, a protein synthesis inhibitor. The mutant proteins also formed heterodimers with wild-type HARS1, raising the possibility that CMT-HARS1 mutations cause disease through a dominant-negative mechanism. Overall, these findings support the hypothesis that CMT-HARS1 alleles exert their toxic effect in a neuronal context, and lead to dysregulated protein synthesis. These studies demonstrate the value of zebrafish as a model for studying mutant alleles associated with CMT, and for characterizing the processes that lead to peripheral nervous system dysfunction.
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Affiliation(s)
- Patrick Mullen
- Department of Biochemistry, University of Vermont, Burlington, VT, USA
| | - Jamie A Abbott
- Department of Biochemistry, University of Vermont, Burlington, VT, USA
| | - Theresa Wellman
- Department of Pharmacology, University of Vermont, Burlington, VT, USA
| | - Mahafuza Aktar
- Department of Biochemistry, University of Vermont, Burlington, VT, USA
| | - Christian Fjeld
- Department of Biochemistry, University of Vermont, Burlington, VT, USA
| | - Borries Demeler
- Department of Chemistry & Biochemistry, University of Lethbridge, Canada
| | - Alicia M Ebert
- Department of Biology, University of Vermont, Burlington, VT, USA
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20
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Caillet-Saguy C, Brûlé S, Wolff N, Raynal B. PDZ Sample Quality Assessment by Biochemical and Biophysical Characterizations. Methods Mol Biol 2021; 2256:89-124. [PMID: 34014518 DOI: 10.1007/978-1-0716-1166-1_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
PDZ domains are small globular domains involved in protein-protein interactions. They participate in a wide range of critical cellular processes. These domains, very abundant in the human proteome, are widely studied by high-throughput interactomics approaches and by biophysical and structural methods. However, the quality of the results is strongly related to the optimal folding and solubility of the domains. We provide here a detailed description of protocols for a strict quality assessment of the PDZ constructs. We describe appropriate experimental approaches that have been selected to overcome the small size of such domains to check the purity, identity, homogeneity, stability, and folding of samples.
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Affiliation(s)
| | - Sébastien Brûlé
- Institut Pasteur, Plate-forme de Biophysique Moléculaire, CNRS UMR 3528, Paris, France
| | - Nicolas Wolff
- Institut Pasteur, Unité Récepteurs-Canaux, CNRS UMR 3571, Paris, France.
| | - Bertrand Raynal
- Institut Pasteur, Plate-forme de Biophysique Moléculaire, CNRS UMR 3528, Paris, France
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21
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Nelson CR, Mrozowich T, Park SM, D’souza S, Henrickson A, Vigar JRJ, Wieden HJ, Owens RJ, Demeler B, Patel TR. Human DDX17 Unwinds Rift Valley Fever Virus Non-Coding RNAs. Int J Mol Sci 2020; 22:E54. [PMID: 33374561 PMCID: PMC7793125 DOI: 10.3390/ijms22010054] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 12/15/2020] [Accepted: 12/21/2020] [Indexed: 01/20/2023] Open
Abstract
Rift Valley fever virus (RVFV) is a mosquito-transmitted virus from the Bunyaviridae family that causes high rates of mortality and morbidity in humans and ruminant animals. Previous studies indicated that DEAD-box helicase 17 (DDX17) restricts RVFV replication by recognizing two primary non-coding RNAs in the S-segment of the genome: the intergenic region (IGR) and 5' non-coding region (NCR). However, we lack molecular insights into the direct binding of DDX17 with RVFV non-coding RNAs and information on the unwinding of both non-coding RNAs by DDX17. Therefore, we performed an extensive biophysical analysis of the DDX17 helicase domain (DDX17135-555) and RVFV non-coding RNAs, IGR and 5' NCR. The homogeneity studies using analytical ultracentrifugation indicated that DDX17135-555, IGR, and 5' NCR are pure. Next, we performed small-angle X-ray scattering (SAXS) experiments, which suggested that DDX17 and both RNAs are homogenous as well. SAXS analysis also demonstrated that DDX17 is globular to an extent, whereas the RNAs adopt an extended conformation in solution. Subsequently, microscale thermophoresis (MST) experiments were performed to investigate the direct binding of DDX17 to the non-coding RNAs. The MST experiments demonstrated that DDX17 binds with the IGR and 5' NCR with a dissociation constant of 5.77 ± 0.15 µM and 9.85 ± 0.11 µM, respectively. As DDX17135-555 is an RNA helicase, we next determined if it could unwind IGR and NCR. We developed a helicase assay using MST and fluorescently-labeled oligos, which suggested DDX17135-555 can unwind both RNAs. Overall, our study provides direct evidence of DDX17135-555 interacting with and unwinding RVFV non-coding regions.
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Affiliation(s)
- Corey R. Nelson
- Department of Chemistry and Biochemistry, Alberta RNA Research and Training Institute, University of Lethbridge, 4401 University Drive, Lethbridge, AB T1K 3M4, Canada; (C.R.N.); (T.M.); (S.M.P.); (A.H.); (J.R.J.V.); (H.-J.W.); (B.D.)
| | - Tyler Mrozowich
- Department of Chemistry and Biochemistry, Alberta RNA Research and Training Institute, University of Lethbridge, 4401 University Drive, Lethbridge, AB T1K 3M4, Canada; (C.R.N.); (T.M.); (S.M.P.); (A.H.); (J.R.J.V.); (H.-J.W.); (B.D.)
| | - Sean M. Park
- Department of Chemistry and Biochemistry, Alberta RNA Research and Training Institute, University of Lethbridge, 4401 University Drive, Lethbridge, AB T1K 3M4, Canada; (C.R.N.); (T.M.); (S.M.P.); (A.H.); (J.R.J.V.); (H.-J.W.); (B.D.)
| | - Simmone D’souza
- Department of Microbiology, Immunology and Infectious Disease, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 1N4, Canada;
| | - Amy Henrickson
- Department of Chemistry and Biochemistry, Alberta RNA Research and Training Institute, University of Lethbridge, 4401 University Drive, Lethbridge, AB T1K 3M4, Canada; (C.R.N.); (T.M.); (S.M.P.); (A.H.); (J.R.J.V.); (H.-J.W.); (B.D.)
| | - Justin R. J. Vigar
- Department of Chemistry and Biochemistry, Alberta RNA Research and Training Institute, University of Lethbridge, 4401 University Drive, Lethbridge, AB T1K 3M4, Canada; (C.R.N.); (T.M.); (S.M.P.); (A.H.); (J.R.J.V.); (H.-J.W.); (B.D.)
| | - Hans-Joachim Wieden
- Department of Chemistry and Biochemistry, Alberta RNA Research and Training Institute, University of Lethbridge, 4401 University Drive, Lethbridge, AB T1K 3M4, Canada; (C.R.N.); (T.M.); (S.M.P.); (A.H.); (J.R.J.V.); (H.-J.W.); (B.D.)
| | - Raymond J. Owens
- Research Complex at Harwell, R92 Rutherford Appleton Laboratories, Harwell, Oxford OX1 0QX, UK;
| | - Borries Demeler
- Department of Chemistry and Biochemistry, Alberta RNA Research and Training Institute, University of Lethbridge, 4401 University Drive, Lethbridge, AB T1K 3M4, Canada; (C.R.N.); (T.M.); (S.M.P.); (A.H.); (J.R.J.V.); (H.-J.W.); (B.D.)
- Department of Chemistry and Biochemistry, University of Montana, Missoula, MT 59812, USA
- NorthWest Biophysics Consortium, University of Lethbridge, University of Lethbridge, 4401 University Drive, Lethbridge, AB T1K 3M4, Canada
| | - Trushar R. Patel
- Department of Chemistry and Biochemistry, Alberta RNA Research and Training Institute, University of Lethbridge, 4401 University Drive, Lethbridge, AB T1K 3M4, Canada; (C.R.N.); (T.M.); (S.M.P.); (A.H.); (J.R.J.V.); (H.-J.W.); (B.D.)
- Department of Microbiology, Immunology and Infectious Disease, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 1N4, Canada;
- Li Ka Shing Institute of Virology and Discovery Lab, University of Alberta, Edmonton, AB T6G 2E1, Canada
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22
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Edwards GB, Muthurajan UM, Bowerman S, Luger K. Analytical Ultracentrifugation (AUC): An Overview of the Application of Fluorescence and Absorbance AUC to the Study of Biological Macromolecules. CURRENT PROTOCOLS IN MOLECULAR BIOLOGY 2020; 133:e131. [PMID: 33351266 PMCID: PMC7781197 DOI: 10.1002/cpmb.131] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The biochemical and biophysical investigation of proteins, nucleic acids, and the assemblies that they form yields essential information to understand complex systems. Analytical ultracentrifugation (AUC) represents a broadly applicable and information-rich method for investigating macromolecular characteristics such as size, shape, stoichiometry, and binding properties, all in the true solution-state environment that is lacking in most orthogonal methods. Despite this, AUC remains underutilized relative to its capabilities and potential in the fields of biochemistry and molecular biology. Although there has been a rapid development of computing power and AUC analysis tools in this millennium, fewer advancements have occurred in development of new applications of the technique, leaving these powerful instruments underappreciated and underused in many research institutes. With AUC previously limited to absorbance and Rayleigh interference optics, the addition of fluorescence detection systems has greatly enhanced the applicability of AUC to macromolecular systems that are traditionally difficult to characterize. This overview provides a resource for novices, highlighting the potential of AUC and encouraging its use in their research, as well as for current users, who may benefit from our experience. We discuss the strengths of fluorescence-detected AUC and demonstrate the power of even simple AUC experiments to answer practical and fundamental questions about biophysical properties of macromolecular assemblies. We address the development and utility of AUC, explore experimental design considerations, present case studies investigating properties of biological macromolecules that are of common interest to researchers, and review popular analysis approaches. © 2020 The Authors.
