1
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Schuck P, To SC, Zhao H. An automated interface for sedimentation velocity analysis in SEDFIT. PLoS Comput Biol 2023; 19:e1011454. [PMID: 37669309 PMCID: PMC10503714 DOI: 10.1371/journal.pcbi.1011454] [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: 05/15/2023] [Revised: 09/15/2023] [Accepted: 08/22/2023] [Indexed: 09/07/2023] Open
Abstract
Sedimentation velocity analytical ultracentrifugation (SV-AUC) is an indispensable tool for the study of particle size distributions in biopharmaceutical industry, for example, to characterize protein therapeutics and vaccine products. In particular, the diffusion-deconvoluted sedimentation coefficient distribution analysis, in the software SEDFIT, has found widespread applications due to its relatively high resolution and sensitivity. However, a lack of suitable software compatible with Good Manufacturing Practices (GMP) has hampered the use of SV-AUC in this regulatory environment. To address this, we have created an interface for SEDFIT so that it can serve as an automatically spawned module with controlled data input through command line parameters and output of key results in files. The interface can be integrated in custom GMP compatible software, and in scripts that provide documentation and meta-analyses for replicate or related samples, for example, to streamline analysis of large families of experimental data, such as binding isotherm analyses in the study of protein interactions. To test and demonstrate this approach we provide a MATLAB script mlSEDFIT.
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Affiliation(s)
- Peter Schuck
- Laboratory of Dynamics of Macromolecular Assembly, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Samuel C. To
- Laboratory of Dynamics of Macromolecular Assembly, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Huaying Zhao
- Laboratory of Dynamics of Macromolecular Assembly, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, Maryland, United States of America
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2
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Schuck P, To SC, Zhao H. An automated interface for sedimentation velocity analysis in SEDFIT. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.14.540690. [PMID: 37425873 PMCID: PMC10327192 DOI: 10.1101/2023.05.14.540690] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/11/2023]
Abstract
Sedimentation velocity analytical ultracentrifugation (SV-AUC) is an indispensable tool for the study of particle size distributions in biopharmaceutical industry, for example, to characterize protein therapeutics and vaccine products. In particular, the diffusion-deconvoluted sedimentation coefficient distribution analysis, in the software SEDFIT, has found widespread applications due to its relatively high resolution and sensitivity. However, a lack of available software compatible with Good Manufacturing Practices (GMP) has hampered the use of SV-AUC in this regulatory environment. To address this, we have created an interface for SEDFIT so that it can serve as an automatically spawned module with controlled data input through command line parameters and output of key results in files. The interface can be integrated in custom GMP compatible software, and in scripts that provide documentation and meta-analyses for replicate or related samples, for example, to streamline analysis of large families of experimental data, such as binding isotherm analyses in the study of protein interactions. To test and demonstrate this approach we provide a MATLAB script mlSEDFIT.
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Affiliation(s)
- Peter Schuck
- Laboratory of Dynamics of Macromolecular Assembly, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD 20892, USA
| | - Samuel C. To
- Laboratory of Dynamics of Macromolecular Assembly, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD 20892, USA
| | - Huaying Zhao
- Laboratory of Dynamics of Macromolecular Assembly, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD 20892, USA
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3
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Illuminating Intrinsically Disordered Proteins with Integrative Structural Biology. Biomolecules 2023; 13:biom13010124. [PMID: 36671509 PMCID: PMC9856150 DOI: 10.3390/biom13010124] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 01/01/2023] [Accepted: 01/04/2023] [Indexed: 01/11/2023] Open
Abstract
Intense study of intrinsically disordered proteins (IDPs) did not begin in earnest until the late 1990s when a few groups, working independently, convinced the community that these 'weird' proteins could have important functions. Over the past two decades, it has become clear that IDPs play critical roles in a multitude of biological phenomena with prominent examples including coordination in signaling hubs, enabling gene regulation, and regulating ion channels, just to name a few. One contributing factor that delayed appreciation of IDP functional significance is the experimental difficulty in characterizing their dynamic conformations. The combined application of multiple methods, termed integrative structural biology, has emerged as an essential approach to understanding IDP phenomena. Here, we review some of the recent applications of the integrative structural biology philosophy to study IDPs.
