1
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Breunig SL, Chapman AM, LeBon J, Quijano JC, Ranasinghe M, Rawson J, Demeler B, Ku HT, Tirrell DA. 4S-fluorination of ProB29 in insulin lispro slows fibril formation. J Biol Chem 2024; 300:107332. [PMID: 38703998 PMCID: PMC11154709 DOI: 10.1016/j.jbc.2024.107332] [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] [Received: 11/21/2023] [Revised: 04/02/2024] [Accepted: 04/09/2024] [Indexed: 05/06/2024] Open
Abstract
Recombinant insulin is a life-saving therapeutic for millions of patients affected by diabetes mellitus. Standard mutagenesis has led to insulin variants with improved control of blood glucose; for instance, the fast-acting insulin lispro contains two point mutations that suppress dimer formation and expedite absorption. However, insulins undergo irreversible denaturation, a process accelerated for the insulin monomer. Here we replace ProB29 of insulin lispro with 4R-fluoroproline, 4S-fluoroproline, and 4,4-difluoroproline. All three fluorinated lispro variants reduce blood glucose in diabetic mice, exhibit similar secondary structure as measured by CD, and rapidly dissociate from the zinc- and resorcinol-bound hexamer upon dilution. Notably, however, we find that 4S-fluorination of ProB29 delays the formation of undesired insulin fibrils that can accumulate at the injection site in vivo and can complicate insulin production and storage. These results demonstrate how subtle molecular changes achieved through non-canonical amino acid mutagenesis can improve the stability of protein therapeutics.
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Affiliation(s)
- Stephanie L Breunig
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California, USA
| | - Alex M Chapman
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California, USA
| | - Jeanne LeBon
- Department of Translational Research and Cellular Therapeutics, Arthur Riggs Diabetes and Metabolism Research Institute, Beckman Research Institute City of Hope, Duarte, California, USA
| | - Janine C Quijano
- Department of Translational Research and Cellular Therapeutics, Arthur Riggs Diabetes and Metabolism Research Institute, Beckman Research Institute City of Hope, Duarte, California, USA
| | - Maduni Ranasinghe
- Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, Alberta, Canada
| | - Jeffrey Rawson
- Department of Translational Research and Cellular Therapeutics, Arthur Riggs Diabetes and Metabolism Research Institute, Beckman Research Institute City of Hope, Duarte, California, USA
| | - Borries Demeler
- Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, Alberta, Canada; Department of Chemistry and Biochemistry, University of Montana, Missoula, Montana, USA
| | - Hsun Teresa Ku
- Department of Translational Research and Cellular Therapeutics, Arthur Riggs Diabetes and Metabolism Research Institute, Beckman Research Institute City of Hope, Duarte, California, USA; Irell & Manella Graduate School of Biological Science, City of Hope, Duarte, California, USA
| | - David A Tirrell
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California, USA.
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2
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Johnson CN, Sojitra KA, Sohn EJ, Moreno-Romero AK, Baudin A, Xu X, Mittal J, Libich DS. Insights into Molecular Diversity within the FUS/EWS/TAF15 Protein Family: Unraveling Phase Separation of the N-Terminal Low-Complexity Domain from RNA-Binding Protein EWS. J Am Chem Soc 2024; 146:8071-8085. [PMID: 38492239 PMCID: PMC11156192 DOI: 10.1021/jacs.3c12034] [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: 03/18/2024]
Abstract
The FET protein family, comprising FUS, EWS, and TAF15, plays crucial roles in mRNA maturation, transcriptional regulation, and DNA damage response. Clinically, they are linked to Ewing family tumors and neurodegenerative diseases such as amyotrophic lateral sclerosis. The fusion protein EWS::FLI1, the causative mutation of Ewing sarcoma, arises from a genomic translocation that fuses a portion of the low-complexity domain (LCD) of EWS (EWSLCD) with the DNA binding domain of the ETS transcription factor FLI1. This fusion protein modifies transcriptional programs and disrupts native EWS functions, such as splicing. The exact role of the intrinsically disordered EWSLCD remains a topic of active investigation, but its ability to phase separate and form biomolecular condensates is believed to be central to EWS::FLI1's oncogenic properties. Here, we used paramagnetic relaxation enhancement NMR, microscopy, and all-atom molecular dynamics (MD) simulations to better understand the self-association and phase separation tendencies of the EWSLCD. Our NMR data and mutational analysis suggest that a higher density and proximity of tyrosine residues amplify the likelihood of condensate formation. MD simulations revealed that the tyrosine-rich termini exhibit compact conformations with unique contact networks and provided critical input on the relationship between contacts formed within a single molecule (intramolecular) and inside the condensed phase (intermolecular). These findings enhance our understanding of FET proteins' condensate-forming capabilities and underline differences between EWS, FUS, and TAF15.
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Affiliation(s)
- Courtney N. Johnson
- Greehey Children’s Cancer Research Institute, The University of Texas Health Science Center at San Antonio, San Antonio, Texas, 78229, United States
- Department of Biochemistry and Structural Biology, The University of Texas Health Science Center at San Antonio, San Antonio, Texas, 78229, United States
| | - Kandarp A Sojitra
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, Texas 77843, United States
| | - Erich J. Sohn
- Greehey Children’s Cancer Research Institute, The University of Texas Health Science Center at San Antonio, San Antonio, Texas, 78229, United States
- Department of Biochemistry and Structural Biology, The University of Texas Health Science Center at San Antonio, San Antonio, Texas, 78229, United States
| | - Alma K. Moreno-Romero
- Greehey Children’s Cancer Research Institute, The University of Texas Health Science Center at San Antonio, San Antonio, Texas, 78229, United States
- Department of Biochemistry and Structural Biology, The University of Texas Health Science Center at San Antonio, San Antonio, Texas, 78229, United States
| | - Antoine Baudin
- Greehey Children’s Cancer Research Institute, The University of Texas Health Science Center at San Antonio, San Antonio, Texas, 78229, United States
- Department of Biochemistry and Structural Biology, The University of Texas Health Science Center at San Antonio, San Antonio, Texas, 78229, United States
| | - Xiaoping Xu
- Greehey Children’s Cancer Research Institute, The University of Texas Health Science Center at San Antonio, San Antonio, Texas, 78229, United States
- Department of Biochemistry and Structural Biology, The University of Texas Health Science Center at San Antonio, San Antonio, Texas, 78229, United States
| | - Jeetain Mittal
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, Texas 77843, United States
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
- Interdisciplinary Graduate Program in Genetics and Genomics, Texas A&M University, College Station, Texas 77843, United States
| | - David S. Libich
- Greehey Children’s Cancer Research Institute, The University of Texas Health Science Center at San Antonio, San Antonio, Texas, 78229, United States
- Department of Biochemistry and Structural Biology, The University of Texas Health Science Center at San Antonio, San Antonio, Texas, 78229, United States
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3
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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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4
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Krahn N, Zhang J, Melnikov SV, Tharp JM, Villa A, Patel A, Howard R, Gabir H, Patel T, Stetefeld J, Puglisi J, Söll D. tRNA shape is an identity element for an archaeal pyrrolysyl-tRNA synthetase from the human gut. Nucleic Acids Res 2024; 52:513-524. [PMID: 38100361 PMCID: PMC10810272 DOI: 10.1093/nar/gkad1188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 11/23/2023] [Accepted: 11/29/2023] [Indexed: 12/17/2023] Open
Abstract
Protein translation is orchestrated through tRNA aminoacylation and ribosomal elongation. Among the highly conserved structure of tRNAs, they have distinguishing features which promote interaction with their cognate aminoacyl tRNA synthetase (aaRS). These key features are referred to as identity elements. In our study, we investigated the tRNA:aaRS pair that installs the 22nd amino acid, pyrrolysine (tRNAPyl:PylRS). Pyrrolysyl-tRNA synthetases (PylRSs) are naturally encoded in some archaeal and bacterial genomes to acylate tRNAPyl with pyrrolysine. Their large amino acid binding pocket and poor recognition of the tRNA anticodon have been instrumental in incorporating >200 noncanonical amino acids. PylRS enzymes can be divided into three classes based on their genomic structure. Two classes contain both an N-terminal and C-terminal domain, however the third class (ΔpylSn) lacks the N-terminal domain. In this study we explored the tRNA identity elements for a ΔpylSn tRNAPyl from Candidatus Methanomethylophilus alvus which drives the orthogonality seen with its cognate PylRS (MaPylRS). From aminoacylation and translation assays we identified five key elements in ΔpylSn tRNAPyl necessary for MaPylRS activity. The absence of a base (position 8) and a G-U wobble pair (G28:U42) were found to affect the high-resolution structure of the tRNA, while molecular dynamic simulations led us to acknowledge the rigidity imparted from the G-C base pairs (G3:C70 and G5:C68).