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Affiliation(s)
| | - Uma M. Muthurajan
- Department of BiochemistryUniversity of Colorado BoulderBoulderColorado
| | - Samuel Bowerman
- Department of BiochemistryUniversity of Colorado BoulderBoulderColorado
- Howard Hughes Medical InstituteUniversity of Colorado BoulderBoulderColorado
| | - Karolin Luger
- Department of BiochemistryUniversity of Colorado BoulderBoulderColorado
- Howard Hughes Medical InstituteUniversity of Colorado BoulderBoulderColorado
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23
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Patil SM, Nguyen J, Keire DA, Chen K. Sedimentation Velocity Analytical Ultracentrifugation Analysis of Marketed Rituximab Drug Product Size Distribution. Pharm Res 2020; 37:238. [PMID: 33155155 DOI: 10.1007/s11095-020-02961-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Accepted: 10/22/2020] [Indexed: 10/23/2022]
Abstract
PURPOSE Analytical methods suitable for intact drug products are often necessary to evaluate the equivalence in physicochemical properties between two drug products (DP) containing the same drug substance (DS), e.g., an innovator biologic drug and its proposed biosimilar. Analytical Ultracentrifugation (AUC) is a biophysics technique applied to the analysis of size and shape of biomolecules. However, the application of AUC to formulated monoclonal antibody (mAb) DP at high concentration has not been reported. METHODS A sedimentation velocity (SV) AUC procedure with a short-pathlength centerpiece was applied to two marketed rituximab DPs, Rituxan® (US) and Reditux® (India), without any buffer exchange or dilution. Detailed precision analysis was performed. RESULTS Highly reproducible sedimentation coefficient values (S) and peak areas were obtained for the dominant (> 84%) monomeric rituximab peak. The minor mAb fragment peaks had large variation in both S values and peak areas (3-12%). The identification of oligomer peaks was only reproducible once the abundance was higher than 2%. CONCLUSIONS SV-AUC provides an orthogonal characterization tool for protein size distribution, composition and assay, which could be informative for biosimilar drug developers who mostly only have access to formulated mAb. However, AUC needs thorough validation on its accuracy, precision and sensitivity.
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Affiliation(s)
- Sharadrao M Patil
- Division of Complex Drug Analysis, Office of Testing and Research, Office of Pharmaceutical Quality, Center for Drug Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, Maryland, 20993, USA.
| | - John Nguyen
- Division of Complex Drug Analysis, Office of Testing and Research, Office of Pharmaceutical Quality, Center for Drug Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, Maryland, 20993, USA
| | - David A Keire
- Office of Testing and Research, Office of Pharmaceutical Quality, Center for Drug Evaluation and Research, U.S. Food and Drug Administration, St. Louis, Missouri, 63110, USA
| | - Kang Chen
- Division of Complex Drug Analysis, Office of Testing and Research, Office of Pharmaceutical Quality, Center for Drug Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, Maryland, 20993, USA.
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24
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Savelyev A, Gorbet GE, Henrickson A, Demeler B. Moving analytical ultracentrifugation software to a good manufacturing practices (GMP) environment. PLoS Comput Biol 2020; 16:e1007942. [PMID: 32559250 PMCID: PMC7347214 DOI: 10.1371/journal.pcbi.1007942] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Revised: 07/09/2020] [Accepted: 05/11/2020] [Indexed: 01/19/2023] Open
Abstract
Recent advances in instrumentation have moved analytical ultracentrifugation (AUC) closer to a possible validation in a Good Manufacturing Practices (GMP) environment. In order for AUC to be validated for a GMP environment, stringent requirements need to be satisfied; analysis procedures must be evaluated for consistency and reproducibility, and GMP capable data acquisition software needs to be developed and validated. These requirements extend to multiple regulatory aspects, covering documentation of instrument hardware functionality, data handling and software for data acquisition and data analysis, process control, audit trails and automation. Here we review the requirements for GMP validation of data acquisition software and illustrate software solutions based on UltraScan that address these requirements as far as they relate to the operation and data handling in conjunction with the latest analytical ultracentrifuge, the Optima AUC by Beckman Coulter. The software targets the needs of regulatory agencies, where AUC plays a critical role in the solution-based characterization of biopolymers and macromolecular assemblies. Biopharmaceutical and regulatory agencies rely heavily on this technique for characterizations of pharmaceutical formulations, biosimilars, injectables, nanoparticles, and other soluble therapeutics. Because of its resolving power, AUC is a favorite application, despite the current lack of GMP validation. We believe that recent advances in standards, hardware, and software presented in this work manage to bridge this gap and allow AUC to be routinely used in a GMP environment. AUC has great potential to provide more detailed information, at higher resolution, and with greater confidence than other analytical techniques, and our software satisfies an urgent need for AUC operation in the GMP environment. The software, including documentation, are publicly available for free download from Github. The multi-platform software is licensed by the LGPL v.3 open source license and supports Windows, Mac and Linux platforms. Installation instructions and a mailing list are available from ultrascan.aucsolutions.com.
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Affiliation(s)
- Alexey Savelyev
- University of Montana, Dept. of Chemistry, Missoula, Montana, United States of America
| | | | - Amy Henrickson
- University of Lethbridge, Dept. of Chemistry and Biochemistry, Lethbridge, Alberta, Canada
| | - Borries Demeler
- University of Montana, Dept. of Chemistry, Missoula, Montana, United States of America
- AUC Solutions, Houston, Texas, United States of America
- University of Lethbridge, Dept. of Chemistry and Biochemistry, Lethbridge, Alberta, Canada
- * E-mail:
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25
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Abstract
Bromodomain-containing proteins are often part of chromatin-modifying complexes, and their activity can lead to altered expression of genes that drive cancer, inflammation and neurological disorders in humans. Bromodomain-PHD finger protein 1 (BRPF1) is part of the MOZ (monocytic leukemic zinc-finger protein) HAT (histone acetyltransferase) complex, which is associated with chromosomal translocations known to contribute to the development of acute myeloid leukemia (AML). BRPF1 contains a unique combination of chromatin reader domains including two plant homeodomain (PHD) fingers separated by a zinc knuckle (PZP domain), a bromodomain, and a proline-tryptophan-tryptophan-proline (PWWP) domain. BRPF1 is known to recruit the MOZ HAT complex to chromatin by recognizing acetylated lysine residues on the N-terminal histone tail region through its bromodomain. However, histone proteins can contain several acetylation modifications on their N-terminus, and it is unknown how additional marks influence bromodomain recruitment to chromatin. Here, we identify the BRPF1 bromodomain as a selective reader of di-acetyllysine modifications on histone H4. We used ITC assays to characterize the binding of di-acetylated histone ligands to the BRPF1 bromodomain and found that the domain binds preferentially to histone peptides H4K5acK8ac and H4K5acK12ac. Analytical ultracentrifugation (AUC) experiments revealed that the monomeric state of the BRPF1 bromodomain coordinates di-acetylated histone ligands. NMR chemical shift perturbation studies, along with binding and mutational analyses, revealed non-canonical regions of the bromodomain-binding pocket that are important for histone tail recognition. Together, our findings provide critical information on how the combinatorial action of post-translational modifications can modulate BRPF1 bromodomain binding and specificity.
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26
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Adusei-Danso F, Khaja FT, DeSantis M, Jeffrey PD, Dubnau E, Demeler B, Neiditch MB, Dubnau D. Structure-Function Studies of the Bacillus subtilis Ric Proteins Identify the Fe-S Cluster-Ligating Residues and Their Roles in Development and RNA Processing. mBio 2019; 10:e01841-19. [PMID: 31530674 PMCID: PMC6751060 DOI: 10.1128/mbio.01841-19] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Accepted: 08/26/2019] [Indexed: 01/01/2023] Open
Abstract
In Bacillus subtilis, the RicA (YmcA), RicF (YlbF), and RicT (YaaT) proteins accelerate the phosphorylation of the transcription factor Spo0A, contributing to genetic competence, sporulation, and biofilm formation, and are also essential for the correct maturation of several protein-encoding and riboswitch RNAs. These proteins form a stable complex (RicAFT) that carries two [4Fe-4S]+2 clusters. We show here that the complex is a 1:1:1 heterotrimer, and we present the X-ray crystal structures of a RicAF heterotetramer and of a RicA dimer. We also demonstrate that one of the Fe-S clusters (cluster 1) is ligated by cysteine residues donated exclusively by RicT and can be retained when the RicT monomer is purified by itself. Cluster 2 is ligated by C167 from RicT, by C134 and C146 located near the C terminus of RicF, and by C141 at the C terminus of RicA. These findings imply the following novel arrangement: adjacent RicT residues C166 and 167 ligate clusters 1 and 2, respectively, while cluster 2 is ligated by cysteine residues from RicT, RicA, and RicF. Thus, the two clusters must lie close to one another and at the interface of the RicAFT protomers. We also show that the cluster-ligating cysteine residues, and therefore most likely both Fe-S clusters, are essential for cggR-gapA mRNA maturation, for the regulation of ricF transcript stability, and for several Ric-associated developmental phenotypes, including competence for transformation, biofilm formation, and sporulation. Finally, we present evidence that RicAFT, RicAF, and RicA and the RicT monomer may play distinct regulatory roles in vivoIMPORTANCE The RicA, RicF, and RicT proteins are widely conserved among the firmicute bacteria and play multiple roles in Bacillus subtilis Among the phenotypes associated with the inactivation of these proteins are the inability to be genetically transformed or to form biofilms, a decrease in sporulation frequency, and changes in the stability and maturation of multiple RNA species. Despite their importance, the molecular mechanisms of Ric protein activities have not been elucidated and the roles of the two iron-sulfur clusters on the complex of the three proteins are not understood. To unravel the mechanisms of Ric action, molecular characterization of the complex and of its constituent proteins is essential. This report represents a major step toward understanding the structures of the Ric proteins, the arrangement and roles of the Fe-S clusters, and the phenotypes associated with Ric mutations.
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Affiliation(s)
- Felix Adusei-Danso
- Department of Microbiology, Biochemistry and Molecular Genetics, New Jersey Medical School, Rutgers University, Newark, New Jersey, USA
| | - Faisal Tarique Khaja
- Public Health Research Center of New Jersey Medical School, Newark, New Jersey, USA
| | - Micaela DeSantis
- Public Health Research Center of New Jersey Medical School, Newark, New Jersey, USA
| | - Philip D Jeffrey
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, USA
| | - Eugenie Dubnau
- Public Health Research Center of New Jersey Medical School, Newark, New Jersey, USA
| | - Borries Demeler
- Department of Chemistry & Biochemistry, The University of Lethbridge, Alberta, Canada
| | - Matthew B Neiditch
- Department of Microbiology, Biochemistry and Molecular Genetics, New Jersey Medical School, Rutgers University, Newark, New Jersey, USA
| | - David Dubnau
- Public Health Research Center of New Jersey Medical School, Newark, New Jersey, USA
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27
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Sequence Reversal Prevents Chain Collapse and Yields Heat-Sensitive Intrinsic Disorder. Biophys J 2019; 115:328-340. [PMID: 30021108 DOI: 10.1016/j.bpj.2018.06.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Revised: 05/15/2018] [Accepted: 06/04/2018] [Indexed: 11/20/2022] Open
Abstract
Sequence patterns of charge, hydrophobicity, hydrogen bonding, and other amino acid physicochemical properties contribute to mechanisms of protein folding, but how sequence composition and patterns influence the conformational dynamics of the denatured state ensemble is not fully understood. To investigate structure-sequence relationships in the denatured state, we reversed the sequence of staphylococcal nuclease and characterized its structure, thermodynamic character, and hydrodynamic radius using circular dichroism spectroscopy, dynamic light scattering, analytical ultracentrifugation, and size-exclusion chromatography as a function of temperature. The macromolecular size of "Retro-nuclease" is highly expanded in solution with characteristics similar to biological intrinsically disordered proteins. In contradistinction to a disordered state, Retro-nuclease exhibits a broad sigmoid transition of its hydrodynamic dimensions as temperature is increased, indicating a thermodynamically controlled compaction. Counterintuitively, the magnitude of these temperature-induced hydrodynamic changes exceed that observed from thermal denaturation of folded unaltered staphylococcal nuclease. Undetectable by calorimetry and intrinsic tryptophan fluorescence, the lack of heat capacity or fluorescence changes throughout the thermal transition indicate canonical hydrophobic collapse did not drive the Retro-nuclease structural transitions. Temperature-dependent circular dichroism spectroscopy performed on Retro-nuclease and computer simulations correlate to temperature sensitivity in the intrinsic sampling of backbone conformations for polyproline II and α-helix. The experimental results indicate a role for sequence direction in mediating the collapse of the polypeptide chain, whereas the simulation trends illustrate the generality of the observed heat effects on disordered protein structure.