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4
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Lenda R, Padjasek M, Krężel A, Ożyhar A, Bystranowska D. Does one plus one always equal two? Structural differences between nesfatin-1, -2, and nesfatin-1/2. Cell Commun Signal 2022; 20:163. [PMID: 36280843 PMCID: PMC9590162 DOI: 10.1186/s12964-022-00980-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 09/27/2022] [Indexed: 11/10/2022] Open
Abstract
Nesfatin-1 and -2 are produced from a reaction in which the N-terminus of human Nucleobindin-2 undergoes proteolytical processing. To date, Nucleobindin-2 and/or nesfatin-1 have only been shown to act as peptide hormones. On the other hand, the purpose of nesfatin-2 remains unknown. Since Nucleobindin-2/nesfatin-1 is thought impact the control of a wide range of physiological processes, including energy homeostasis, neurodegenerative processes and carcinogenesis, its ligands/interactions deserve special studies and attention. However, there are no reports about the molecular properties of the proteolytical products of human Nucleobindin-2 in the literature. Hence, this study aimed to analyze the effect of Zn(II) and Ca(II) on human nesfatin-1, -2, and -1/2 structures. Herein, we report that human nesfatin-1 is a member of the intrinsically disordered protein family, as indicated by circular dichroism and analytical ultracentrifugation experiments. In contrast, we found that the human nesfatin-2 and nesfatin-1/2 structures were globular with intrinsically disordered regions. Under Zn(II) treatment, we observed concentration-dependent structurization and compaction of intrinsically disordered nesfatin-1 and its propensity for oligomerization, as well as destabilization of both nesfatin-2 and nesfatin-1/2. Furthermore, dissociation constants for Zn(II) binding by nesfatin-1, nesfatin-2, and nesfatin-1/2 were also reported. Moreover, structurally distinct nesfatin-1 and -2 seem to be interdependent when linked together, as indicated by the observed molecular properties of nesfatin-1/2, which in turn are not a simple sum of the properties exhibited by the former peptides. Thus, herein, we shed new light on the molecular behavior of human nesfatins, which might help to elucidate the complex function of those peptides. Video abstract.
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Affiliation(s)
- Rafał Lenda
- grid.7005.20000 0000 9805 3178Department of Biochemistry, Molecular Biology and Biotechnology, Faculty of Chemistry, Wrocław University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wrocław, Poland
| | - Michał Padjasek
- grid.8505.80000 0001 1010 5103Department of Chemical Biology, Faculty of Biotechnology, University of Wrocław, Joliot-Curie 14a, 50-383 Wrocław, Poland
| | - Artur Krężel
- grid.8505.80000 0001 1010 5103Department of Chemical Biology, Faculty of Biotechnology, University of Wrocław, Joliot-Curie 14a, 50-383 Wrocław, Poland
| | - Andrzej Ożyhar
- grid.7005.20000 0000 9805 3178Department of Biochemistry, Molecular Biology and Biotechnology, Faculty of Chemistry, Wrocław University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wrocław, Poland
| | - Dominika Bystranowska
- grid.7005.20000 0000 9805 3178Department of Biochemistry, Molecular Biology and Biotechnology, Faculty of Chemistry, Wrocław University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wrocław, Poland
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5
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Baker K, Kwok E, Reardon P, Rodriguez DJ, Rolland AD, Wilson JW, Prell JS, Nyarko A. Yorkie-Warts Complexes are an Ensemble of Interconverting Conformers Formed by Multivalent Interactions. J Mol Biol 2020; 433:166776. [PMID: 33383033 DOI: 10.1016/j.jmb.2020.166776] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 11/18/2020] [Accepted: 12/16/2020] [Indexed: 11/17/2022]
Abstract
Multiple copies of WW domains and PPXY motif sequences are often reciprocally presented by regulatory proteins that interact at crucial regulatory steps in the cell life cycle. While biophysical studies of single WW domain-single PPXY motif complexes abound in the literature, the molecular mechanisms of multivalent WW domain-PPXY assemblies are still poorly understood. By way of investigating such assemblies, we characterized the multivalent association of the entire cognate binding domains, two WW sequences and five PPXY motifs respectively, of the Yorkie transcription coactivator and the Warts tumor suppressor. Isothermal titration calorimetry, sedimentation velocity, size-exclusion chromatography coupled to multi-angle light scattering and native-state mass spectrometry of Yorkie WW domains interactions with the full-length Warts PPXY domain, and numerous PPXY motif variants of Warts show that the two proteins assemble via binding of tandem WW domains to adjacent PPXY pairs to produce an ensemble of interconverting complexes of variable stoichiometries, binding energetics and WW domain occupancy. Apparently, the Yorkie tandem WW domains first target the two adjacent PPXY motifs at the C-terminus of the Warts polypeptide and additional WW domains bind unoccupied motifs. Similar ensembles of interconverting conformers may be common in multivalent WW domain-PPXY interactions to promote the adaptability and versatility of WW domain-PPXY mediated cellular processes.