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Affiliation(s)
- Natalie Krahn
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | - Jingji Zhang
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Sergey V Melnikov
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - Jeffery M Tharp
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | - Alessandra Villa
- PDC-Center for High Performance Computing, KTH-Royal Institute of Technology, Stockholm, SE-100 44, Sweden
| | - Armaan Patel
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | - Rebecca J Howard
- Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, Solna, SE-171 65, Sweden
| | - Haben Gabir
- Department of Chemistry, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
| | - Trushar R Patel
- Department of Chemistry and Biochemistry, Alberta RNA Research and Training Institute, University of Lethbridge, Lethbridge, AB T1K 2E1, Canada
- Li Ka Shing Institute of Virology, University of Alberta, Edmonton, AB T6G 2E1, Canada
- Department of Microbiology, Immunology & Infectious Diseases, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada
| | - Jörg Stetefeld
- Department of Chemistry, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
- Department of Microbiology, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
| | - Joseph Puglisi
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Dieter Söll
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
- Department of Chemistry, Yale University, New Haven, CT 06520, USA
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5
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Gabir H, Gupta M, Meier M, Heide F, Koch M, Stetefeld J, Demeler B. Investigation of dynamic solution interactions between NET-1 and UNC-5B by multi-wavelength analytical ultracentrifugation. EUROPEAN BIOPHYSICS JOURNAL : EBJ 2023; 52:473-481. [PMID: 36939874 PMCID: PMC10509325 DOI: 10.1007/s00249-023-01644-1] [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: 12/25/2022] [Revised: 02/27/2023] [Accepted: 03/03/2023] [Indexed: 03/21/2023]
Abstract
NET-1 is a key chemotropic ligand that signals commissural axon migration and change in direction. NET-1 and its receptor UNC-5B switch axon growth cones from attraction to repulsion. The biophysical properties of the NET-1 + UNC-5B complex have been poorly characterized. Using multi-wavelength-AUC by adding a fluorophore to UNC-5B, we were able to separate the UNC-5B sedimentation from NET-1. Using both multi-wavelength- and single-wavelength AUC, we investigated NET-1 and UNC-5B hydrodynamic parameters and complex formation. The sedimentation velocity experiments show that NET-1 exists in a monomer-dimer equilibrium. A close study of the association shows that NET-1 forms a pH-sensitive dimer that interacts in an anti-parallel orientation. UNC-5B can form equimolar NET-1 + UNC-5B heterocomplexes with both monomeric and dimeric NET-1.
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Affiliation(s)
- Haben Gabir
- Department of Chemistry, University of Manitoba, Winnipeg, MB, Canada
| | | | - Markus Meier
- Department of Chemistry, University of Manitoba, Winnipeg, MB, Canada
| | - Fabian Heide
- Department of Chemistry, University of Manitoba, Winnipeg, MB, Canada
| | - Manuel Koch
- Medical Faculty, Institute for Dental Research and Oral Musculoskeletal Biology, University of Cologne, Cologne, Germany
| | - Joerg Stetefeld
- Department of Chemistry, University of Manitoba, Winnipeg, MB, Canada
| | - 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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Prasad P, Hunt LA, Pall AE, Ranasinghe M, Williams AE, Stemmler TL, Demeler B, Hammer NI, Chakraborty S. Photocatalytic Hydrogen Evolution by a De Novo Designed Metalloprotein that Undergoes Ni-Mediated Oligomerization Shift. Chemistry 2023; 29:e202202902. [PMID: 36440875 PMCID: PMC10308963 DOI: 10.1002/chem.202202902] [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: 09/16/2022] [Revised: 11/25/2022] [Accepted: 11/28/2022] [Indexed: 11/29/2022]
Abstract
De novo metalloprotein design involves the construction of proteins guided by specific repeat patterns of polar and apolar residues, which, upon self-assembly, provide a suitable environment to bind metals and produce artificial metalloenzymes. While a wide range of functionalities have been realized in de novo designed metalloproteins, the functional repertoire of such constructs towards alternative energy-relevant catalysis is currently limited. Here we show the application of de novo approach to design a functional H2 evolving protein. The design involved the assembly of an amphiphilic peptide featuring cysteines at tandem a/d sites of each helix. Intriguingly, upon NiII addition, the oligomers shift from a major trimeric assembly to a mix of dimers and trimers. The metalloprotein produced H2 photocatalytically with a bell-shape pH dependence, having a maximum activity at pH 5.5. Transient absorption spectroscopy is used to determine the timescales of electron transfer as a function of pH. Selective outer sphere mutations are made to probe how the local environment tunes activity. A preferential enhancement of activity is observed via steric modulation above the NiII site, towards the N-termini, compared to below the NiII site towards the C-termini.
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Affiliation(s)
- Pallavi Prasad
- Department of Chemistry and Biochemistry, The University of Mississippi, University, MS, 38677 (USA)
| | - Leigh Anna Hunt
- Department of Chemistry and Biochemistry, The University of Mississippi, University, MS, 38677 (USA)
| | - Ashley E. Pall
- Department of Pharmaceutical Sciences, Wayne State University, 259 Mack Avenue, Detroit, MI, 48201-2417 (USA)
| | - Maduni Ranasinghe
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401,University Dr W, Lethbridge, AB T1K 6T5 (CA)
| | - Ashley E. Williams
- Department of Chemistry and Biochemistry, The University of Mississippi, University, MS, 38677 (USA)
| | - Timothy L. Stemmler
- Department of Pharmaceutical Sciences, Wayne State University, 259 Mack Avenue, Detroit, MI, 48201-2417 (USA)
| | - Borries Demeler
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401,University Dr W, Lethbridge, AB T1K 6T5 (CA)
| | - Nathan I. Hammer
- Department of Chemistry and Biochemistry, The University of Mississippi, University, MS, 38677 (USA)
| | - Saumen Chakraborty
- Department of Chemistry and Biochemistry, The University of Mississippi, University, MS, 38677 (USA)
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7
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Structure-function studies reveal ComEA contains an oligomerization domain essential for transformation in gram-positive bacteria. Nat Commun 2022; 13:7724. [PMID: 36513643 PMCID: PMC9747964 DOI: 10.1038/s41467-022-35129-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 11/18/2022] [Indexed: 12/15/2022] Open
Abstract
An essential step in bacterial transformation is the uptake of DNA into the periplasm, across the thick peptidoglycan cell wall of Gram-positive bacteria, or the outer membrane and thin peptidoglycan layer of Gram-negative bacteria. ComEA, a DNA-binding protein widely conserved in transformable bacteria, is required for this uptake step. Here we determine X-ray crystal structures of ComEA from two Gram-positive species, Bacillus subtilis and Geobacillus stearothermophilus, identifying a domain that is absent in Gram-negative bacteria. X-ray crystallographic, genetic, and analytical ultracentrifugation (AUC) analyses reveal that this domain drives ComEA oligomerization, which we show is required for transformation. We use multi-wavelength AUC (MW-AUC) to characterize the interaction between DNA and the ComEA DNA-binding domain. Finally, we present a model for the interaction of the ComEA DNA-binding domain with DNA, suggesting that ComEA oligomerization may provide a pulling force that drives DNA uptake across the thick cell walls of Gram-positive bacteria.