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28
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Novel combinations of experimental and computational analysis tested on the binding of metalloprotoporphyrins to albumin. Int J Biol Macromol 2019; 134:445-457. [PMID: 31078597 DOI: 10.1016/j.ijbiomac.2019.05.060] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Revised: 05/08/2019] [Accepted: 05/08/2019] [Indexed: 02/02/2023]
Abstract
The evidence that Human Serum Albumin (HSA) binds metal ions and organometallic compounds has generated interest in its physiological role as a metalloprotein and as a vehicle for synthetic biology applications (e.g., synthetic blood and solar energy conversion). HSA has been shown to bind metallo-porphyrins, however, the structural details of such interactions are available only for the HSA:heme complex. A typical challenge for studying the interaction of proteins with metalloporphyrins is the poor solubility of the ligands that affect the characterization the complexes. The manuscript shows that a combination of dialysis and centrifugation yields aqueous solutions that contain >90% HSA:porphyrin complexes and virtually eliminate aggregated ligands. The removal of aggregates increases the quality of the optical spectroscopy data which, in turn, yield more accurate binding constants (~0.1 and 2.1 × 106 M-1) and reveal FRET between Trp214 and the porphyrins. The Trp-porphyrin distance was estimated to be within the 28-34 Å range and was used to guide the search of binding sites through a novel feedback approach with docking simulations. Results suggest while some protoporphyrins (metal-free, Fe(III)PPIX and Mg(II)PPIX) bind HSA at the heme site, others (Zn(II)PPIX, Mn(III)PPIX and Sn(IV)PPIX) are more likely to bind the Cys34.
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29
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Dcona MM, Damle PK, Zarate-Perez F, Morris BL, Nawaz Z, Dennis MJ, Deng X, Korwar S, Singh SJ, Ellis KC, Royer WE, Bandyopadhyay D, Escalante C, Grossman SR. Active-Site Tryptophan, the Target of Antineoplastic C-Terminal Binding Protein Inhibitors, Mediates Inhibitor Disruption of CtBP Oligomerization and Transcription Coregulatory Activities. Mol Pharmacol 2019; 96:99-108. [PMID: 31036695 DOI: 10.1124/mol.118.114363] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Accepted: 04/21/2019] [Indexed: 01/20/2023] Open
Abstract
C-terminal binding proteins (CtBP1/2) are oncogenic transcriptional coregulators and dehydrogenases often overexpressed in multiple solid tumors, including breast, colon, and ovarian cancer, and associated with poor survival. CtBPs act by repressing expression of genes responsible for apoptosis (e.g., PUMA, BIK) and metastasis-associated epithelial-mesenchymal transition (e.g., CDH1), and by activating expression of genes that promote migratory and invasive properties of cancer cells (e.g., TIAM1) and genes responsible for enhanced drug resistance (e.g., MDR1). CtBP's transcriptional functions are also critically dependent on oligomerization and nucleation of transcriptional complexes. Recently, we have developed a family of CtBP dehydrogenase inhibitors, based on the parent 2-hydroxyimino-3-phenylpropanoic acid (HIPP), that specifically disrupt cancer cell viability, abrogate CtBP's transcriptional function, and block polyp formation in a mouse model of intestinal polyposis that depends on CtBP's oncogenic functions. Crystallographic analysis revealed that HIPP interacts with CtBP1/2 at a conserved active site tryptophan (W318/324; CtBP1/2) that is unique among eukaryotic D2-dehydrogenases. To better understand the mechanism of action of HIPP-class inhibitors, we investigated the contribution of W324 to CtBP2's biochemical and physiologic activities utilizing mutational analysis. Indeed, W324 was necessary for CtBP2 self-association, as shown by analytical ultracentrifugation and in vivo cross-linking. Additionally, W324 supported CtBP's association with the transcriptional corepressor CoREST, and was critical for CtBP2 induction of cell motility. Notably, the HIPP derivative 4-chloro-HIPP biochemically and biologically phenocopied mutational inactivation of CtBP2 W324. Our data support further optimization of W318/W324-interacting CtBP dehydrogenase inhibitors that are emerging as a novel class of cancer cell-specific therapeutic.
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Affiliation(s)
- M Michael Dcona
- Departments of Internal Medicine (M.M.D., P.K.D., Z.N., M.J.D., S.J.S., S.R.G.), Human and Molecular Genetics (B.L.M., S.R.G.), Physiology and Biophysics (F.Z.-P., C.E.), Medicinal Chemistry (S.K., K.C.E.), and Biostatistics (X.D., D.B.) and Massey Cancer Center (K.C.E., D.B., C.E., S.R.G.), Virginia Commonwealth University, Richmond, Virginia; and Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts (W.E.R.)
| | - Priyadarshan K Damle
- Departments of Internal Medicine (M.M.D., P.K.D., Z.N., M.J.D., S.J.S., S.R.G.), Human and Molecular Genetics (B.L.M., S.R.G.), Physiology and Biophysics (F.Z.-P., C.E.), Medicinal Chemistry (S.K., K.C.E.), and Biostatistics (X.D., D.B.) and Massey Cancer Center (K.C.E., D.B., C.E., S.R.G.), Virginia Commonwealth University, Richmond, Virginia; and Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts (W.E.R.)
| | - Francisco Zarate-Perez
- Departments of Internal Medicine (M.M.D., P.K.D., Z.N., M.J.D., S.J.S., S.R.G.), Human and Molecular Genetics (B.L.M., S.R.G.), Physiology and Biophysics (F.Z.-P., C.E.), Medicinal Chemistry (S.K., K.C.E.), and Biostatistics (X.D., D.B.) and Massey Cancer Center (K.C.E., D.B., C.E., S.R.G.), Virginia Commonwealth University, Richmond, Virginia; and Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts (W.E.R.)
| | - Benjamin L Morris
- Departments of Internal Medicine (M.M.D., P.K.D., Z.N., M.J.D., S.J.S., S.R.G.), Human and Molecular Genetics (B.L.M., S.R.G.), Physiology and Biophysics (F.Z.-P., C.E.), Medicinal Chemistry (S.K., K.C.E.), and Biostatistics (X.D., D.B.) and Massey Cancer Center (K.C.E., D.B., C.E., S.R.G.), Virginia Commonwealth University, Richmond, Virginia; and Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts (W.E.R.)
| | - Zaid Nawaz
- Departments of Internal Medicine (M.M.D., P.K.D., Z.N., M.J.D., S.J.S., S.R.G.), Human and Molecular Genetics (B.L.M., S.R.G.), Physiology and Biophysics (F.Z.-P., C.E.), Medicinal Chemistry (S.K., K.C.E.), and Biostatistics (X.D., D.B.) and Massey Cancer Center (K.C.E., D.B., C.E., S.R.G.), Virginia Commonwealth University, Richmond, Virginia; and Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts (W.E.R.)
| | - Michael J Dennis
- Departments of Internal Medicine (M.M.D., P.K.D., Z.N., M.J.D., S.J.S., S.R.G.), Human and Molecular Genetics (B.L.M., S.R.G.), Physiology and Biophysics (F.Z.-P., C.E.), Medicinal Chemistry (S.K., K.C.E.), and Biostatistics (X.D., D.B.) and Massey Cancer Center (K.C.E., D.B., C.E., S.R.G.), Virginia Commonwealth University, Richmond, Virginia; and Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts (W.E.R.)
| | - Xiaoyan Deng
- Departments of Internal Medicine (M.M.D., P.K.D., Z.N., M.J.D., S.J.S., S.R.G.), Human and Molecular Genetics (B.L.M., S.R.G.), Physiology and Biophysics (F.Z.-P., C.E.), Medicinal Chemistry (S.K., K.C.E.), and Biostatistics (X.D., D.B.) and Massey Cancer Center (K.C.E., D.B., C.E., S.R.G.), Virginia Commonwealth University, Richmond, Virginia; and Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts (W.E.R.)
| | - Sudha Korwar
- Departments of Internal Medicine (M.M.D., P.K.D., Z.N., M.J.D., S.J.S., S.R.G.), Human and Molecular Genetics (B.L.M., S.R.G.), Physiology and Biophysics (F.Z.-P., C.E.), Medicinal Chemistry (S.K., K.C.E.), and Biostatistics (X.D., D.B.) and Massey Cancer Center (K.C.E., D.B., C.E., S.R.G.), Virginia Commonwealth University, Richmond, Virginia; and Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts (W.E.R.)
| | - Sahib J Singh
- Departments of Internal Medicine (M.M.D., P.K.D., Z.N., M.J.D., S.J.S., S.R.G.), Human and Molecular Genetics (B.L.M., S.R.G.), Physiology and Biophysics (F.Z.-P., C.E.), Medicinal Chemistry (S.K., K.C.E.), and Biostatistics (X.D., D.B.) and Massey Cancer Center (K.C.E., D.B., C.E., S.R.G.), Virginia Commonwealth University, Richmond, Virginia; and Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts (W.E.R.)
| | - Keith C Ellis
- Departments of Internal Medicine (M.M.D., P.K.D., Z.N., M.J.D., S.J.S., S.R.G.), Human and Molecular Genetics (B.L.M., S.R.G.), Physiology and Biophysics (F.Z.-P., C.E.), Medicinal Chemistry (S.K., K.C.E.), and Biostatistics (X.D., D.B.) and Massey Cancer Center (K.C.E., D.B., C.E., S.R.G.), Virginia Commonwealth University, Richmond, Virginia; and Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts (W.E.R.)