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Affiliation(s)
- Kasie Baker
- Department of Biochemistry & Biophysics, Oregon State University, Corvallis, OR 97331, USA
| | - Ethiene Kwok
- Department of Biochemistry & Biophysics, Oregon State University, Corvallis, OR 97331, USA
| | - Patrick Reardon
- Department of Biochemistry & Biophysics, Oregon State University, Corvallis, OR 97331, USA
| | - Diego J Rodriguez
- Department of Biochemistry & Biophysics, Oregon State University, Corvallis, OR 97331, USA
| | - Amber D Rolland
- Department of Chemistry & Biochemistry, University of Oregon, Eugene, OR 97403, USA; Institute of Molecular Biology, University of Oregon, Eugene, OR 97403, USA
| | - Jesse W Wilson
- Department of Chemistry & Biochemistry, University of Oregon, Eugene, OR 97403, USA; Institute of Molecular Biology, University of Oregon, Eugene, OR 97403, USA
| | - James S Prell
- Department of Chemistry & Biochemistry, University of Oregon, Eugene, OR 97403, USA; Materials Science Institute, University of Oregon, Eugene, OR 97403, USA
| | - Afua Nyarko
- Department of Biochemistry & Biophysics, Oregon State University, Corvallis, OR 97331, USA.
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6
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Sedimentation Velocity Methods for the Characterization of Protein Heterogeneity and Protein Affinity Interactions. Methods Mol Biol 2020. [PMID: 33301117 DOI: 10.1007/978-1-0716-1126-5_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/07/2023]
Abstract
Sedimentation velocity analytical ultracentrifugation is a powerful and versatile tool for the characterization of proteins and macromolecular complexes in solution. The direct modeling of the sedimentation process using modern computational strategies allows among others to assess the homogeneity/heterogeneity state of protein samples and to characterize protein associations. In this chapter, we will provide theoretical backgrounds and protocols to analyze the size distribution of protein samples and to determine the affinity of protein-protein hetero-associations.
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7
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The Anti-Inflammatory Protein TNIP1 Is Intrinsically Disordered with Structural Flexibility Contributed by Its AHD1-UBAN Domain. Biomolecules 2020; 10:biom10111531. [PMID: 33182596 PMCID: PMC7697625 DOI: 10.3390/biom10111531] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 11/04/2020] [Accepted: 11/05/2020] [Indexed: 01/02/2023] Open
Abstract
TNFAIP3 interacting protein 1 (TNIP1) interacts with numerous non-related cellular, viral, and bacterial proteins. TNIP1 is also linked with multiple chronic inflammatory disorders on the gene and protein levels, through numerous single-nucleotide polymorphisms and reduced protein amounts. Despite the importance of TNIP1 function, there is limited investigation as to how its conformation may impact its apparent multiple roles. Hub proteins like TNIP1 are often intrinsically disordered proteins. Our initial in silico assessments suggested TNIP1 is natively unstructured, featuring numerous potentials intrinsically disordered regions, including the ABIN homology domain 1-ubiquitin binding domain in ABIN proteins and NEMO (AHD1-UBAN) domain associated with its anti-inflammatory function. Using multiple biophysical approaches, we demonstrate the structural flexibility of full-length TNIP1 and the AHD1-UBAN domain. We present evidence the AHD1-UBAN domain exists primarily as a pre-molten globule with limited secondary structure in solution. Data presented here suggest the previously described coiled-coil conformation of the crystallized UBAN-only region may represent just one of possibly multiple states for the AHD1-UBAN domain in solution. These data also characterize the AHD1-UBAN domain in solution as mostly monomeric with potential to undergo oligomerization under specific environmental conditions (e.g., binding partner availability, pH-dependence). This proposed intrinsic disorder across TNIP1 and within the AHD1-UBAN region is likely to impact TNIP1 function and interaction with its multiple partners.