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8
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Zhou XE, Schultz CR, Suino Powell K, Henrickson A, Lamp J, Brunzelle JS, Demeler B, Vega IE, Bachmann AS, Melcher K. Structure and Enzymatic Activity of an Intellectual Disability-Associated Ornithine Decarboxylase Variant, G84R. ACS OMEGA 2022; 7:34665-34675. [PMID: 36188294 PMCID: PMC9520691 DOI: 10.1021/acsomega.2c04702] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 08/30/2022] [Indexed: 06/13/2023]
Abstract
Ornithine decarboxylase (ODC) is a rate-limiting enzyme for the synthesis of polyamines (PAs). PAs are required for proliferation, and increased ODC activity is associated with cancer and neural over-proliferation. ODC levels and activity are therefore tightly regulated, including through the ODC-specific inhibitor, antizyme AZ1. Recently, ODC G84R has been reported as a partial loss-of-function variant that is associated with intellectual disability and seizures. However, G84 is distant from both the catalytic center and the ODC homodimerization interface. To understand how G84R modulates ODC activity, we have determined the crystal structure of ODC G84R in both the presence and the absence of the cofactor pyridoxal 5-phosphate. The structures show that the replacement of G84 by arginine leads to hydrogen bond formation of R84 with F420, the last residue of the ODC C-terminal helix, a structural element that is involved in the AZ1-mediated proteasomal degradation of ODC. In contrast, the catalytic center is essentially indistinguishable from that of wildtype ODC. We therefore reanalyzed the catalytic activity of ODC G84R and found that it is rescued when the protein is purified in the presence of a reducing agent to mimic the reducing environment of the cytoplasm. This suggests that R84 may exert its neurological effects not through reducing ODC catalytic activity but through misregulation of its AZ1-mediated proteasomal degradation.
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Affiliation(s)
- X. Edward Zhou
- Department
of Structural Biology, Van Andel Institute, Grand Rapids, Michigan 49503, United States
| | - Chad R. Schultz
- Department
of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, Michigan 49546, United States
| | - Kelly Suino Powell
- Department
of Structural Biology, Van Andel Institute, Grand Rapids, Michigan 49503, United States
| | - Amy Henrickson
- Department
of Chemistry and Biochemistry, The University
of Lethbridge, Lethbridge, AB T1K3M4, Canada
| | - Jared Lamp
- Department
of Translational Neuroscience, Integrated Mass Spectrometry Unit,
College of Human Medicine, Michigan State
University, Grand
Rapids, Michigan 49503, United States
| | - Joseph S. Brunzelle
- Northwestern
University Synchrotron Research Center, Life Sciences Collaborative
Access Team, Northwestern University, Argonne, Illinois 60439, United States
| | - Borries Demeler
- Department
of Chemistry and Biochemistry, The University
of Lethbridge, Lethbridge, AB T1K3M4, Canada
- Department
of Chemistry and Biochemistry, The University
of Montana, Missoula, Montana 59812, United
States
| | - Irving E. Vega
- Department
of Translational Neuroscience, Integrated Mass Spectrometry Unit,
College of Human Medicine, Michigan State
University, Grand
Rapids, Michigan 49503, United States
| | - André S. Bachmann
- Department
of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, Michigan 49546, United States
| | - Karsten Melcher
- Department
of Structural Biology, Van Andel Institute, Grand Rapids, Michigan 49503, United States
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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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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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11
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Turk LS, Mitchell D, Comoletti D. Purification of a heterodimeric Reelin construct to investigate binding stoichiometry. EUROPEAN BIOPHYSICS JOURNAL : EBJ 2020; 49:773-779. [PMID: 33057791 PMCID: PMC7701066 DOI: 10.1007/s00249-020-01465-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 08/25/2020] [Accepted: 09/14/2020] [Indexed: 01/01/2023]
Abstract
Reelin is a secreted glycoprotein that is integral in neocortex development and synaptic function. Reelin exists as a homodimer with two chains linked by a disulfide bond at cysteine 2101, a feature that is vital to the protein's function. This is highlighted by the fact that only dimeric Reelin can elicit efficient, canonical signaling, even though a mutated (C2101A) monomeric construct of Reelin retains the capacity to bind to its receptors. Receptor clustering has been shown to be important in the signaling pathway, however direct evidence regarding the stoichiometry of Reelin-receptor binding interaction is lacking. Here we describe the construction and purification of a heterodimeric Reelin construct to investigate the stoichiometry of Reelin-receptor binding and how it affects Reelin pathway signaling. We have devised different strategies and have finalized a protocol to produce a heterodimer of Reelin's central fragment using differential tagging and tandem affinity chromatography, such that chain A is wild type in amino acid sequence whereas chain B includes a receptor binding site mutation (K2467A). We also validate that the heterodimer is capable of binding to the extracellular domain of one of Reelin's known receptors, calculating the KD of the interaction. This heterodimeric construct will enable us to understand in greater detail the mechanism by which Reelin interacts with its known receptors and initiates pathway signaling.
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Affiliation(s)
- Liam S Turk
- Child Health Institute of New Jersey, New Brunswick, NJ, 08901, USA.
- Department of Neuroscience and Cell Biology, 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, 6012, New Zealand.
| | - Daniel Mitchell
- School of Biological Sciences, Victoria University of Wellington, Wellington, 6012, New Zealand
| | - Davide Comoletti
- Child Health Institute of New Jersey, New Brunswick, NJ, 08901, USA.
- Department of Neuroscience and Cell Biology, 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, 6012, New Zealand.
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12
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Fedorov D, Batys P, Hayes DB, Sammalkorpi M, Linder MB. Analyzing the weak dimerization of a cellulose binding module by analytical ultracentrifugation. Int J Biol Macromol 2020; 163:1995-2004. [PMID: 32937156 DOI: 10.1016/j.ijbiomac.2020.09.054] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Revised: 09/01/2020] [Accepted: 09/08/2020] [Indexed: 12/22/2022]
Abstract
Cellulose binding modules (CBMs) are found widely in different proteins that act on cellulose. Because they allow a very easy way of binding recombinant proteins to cellulose, they have become widespread in many biotechnological applications involving cellulose. One commonly used variant is the CBMCipA from Clostridium thermocellum. Here we studied the oligomerization behavior of CBMCipA, as such solution association may have an impact on its use. As the principal approach, we used sedimentation velocity and sedimentation equilibrium analytical ultracentrifugation. To enhance our understanding of the possible interactions, we used molecular dynamics simulations. By analysis of the sedimentation velocity data by a discrete model genetic algorithm and by building a binding isotherm based on weight average sedimentation coefficient and by global fitting of sedimentation equilibrium data we found that the CBMCipA shows a weak dimerization interaction with a dissociation constant KD of 90 ± 30 μM. As the KD of CBMCipA binding to cellulose is below 1 μM, we conclude that the dimerization is unlikely to affect cellulose binding. However, at high concentrations used in some applications of the CBMCipA, its dimerization is likely to have a marked effect on its solution behavior.
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Affiliation(s)
- Dmitrii Fedorov
- Department of Bioproducts and Biosystems, School of Chemical Engineering, Aalto University, Box 16100, 00076-Aalto Espoo, Finland
| | - Piotr Batys
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Niezapominajek 8, PL-30239 Krakow, Poland
| | - David B Hayes
- International Solidarity of Scientists, LLC, Gorham, NH, USA
| | - Maria Sammalkorpi
- Department of Bioproducts and Biosystems, School of Chemical Engineering, Aalto University, Box 16100, 00076-Aalto Espoo, Finland; Department of Chemistry and Materials Science, School of Chemical Engineering, Aalto University, Box 16100, 00076-Aalto Espoo, Finland
| | - Markus B Linder
- Department of Bioproducts and Biosystems, School of Chemical Engineering, Aalto University, Box 16100, 00076-Aalto Espoo, Finland.
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13
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Stoutjesdyk M, Henrickson A, Minors G, Demeler B. A calibration disk for the correction of radial errors from chromatic aberration and rotor stretch in the Optima AUC™ analytical ultracentrifuge. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2020; 49:701-709. [DOI: 10.1007/s00249-020-01434-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Revised: 04/15/2020] [Accepted: 04/28/2020] [Indexed: 01/17/2023]
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14
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Mitra S, Demeler B. Probing RNA-Protein Interactions and RNA Compaction by Sedimentation Velocity Analytical Ultracentrifugation. Methods Mol Biol 2020; 2113:281-317. [PMID: 32006321 PMCID: PMC10958623 DOI: 10.1007/978-1-0716-0278-2_19] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Recent advances in multi-wavelength analytical ultracentrifugation (MWL-AUC) combine the power of an exquisitely sensitive hydrodynamic-based separation technique with the added dimension of spectral separation. This added dimension has opened up new doors to much improved characterization of multiple, interacting species in solution. When applied to structural investigations of RNA, MWL-AUC can precisely report on the hydrodynamic radius and the overall shape of an RNA molecule by enabling precise measurements of its sedimentation and diffusion coefficients and identify the stoichiometry of interacting components based on spectral decomposition. Information provided in this chapter will allow an investigator to design experiments for probing ion and/or protein-induced global conformational changes of an RNA molecule and exploit spectral differences between proteins and RNA to characterize their interactions in a physiological solution environment.