| | - William E Royer
- Departments of Internal Medicine (M.M.D., P.K.D., Z.N., M.J.D., S.J.S., S.R.G.), Human and Molecular Genetics (B.L.M., S.R.G.), Physiology and Biophysics (F.Z.-P., C.E.), Medicinal Chemistry (S.K., K.C.E.), and Biostatistics (X.D., D.B.) and Massey Cancer Center (K.C.E., D.B., C.E., S.R.G.), Virginia Commonwealth University, Richmond, Virginia; and Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts (W.E.R.)
| | - Dipankar Bandyopadhyay
- Departments of Internal Medicine (M.M.D., P.K.D., Z.N., M.J.D., S.J.S., S.R.G.), Human and Molecular Genetics (B.L.M., S.R.G.), Physiology and Biophysics (F.Z.-P., C.E.), Medicinal Chemistry (S.K., K.C.E.), and Biostatistics (X.D., D.B.) and Massey Cancer Center (K.C.E., D.B., C.E., S.R.G.), Virginia Commonwealth University, Richmond, Virginia; and Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts (W.E.R.)
| | - Carlos Escalante
- Departments of Internal Medicine (M.M.D., P.K.D., Z.N., M.J.D., S.J.S., S.R.G.), Human and Molecular Genetics (B.L.M., S.R.G.), Physiology and Biophysics (F.Z.-P., C.E.), Medicinal Chemistry (S.K., K.C.E.), and Biostatistics (X.D., D.B.) and Massey Cancer Center (K.C.E., D.B., C.E., S.R.G.), Virginia Commonwealth University, Richmond, Virginia; and Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts (W.E.R.)
| | - Steven R Grossman
- Departments of Internal Medicine (M.M.D., P.K.D., Z.N., M.J.D., S.J.S., S.R.G.), Human and Molecular Genetics (B.L.M., S.R.G.), Physiology and Biophysics (F.Z.-P., C.E.), Medicinal Chemistry (S.K., K.C.E.), and Biostatistics (X.D., D.B.) and Massey Cancer Center (K.C.E., D.B., C.E., S.R.G.), Virginia Commonwealth University, Richmond, Virginia; and Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts (W.E.R.)
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30
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Bansal A, Karanth NM, Demeler B, Schindelin H, Sarma SP. Crystallographic Structures of IlvN·Val/Ile Complexes: Conformational Selectivity for Feedback Inhibition of Aceto Hydroxy Acid Synthases. Biochemistry 2019; 58:1992-2008. [PMID: 30887800 PMCID: PMC6668035 DOI: 10.1021/acs.biochem.9b00050] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Conformational factors that predicate selectivity for valine or isoleucine binding to IlvN leading to the regulation of aceto hydroxy acid synthase I (AHAS I) of Escherichia coli have been determined for the first time from high-resolution (1.9-2.43 Å) crystal structures of IlvN·Val and IlvN·Ile complexes. The valine and isoleucine ligand binding pockets are located at the dimer interface. In the IlvN·Ile complex, among residues in the binding pocket, the side chain of Cys43 is 2-fold disordered (χ1 angles of gauche- and trans). Only one conformation can be observed for the identical residue in the IlvN·Val complexes. In a reversal, the side chain of His53, located at the surface of the protein, exhibits two conformations in the IlvN·Val complex. The concerted conformational switch in the side chains of Cys43 and His53 may play an important role in the regulation of the AHAS I holoenzyme activity. A significant result is the establishment of the subunit composition in the AHAS I holoenzyme by analytical ultracentrifugation. Solution nuclear magnetic resonance and analytical ultracentrifugation experiments have also provided important insights into the hydrodynamic properties of IlvN in the ligand-free and -bound states. The structural and biophysical data unequivocally establish the molecular basis for differential binding of the ligands to IlvN and a rationale for the resistance of IlvM to feedback inhibition by the branched-chain amino acids.
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Affiliation(s)
- Akanksha Bansal
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, Karnataka 560012, India
| | - N. Megha Karanth
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, Karnataka 560012, India
| | - Borries Demeler
- Department of Biochemistry and Structural Biology, The University of Texas Health Science Center at San Antonio, Mailcode 7760, 7703 Floyd Curl Drive, San Antonio, Texas 78229-3900, United States
| | - Hermann Schindelin
- Rudolf Virchow Centre for Experimental Biomedicine, Institute of Structural Biology, University of Wuerzburg, Josef-Schneider-Strasse 2, D-97080 Wuerzburg, Germany
| | - Siddhartha P. Sarma
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, Karnataka 560012, India
- NMR Research Center, Indian Institute of Science, Bangalore, Karnataka 560012, India
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31
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Ranaivoson FM, Turk LS, Ozgul S, Kakehi S, von Daake S, Lopez N, Trobiani L, De Jaco A, Denissova N, Demeler B, Özkan E, Montelione GT, Comoletti D. A Proteomic Screen of Neuronal Cell-Surface Molecules Reveals IgLONs as Structurally Conserved Interaction Modules at the Synapse. Structure 2019; 27:893-906.e9. [PMID: 30956130 DOI: 10.1016/j.str.2019.03.004] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Revised: 01/10/2019] [Accepted: 03/07/2019] [Indexed: 12/21/2022]
Abstract
In the developing brain, cell-surface proteins play crucial roles, but their protein-protein interaction network remains largely unknown. A proteomic screen identified 200 interactions, 89 of which were not previously published. Among these interactions, we find that the IgLONs, a family of five cell-surface neuronal proteins implicated in various human disorders, interact as homo- and heterodimers. We reveal their interaction patterns and report the dimeric crystal structures of Neurotrimin (NTRI), IgLON5, and the neuronal growth regulator 1 (NEGR1)/IgLON5 complex. We show that IgLONs maintain an extended conformation and that their dimerization occurs through the first Ig domain of each monomer and is Ca2+ independent. Cell aggregation shows that NTRI and NEGR1 homo- and heterodimerize in trans. Taken together, we report 89 unpublished cell-surface ligand-receptor pairs and describe structural models of trans interactions of IgLONs, showing that their structures are compatible with a model of interaction across the synaptic cleft.
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Affiliation(s)
| | - Liam S Turk
- Child Health Institute of New Jersey, New Brunswick, NJ 08901, USA
| | - Sinem Ozgul
- Child Health Institute of New Jersey, New Brunswick, NJ 08901, USA
| | - Sumie Kakehi
- Child Health Institute of New Jersey, New Brunswick, NJ 08901, USA
| | | | - Nicole Lopez
- Child Health Institute of New Jersey, New Brunswick, NJ 08901, USA
| | - Laura Trobiani
- Department of Biology and Biotechnology "Charles Darwin" and Pasteur Institute - Cenci Bolognetti Foundation, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185 Rome, Italy
| | - Antonella De Jaco
- Department of Biology and Biotechnology "Charles Darwin" and Pasteur Institute - Cenci Bolognetti Foundation, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185 Rome, Italy
| | - Natalia Denissova
- Department of Molecular Biology and Biochemistry and Center for Advanced Biotechnology and Medicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Borries Demeler
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive, Lethbridge, AB T1K 3M4, Canada
| | - Engin Özkan
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL 60637, USA
| | - Gaetano T Montelione
- Department of Molecular Biology and Biochemistry and Center for Advanced Biotechnology and Medicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA; Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Davide Comoletti
- Child Health Institute of New Jersey, New Brunswick, NJ 08901, USA; Departments of Neuroscience and Cell Biology Robert Wood Johnson Medical School, Rutgers, The State University of New Jersey, New Brunswick, NJ 08901, USA; Department of Pediatrics, Robert Wood Johnson Medical School, Rutgers, The State University of New Jersey, New Brunswick, NJ 08901, USA; School of Biological Sciences, Victoria University of Wellington, Wellington 6140, New Zealand.
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32
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Swygert SG, Senapati S, Bolukbasi MF, Wolfe SA, Lindsay S, Peterson CL. SIR proteins create compact heterochromatin fibers. Proc Natl Acad Sci U S A 2018; 115:12447-12452. [PMID: 30455303 PMCID: PMC6298083 DOI: 10.1073/pnas.1810647115] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Heterochromatin is a silenced chromatin region essential for maintaining genomic stability and driving developmental processes. The complicated structure and dynamics of heterochromatin have rendered it difficult to characterize. In budding yeast, heterochromatin assembly requires the SIR proteins-Sir3, believed to be the primary structural component of SIR heterochromatin, and the Sir2-4 complex, responsible for the targeted recruitment of SIR proteins and the deacetylation of lysine 16 of histone H4. Previously, we found that Sir3 binds but does not compact nucleosomal arrays. Here we reconstitute chromatin fibers with the complete complement of SIR proteins and use sedimentation velocity, molecular modeling, and atomic force microscopy to characterize the stoichiometry and conformation of SIR chromatin fibers. In contrast to fibers with Sir3 alone, our results demonstrate that SIR arrays are highly compact. Strikingly, the condensed structure of SIR heterochromatin fibers requires both the integrity of H4K16 and an interaction between Sir3 and Sir4. We propose a model in which a dimer of Sir3 bridges and stabilizes two adjacent nucleosomes, while a Sir2-4 heterotetramer interacts with Sir3 associated with a nucleosomal trimer, driving fiber compaction.