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8
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Porębska A, Różycka M, Hołubowicz R, Szewczuk Z, Ożyhar A, Dobryszycki P. Functional derivatives of human dentin matrix protein 1 modulate morphology of calcium carbonate crystals. FASEB J 2020; 34:6147-6165. [PMID: 32190922 DOI: 10.1096/fj.201901999r] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Revised: 02/07/2020] [Accepted: 02/21/2020] [Indexed: 12/23/2022]
Abstract
Dentin matrix protein 1 (DMP1) is an acidic, extracellular matrix protein essential for biomineralization of calcium phosphate, in bone and dentin. It is proteolytically processed into two fragments, 44K and 56K. Recently, the presence of DMP1 was noticed in inner ear, specifically in otoconia, which are calcium carbonate biominerals involved in sensing of balance. In this study, the solution structure and biomineralization activity of otoconial 44K and 56K fragments toward calcium carbonate were investigated. The results of analytical ultracentrifugation, circular dichroism, and gel filtration indicated that DMP1 fragments are disordered in solution. Notably, 56K formed oligomers in the presence of calcium ions. It was also observed that both fragments influenced the crystal growth by in vitro biomineralization assay and scanning electron microscopy. In addition, they sequester the calcium ions during the calcite formation. Calcium carbonate crystals precipitated in vitro changed their size and shape in the presence of DMP1 fragments. Oligomerization propensity of 56K may significantly enhance this function. Our study indicates that intrinsically disordered DMP1 has a previously unknown regulatory function for biomineralization of otoconia.
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Affiliation(s)
- Aleksandra Porębska
- Department of Biochemistry, Molecular Biology and Biotechnology, Faculty of Chemistry, Wrocław University of Science and Technology, Wrocław, Poland
| | - Mirosława Różycka
- Department of Biochemistry, Molecular Biology and Biotechnology, Faculty of Chemistry, Wrocław University of Science and Technology, Wrocław, Poland
| | - Rafał Hołubowicz
- Department of Biochemistry, Molecular Biology and Biotechnology, Faculty of Chemistry, Wrocław University of Science and Technology, Wrocław, Poland
| | | | - Andrzej Ożyhar
- Department of Biochemistry, Molecular Biology and Biotechnology, Faculty of Chemistry, Wrocław University of Science and Technology, Wrocław, Poland
| | - Piotr Dobryszycki
- Department of Biochemistry, Molecular Biology and Biotechnology, Faculty of Chemistry, Wrocław University of Science and Technology, Wrocław, Poland
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9
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Medve L, Achilli S, Guzman‐Caldentey J, Thépaut M, Senaldi L, Le Roy A, Sattin S, Ebel C, Vivès C, Martin‐Santamaria S, Bernardi A, Fieschi F. Enhancing Potency and Selectivity of a DC-SIGN Glycomimetic Ligand by Fragment-Based Design: Structural Basis. Chemistry 2019; 25:14659-14668. [PMID: 31469191 PMCID: PMC6899773 DOI: 10.1002/chem.201903391] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Revised: 08/28/2019] [Indexed: 12/22/2022]
Abstract
Chemical modification of pseudo-dimannoside ligands guided by fragment-based design allowed for the exploitation of an ammonium-binding region in the vicinity of the mannose-binding site of DC-SIGN, leading to the synthesis of a glycomimetic antagonist (compound 16) of unprecedented affinity and selectivity against the related lectin langerin. Here, the computational design of pseudo-dimannoside derivatives as DC-SIGN ligands, their synthesis, their evaluation as DC-SIGN selective antagonists, the biophysical characterization of the DC-SIGN/16 complex, and the structural basis for the ligand activity are presented. On the way to the characterization of this ligand, an unusual bridging interaction within the crystals shed light on the plasticity and potential secondary binding sites within the DC-SIGN carbohydrate recognition domain.