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Affiliation(s)
- Somdeb Mitra
- Department of Chemistry, New York University, New York, NY, USA.
| | - Borries Demeler
- Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, AB, Canada
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15
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Crowther JM, Cross PJ, Oliver MR, Leeman MM, Bartl AJ, Weatherhead AW, North RA, Donovan KA, Griffin MDW, Suzuki H, Hudson AO, Kasanmascheff M, Dobson RCJ. Structure-function analyses of two plant meso-diaminopimelate decarboxylase isoforms reveal that active-site gating provides stereochemical control. J Biol Chem 2019; 294:8505-8515. [PMID: 30962284 DOI: 10.1074/jbc.ra118.006825] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Revised: 03/26/2019] [Indexed: 11/06/2022] Open
Abstract
meso-Diaminopimelate decarboxylase catalyzes the decarboxylation of meso-diaminopimelate, the final reaction in the diaminopimelate l-lysine biosynthetic pathway. It is the only known pyridoxal-5-phosphate-dependent decarboxylase that catalyzes the removal of a carboxyl group from a d-stereocenter. Currently, only prokaryotic orthologs have been kinetically and structurally characterized. Here, using complementation and kinetic analyses of enzymes recombinantly expressed in Escherichia coli, we have functionally tested two putative eukaryotic meso-diaminopimelate decarboxylase isoforms from the plant species Arabidopsis thaliana We confirm they are both functional meso-diaminopimelate decarboxylases, although with lower activities than those previously reported for bacterial orthologs. We also report in-depth X-ray crystallographic structural analyses of each isoform at 1.9 and 2.4 Å resolution. We have captured the enzyme structure of one isoform in an asymmetric configuration, with one ligand-bound monomer and the other in an apo-form. Analytical ultracentrifugation and small-angle X-ray scattering solution studies reveal that A. thaliana meso-diaminopimelate decarboxylase adopts a homodimeric assembly. On the basis of our structural analyses, we suggest a mechanism whereby molecular interactions within the active site transduce conformational changes to the active-site loop. These conformational differences are likely to influence catalytic activity in a way that could allow for d-stereocenter selectivity of the substrate meso-diaminopimelate to facilitate the synthesis of l-lysine. In summary, the A. thaliana gene loci At3g14390 and At5g11880 encode functional. meso-diaminopimelate decarboxylase enzymes whose structures provide clues to the stereochemical control of the decarboxylation reaction catalyzed by these eukaryotic proteins.
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Affiliation(s)
- Jennifer M Crowther
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch 8140, New Zealand; School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3JG, Scotland, United Kingdom
| | - Penelope J Cross
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch 8140, New Zealand
| | - Michael R Oliver
- School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3JG, Scotland, United Kingdom
| | - Mary M Leeman
- Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology (RIT), Rochester, New York 14623
| | - Austin J Bartl
- Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology (RIT), Rochester, New York 14623
| | - Anthony W Weatherhead
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch 8140, New Zealand
| | - Rachel A North
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch 8140, New Zealand
| | - Katherine A Donovan
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02215
| | - Michael D W Griffin
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Hironori Suzuki
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch 8140, New Zealand
| | - André O Hudson
- Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology (RIT), Rochester, New York 14623.
| | - Müge Kasanmascheff
- Department of Chemistry and Chemical Biology, Technical University of Dortmund, D-44227 Dortmund, Germany.
| | - Renwick C J Dobson
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch 8140, New Zealand; Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria 3010, Australia.
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16
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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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17
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Atkinson SC, Dogovski C, Wood K, Griffin MDW, Gorman MA, Hor L, Reboul CF, Buckle AM, Wuttke J, Parker MW, Dobson RCJ, Perugini MA. Substrate Locking Promotes Dimer-Dimer Docking of an Enzyme Antibiotic Target. Structure 2018; 26:948-959.e5. [PMID: 29804823 DOI: 10.1016/j.str.2018.04.014] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2018] [Revised: 02/27/2018] [Accepted: 04/19/2018] [Indexed: 11/19/2022]
Abstract
Protein dynamics manifested through structural flexibility play a central role in the function of biological molecules. Here we explore the substrate-mediated change in protein flexibility of an antibiotic target enzyme, Clostridium botulinum dihydrodipicolinate synthase. We demonstrate that the substrate, pyruvate, stabilizes the more active dimer-of-dimers or tetrameric form. Surprisingly, there is little difference between the crystal structures of apo and substrate-bound enzyme, suggesting protein dynamics may be important. Neutron and small-angle X-ray scattering experiments were used to probe substrate-induced dynamics on the sub-second timescale, but no significant changes were observed. We therefore developed a simple technique, coined protein dynamics-mass spectrometry (ProD-MS), which enables measurement of time-dependent alkylation of cysteine residues. ProD-MS together with X-ray crystallography and analytical ultracentrifugation analyses indicates that pyruvate locks the conformation of the dimer that promotes docking to the more active tetrameric form, offering insight into ligand-mediated stabilization of multimeric enzymes.
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Affiliation(s)
- Sarah C Atkinson
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia; Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, 30 Flemington Road, University of Melbourne, Parkville, VIC 3010, Australia
| | - Con Dogovski
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, 30 Flemington Road, University of Melbourne, Parkville, VIC 3010, Australia
| | - Kathleen Wood
- Australian Nuclear Science and Technology Organisation, Lucas Heights, NSW 2234, Australia
| | - Michael D W Griffin
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, 30 Flemington Road, University of Melbourne, Parkville, VIC 3010, Australia
| | - Michael A Gorman
- ACRF Rational Drug Discovery Centre, St. Vincent's Institute of Medical Research, Fitzroy, VIC 3065, Australia
| | - Lilian Hor
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, 30 Flemington Road, University of Melbourne, Parkville, VIC 3010, Australia; Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC 3086, Australia; ARC Centre of Excellence in Advanced Molecular Imaging, La Trobe University, Melbourne, VIC 3086, Australia
| | - Cyril F Reboul
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia
| | - Ashley M Buckle
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia
| | - Joachim Wuttke
- Juelich Centre for Neutron Science (JCNS), at Heinz Maier-Leibnitz Zentrum (MLZ), Forschungszentrum Juelich GmbH, Lichtenstrasse 1, Garching 85 747, Germany
| | - Michael W Parker
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, 30 Flemington Road, University of Melbourne, Parkville, VIC 3010, Australia; ACRF Rational Drug Discovery Centre, St. Vincent's Institute of Medical Research, Fitzroy, VIC 3065, Australia
| | - Renwick C J Dobson
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, 30 Flemington Road, University of Melbourne, Parkville, VIC 3010, Australia; Biomolecular Interaction Centre, School of Biological Sciences, University of Canterbury, Private Bag, Christchurch 4800, New Zealand
| | - Matthew A Perugini
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, 30 Flemington Road, University of Melbourne, Parkville, VIC 3010, Australia; Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC 3086, Australia.
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18
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Crowther JM, Allison JR, Smolenski GA, Hodgkinson AJ, Jameson GB, Dobson RCJ. The self-association and thermal denaturation of caprine and bovine β-lactoglobulin. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2018; 47:739-750. [PMID: 29663020 DOI: 10.1007/s00249-018-1300-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Revised: 02/27/2018] [Accepted: 04/10/2018] [Indexed: 11/29/2022]
Abstract
Milk components, such as proteins and lipids, have different physicochemical properties depending upon the mammalian species from which they come. Understanding the different responses of these milks to digestion, processing, and differences in their immunogenicity requires detailed knowledge of these physicochemical properties. Here we report on the oligomeric state of β-lactoglobulin from caprine milk, the most abundant protein present in the whey fraction. At pH 2.5 caprine β-lactoglobulin is predominantly monomeric, whereas bovine β-lactoglobulin exists in a monomer-dimer equilibrium at the same protein concentrations. This behaviour was also observed in molecular dynamics simulations and can be rationalised in terms of the amino acid substitutions present between caprine and bovine β-lactoglobulin that result in a greater positive charge on each subunit of caprine β-lactoglobulin at low pH. The denaturation of β-lactoglobulin when milk is heat-treated contributes to the fouling of heat-exchange surfaces, reducing yields and increasing cleaning costs. The bovine and caprine orthologues of β-lactoglobulin display different responses to thermal treatment, with caprine β-lactoglobulin precipitating at higher pH values than bovine β-lactoglobulin (pH 7.1 compared to pH 5.6) that are closer to the natural pH of these milks (pH 6.7). This property of caprine β-lactoglobulin likely contributes to the reduced heat stability of caprine milk compared to bovine milk at its natural pH.