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Affiliation(s)
- Sarah G Swygert
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605
| | - Subhadip Senapati
- Center for Single Molecule Biophysics, Biodesign Institute, Arizona State University, Tempe, AZ 85287
| | - Mehmet F Bolukbasi
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01655
| | - Scot A Wolfe
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01655
| | - Stuart Lindsay
- Center for Single Molecule Biophysics, Biodesign Institute, Arizona State University, Tempe, AZ 85287
| | - Craig L Peterson
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605;
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33
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Structural and functional characterisation of the entry point to pyocyanin biosynthesis in Pseudomonas aeruginosa defines a new 3-deoxy-d-arabino-heptulosonate 7-phosphate synthase subclass. Biosci Rep 2018; 38:BSR20181605. [PMID: 30242059 PMCID: PMC6435475 DOI: 10.1042/bsr20181605] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2018] [Revised: 09/17/2018] [Accepted: 09/20/2018] [Indexed: 12/12/2022] Open
Abstract
In Pseudomonas aeruginosa (Pae), the shikimate pathway end product, chorismate, serves as the last common precursor for the biosynthesis of both primary aromatic metabolites, including phenylalanine, tyrosine and tryptophan, and secondary aromatic metabolites, including phenazine-1-carboxylic acid (PCA) and pyocyanin (PYO). The enzyme 3-deoxy-d-arabino-heptulosonate 7-phosphate synthase (DAH7PS) catalyses the first committed step of the shikimate pathway, en route to chorismate. P. aeruginosa expresses multiple, distinct DAH7PSs that are associated with either primary or secondary aromatic compound biosynthesis. Here we report the structure of a type II DAH7PS, encoded by phzC as part of the duplicated phenazine biosynthetic cluster, from P. aeruginosa (PAO1) revealing for the first time the structure of a type II DAH7PS involved in secondary metabolism. The omission of the structural elements α2a and α2b, relative to other characterised type II DAH7PSs, leads to the formation of an alternative, dimeric, solution-state structure for this type II DAH7PS with an oligomeric interface that has not previously been characterised and that does not facilitate the formation of aromatic amino acid allosteric binding sites. The sequence similarity and, in particular, the common N-terminal extension suggest a common origin for the type II DAH7PSs from P. aeruginosa. The results described in the present study support an expanded classification of the type II DAH7PSs as type IIA and type IIB based on sequence characteristics, structure and function of the resultant proteins, and on defined physiological roles within primary or secondary metabolism.
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34
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North RA, Wahlgren WY, Remus DM, Scalise M, Kessans SA, Dunevall E, Claesson E, Soares da Costa TP, Perugini MA, Ramaswamy S, Allison JR, Indiveri C, Friemann R, Dobson RCJ. The Sodium Sialic Acid Symporter From Staphylococcus aureus Has Altered Substrate Specificity. Front Chem 2018; 6:233. [PMID: 30023356 PMCID: PMC6039549 DOI: 10.3389/fchem.2018.00233] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Accepted: 06/01/2018] [Indexed: 11/13/2022] Open
Abstract
Mammalian cell surfaces are decorated with complex glycoconjugates that terminate with negatively charged sialic acids. Commensal and pathogenic bacteria can use host-derived sialic acids for a competitive advantage, but require a functional sialic acid transporter to import the sugar into the cell. This work investigates the sodium sialic acid symporter (SiaT) from Staphylococcus aureus (SaSiaT). We demonstrate that SaSiaT rescues an Escherichia coli strain lacking its endogenous sialic acid transporter when grown on the sialic acids N-acetylneuraminic acid (Neu5Ac) or N-glycolylneuraminic acid (Neu5Gc). We then develop an expression, purification and detergent solubilization system for SaSiaT and demonstrate that the protein is largely monodisperse in solution with a stable monomeric oligomeric state. Binding studies reveal that SaSiaT has a higher affinity for Neu5Gc over Neu5Ac, which was unexpected and is not seen in another SiaT homolog. We develop a homology model and use comparative sequence analyses to identify substitutions in the substrate-binding site of SaSiaT that may explain the altered specificity. SaSiaT is shown to be electrogenic, and transport is dependent upon more than one Na+ ion for every sialic acid molecule. A functional sialic acid transporter is essential for the uptake and utilization of sialic acid in a range of pathogenic bacteria, and developing new inhibitors that target these transporters is a valid mechanism for inhibiting bacterial growth. By demonstrating a route to functional recombinant SaSiaT, and developing the in vivo and in vitro assay systems, our work underpins the design of inhibitors to this transporter.
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Affiliation(s)
- Rachel A North
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand.,Biomolecular Interaction Centre, University of Canterbury, Christchurch, New Zealand.,Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Weixiao Y Wahlgren
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden.,Centre for Antibiotic Resistance Research, University of Gothenburg, Gothenburg, Sweden
| | - Daniela M Remus
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand.,Biomolecular Interaction Centre, University of Canterbury, Christchurch, New Zealand
| | - Mariafrancesca Scalise
- Unit of Biochemistry and Molecular Biotechnology, Department DiBEST (Biologia, Ecologia, Scienze della Terra), University of Calabria, Arcavacata di Rende, Italy
| | - Sarah A Kessans
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand.,Biomolecular Interaction Centre, University of Canterbury, Christchurch, New Zealand
| | - Elin Dunevall
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Elin Claesson
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Tatiana P Soares da Costa
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC, Australia
| | - Matthew A Perugini
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC, Australia
| | - S Ramaswamy
- The Institute for Stem Cell Biology and Regenerative Medicine, Bangalore, India
| | - Jane R Allison
- Biomolecular Interaction Centre, University of Canterbury, Christchurch, New Zealand.,Centre for Theoretical Chemistry and Physics, Institute of Natural and Mathematical Sciences, Massey University, Auckland, New Zealand.,Maurice Wilkins Centre for Molecular Biodiscovery, University of Auckland, Auckland, New Zealand
| | - Cesare Indiveri
- Unit of Biochemistry and Molecular Biotechnology, Department DiBEST (Biologia, Ecologia, Scienze della Terra), University of Calabria, Arcavacata di Rende, Italy
| | - Rosmarie Friemann
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden.,Centre for Antibiotic Resistance Research, University of Gothenburg, Gothenburg, Sweden
| | - Renwick C J Dobson
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand.,Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, VIC, Australia
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35
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Two-dimensional grid optimization for sedimentation velocity analysis in the analytical ultracentrifuge. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2018; 47:837-844. [PMID: 29777290 DOI: 10.1007/s00249-018-1309-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Revised: 04/17/2018] [Accepted: 05/02/2018] [Indexed: 10/16/2022]
Abstract
Sedimentation velocity experiments performed in the analytical ultracentrifuge are modeled using finite-element solutions of the Lamm equation. During modeling, three fundamental parameters are optimized: the sedimentation coefficients, the diffusion coefficients, and the partial concentrations of all solutes present in a mixture. A general modeling approach consists of fitting the partial concentrations of solutes defined in a two-dimensional grid of sedimentation and diffusion coefficient combinations that cover the range of possible solutes for a given mixture. An increasing number of grid points increase the resolution of the model produced by the subsequent analysis, with denser grids giving rise to a very large system of equations. Here, we evaluate the efficiency and resolution of several regular grids and show that traditionally defined grids tend to provide inadequate coverage in one region of the grid, while at the same time being computationally wasteful in other sections of the grid. We describe a rapid and systematic approach for generating efficient two-dimensional analysis grids that balance optimal information content and model resolution for a given signal-to-noise ratio with improved calculation efficiency. These findings are general and apply to one- and two-dimensional grids, although they no longer represent regular grids. We provide a recipe for an improved grid-point spacing in both directions which eliminates unnecessary points, while at the same time providing a more uniform resolution that can be scaled based on the stochastic noise in the experimental data.
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36
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Multi-speed sedimentation velocity simulations with UltraScan-III. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2018; 47:815-823. [PMID: 29748855 DOI: 10.1007/s00249-018-1308-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Revised: 04/22/2018] [Accepted: 05/02/2018] [Indexed: 10/16/2022]
Abstract
Recent developments in the UltraScan-III software make it possible to model multi-speed analytical ultracentrifugation sedimentation velocity experiments using finite-element solutions of the Lamm equation. Using simulated data, we demonstrate here how these innovations can be used to enhance the resolution of sedimentation velocity experiments when compared to single-speed experiments. Using heterogeneous systems covering as much as five orders of magnitude in molar mass and fivefold in anisotropy, we compare results from runs performed at multiple speeds to those obtained from single-speed experiments, fitted individually and analyzed globally over multiple speeds, and quantify resolution for sample heterogeneous in size and anisotropy. We also provide guidance on the design of multi-speed experiments and offer a program that can be used to deduce optimal spacing of rotor speeds and speed step durations when a few parameters from the experiment can be estimated. These include the meniscus position, the sedimentation coefficient of the largest species in a mixture, and a solute distribution. Our results show that errors observed in the determination of hydrodynamic parameters for system with great heterogeneity are markedly reduced when multi-speed analysis is employed.
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37
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Johnson CN, Gorbet GE, Ramsower H, Urquidi J, Brancaleon L, Demeler B. Multi-wavelength analytical ultracentrifugation of human serum albumin complexed with porphyrin. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2018; 47:789-797. [PMID: 29675648 DOI: 10.1007/s00249-018-1301-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Revised: 03/26/2018] [Accepted: 04/10/2018] [Indexed: 11/30/2022]
Abstract
The new Beckman Coulter Optima AUC instrument, which features multi-wavelength detection that couples the hydrodynamic separation of colloidal mixtures to spectral deconvolution of interacting and non-interacting solutes present in a mixture, was used to analyze the composition of human serum albumin (HSA) bound to metallo-protoporphyrin. We present new methods implemented in UltraScan that permit Optima AUC-derived multi-wavelength data to be spectrally decomposed in the same fashion as has been made possible for the Cölfen detector earlier. We demonstrate this approach by spectrally separating sedimentation velocity experimental data from mixtures of apo-HSA and HSA complexed to different metallo-protoporphyrins. We further demonstrate how multi-wavelength AUC can accurately recover percentages of metallo-protoporphyrin-bound HSA and apo-HSA from mixtures and how multi-wavelength AUC permits the calculation of molar extinction coefficients for porphyrins bound to HSA. The presented method has broad applicability to other complex systems where mixtures of molecules with different spectral properties need to be characterized.
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Affiliation(s)
- Courtney N Johnson
- Department of Biochemistry and Structural Biology, UTHSCSA, San Antonio, TX, USA
| | - Gary E Gorbet
- Department of Biochemistry and Structural Biology, UTHSCSA, San Antonio, TX, USA
| | - Heidi Ramsower
- Department of Physics and Astronomy, UTSA, San Antonio, TX, USA
| | - Julio Urquidi
- Department of Physics and Astronomy, UTSA, San Antonio, TX, USA
| | | | - Borries Demeler
- Department of Biochemistry and Structural Biology, UTHSCSA, San Antonio, TX, USA.
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38
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Gorbet GE, Mohapatra S, Demeler B. Multi-speed sedimentation velocity implementation in UltraScan-III. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2018; 47:825-835. [PMID: 29610996 DOI: 10.1007/s00249-018-1297-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Revised: 03/17/2018] [Accepted: 03/26/2018] [Indexed: 11/28/2022]
Abstract
A framework for the global analysis of multi-speed analytical ultracentrifugation sedimentation velocity experiments is presented. We discuss extensions to the adaptive space-time finite element fitting methods implemented in UltraScan-III to model sedimentation velocity experiments where a single run is performed at multiple rotor speeds, and describe extensions in the optimization routines used for fitting experimental data collected at arbitrary multi-speed profiles. Our implementation considers factors such as speed dependent rotor stretching, the resulting radial shifting of the finite element solution's boundary conditions, and changes in the associated time-invariant noise. We also address the calculation of acceleration rates and acceleration zones from existing radial acceleration and time records, as well as utilization of the time state object available at high temporal resolution from the new Beckman Optima AUC instrument. Analysis methods in UltraScan-III support unconstrained models that extract reliable information for both the sedimentation and the diffusion coefficients. These methods do not rely on any assumptions and allow for arbitrary variations in both sedimentation and diffusion transport. We have adapted these routines for the multi-speed case, and developed optimized and general grid based fitting methods to handle changes in the information content of the simulation matrix for different speed steps. New graphical simulation tools are presented that assist the investigator to estimate suitable grid metrics and evaluate information content based on edit profiles for individual experiments.