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Affiliation(s)
- Laura Medve
- Dipartimento di ChimicaUniversità degli Studi di Milanovia Golgi 1920133MilanoItaly
| | - Silvia Achilli
- Université Grenoble AlpesCNRS, CEAInstitut de Biologie Structurale38044GrenobleFrance
| | - Joan Guzman‐Caldentey
- Department of Structural and Chemical Biology, Centro de Investigaciones BiologicasCIB-CSICC/Ramiro de Maeztu, 928040MadridSpain
| | - Michel Thépaut
- Université Grenoble AlpesCNRS, CEAInstitut de Biologie Structurale38044GrenobleFrance
| | - Luca Senaldi
- Dipartimento di ChimicaUniversità degli Studi di Milanovia Golgi 1920133MilanoItaly
| | - Aline Le Roy
- Université Grenoble AlpesCNRS, CEAInstitut de Biologie Structurale38044GrenobleFrance
| | - Sara Sattin
- Dipartimento di ChimicaUniversità degli Studi di Milanovia Golgi 1920133MilanoItaly
| | - Christine Ebel
- Université Grenoble AlpesCNRS, CEAInstitut de Biologie Structurale38044GrenobleFrance
| | - Corinne Vivès
- Université Grenoble AlpesCNRS, CEAInstitut de Biologie Structurale38044GrenobleFrance
| | - Sonsoles Martin‐Santamaria
- Department of Structural and Chemical Biology, Centro de Investigaciones BiologicasCIB-CSICC/Ramiro de Maeztu, 928040MadridSpain
| | - Anna Bernardi
- Dipartimento di ChimicaUniversità degli Studi di Milanovia Golgi 1920133MilanoItaly
| | - Franck Fieschi
- Université Grenoble AlpesCNRS, CEAInstitut de Biologie Structurale38044GrenobleFrance
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The MurG glycosyltransferase provides an oligomeric scaffold for the cytoplasmic steps of peptidoglycan biosynthesis in the human pathogen Bordetella pertussis. Sci Rep 2019; 9:4656. [PMID: 30874582 PMCID: PMC6420597 DOI: 10.1038/s41598-019-40966-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Accepted: 02/19/2019] [Indexed: 11/09/2022] Open
Abstract
Peptidoglycan is a major component of the bacterial cell wall and thus a major determinant of cell shape. Its biosynthesis is initiated by several sequential reactions catalyzed by cytoplasmic Mur enzymes. Mur ligases (MurC, -D, -E, and -F) are essential for bacteria, metabolize molecules not present in eukaryotes, and are structurally and biochemically tractable. However, although many Mur inhibitors have been developed, few have shown promising antibacterial activity, prompting the hypothesis that within the cytoplasm, Mur enzymes could exist as a complex whose architecture limits access of small molecules to their active sites. This suggestion is supported by the observation that in many bacteria, mur genes are present in a single operon, and pairs of these genes often are fused to generate a single polypeptide. Here, we explored this genetic arrangement in the human pathogen Bordetella pertussis and show that MurE and MurF are expressed as a single, bifunctional protein. EM, small angle X-ray scattering (SAXS), and analytical centrifugation (AUC) revealed that the MurE–MurF fusion displays an elongated, flexible structure that can dimerize. Moreover, MurE–MurF interacted with the peripheral glycosyltransferase MurG, which formed discrete oligomers resembling 4- or 5-armed stars in EM images. The oligomeric structure of MurG may allow it to play a bona fide scaffolding role for a potential Mur complex, facilitating the efficient conveyance of peptidoglycan-building blocks toward the inner membrane leaflet. Our findings shed light on the structural determinants of a peptidoglycan formation complex involving Mur enzymes in bacterial cell wall formation.
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11
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Lee EF, Perugini MA, Pettikiriarachchi A, Evangelista M, Keizer DW, Yao S, Fairlie WD. The BECN1 N-terminal domain is intrinsically disordered. Autophagy 2016; 12:460-71. [PMID: 27046249 PMCID: PMC4836020 DOI: 10.1080/15548627.2016.1140292] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2014] [Revised: 12/16/2015] [Accepted: 01/04/2016] [Indexed: 10/22/2022] Open
Abstract
BECN1/Beclin 1 has a critical role in the early stages of autophagosome formation. Recently, structures of its central and C-terminal domains were reported, however, little structural information is available on the N-terminal domain, comprising a third of the protein. This lack of structural information largely stems from the inability to produce this region in a purified form. Here, we describe the expression and purification of the N-terminal domain of BECN1 (residues 1 to 150) and detailed biophysical characterization, including NMR spectroscopy. Combined, our studies demonstrated at the atomic level that the BECN1 N-terminal domain is intrinsically disordered, and apart from the BH3 subdomain, remains disordered following interaction with a binding partner, BCL2L1/BCL-XL. In addition, the BH3 domain α-helix induced upon interaction with BCL2L1 reverts to a disordered state when the complex is dissociated by exposure to a competitive inhibitor. No significant interactions between N- and C-terminal domains were detected.