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Affiliation(s)
- Jennifer M Crowther
- School of Biological Sciences, University of Canterbury, PO Box 4800, Christchurch, 8140, New Zealand
- Biomolecular Interaction Centre, University of Canterbury, Christchurch, New Zealand
| | - 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
| | - Grant A Smolenski
- Food and Bio-Based Products, AgResearch Limited, Ruakura Research Centre, Hamilton, New Zealand
- MS3 Solutions Ltd, Ruakura Research Centre, Hamilton, 3240, New Zealand
| | - Alison J Hodgkinson
- Food and Bio-Based Products, AgResearch Limited, Ruakura Research Centre, Hamilton, New Zealand
| | - Geoffrey B Jameson
- Biomolecular Interaction Centre, University of Canterbury, Christchurch, New Zealand
- Institute of Fundamental Sciences, Massey University, Palmerston North, New Zealand
- The Riddet Institute, Massey University, Palmerston North, New Zealand
| | - Renwick C J Dobson
- School of Biological Sciences, University of Canterbury, PO Box 4800, Christchurch, 8140, New Zealand.
- Biomolecular Interaction Centre, University of Canterbury, Christchurch, New Zealand.
- The Riddet Institute, Massey University, Palmerston North, New Zealand.
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, VIC, Australia.
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19
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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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20
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Adkins NL, Swygert SG, Kaur P, Niu H, Grigoryev SA, Sung P, Wang H, Peterson CL. Nucleosome-like, Single-stranded DNA (ssDNA)-Histone Octamer Complexes and the Implication for DNA Double Strand Break Repair. J Biol Chem 2017; 292:5271-5281. [PMID: 28202543 DOI: 10.1074/jbc.m117.776369] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Revised: 02/13/2017] [Indexed: 11/06/2022] Open
Abstract
Repair of DNA double strand breaks (DSBs) is key for maintenance of genome integrity. When DSBs are repaired by homologous recombination, DNA ends can undergo extensive processing, producing long stretches of single-stranded DNA (ssDNA). In vivo, DSB processing occurs in the context of chromatin, and studies indicate that histones may remain associated with processed DSBs. Here we demonstrate that histones are not evicted from ssDNA after in vitro chromatin resection. In addition, we reconstitute histone-ssDNA complexes (termed ssNucs) with ssDNA and recombinant histones and analyze these particles by a combination of native gel electrophoresis, sedimentation velocity, electron microscopy, and a recently developed electrostatic force microscopy technique, DREEM (dual-resonance frequency-enhanced electrostatic force microscopy). The reconstituted ssNucs are homogenous and relatively stable, and DREEM reveals ssDNA wrapping around histones. We also find that histone octamers are easily transferred in trans from ssNucs to either double-stranded DNA or ssDNA. Furthermore, the Fun30 remodeling enzyme, which has been implicated in DNA repair, binds ssNucs preferentially over nucleosomes, and ssNucs are effective at activating Fun30 ATPase activity. Our results indicate that ssNucs may be a hallmark of processes that generate ssDNA, and that posttranslational modification of ssNucs may generate novel signaling platforms involved in genome stability.
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Affiliation(s)
- Nicholas L Adkins
- From the Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts 01605
| | - Sarah G Swygert
- From the Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts 01605
| | - Parminder Kaur
- the Department of Physics.,Center for Human Health and the Environment, North Carolina State University, Raleigh, North Carolina 27695
| | - Hengyao Niu
- the Department Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, Connecticut 06520, and
| | - Sergei A Grigoryev
- the Department of Biochemistry and Molecular Biology, Pennsylvania State University College of Medicine, Hershey, Pennsylvania 17033
| | - Patrick Sung
- the Department Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, Connecticut 06520, and
| | - Hong Wang
- the Department of Physics.,Center for Human Health and the Environment, North Carolina State University, Raleigh, North Carolina 27695
| | - Craig L Peterson
- From the Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts 01605,
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21
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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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22
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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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Patel TR, Winzor DJ, Scott DJ. Analytical ultracentrifugation: A versatile tool for the characterisation of macromolecular complexes in solution. Methods 2016; 95:55-61. [DOI: 10.1016/j.ymeth.2015.11.006] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2015] [Revised: 11/05/2015] [Accepted: 11/07/2015] [Indexed: 12/25/2022] Open
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24
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Abstract
The ATPases associated with diverse cellular activities (AAA+) is a large superfamily of proteins involved in a broad array of biological processes. Many members of this family require nucleotide binding to assemble into their final active hexameric form. We have been studying two example members, Escherichia coli ClpA and ClpB. These two enzymes are active as hexameric rings that both require nucleotide binding for assembly. Our studies have shown that they both reside in a monomer, dimer, tetramer, and hexamer equilibrium, and this equilibrium is thermodynamically linked to nucleotide binding. Moreover, we are finding that the kinetics of the assembly reaction are very different for the two enzymes. Here, we present our strategy for determining the self-association constants in the absence of nucleotide to set the stage for the analysis of nucleotide binding from other experimental approaches including analytical ultracentrifugation.
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Affiliation(s)
- JiaBei Lin
- Department of Chemistry, The University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Aaron L Lucius
- Department of Chemistry, The University of Alabama at Birmingham, Birmingham, Alabama, USA.
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25
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Ranaivoson FM, Liu Q, Martini F, Bergami F, von Daake S, Li S, Lee D, Demeler B, Hendrickson WA, Comoletti D. Structural and Mechanistic Insights into the Latrophilin3-FLRT3 Complex that Mediates Glutamatergic Synapse Development. Structure 2015; 23:1665-1677. [PMID: 26235031 DOI: 10.1016/j.str.2015.06.022] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2014] [Revised: 06/09/2015] [Accepted: 06/21/2015] [Indexed: 10/23/2022]
Abstract
Latrophilins (LPHNs) are adhesion-like G-protein-coupled receptors implicated in attention-deficit/hyperactivity disorder. Recently, LPHN3 was found to regulate excitatory synapse number through trans interactions with fibronectin leucine-rich repeat transmembrane 3 (FLRT3). By isothermal titration calorimetry, we determined that only the olfactomedin (OLF) domain of LPHN3 is necessary for FLRT3 association. By multi-crystal native single-wavelength anomalous diffraction phasing, we determined the crystal structure of the OLF domain. This structure is a five-bladed β propeller with a Ca(2+) ion bound in the central pore, which is capped by a mobile loop that allows the ion to exchange with the solvent. The crystal structure of the OLF/FLRT3 complex shows that LPHN3-OLF in the closed state binds with high affinity to the concave face of FLRT3-LRR with a combination of hydrophobic and charged residues. Our study provides structural and functional insights into the molecular mechanism underlying the contribution of LPHN3/FLRT3 to the development of glutamatergic synapses.
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Affiliation(s)
- Fanomezana M Ranaivoson
- Child Health Institute of New Jersey and Department of Neuroscience and Cell Biology, Robert Wood Johnson Medical School, Rutgers University, 89 French Street, New Brunswick, NJ 08901, USA
| | - Qun Liu
- New York Structural Biology Center, NSLSII, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Francesca Martini
- Child Health Institute of New Jersey and Department of Neuroscience and Cell Biology, Robert Wood Johnson Medical School, Rutgers University, 89 French Street, New Brunswick, NJ 08901, USA
| | - Francesco Bergami
- Child Health Institute of New Jersey and Department of Neuroscience and Cell Biology, Robert Wood Johnson Medical School, Rutgers University, 89 French Street, New Brunswick, NJ 08901, USA
| | - Sventja von Daake
- Child Health Institute of New Jersey and Department of Neuroscience and Cell Biology, Robert Wood Johnson Medical School, Rutgers University, 89 French Street, New Brunswick, NJ 08901, USA
| | - Sheng Li
- Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - David Lee
- Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Borries Demeler
- The University of Texas Health Science Center at San Antonio, Department of Biochemistry, San Antonio, TX 78229, USA
| | - Wayne A Hendrickson
- New York Structural Biology Center, NSLSII, Brookhaven National Laboratory, Upton, NY 11973, USA; Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
| | - Davide Comoletti
- Child Health Institute of New Jersey and Department of Neuroscience and Cell Biology, Robert Wood Johnson Medical School, Rutgers University, 89 French Street, New Brunswick, NJ 08901, USA; Department of Pediatrics, Robert Wood Johnson Medical School, Rutgers University, New Brunswick, NJ 08901, USA.