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Affiliation(s)
- Gary E Gorbet
- University of Texas Health Science Center, San Antonio, USA
| | | | - Borries Demeler
- University of Texas Health Science Center, San Antonio, USA.
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39
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Abbott JA, Meyer-Schuman R, Lupo V, Feely S, Mademan I, Oprescu SN, Griffin LB, Alberti MA, Casasnovas C, Aharoni S, Basel-Vanagaite L, Züchner S, De Jonghe P, Baets J, Shy ME, Espinós C, Demeler B, Antonellis A, Francklyn C. Substrate interaction defects in histidyl-tRNA synthetase linked to dominant axonal peripheral neuropathy. Hum Mutat 2018; 39:415-432. [PMID: 29235198 PMCID: PMC5983030 DOI: 10.1002/humu.23380] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Revised: 12/01/2017] [Accepted: 12/07/2017] [Indexed: 11/09/2022]
Abstract
Histidyl-tRNA synthetase (HARS) ligates histidine to cognate tRNA molecules, which is required for protein translation. Mutations in HARS cause the dominant axonal peripheral neuropathy Charcot-Marie-Tooth disease type 2W (CMT2W); however, the precise molecular mechanism remains undefined. Here, we investigated three HARS missense mutations associated with CMT2W (p.Tyr330Cys, p.Ser356Asn, and p.Val155Gly). The three mutations localize to the HARS catalytic domain and failed to complement deletion of the yeast ortholog (HTS1). Enzyme kinetics, differential scanning fluorimetry (DSF), and analytical ultracentrifugation (AUC) were employed to assess the effect of these substitutions on primary aminoacylation function and overall dimeric structure. Notably, the p.Tyr330Cys, p.Ser356Asn, and p.Val155Gly HARS substitutions all led to reduced aminoacylation, providing a direct connection between CMT2W-linked HARS mutations and loss of canonical ARS function. While DSF assays revealed that only one of the variants (p.Val155Gly) was less thermally stable relative to wild-type, all three HARS mutants formed stable dimers, as measured by AUC. Our work represents the first biochemical analysis of CMT-associated HARS mutations and underscores how loss of the primary aminoacylation function can contribute to disease pathology.
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Affiliation(s)
- Jamie A. Abbott
- Department of Biochemistry, University of Vermont, College of Medicine, Burlington, Vermont
| | - Rebecca Meyer-Schuman
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, Michigan
| | - Vincenzo Lupo
- Unit of Genetics and Genomics of Neuromuscular Disorders, Centro de Investigación Príncipe Felipe (CIPF), Valencia, Spain
| | - Shawna Feely
- Department of Neurology, University of Iowa Hospitals and Clinics, Iowa City, Iowa
| | - Inès Mademan
- Neurogenetics Group, Center for Molecular Neurology, VIB, Antwerp, Belgium
- Laboratory of Neuromuscular Pathology, Institute Born-Bunge, University of Antwerp, Antwerpen, Belgium
| | - Stephanie N. Oprescu
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, Michigan
| | - Laurie B. Griffin
- Cellular and Molecular Biology Program, University of Michigan Medical School, Ann Arbor, Michigan
- Medical Scientist Training Program, University of Michigan Medical School, Ann Arbor, Michigan
| | - M. Antonia Alberti
- Department of Neurology, Hospital Universitario de Bellvitge, Barcelona, Spain
| | - Carlos Casasnovas
- Department of Neurology, Hospital Universitario de Bellvitge, Barcelona, Spain
| | - Sharon Aharoni
- Institute of Child Neurology, Schneider Children’s Medical Center of Israel, Petah Tikva, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Lina Basel-Vanagaite
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- Raphael Recanati Genetic Institute, Rabin Medical Center, Beilinson Campus, Petah Tikva, Israel
- Pediatric Genetics Unit, Schneider Children’s Medical Center, Petah Tikva, Israel
- Felsenstein Medical Research Center, Rabin Medical Center, Petah Tikva, Israel
| | - Stephan Züchner
- Dr John T McDonald Foundation Department of Human Genetics & John P Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, Florida
| | - Peter De Jonghe
- Neurogenetics Group, Center for Molecular Neurology, VIB, Antwerp, Belgium
- Laboratory of Neuromuscular Pathology, Institute Born-Bunge, University of Antwerp, Antwerpen, Belgium
- Department of Neurology, Antwerp University Hospital, Antwerpen, Belgium
| | - Jonathan Baets
- Neurogenetics Group, Center for Molecular Neurology, VIB, Antwerp, Belgium
- Laboratory of Neuromuscular Pathology, Institute Born-Bunge, University of Antwerp, Antwerpen, Belgium
- Department of Neurology, Antwerp University Hospital, Antwerpen, Belgium
| | - Michael E. Shy
- Department of Neurology, University of Iowa Hospitals and Clinics, Iowa City, Iowa
| | - Carmen Espinós
- Unit of Genetics and Genomics of Neuromuscular Disorders, Centro de Investigación Príncipe Felipe (CIPF), Valencia, Spain
| | - Borries Demeler
- Department of Biochemistry, The University of Texas Health Sciences at San Antonio, San Antonio, Texas
| | - Anthony Antonellis
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, Michigan
- Cellular and Molecular Biology Program, University of Michigan Medical School, Ann Arbor, Michigan
| | - Christopher Francklyn
- Department of Biochemistry, University of Vermont, College of Medicine, Burlington, Vermont
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40
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Tian S, Yu G, He H, Zhao Y, Liu P, Marshall AG, Demeler B, Stagg SM, Li H. Pih1p-Tah1p Puts a Lid on Hexameric AAA+ ATPases Rvb1/2p. Structure 2017; 25:1519-1529.e4. [PMID: 28919439 PMCID: PMC6625358 DOI: 10.1016/j.str.2017.08.002] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Revised: 06/11/2017] [Accepted: 08/07/2017] [Indexed: 11/21/2022]
Abstract
The Saccharomyces cerevisiae (Sc) R2TP complex affords an Hsp90-mediated and nucleotide-driven chaperone activity to proteins of small ribonucleoprotein particles (snoRNPs). The current lack of structural information on the ScR2TP complex, however, prevents a mechanistic understanding of this biological process. We characterized the structure of the ScR2TP complex made up of two AAA+ ATPases, Rvb1/2p, and two Hsp90 binding proteins, Tah1p and Pih1p, and its interaction with the snoRNP protein Nop58p by a combination of analytical ultracentrifugation, isothermal titration calorimetry, chemical crosslinking, hydrogen-deuterium exchange, and cryoelectron microscopy methods. We find that Pih1p-Tah1p interacts with Rvb1/2p cooperatively through the nucleotide-sensitive domain of Rvb1/2p. Nop58p further binds Pih1p-Tahp1 on top of the dome-shaped R2TP. Consequently, nucleotide binding releases Pih1p-Tah1p from Rvb1/2p, which offers a mechanism for nucleotide-driven binding and release of snoRNP intermediates.
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Affiliation(s)
- Shaoxiong Tian
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL 32306, USA
| | - Ge Yu
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL 32306, USA
| | - Huan He
- Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306, USA
| | - Yu Zhao
- Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306, USA
| | - Peilu Liu
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL 32306, USA
| | - Alan G Marshall
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL 32306, USA; Ion Cyclotron Resonance Program, The National High Magnetic Field Laboratory, Tallahassee, FL 32310, USA
| | - Borries Demeler
- Department of Biochemistry, The University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Scott M Stagg
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL 32306, USA; Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306, USA
| | - Hong Li
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL 32306, USA; Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306, USA.
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41
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Kim SK, Barron L, Hinck CS, Petrunak EM, Cano KE, Thangirala A, Iskra B, Brothers M, Vonberg M, Leal B, Richter B, Kodali R, Taylor AB, Du S, Barnes CO, Sulea T, Calero G, Hart PJ, Hart MJ, Demeler B, Hinck AP. An engineered transforming growth factor β (TGF-β) monomer that functions as a dominant negative to block TGF-β signaling. J Biol Chem 2017; 292:7173-7188. [PMID: 28228478 PMCID: PMC5409485 DOI: 10.1074/jbc.m116.768754] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Revised: 02/12/2017] [Indexed: 11/06/2022] Open
Abstract
The transforming growth factor β isoforms, TGF-β1, -β2, and -β3, are small secreted homodimeric signaling proteins with essential roles in regulating the adaptive immune system and maintaining the extracellular matrix. However, dysregulation of the TGF-β pathway is responsible for promoting the progression of several human diseases, including cancer and fibrosis. Despite the known importance of TGF-βs in promoting disease progression, no inhibitors have been approved for use in humans. Herein, we describe an engineered TGF-β monomer, lacking the heel helix, a structural motif essential for binding the TGF-β type I receptor (TβRI) but dispensable for binding the other receptor required for TGF-β signaling, the TGF-β type II receptor (TβRII), as an alternative therapeutic modality for blocking TGF-β signaling in humans. As shown through binding studies and crystallography, the engineered monomer retained the same overall structure of native TGF-β monomers and bound TβRII in an identical manner. Cell-based luciferase assays showed that the engineered monomer functioned as a dominant negative to inhibit TGF-β signaling with a Ki of 20-70 nm Investigation of the mechanism showed that the high affinity of the engineered monomer for TβRII, coupled with its reduced ability to non-covalently dimerize and its inability to bind and recruit TβRI, enabled it to bind endogenous TβRII but prevented it from binding and recruiting TβRI to form a signaling complex. Such engineered monomers provide a new avenue to probe and manipulate TGF-β signaling and may inform similar modifications of other TGF-β family members.