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Affiliation(s)
- Erinna F. Lee
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, Victoria, Australia
- Olivia Newton-John Cancer Research Institute, Heidelberg, Victoria, Australia
- School of Cancer Medicine, La Trobe University, Melbourne, Victoria, Australia
- Department of Chemistry and Physics, La Trobe Institute for Molecular Science, Melbourne, Victoria, Australia
| | - Matthew A. Perugini
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, Australia
| | | | - Marco Evangelista
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Olivia Newton-John Cancer Research Institute, Heidelberg, Victoria, Australia
| | - David W. Keizer
- Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, Victoria, Australia
| | - Shenggen Yao
- Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, Victoria, Australia
| | - W. Douglas Fairlie
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, Victoria, Australia
- Olivia Newton-John Cancer Research Institute, Heidelberg, Victoria, Australia
- School of Cancer Medicine, La Trobe University, Melbourne, Victoria, Australia
- Department of Chemistry and Physics, La Trobe Institute for Molecular Science, Melbourne, Victoria, Australia
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12
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Różycka M, Wojtas M, Jakób M, Stigloher C, Grzeszkowiak M, Mazur M, Ożyhar A. Intrinsically disordered and pliable Starmaker-like protein from medaka (Oryzias latipes) controls the formation of calcium carbonate crystals. PLoS One 2014; 9:e114308. [PMID: 25490041 PMCID: PMC4260845 DOI: 10.1371/journal.pone.0114308] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2014] [Accepted: 11/07/2014] [Indexed: 01/31/2023] Open
Abstract
Fish otoliths, biominerals composed of calcium carbonate with a small amount of organic matrix, are involved in the functioning of the inner ear. Starmaker (Stm) from zebrafish (Danio rerio) was the first protein found to be capable of controlling the formation of otoliths. Recently, a gene was identified encoding the Starmaker-like (Stm-l) protein from medaka (Oryzias latipes), a putative homologue of Stm and human dentine sialophosphoprotein. Although there is no sequence similarity between Stm-l and Stm, Stm-l was suggested to be involved in the biomineralization of otoliths, as had been observed for Stm even before. The molecular properties and functioning of Stm-l as a putative regulatory protein in otolith formation have not been characterized yet. A comprehensive biochemical and biophysical analysis of recombinant Stm-l, along with in silico examinations, indicated that Stm-l exhibits properties of a coil-like intrinsically disordered protein. Stm-l possesses an elongated and pliable structure that is able to adopt a more ordered and rigid conformation under the influence of different factors. An in vitro assay of the biomineralization activity of Stm-l indicated that Stm-l affected the size, shape and number of calcium carbonate crystals. The functional significance of intrinsically disordered properties of Stm-l and the possible role of this protein in controlling the formation of calcium carbonate crystals is discussed.