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27
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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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28
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Ligand binding reveals a role for heme in translationally-controlled tumor protein dimerization. PLoS One 2014; 9:e112823. [PMID: 25396429 PMCID: PMC4232476 DOI: 10.1371/journal.pone.0112823] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2014] [Accepted: 10/16/2014] [Indexed: 11/19/2022] Open
Abstract
The translationally-controlled tumor protein (TCTP) is a highly conserved, ubiquitously expressed, abundant protein that is broadly distributed among eukaryotes. Its biological function spans numerous cellular processes ranging from regulation of the cell cycle and microtubule stabilization to cell growth, transformation, and death processes. In this work, we propose a new function for TCTP as a “buffer protein” controlling cellular homeostasis. We demonstrate that binding of hemin to TCTP is mediated by a conserved His-containing motif (His76His77) followed by dimerization, an event that involves ligand-mediated conformational changes and that is necessary to trigger TCTP's cytokine-like activity. Mutation in both His residues to Ala prevents hemin from binding and abrogates oligomerization, suggesting that the ligand site localizes at the interface of the oligomer. Unlike heme, binding of Ca2+ ligand to TCTP does not alter its monomeric state; although, Ca2+ is able to destabilize an existing TCTP dimer created by hemin addition. In agreement with TCTP's proposed buffer function, ligand binding occurs at high concentration, allowing the “buffer” condition to be dissociated from TCTP's role as a component of signal transduction mechanisms.
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29
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Papsdorf K, Sacherl J, Richter K. The balanced regulation of Hsc70 by DNJ-13 and UNC-23 is required for muscle functionality. J Biol Chem 2014; 289:25250-61. [PMID: 25053410 DOI: 10.1074/jbc.m114.565234] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The molecular chaperone Hsc70 assists in the folding of non-native proteins together with its J domain- and BAG domain-containing cofactors. In Caenorhabditis elegans, two BAG domain-containing proteins can be identified, one of them being UNC-23, whose mutation induces severe motility dysfunctions. Using reporter strains, we find that the full-length UNC-23, in contrast to C-terminal fragments, localizes specifically to the muscular attachment sites. C-terminal fragments of UNC-23 instead perform all Hsc70-related functions, like ATPase stimulation and regulation of folding activity, albeit with lower affinity than BAG-1. Interestingly, overexpression of CFP-Hsc70 can induce muscular defects in wild-type nematodes that phenocopy the knockout of its cofactor UNC-23. Strikingly, the motility dysfunction in the unc-23 mutated strain can be cured specifically by down-regulation of the antagonistic Hsc70 cochaperone DNJ-13, implying that the severe phenotype is caused by misregulation of the Hsc70 cycle. These findings point out that the balanced action of cofactors in the ATP-driven cycle of Hsc70 is crucial for the contribution of Hsc70 to muscle functionality.
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Affiliation(s)
- Katharina Papsdorf
- From the Department of Biotechnology and Center for Integrated Protein Science Munich (CIPS), Technische Universität München, Lichtenbergstrasse 4, 85748 Garching, Germany
| | - Julia Sacherl
- From the Department of Biotechnology and Center for Integrated Protein Science Munich (CIPS), Technische Universität München, Lichtenbergstrasse 4, 85748 Garching, Germany
| | - Klaus Richter
- From the Department of Biotechnology and Center for Integrated Protein Science Munich (CIPS), Technische Universität München, Lichtenbergstrasse 4, 85748 Garching, Germany
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30
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Clingman CC, Deveau LM, Hay SA, Genga RM, Shandilya SMD, Massi F, Ryder SP. Allosteric inhibition of a stem cell RNA-binding protein by an intermediary metabolite. eLife 2014; 3. [PMID: 24935936 PMCID: PMC4094780 DOI: 10.7554/elife.02848] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2014] [Accepted: 06/15/2014] [Indexed: 01/22/2023] Open
Abstract
Gene expression and metabolism are coupled at numerous levels. Cells must sense and respond to nutrients in their environment, and specialized cells must synthesize metabolic products required for their function. Pluripotent stem cells have the ability to differentiate into a wide variety of specialized cells. How metabolic state contributes to stem cell differentiation is not understood. In this study, we show that RNA-binding by the stem cell translation regulator Musashi-1 (MSI1) is allosterically inhibited by 18-22 carbon ω-9 monounsaturated fatty acids. The fatty acid binds to the N-terminal RNA Recognition Motif (RRM) and induces a conformational change that prevents RNA association. Musashi proteins are critical for development of the brain, blood, and epithelium. We identify stearoyl-CoA desaturase-1 as a MSI1 target, revealing a feedback loop between ω-9 fatty acid biosynthesis and MSI1 activity. We propose that other RRM proteins could act as metabolite sensors to couple gene expression changes to physiological state.
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Affiliation(s)
- Carina C Clingman
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, United States
| | - Laura M Deveau
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, United States
| | - Samantha A Hay
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, United States
| | - Ryan M Genga
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, United States
| | - Shivender M D Shandilya
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, United States
| | - Francesca Massi
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, United States
| | - Sean P Ryder
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, United States
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31
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Eckl JM, Drazic A, Rutz DA, Richter K. Nematode Sgt1-homologue D1054.3 binds open and closed conformations of Hsp90 via distinct binding sites. Biochemistry 2014; 53:2505-14. [PMID: 24660900 DOI: 10.1021/bi5000542] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Heat shock protein 90 (Hsp90) is a highly conserved ATP-driven machine involved in client protein maturation, folding, and activation. The chaperone is supported by a set of cochaperones that confer client specificities. One of those proteins is the suppressor of G2 allele of skp1 (Sgt1), which participates together with Hsp90 in the immune responses of plants. Sgt1 consists of three domains: a TPR-, CS-, and SGS-domain, conserved in plants, yeast, and humans. The TPR-domain though is lacking in nematodes and insects. We observe that the Caenorhabditis elegans Sgt1 homologue D1054.3 binds to Hsp90 in the absence of nucleotides but much stronger in the presence of ATP and ATPγS. The latter binding mode is similar to p23, another CS-domain containing Hsp90 cofactor, even though binding is not observable for p23 in the absence of nucleotides. We use point mutations in Hsp90, which accumulate different conformations in the ATPase cycle, to differentiate between binding to open and closed Hsp90 conformations. These data support a strong contribution of the Hsp90 conformation to Sgt1 binding and highlight the ability of this cofactor to interact with all known Hsp90 conformations albeit with different affinities.
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Affiliation(s)
- Julia M Eckl
- Department of Chemistry, Technische Universität München , 85748 Garching, Germany
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32
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Abstract
![]()
This
contribution reports solution-phase structural studies of
oligomers of a family of peptides derived from the β-amyloid
peptide (Aβ). We had previously reported the X-ray crystallographic
structures of the oligomers and oligomer assemblies formed in the
solid state by a macrocyclic β-sheet peptide containing the
Aβ15–23 nonapeptide. In the current study,
we set out to determine its assembly in aqueous solution. In the solid
state, macrocyclic β-sheet peptide 1 assembles
to form hydrogen-bonded dimers that further assemble in a sandwich-like
fashion to form tetramers through hydrophobic interactions between
the faces bearing V18 and F20. In aqueous solution,
macrocyclic β-sheet peptide 1 and homologue 2a form hydrogen-bonded dimers that assemble to form tetramers
through hydrophobic interactions between the faces bearing L17, F19, and A21. In the solid state, the hydrogen-bonded
dimers are antiparallel, and the β-strands are fully aligned,
with residues 17–23 of one of the macrocycles aligned with
residues 23–17 of the other. In solution, residues 17–23
of the hydrogen-bonded dimers are shifted out of alignment by two
residues toward the C-termini. The two hydrogen-bonded dimers are
nearly orthogonal in the solid state, while in solution the dimers
are only slightly rotated. The differing morphology of the solution-state
and solid-state tetramers is significant, because it may provide a
glimpse into some of the structural bases for polymorphism among Aβ
oligomers in Alzheimer’s disease.