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Affiliation(s)
- Sun Kyung Kim
- the Departments of Biochemistry and Structural Biology and
| | | | - Cynthia S Hinck
- From the Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15260
| | - Elyse M Petrunak
- From the Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15260
| | - Kristin E Cano
- the Departments of Biochemistry and Structural Biology and
| | | | - Brian Iskra
- the Departments of Biochemistry and Structural Biology and
| | - Molly Brothers
- the Departments of Biochemistry and Structural Biology and
| | | | - Belinda Leal
- the Departments of Biochemistry and Structural Biology and
| | - Blair Richter
- the Departments of Biochemistry and Structural Biology and
| | - Ravindra Kodali
- From the Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15260
| | | | - Shoucheng Du
- From the Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15260
| | - Christopher O Barnes
- From the Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15260
| | - Traian Sulea
- the National Research Council, Human Health Therapeutics Portfolio, Montréal, Quebec H4P 2R2, Canada
| | - Guillermo Calero
- From the Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15260
| | - P John Hart
- the Departments of Biochemistry and Structural Biology and
| | - Matthew J Hart
- Center for Innovative Drug Discovery, University of Texas Health Science Center, San Antonio, Texas 78229-3900, and
| | | | - Andrew P Hinck
- From the Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15260,
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42
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Fan Y, Guo YR, Yuan W, Zhou Y, Holt MV, Wang T, Demeler B, Young NL, Zhong W, Tao YJ. Structure of a pentameric virion-associated fiber with a potential role in Orsay virus entry to host cells. PLoS Pathog 2017; 13:e1006231. [PMID: 28241071 PMCID: PMC5344674 DOI: 10.1371/journal.ppat.1006231] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2016] [Revised: 03/09/2017] [Accepted: 02/10/2017] [Indexed: 11/25/2022] Open
Abstract
Despite the wide use of Caenorhabditis elegans as a model organism, the first virus naturally infecting this organism was not discovered until six years ago. The Orsay virus and its related nematode viruses have a positive-sense RNA genome, encoding three proteins: CP, RdRP, and a novel δ protein that shares no homology with any other proteins. δ can be expressed either as a free δ or a CP-δ fusion protein by ribosomal frameshift, but the structure and function of both δ and CP-δ remain unknown. Using a combination of electron microscopy, X-ray crystallography, computational and biophysical analyses, here we show that the Orsay δ protein forms a ~420-Å long, pentameric fiber with an N-terminal α-helical bundle, a β-stranded filament in the middle, and a C-terminal head domain. The pentameric nature of the δ fiber has been independently confirmed by both mass spectrometry and analytical ultracentrifugation. Recombinant Orsay capsid containing CP-δ shows protruding long fibers with globular heads at the distal end. Mutant viruses with disrupted CP-δ fibers were generated by organism-based reverse genetics. These viruses were found to be either non-viable or with poor infectivity according to phenotypic and qRT-PCR analyses. Furthermore, addition of purified δ proteins to worm culture greatly reduced Orsay infectivity in a sequence-specific manner. Based on the structure resemblance between the Orsay CP-δ fiber and the fibers from reovirus and adenovirus, we propose that CP-δ functions as a cell attachment protein to mediate Orsay entry into worm intestine cells.
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Affiliation(s)
- Yanlin Fan
- Department of BioSciences, Rice University, MS-140, Houston, Texas, United States of America
| | - Yusong R. Guo
- Department of BioSciences, Rice University, MS-140, Houston, Texas, United States of America
| | - Wang Yuan
- Department of BioSciences, Rice University, MS-140, Houston, Texas, United States of America
| | - Ying Zhou
- Department of BioSciences, Rice University, MS-140, Houston, Texas, United States of America
| | - Matthew V. Holt
- Verna & Marrs McLean Department of Biochemistry & Molecular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX, United States of America
| | - Tao Wang
- Verna & Marrs McLean Department of Biochemistry & Molecular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX, United States of America
| | - Borries Demeler
- The University of Texas Health Science Center at San Antonio, Department of Biochemistry, MC 7760, 7703 Floyd Curl Drive, San Antonio, Texas, United States of America
| | - Nicolas L. Young
- Verna & Marrs McLean Department of Biochemistry & Molecular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX, United States of America
- Department of Molecular and Cellular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX, United States of America
| | - Weiwei Zhong
- Department of BioSciences, Rice University, MS-140, Houston, Texas, United States of America
| | - Yizhi J. Tao
- Department of BioSciences, Rice University, MS-140, Houston, Texas, United States of America
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43
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Zhang J, Pearson JZ, Gorbet GE, Cölfen H, Germann MW, Brinton MA, Demeler B. Spectral and Hydrodynamic Analysis of West Nile Virus RNA-Protein Interactions by Multiwavelength Sedimentation Velocity in the Analytical Ultracentrifuge. Anal Chem 2017; 89:862-870. [PMID: 27977168 PMCID: PMC5505516 DOI: 10.1021/acs.analchem.6b03926] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Interactions between nucleic acids and proteins are critical for many cellular processes, and their study is of utmost importance to many areas of biochemistry, cellular biology, and virology. Here, we introduce a new analytical method based on sedimentation velocity (SV) analytical ultracentrifugation, in combination with a novel multiwavelength detector to characterize such interactions. We identified the stoichiometry and molar mass of a complex formed during the interaction of a West Nile virus RNA stem loop structure with the human T cell-restricted intracellular antigen-1 related protein. SV has long been proven as a powerful technique for studying dynamic assembly processes under physiological conditions in solution. Here, we demonstrate, for the first time, how the new multiwavelength technology can be exploited to study protein-RNA interactions, and show how the spectral information derived from the new detector complements the traditional hydrodynamic information from analytical ultracentrifugation. Our method allows the protein and nucleic acid signals to be separated by spectral decomposition such that sedimentation information from each individual species, including any complexes, can be clearly identified based on their spectral signatures. The method presented here extends to any interacting system where the interaction partners are spectrally separable.
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Affiliation(s)
- Jin Zhang
- Georgia State University, Department of Chemistry, 50 Decatur St. SE, Atlanta, Georgia 30303, United States
- Georgia State University, Department of Biology, P.O. 4010, Atlanta, Georgia 30303, United States
| | - Joseph Z. Pearson
- University of Konstanz, Department of Chemistry, Physical Chemistry, Universitätsstraße 10, Box 714, D-78457 Konstanz, Germany
| | - Gary E. Gorbet
- The University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Drive, MC 7760, San Antonio, Texas 78229-3901, United States
| | - Helmut Cölfen
- University of Konstanz, Department of Chemistry, Physical Chemistry, Universitätsstraße 10, Box 714, D-78457 Konstanz, Germany
| | - Markus W. Germann
- Georgia State University, Department of Chemistry, 50 Decatur St. SE, Atlanta, Georgia 30303, United States
- Georgia State University, Department of Biology, P.O. 4010, Atlanta, Georgia 30303, United States
| | - Margo A. Brinton
- Georgia State University, Department of Biology, P.O. 4010, Atlanta, Georgia 30303, United States
| | - Borries Demeler
- The University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Drive, MC 7760, San Antonio, Texas 78229-3901, United States
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44
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Smirnova E, Kwan JJ, Siu R, Gao X, Zoidl G, Demeler B, Saridakis V, Donaldson LW. A new mode of SAM domain mediated oligomerization observed in the CASKIN2 neuronal scaffolding protein. Cell Commun Signal 2016; 14:17. [PMID: 27549312 PMCID: PMC4994250 DOI: 10.1186/s12964-016-0140-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2016] [Accepted: 08/12/2016] [Indexed: 11/18/2022] Open
Abstract
Background CASKIN2 is a homolog of CASKIN1, a scaffolding protein that participates in a signaling network with CASK (calcium/calmodulin-dependent serine kinase). Despite a high level of homology between CASKIN2 and CASKIN1, CASKIN2 cannot bind CASK due to the absence of a CASK Interaction Domain and consequently, may have evolved undiscovered structural and functional distinctions. Results We demonstrate that the crystal structure of the Sterile Alpha Motif (SAM) domain tandem (SAM1-SAM2) oligomer from CASKIN2 is different than CASKIN1, with the minimal repeating unit being a dimer, rather than a monomer. Analytical ultracentrifugation sedimentation velocity methods revealed differences in monomer/dimer equilibria across a range of concentrations and ionic strengths for the wild type CASKIN2 SAM tandem and a structure-directed double mutant that could not oligomerize. Further distinguishing CASKIN2 from CASKIN1, EGFP-tagged SAM tandem proteins expressed in Neuro2a cells produced punctae that were distinct both in shape and size. Conclusions This study illustrates a new way in which neuronal SAM domains can assemble into large macromolecular assemblies that might concentrate and amplify synaptic responses. Electronic supplementary material The online version of this article (doi:10.1186/s12964-016-0140-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ekaterina Smirnova
- Department of Biology, York University, 4700 Keele Street, Toronto, ON, M3J 1P3, Canada
| | - Jamie J Kwan
- Department of Biology, York University, 4700 Keele Street, Toronto, ON, M3J 1P3, Canada
| | - Ryan Siu
- Department of Biology, York University, 4700 Keele Street, Toronto, ON, M3J 1P3, Canada
| | - Xin Gao
- Division of Computer, Computational Bioscience Research Center, Electrical and Mathematical Science and Engineering, King Abdullah University of Science and Technology, Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Georg Zoidl
- Department of Biology, York University, 4700 Keele Street, Toronto, ON, M3J 1P3, Canada.,Department of Psychology, York University, 4700 Keele Street, Toronto, ON, M3J 1P3, Canada
| | - Borries Demeler
- Department of Biochemistry, University of Texas Health Science Center at San Antonio, 7760 Floyd Curl Drive, San Antonio, TX, 78229-3900, USA
| | - Vivian Saridakis
- Department of Biology, York University, 4700 Keele Street, Toronto, ON, M3J 1P3, Canada
| | - Logan W Donaldson
- Department of Biology, York University, 4700 Keele Street, Toronto, ON, M3J 1P3, Canada.
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45
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Rubio-Marrero EN, Vincelli G, Jeffries CM, Shaikh TR, Pakos IS, Ranaivoson FM, von Daake S, Demeler B, De Jaco A, Perkins G, Ellisman MH, Trewhella J, Comoletti D. Structural Characterization of the Extracellular Domain of CASPR2 and Insights into Its Association with the Novel Ligand Contactin1. J Biol Chem 2016; 291:5788-5802. [PMID: 26721881 PMCID: PMC4786715 DOI: 10.1074/jbc.m115.705681] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2015] [Revised: 12/28/2015] [Indexed: 01/06/2023] Open
Abstract
Contactin-associated protein-like 2 (CNTNAP2) encodes for CASPR2, a multidomain single transmembrane protein belonging to the neurexin superfamily that has been implicated in a broad range of human phenotypes including autism and language impairment. Using a combination of biophysical techniques, including small angle x-ray scattering, single particle electron microscopy, analytical ultracentrifugation, and bio-layer interferometry, we present novel structural and functional data that relate the architecture of the extracellular domain of CASPR2 to a previously unknown ligand, Contactin1 (CNTN1). Structurally, CASPR2 is highly glycosylated and has an overall compact architecture. Functionally, we show that CASPR2 associates with micromolar affinity with CNTN1 but, under the same conditions, it does not interact with any of the other members of the contactin family. Moreover, by using dissociated hippocampal neurons we show that microbeads loaded with CASPR2, but not with a deletion mutant, co-localize with transfected CNTN1, suggesting that CNTN1 is an endogenous ligand for CASPR2. These data provide novel insights into the structure and function of CASPR2, suggesting a complex role of CASPR2 in the nervous system.