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Affiliation(s)
- Mirosława Różycka
- Department of Biochemistry, Faculty of Chemistry, Wrocław University of Technology, Wrocław, Poland
| | - Magdalena Wojtas
- Department of Biochemistry, Faculty of Chemistry, Wrocław University of Technology, Wrocław, Poland
| | - Michał Jakób
- Department of Biochemistry, Faculty of Chemistry, Wrocław University of Technology, Wrocław, Poland
| | - Christian Stigloher
- Division of Electron Microscopy, Biocenter, University of Würzburg, Würzburg, Germany
| | - Mikołaj Grzeszkowiak
- NanoBioMedical Centre and Department of Macromolecular Physics, Faculty of Physics, Adam Mickiewicz University, Poznań, Poland
| | - Maciej Mazur
- Department of Chemistry, University of Warsaw, Warsaw, Poland
| | - Andrzej Ożyhar
- Department of Biochemistry, Faculty of Chemistry, Wrocław University of Technology, Wrocław, Poland
- * E-mail:
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13
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Noval MG, Gallo M, Perrone S, Salvay AG, Chemes LB, de Prat-Gay G. Conformational dissection of a viral intrinsically disordered domain involved in cellular transformation. PLoS One 2013; 8:e72760. [PMID: 24086265 PMCID: PMC3785498 DOI: 10.1371/journal.pone.0072760] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2013] [Accepted: 07/14/2013] [Indexed: 12/25/2022] Open
Abstract
Intrinsic disorder is abundant in viral genomes and provides conformational plasticity to its protein products. In order to gain insight into its structure-function relationships, we carried out a comprehensive analysis of structural propensities within the intrinsically disordered N-terminal domain from the human papillomavirus type-16 E7 oncoprotein (E7N). Two E7N segments located within the conserved CR1 and CR2 regions present transient α-helix structure. The helix in the CR1 region spans residues L8 to L13 and overlaps with the E2F mimic linear motif. The second helix, located within the highly acidic CR2 region, presents a pH-dependent structural transition. At neutral pH the helix spans residues P17 to N29, which include the retinoblastoma tumor suppressor LxCxE binding motif (residues 21-29), while the acidic CKII-PEST region spanning residues E33 to I38 populates polyproline type II (PII) structure. At pH 5.0, the CR2 helix propagates up to residue I38 at the expense of loss of PII due to charge neutralization of acidic residues. Using truncated forms of HPV-16 E7, we confirmed that pH-induced changes in α-helix content are governed by the intrinsically disordered E7N domain. Interestingly, while at both pH the region encompassing the LxCxE motif adopts α-helical structure, the isolated 21-29 fragment including this stretch is unable to populate an α-helix even at high TFE concentrations. Thus, the E7N domain can populate dynamic but discrete structural ensembles by sampling α-helix-coil-PII-ß-sheet structures. This high plasticity may modulate the exposure of linear binding motifs responsible for its multi-target binding properties, leading to interference with key cell signaling pathways and eventually to cellular transformation by the virus.
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Affiliation(s)
- María G. Noval
- Protein Structure-Function and Engineering Laboratory, Fundación Instituto Leloir and IIBBA- CONICET, Buenos Aires, Argentina
| | - Mariana Gallo
- NMR Laboratory, Fundación Instituto Leloir and IIBBA-CONICET, Buenos Aires, Argentina
| | - Sebastián Perrone
- Protein Structure-Function and Engineering Laboratory, Fundación Instituto Leloir and IIBBA- CONICET, Buenos Aires, Argentina
| | - Andres G. Salvay
- Institute of Physics of Liquids and Biological Systems, Universidad Nacional de La Plata, La Plata, Argentina
- Department of Science and Technology, Universidad Nacional de Quilmes, Bernal, Argentina
| | - Lucía B. Chemes
- Protein Structure-Function and Engineering Laboratory, Fundación Instituto Leloir and IIBBA- CONICET, Buenos Aires, Argentina
| | - Gonzalo de Prat-Gay
- Protein Structure-Function and Engineering Laboratory, Fundación Instituto Leloir and IIBBA- CONICET, Buenos Aires, Argentina
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14
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Ghirlando R, Balbo A, Piszczek G, Brown PH, Lewis MS, Brautigam CA, Schuck P, Zhao H. Improving the thermal, radial, and temporal accuracy of the analytical ultracentrifuge through external references. Anal Biochem 2013; 440:81-95. [PMID: 23711724 PMCID: PMC3826449 DOI: 10.1016/j.ab.2013.05.011] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2013] [Revised: 05/08/2013] [Accepted: 05/10/2013] [Indexed: 11/21/2022]
Abstract
Sedimentation velocity (SV) is a method based on first principles that provides a precise hydrodynamic characterization of macromolecules in solution. Due to recent improvements in data analysis, the accuracy of experimental SV data emerges as a limiting factor in its interpretation. Our goal was to unravel the sources of experimental error and develop improved calibration procedures. We implemented the use of a Thermochron iButton temperature logger to directly measure the temperature of a spinning rotor and detected deviations that can translate into an error of as much as 10% in the sedimentation coefficient. We further designed a precision mask with equidistant markers to correct for instrumental errors in the radial calibration that were observed to span a range of 8.6%. The need for an independent time calibration emerged with use of the current data acquisition software (Zhao et al., Anal. Biochem., 437 (2013) 104-108), and we now show that smaller but significant time errors of up to 2% also occur with earlier versions. After application of these calibration corrections, the sedimentation coefficients obtained from 11 instruments displayed a significantly reduced standard deviation of approximately 0.7%. This study demonstrates the need for external calibration procedures and regular control experiments with a sedimentation coefficient standard.