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Affiliation(s)
- Johnny D Pham
- Department of Chemistry, University of California, Irvine , Irvine, California 92697-2025, United States
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Halling DB, Kenrick SA, Riggs AF, Aldrich RW. Calcium-dependent stoichiometries of the KCa2.2 (SK) intracellular domain/calmodulin complex in solution. ACTA ACUST UNITED AC 2014; 143:231-52. [PMID: 24420768 PMCID: PMC4001768 DOI: 10.1085/jgp.201311007] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Biophysical analyses indicate that the Ca2+-activated K+ channel SK2 binds calmodulin with multiple stoichiometries, distinct from the two SK2-two calmodulin stoichiometry identified by crystallography. Ca2+ activates SK Ca2+-activated K+ channels through the protein Ca2+ sensor, calmodulin (CaM). To understand how SK channels operate, it is necessary to determine how Ca2+ regulates CaM binding to its target on SK. Tagless, recombinant SK peptide (SKp), was purified for binding studies with CaM at low and high Ca2+ concentrations. Composition gradient multi-angle light scattering accurately measures the molar mass, stoichiometry, and affinity of protein complexes. In 2 mM Ca2+, SKp and CaM bind with three different stoichiometries that depend on the molar ratio of SKp:CaM in solution. These complexes include 28 kD 1SKp/1CaM, 39 kD 2SKp/1CaM, and 44 kD 1SKp/2CaM. A 2SKp/2CaM complex, observed in prior crystallographic studies, is absent. At <5 nM Ca2+, 1SKp/1CaM and 2SKp/1CaM were observed; however, 1SKp/2CaM was absent. Analytical ultracentrifugation was used to characterize the physical properties of the three SKp/CaM stoichiometries. In high Ca2+, the sedimentation coefficient is smaller for a 1SKp:1CaM solution than it is for either 2SKp:1CaM or 1SKp:2CaM. At low Ca2+ and at >100 µM protein concentrations, a molar excess of SKp over CaM causes aggregation. Aggregation is not observed in Ca2+ or with CaM in molar excess. In low Ca2+ both 1SKp:1CaM and 1SKp:2CaM solutions have similar sedimentation coefficients, which is consistent with the absence of a 1SKp/2CaM complex in low Ca2+. These results suggest that complexes with stoichiometries other than 2SKp/2CaM are important in gating.
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Affiliation(s)
- D Brent Halling
- Department of Neuroscience, 2 Center for Learning and Memory, The University of Texas at Austin, Austin, TX 78712
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Bjelić S, Wieser M, Frey D, Stirnimann CU, Chance MR, Jaussi R, Steinmetz MO, Kammerer RA. Structural basis for the oligomerization-state switch from a dimer to a trimer of an engineered cortexillin-1 coiled-coil variant. PLoS One 2013; 8:e63370. [PMID: 23691037 PMCID: PMC3653964 DOI: 10.1371/journal.pone.0063370] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2013] [Accepted: 03/30/2013] [Indexed: 11/19/2022] Open
Abstract
Coiled coils are well suited to drive subunit oligomerization and are widely used in applications ranging from basic research to medicine. The optimization of these applications requires a detailed understanding of the molecular determinants that control of coiled-coil formation. Although many of these determinants have been identified and characterized in great detail, a puzzling observation is that their presence does not necessarily correlate with the oligomerization state of a given coiled-coil structure. Thus, other determinants must play a key role. To address this issue, we recently investigated the unrelated coiled-coil domains from GCN4, ATF1 and cortexillin-1 as model systems. We found that well-known trimer-specific oligomerization-state determinants, such as the distribution of isoleucine residues at heptad-repeat core positions or the trimerization motif Arg-h-x-x-h-Glu (where h = hydrophobic amino acid; x = any amino acid), switch the peptide's topology from a dimer to a trimer only when inserted into the trigger sequence, a site indispensable for coiled-coil formation. Because high-resolution structural information could not be obtained for the full-length, three-stranded cortexillin-1 coiled coil, we here report the detailed biophysical and structural characterization of a shorter variant spanning the trigger sequence using circular dichroism, anatytical ultracentrifugation and x-ray crystallography. We show that the peptide forms a stable α-helical trimer in solution. We further determined the crystal structure of an optimised variant at a resolution of 1.65 Å, revealing that the peptide folds into a parallel, three-stranded coiled coil. The two complemented R-IxxIE trimerization motifs and the additional hydrophobic core isoleucine residue adopt the conformations seen in other extensively characterized parallel, three-stranded coiled coils. These findings not only confirm the structural basis for the switch in oligomerization state from a dimer to a trimer observed for the full-length cortexillin-1 coiled-coil domain, but also provide further evidence for a general link between oligomerization-state specificity and trigger-sequence function.
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Affiliation(s)
- Saša Bjelić
- Laboratory of Biomolecular Research, Paul Scherrer Institut, Villigen, Switzerland
- Center for Proteomics & Bioinformatics, Case Western Reserve University, Cleveland, Ohio, United States of America
| | - Mara Wieser
- Laboratory of Biomolecular Research, Paul Scherrer Institut, Villigen, Switzerland
| | - Daniel Frey
- Laboratory of Biomolecular Research, Paul Scherrer Institut, Villigen, Switzerland
| | | | - Mark R. Chance
- Center for Proteomics & Bioinformatics, Case Western Reserve University, Cleveland, Ohio, United States of America
| | - Rolf Jaussi
- Laboratory of Biomolecular Research, Paul Scherrer Institut, Villigen, Switzerland
| | - Michel O. Steinmetz
- Laboratory of Biomolecular Research, Paul Scherrer Institut, Villigen, Switzerland
| | - Richard A. Kammerer
- Laboratory of Biomolecular Research, Paul Scherrer Institut, Villigen, Switzerland
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35
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Wenta N, Vinkemeier U. Characterization of STAT self-association by analytical ultracentrifugation. Methods Mol Biol 2013; 967:203-224. [PMID: 23296732 DOI: 10.1007/978-1-62703-242-1_15] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Multiple experimental tools have demonstrated that cytokine-induced STAT activation entails the transition of dimer conformations rather than de novo dimerization. In this chapter, we describe the utilization of analytical ultracentrifugation (AUC) as a powerful technique for the quantitative analysis of hydro- and thermodynamic properties of STAT proteins in solution. These studies provided a quantitative understanding of dimer stability and conformational transitions associated with the activation of STAT1.
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Affiliation(s)
- Nikola Wenta
- School of Biomedical Sciences, University of Nottingham Medical School, Nottingham, UK
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36
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Krayukhina E, Uchiyama S, Nojima K, Okada Y, Hamaguchi I, Fukui K. Aggregation analysis of pharmaceutical human immunoglobulin preparations using size-exclusion chromatography and analytical ultracentrifugation sedimentation velocity. J Biosci Bioeng 2013; 115:104-10. [DOI: 10.1016/j.jbiosc.2012.07.021] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2012] [Revised: 07/27/2012] [Accepted: 07/31/2012] [Indexed: 10/28/2022]
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Sun L, Edelmann FT, Kaiser CJO, Papsdorf K, Gaiser AM, Richter K. The lid domain of Caenorhabditis elegans Hsc70 influences ATP turnover, cofactor binding and protein folding activity. PLoS One 2012; 7:e33980. [PMID: 22479492 PMCID: PMC3315512 DOI: 10.1371/journal.pone.0033980] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2011] [Accepted: 02/20/2012] [Indexed: 12/27/2022] Open
Abstract
Hsc70 is a conserved ATP-dependent molecular chaperone, which utilizes the energy of ATP hydrolysis to alter the folding state of its client proteins. In contrast to the Hsc70 systems of bacteria, yeast and humans, the Hsc70 system of C. elegans (CeHsc70) has not been studied to date. We find that CeHsc70 is characterized by a high ATP turnover rate and limited by post-hydrolysis nucleotide exchange. This rate-limiting step is defined by the helical lid domain at the C-terminus. A certain truncation in this domain (CeHsc70-Δ545) reduces the turnover rate and renders the hydrolysis step rate-limiting. The helical lid domain also affects cofactor affinities as the lidless mutant CeHsc70-Δ512 binds more strongly to DNJ-13, forming large protein complexes in the presence of ATP. Despite preserving the ability to hydrolyze ATP and interact with its cofactors DNJ-13 and BAG-1, the truncation of the helical lid domain leads to the loss of all protein folding activity, highlighting the requirement of this domain for the functionality of the nematode's Hsc70 protein.