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Affiliation(s)
- Eva N Rubio-Marrero
- From the Child Health Institute of New Jersey and Departments of Neuroscience and Cell Biology and
| | - Gabriele Vincelli
- From the Child Health Institute of New Jersey and Departments of Neuroscience and Cell Biology and
| | - Cy M Jeffries
- the School of Molecular Bioscience, University of Sydney, New South Wales 2006, Australia
| | - Tanvir R Shaikh
- the Structural Biology Programme, Central European Institute of Technology, Masaryk University, 62500 Brno, Czech Republic
| | - Irene S Pakos
- From the Child Health Institute of New Jersey and Departments of Neuroscience and Cell Biology and
| | - Fanomezana M Ranaivoson
- From the Child Health Institute of New Jersey and Departments of Neuroscience and Cell Biology and
| | - Sventja von Daake
- From the Child Health Institute of New Jersey and Departments of Neuroscience and Cell Biology and
| | - Borries Demeler
- the Department of Biochemistry, The University of Texas Health Science Center, San Antonio, Texas 78229
| | - Antonella De Jaco
- the Department of Biology and Biotechnologies "Charles Darwin" and Pasteur Institute-Cenci Bolognetti Foundation, Sapienza University of Rome, Rome, Italy 00185
| | - Guy Perkins
- the National Center for Microscopy and Imaging Research, University of California San Diego, La Jolla, California 92093, and
| | - Mark H Ellisman
- the National Center for Microscopy and Imaging Research, University of California San Diego, La Jolla, California 92093, and
| | - Jill Trewhella
- the School of Molecular Bioscience, University of Sydney, New South Wales 2006, Australia,; the Department of Chemistry, University of Utah, Salt Lake City, Utah 84112
| | - Davide Comoletti
- From the Child Health Institute of New Jersey and Departments of Neuroscience and Cell Biology and; Pediatrics, Robert Wood Johnson Medical School, Rutgers University, New Brunswick, New Jersey 08901,.
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46
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Cryo-EM reveals a novel octameric integrase structure for betaretroviral intasome function. Nature 2016; 530:358-61. [PMID: 26887496 PMCID: PMC4908968 DOI: 10.1038/nature16955] [Citation(s) in RCA: 72] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2015] [Accepted: 12/30/2015] [Indexed: 12/26/2022]
Abstract
Retroviral integrase catalyses the integration of viral DNA into host target DNA, which is an essential step in the life cycle of all retroviruses. Previous structural characterization of integrase-viral DNA complexes, or intasomes, from the spumavirus prototype foamy virus revealed a functional integrase tetramer, and it is generally believed that intasomes derived from other retroviral genera use tetrameric integrase. However, the intasomes of orthoretroviruses, which include all known pathogenic species, have not been characterized structurally. Here, using single-particle cryo-electron microscopy and X-ray crystallography, we determine an unexpected octameric integrase architecture for the intasome of the betaretrovirus mouse mammary tumour virus. The structure is composed of two core integrase dimers, which interact with the viral DNA ends and structurally mimic the integrase tetramer of prototype foamy virus, and two flanking integrase dimers that engage the core structure via their integrase carboxy-terminal domains. Contrary to the belief that tetrameric integrase components are sufficient to catalyse integration, the flanking integrase dimers were necessary for mouse mammary tumour virus integrase activity. The integrase octamer solves a conundrum for betaretroviruses as well as alpharetroviruses by providing critical carboxy-terminal domains to the intasome core that cannot be provided in cis because of evolutionarily restrictive catalytic core domain-carboxy-terminal domain linker regions. The octameric architecture of the intasome of mouse mammary tumour virus provides new insight into the structural basis of retroviral DNA integration.
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47
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48
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Cockburn DW, Orlovsky NI, Foley MH, Kwiatkowski KJ, Bahr CM, Maynard M, Demeler B, Koropatkin NM. Molecular details of a starch utilization pathway in the human gut symbiont Eubacterium rectale. Mol Microbiol 2015; 95:209-30. [PMID: 25388295 PMCID: PMC4437465 DOI: 10.1111/mmi.12859] [Citation(s) in RCA: 81] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/06/2014] [Indexed: 01/07/2023]
Abstract
Eubacterium rectale is a prominent human gut symbiont yet little is known about the molecular strategies this bacterium has developed to acquire nutrients within the competitive gut ecosystem. Starch is one of the most abundant glycans in the human diet, and E. rectale increases in vivo when the host consumes a diet rich in resistant starch, although it is not a primary degrader of this glycan. Here we present the results of a quantitative proteomics study in which we identify two glycoside hydrolase 13 family enzymes, and three ABC transporter solute-binding proteins that are abundant during growth on starch and, we hypothesize, work together at the cell surface to degrade starch and capture the released maltooligosaccharides. EUR_21100 is a multidomain cell wall anchored amylase that preferentially targets starch polysaccharides, liberating maltotetraose, whereas the membrane-associated maltogenic amylase EUR_01860 breaks down maltooligosaccharides longer than maltotriose. The three solute-binding proteins display a range of glycan-binding specificities that ensure the capture of glucose through maltoheptaose and some α1,6-branched glycans. Taken together, we describe a pathway for starch utilization by E. rectale DSM 17629 that may be conserved among other starch-degrading Clostridium cluster XIVa organisms in the human gut.
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Affiliation(s)
- Darrell W. Cockburn
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI 48109
| | - Nicole I. Orlovsky
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI 48109
| | - Matthew H. Foley
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI 48109
| | - Kurt J. Kwiatkowski
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI 48109
| | - Constance M. Bahr
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI 48109
| | - Mallory Maynard
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI 48109
| | - Borries Demeler
- Department of Biochemistry, The University of Texas Health Science Center, San Antonio, TX 78229
| | - Nicole M. Koropatkin
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI 48109
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49
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Gorbet G, Devlin T, Hernandez Uribe BI, Demeler AK, Lindsey ZL, Ganji S, Breton S, Weise-Cross L, Lafer EM, Brookes EH, Demeler B. A parametrically constrained optimization method for fitting sedimentation velocity experiments. Biophys J 2014; 106:1741-50. [PMID: 24739173 DOI: 10.1016/j.bpj.2014.02.022] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2013] [Revised: 02/11/2014] [Accepted: 02/25/2014] [Indexed: 10/25/2022] Open
Abstract
A method for fitting sedimentation velocity experiments using whole boundary Lamm equation solutions is presented. The method, termed parametrically constrained spectrum analysis (PCSA), provides an optimized approach for simultaneously modeling heterogeneity in size and anisotropy of macromolecular mixtures. The solutions produced by PCSA are particularly useful for modeling polymerizing systems, where a single-valued relationship exists between the molar mass of the growing polymer chain and its corresponding anisotropy. The PCSA uses functional constraints to identify this relationship, and unlike other multidimensional grid methods, assures that only a single molar mass can be associated with a given anisotropy measurement. A description of the PCSA algorithm is presented, as well as several experimental and simulated examples that illustrate its utility and capabilities. The performance advantages of the PCSA method in comparison to other methods are documented. The method has been added to the UltraScan-III software suite, which is available for free download from http://www.ultrascan.uthscsa.edu.
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Affiliation(s)
- Gary Gorbet
- The University of Texas Health Science Center at San Antonio, Department of Biochemistry, San Antonio, Texas
| | - Taylor Devlin
- The University of Texas Health Science Center at San Antonio, Department of Biochemistry, San Antonio, Texas
| | - Blanca I Hernandez Uribe
- The University of Texas Health Science Center at San Antonio, Department of Biochemistry, San Antonio, Texas
| | - Aysha K Demeler
- The University of Texas Health Science Center at San Antonio, Department of Biochemistry, San Antonio, Texas
| | - Zachary L Lindsey
- Texas A&M University, Department of Mechanical Engineering, College Station, Texas
| | - Suma Ganji
- The University of Texas Health Science Center at San Antonio, Department of Biochemistry, San Antonio, Texas
| | - Sabrah Breton
- The University of Texas Health Science Center at San Antonio, Department of Biochemistry, San Antonio, Texas
| | - Laura Weise-Cross
- University of North Carolina at Chapel Hill, Department of Pathology and Laboratory Medicine, Chapel Hill, North Carolina
| | - Eileen M Lafer
- The University of Texas Health Science Center at San Antonio, Department of Biochemistry, San Antonio, Texas
| | - Emre H Brookes
- The University of Texas Health Science Center at San Antonio, Department of Biochemistry, San Antonio, Texas
| | - Borries Demeler
- The University of Texas Health Science Center at San Antonio, Department of Biochemistry, San Antonio, Texas.
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Overproduction and biophysical characterization of human HSP70 proteins. Protein Expr Purif 2014; 106:57-65. [PMID: 25266791 DOI: 10.1016/j.pep.2014.09.013] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2014] [Revised: 09/16/2014] [Accepted: 09/18/2014] [Indexed: 11/20/2022]
Abstract
Heat shock proteins (HSP) perform vital cellular functions and modulate cell response pathways to physical and chemical stressors. A key feature of HSP function is the ability to interact with a broad array of protein binding partners as a means to potentiate downstream response pathways or facilitate protein folding. These binding interactions are driven by ATP-dependent conformational rearrangements in HSP proteins. The HSP70 family is evolutionarily conserved and is associated with diabetes and cancer progression and the etiopathogenesis of hepatic, cardiovascular, and neurological disorders in humans. However, functional characterization of human HSP70s has been stymied by difficulties in obtaining large quantities of purified protein. Studies of purified human HSP70 proteins are essential for downstream investigations of protein-protein interactions and in the rational design of novel family-specific therapeutics. Within this work, we present optimized protocols for the heterologous overexpression and purification of either the nucleotide binding domain (NBD) or the nucleotide and substrate binding domains of human HSPA9, HSPA8, and HSPA5 in either Escherichia coli or Saccharomyces cerevisiae. We also include initial biophysical characterization of HSPA9 and HSPA8. This work provides the basis for future biochemical studies of human HSP70 protein function and structure.
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