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Affiliation(s)
- Rodolfo Ghirlando
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, NIH, Bethesda, MD
| | - Andrea Balbo
- Bioengineering and Physical Science Shared Resource, National Institute of Biomedical Imaging and Bioengineering, NIH, Bethesda, MD
| | - Grzegorz Piszczek
- Biochemistry and Biophysics Center, National Heart, Lung and Blood Institute, NIH, Bethesda, MD
| | - Patrick H. Brown
- Bioengineering and Physical Science Shared Resource, National Institute of Biomedical Imaging and Bioengineering, NIH, Bethesda, MD
| | - Marc S. Lewis
- Bioengineering and Physical Science Shared Resource, National Institute of Biomedical Imaging and Bioengineering, NIH, Bethesda, MD
| | - Chad A. Brautigam
- Department of Biophysics, The University of Texas Southwestern Medical Center, Dallas, TX
| | - Peter Schuck
- Dynamics of Macromolecular Assembly Section, Laboratory of Cellular Imaging and Macromolecular Biophysics, National Institute of Biomedical Imaging and Bioengineering, NIH, Bethesda, MD
| | - Huaying Zhao
- Dynamics of Macromolecular Assembly Section, Laboratory of Cellular Imaging and Macromolecular Biophysics, National Institute of Biomedical Imaging and Bioengineering, NIH, Bethesda, MD
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15
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Molecular architecture of the human protein deacetylase Sirt1 and its regulation by AROS and resveratrol. Biosci Rep 2013; 33:BSR20120121. [PMID: 23548308 PMCID: PMC3654483 DOI: 10.1042/bsr20120121] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Sirtuins are NAD+-dependent protein deacetylases regulating metabolism, stress responses and ageing processes. Among the seven mammalian Sirtuins, Sirt1 is the physiologically best-studied isoform. It regulates nuclear functions such as chromatin remodelling and gene transcription, and it appears to mediate beneficial effects of a low calorie diet which can partly be mimicked by the Sirt1 activating polyphenol resveratrol. The molecular details of Sirt1 domain architecture and regulation, however, are little understood. It has a unique N-terminal domain and CTD (C-terminal domain) flanking a conserved Sirtuin catalytic core and these extensions are assumed to mediate Sirt1-specific features such as homo-oligomerization and activation by resveratrol. To analyse the architecture of human Sirt1 and functions of its N- and C-terminal extensions, we recombinantly produced Sirt1 and Sirt1 deletion constructs as well as the AROS (active regulator of Sirt1) protein. We then studied Sirt1 features such as molecular size, secondary structure and stimulation by small molecules and AROS. We find that Sirt1 is monomeric and has extended conformations in its flanking domains, likely disordered especially in the N-terminus, resulting in an increased hydrodynamic radius. Nevertheless, both termini increase Sirt1 deacetylase activity, indicating a regulatory function. We also find an unusual but defined conformation for AROS protein, which fails, however, to stimulate Sirt1. Resveratrol, in contrast, activates the Sirt1 catalytic core independent of the terminal domains, indicating a binding site within the catalytic core and suggesting that small molecule activators for other isoforms might also exist.
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16
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Le Roy A, Nury H, Wiseman B, Sarwan J, Jault JM, Ebel C. Sedimentation velocity analytical ultracentrifugation in hydrogenated and deuterated solvents for the characterization of membrane proteins. Methods Mol Biol 2013; 1033:219-251. [PMID: 23996181 DOI: 10.1007/978-1-62703-487-6_15] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
This chapter is a step-by-step protocol for setting up, realizing, and analyzing sedimentation velocity experiments in hydrogenated and deuterated solvents, in the context of the characterization of membrane protein, in terms of homogeneity, association state, and amount of bound detergent, based on a real case study of the membrane protein BmrA solubilized in n-Dodecyl-β-D-Maltopyranoside) detergent.
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Affiliation(s)
- Aline Le Roy
- Institut de Biologie Structurale, CEA, Grenoble, France
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