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Affiliation(s)
| | | | | | | | | | - Klaus Richter
- Center for Integrated Protein Science Munich (CIPSM) and Department Chemie, Technische Universität München, Garching, Germany
- * E-mail:
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Moody AD, Robblee JP, Bain DL. Dissecting the linkage between transcription factor self-assembly and site-specific DNA binding: the role of the analytical ultracentrifuge. Methods Mol Biol 2012; 796:187-204. [PMID: 22052491 DOI: 10.1007/978-1-61779-334-9_10] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
A long-standing goal of biomedical research has been to determine the quantitative mechanisms responsible for gene regulation and transcriptional activation. These events occur through numerous protein-protein and protein-DNA interactions, many of which are allosterically coupled. For systems where highly purified protein is available, analytical ultracentrifugation provides a means to study these linked reactions, allosteric or otherwise. Sedimentation velocity is an ultracentrifugation technique that provides rigorous insight into protein self-association, homogeneity, and gross structure. Because self-association is often in dynamic equilibrium with other reactions such as DNA binding, an explicit and independent analysis of each interaction is critical to revealing mechanism. This chapter details a protocol for using sedimentation velocity to dissect the linkage between transcription factor self-association and site-specific DNA binding.
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Affiliation(s)
- Amie D Moody
- Department of Pharmaceutical Sciences, University of Colorado, Aurora, CO, USA
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Lee S, Xue Y, Hu J, Wang Y, Liu X, Demeler B, Ha Y. The E2 domains of APP and APLP1 share a conserved mode of dimerization. Biochemistry 2011; 50:5453-64. [PMID: 21574595 DOI: 10.1021/bi101846x] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Amyloid precursor protein (APP) is genetically linked to Alzheimer's disease. APP is a type I membrane protein, and its oligomeric structure is potentially important because this property may play a role in its function or affect the processing of the precursor by the secretases to generate amyloid β-peptide. Several independent studies have shown that APP can form dimers in the cell, but how it dimerizes remains controversial. At least three regions of the precursor, including a centrally located and conserved domain called E2, have been proposed to contribute to dimerization. Here we report two new crystal structures of E2, one from APP and the other from APLP1, a mammalian APP homologue. Comparison with an earlier APP structure, which was determined in a different space group, shows that the E2 domains share a conserved and antiparallel mode of dimerization. Biophysical measurements in solution show that heparin binding induces E2 dimerization. The 2.1 Å resolution electron density map also reveals phosphate ions that are bound to the protein surface. Mutational analysis shows that protein residues interacting with the phosphate ions are also involved in heparin binding. The locations of two of these residues, Arg-369 and His-433, at the dimeric interface suggest a mechanism for heparin-induced protein dimerization.
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Affiliation(s)
- Sangwon Lee
- Department of Pharmacology, Yale School of Medicine, New Haven, Connecticut 06520, USA
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40
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Abstract
PKR is an interferon-induced kinase that plays a pivotal role in the innate immunity pathway for defense against viral infection. PKR is activated to undergo autophosphorylation upon binding to RNAs that contain duplex regions. Some highly structured viral RNAs do not activate and function as PKR inhibitors. In order to define the mechanisms of activation and inhibition of PKR by RNA, it is necessary to characterize the stoichiometries, affinities, and free energy couplings governing the assembly of the relevant complexes. We have found sedimentation velocity analytical ultracentrifugation to be particularly useful in the study of PKR-RNA interactions. Here, we describe protocols for designing and analyzing sedimentation velocity experiments that are generally applicable to studies of protein-nucleic acid interactions. Initially, velocity data obtained at multiple protein:RNA ratios are analyzed using the dc/dt method's to define the association model and to test whether the system is kinetically limited. The sedimentation velocity data obtained at multiple loading concentrations are then globally fitted to this model to determine the relevant association constants. The frictional ratios of the complexes are calculated using the fitted sedimentation coefficients to determine whether the hydrodynamic properties are physically reasonable. We demonstrate the utility of this approach using examples from our studies of PKR interactions with simple dsRNAs, the HIV TAR RNA, and the VAI RNA from adenovirus.
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Affiliation(s)
- C Jason Wong
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut, USA
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Rowe AJ. Ultra-weak reversible protein–protein interactions. Methods 2011; 54:157-66. [DOI: 10.1016/j.ymeth.2011.02.006] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2010] [Revised: 01/15/2011] [Accepted: 02/07/2011] [Indexed: 10/18/2022] Open
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42
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Wang R, Taylor AB, Leal BZ, Chadwell LV, Ilangovan U, Robinson AK, Schirf V, Hart PJ, Lafer EM, Demeler B, Hinck AP, McEwen DG, Kim CA. Polycomb group targeting through different binding partners of RING1B C-terminal domain. Structure 2010; 18:966-75. [PMID: 20696397 DOI: 10.1016/j.str.2010.04.013] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2010] [Revised: 04/21/2010] [Accepted: 04/25/2010] [Indexed: 12/31/2022]
Abstract
RING1B, a Polycomb Group (PcG) protein, binds methylated chromatin through its association with another PcG protein called Polycomb (Pc). However, RING1B can associate with nonmethylated chromatin suggesting an alternate mechanism for RING1B interaction with chromatin. Here, we demonstrate that two proteins with little sequence identity between them, the Pc cbox domain and RYBP, bind the same surface on the C-terminal domain of RING1B (C-RING1B). Pc cbox and RYBP each fold into a nearly identical, intermolecular beta sheet with C-RING1B and a loop structure which are completely different in the two proteins. Both the beta sheet and loop are required for stable binding and transcription repression. Further, a mutation engineered to disrupt binding on the Drosophila dRING1 protein prevents chromatin association and PcG function in vivo. These results suggest that PcG targeting to different chromatin locations relies, in part, on binding partners of C-RING1B that are diverse in sequence and structure.
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Affiliation(s)
- Renjing Wang
- Department of Biochemistry, University of Texas Health Science Center at San Antonio, MSC 7760, 7703 Floyd Curl Drive, San Antonio, TX 78229-3990, USA
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Abstract
In this contribution the use of Analytical Ultracentrifugation (AUC) for the modern analysis of colloids is reviewed. Since AUC is a fractionation technique, distributions of the sedimentation coefficient, particle size and shape, molar mass and density can be obtained for particle sizes spanning the entire colloidal range. The Ångström resolution and the reliable statistics with which particle size distributions can be obtained from analytical ultracentrifugation makes this a high resolution analysis technique for the characterization of nanoparticles in solution or suspension. Several examples showing successful applications of AUC to complex problems in colloid science are given to illustrate the broad range and versatility of questions that can be answered by AUC experiments.
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Affiliation(s)
- Karel L Planken
- Max-Planck-Institute of Colloids and Interfaces, Colloid Chemistry, Research Campus Golm, Am Mühlenberg, D-14424 Potsdam, Germany.
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Demeler B. Methods for the design and analysis of sedimentation velocity and sedimentation equilibrium experiments with proteins. ACTA ACUST UNITED AC 2010; Chapter 7:7.13.1-7.13.24. [PMID: 20393977 DOI: 10.1002/0471140864.ps0713s60] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Analytical ultracentrifugation experiments play an integral role in the solution phase characterization of recombinant proteins and other biological macromolecules. This unit discusses the design of sedimentation velocity and sedimentation equilibrium experiments performed with a Beckman Optima XL-A or XL-I analytical ultracentrifuge. Optimal 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.
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Affiliation(s)
- Borries Demeler
- Department of Biochemistry, The University of Texas Health Science Center at San Antonio, San Antonio, Texas, USA
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