1
|
Lill A, Herbst A, Langhans M, Paech S, Hamacher K, Biesalski M, Meckel T, Schmitz K. Investigating Cellulose Binding of Peptides Derived from Carbohydrate Binding Module 1. Biomacromolecules 2024. [PMID: 39103164 DOI: 10.1021/acs.biomac.4c00575] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/07/2024]
Abstract
Carbohydrate-binding modules (CBM) have emerged as useful tools for a wide range of tasks, including the use as purification tags or for cellulose fiber modification. For this purpose, the CBM needs to be attached to a target protein leading to large constructs. We investigated if short peptides from the carbohydrate binding site of CBMs can bind in a similar way as native, full-length CBMs to nanocrystalline cellulose (NCC) or cotton linter paper. We designed our cellulose-binding peptides to be less hydrophobic and shorter than those previously reported. Starting from the binding site of Cel7A-CBM1, we incorporated the essential amino acids involved in cellulose binding into our peptides. These peptides, as well as control peptides with scrambled sequences or a lack of essential amino acids, bound to cellulose with similar affinity as CBM regardless of their secondary structure, sequence, or hydrophobicity. This unspecific mode of cellulose binding displayed by the presented peptides may be exploited to functionalize cellulose-based biomaterials by means of peptide-conjugates.
Collapse
Affiliation(s)
- Annika Lill
- Biological Chemistry, Chemistry Department, Technical University of Darmstadt, Darmstadt 64278, Germany
| | - Alexandra Herbst
- Biological Chemistry, Chemistry Department, Technical University of Darmstadt, Darmstadt 64278, Germany
| | - Markus Langhans
- Macromolecular and Paper Chemistry, Chemistry Department, Technical University of Darmstadt, Darmstadt 64278, Germany
| | - Steffen Paech
- Macromolecular and Paper Chemistry, Chemistry Department, Technical University of Darmstadt, Darmstadt 64278, Germany
| | - Kay Hamacher
- Computational Biology and Simulation, Biology Department, Technical University of Darmstadt, Darmstadt 64287, Germany
| | - Markus Biesalski
- Macromolecular and Paper Chemistry, Chemistry Department, Technical University of Darmstadt, Darmstadt 64278, Germany
| | - Tobias Meckel
- Macromolecular and Paper Chemistry, Chemistry Department, Technical University of Darmstadt, Darmstadt 64278, Germany
| | - Katja Schmitz
- Biological Chemistry, Chemistry Department, Technical University of Darmstadt, Darmstadt 64278, Germany
| |
Collapse
|
2
|
Osman R, Bossu M, Dauvillée D, Spriet C, Liu C, Zeeman SC, D'Hulst C, Bompard C. LIKE EARLY STARVATION 1 interacts with amylopectin during starch biosynthesis. PLANT PHYSIOLOGY 2024; 195:1851-1865. [PMID: 38573555 DOI: 10.1093/plphys/kiae193] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Revised: 03/08/2024] [Accepted: 03/13/2024] [Indexed: 04/05/2024]
Abstract
Starch is the major energy storage compound in plants. Both transient starch and long-lasting storage starch accumulate in the form of insoluble, partly crystalline granules. The structure of these granules is related to the structure of the branched polymer amylopectin: linear chains of glucose units organized in double helices that align to form semicrystalline lamellae, with branching points located in amorphous regions between them. EARLY STARVATION 1 (ESV1) and LIKE EARLY STARVATION 1 (LESV) proteins are involved in the maintenance of starch granule structure and in the phase transition of amylopectin, respectively, in Arabidopsis (Arabidopsis thaliana). These proteins contain a conserved tryptophan-rich C-terminal domain folded into an antiparallel β-sheet, likely responsible for binding of the proteins to starch, and different N-terminal domains whose structure and function are unknown. In this work, we combined biochemical and biophysical approaches to analyze the structures of LESV and ESV1 and their interactions with the different starch polyglucans. We determined that both proteins interact with amylopectin but not with amylose and that only LESV is capable of interacting with amylopectin during starch biosynthesis. While the C-terminal domain interacts with amylopectin in its semicrystalline form, the N-terminal domain of LESV undergoes induced conformational changes that are probably involved in its specific function of mediating glucan phase transition. These results clarify the specific mechanism of action of these 2 proteins in the biosynthesis of starch granules.
Collapse
Affiliation(s)
- Rayan Osman
- Université de Lille, CNRS, UMR 8576-UGSF-Unité de Glycobiologie Structurale et Fonctionnelle, Lille, France
| | - Mélanie Bossu
- Université de Lille, CNRS, UMR 8576-UGSF-Unité de Glycobiologie Structurale et Fonctionnelle, Lille, France
| | - David Dauvillée
- Université de Lille, CNRS, UMR 8576-UGSF-Unité de Glycobiologie Structurale et Fonctionnelle, Lille, France
| | - Corentin Spriet
- Université de Lille, CNRS, UMR 8576-UGSF-Unité de Glycobiologie Structurale et Fonctionnelle, Lille, France
- University Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, US 41-UAR 2014-PLBS, Lille F-59000, France
| | - Chun Liu
- Institute of Molecular Plant Biology, ETH Zurich, Universitätstrasse 2, 8092 Zurich
| | - Samuel C Zeeman
- Institute of Molecular Plant Biology, ETH Zurich, Universitätstrasse 2, 8092 Zurich
| | - Christophe D'Hulst
- Université de Lille, CNRS, UMR 8576-UGSF-Unité de Glycobiologie Structurale et Fonctionnelle, Lille, France
| | - Coralie Bompard
- Université de Lille, CNRS, UMR 8576-UGSF-Unité de Glycobiologie Structurale et Fonctionnelle, Lille, France
| |
Collapse
|
3
|
Jones C. Impact of imperfect data on protein secondary structure estimates from Far-UV circular dichroism spectra. Anal Biochem 2024; 688:115483. [PMID: 38360171 DOI: 10.1016/j.ab.2024.115483] [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: 10/27/2023] [Revised: 02/09/2024] [Accepted: 02/12/2024] [Indexed: 02/17/2024]
Abstract
Circular dichroism [CD] is widely used to rapidly assess protein structure. Deconvolution of the far-UV CD spectrum is widely used to quantify the secondary structural elements [SSEs]. Multiple algorithms are available for this. Imperfections in the experimental CD spectra arising from spectral noise, instrument miscalibration, spectral offsets and non-linearity will impact on the accuracy and precision of derived secondary structure estimates. Analytical validation for use in regulated environments, such as biopharmaceuticals, requires that the impact of imperfect data on these estimates be understood. Limited information on the impact of poor data were available. A series of noise-free simulated spectral datasets with modified intensity, wavelength, noise and intensity linearity and offsets were created from entries in the Protein Circular Dichroism Data Bank. These datasets were analysed using the BeStSel, on-line resource to estimate secondary structure. Data imperfections caused significant change in SSEs, but the spectral range is also important. This study emphasises the importance of analytical method validation and justifiable estimates of uncertainty when reporting results. The datasets created are made available as a resource to validate other secondary structure estimation programs.
Collapse
|
4
|
Godoy Muñoz JM, Neset L, Markússon S, Weber S, Krokengen OC, Sutinen A, Christakou E, Lopez AJ, Bramham CR, Kursula P. Structural characterization of two nanobodies targeting the ligand-binding pocket of human Arc. PLoS One 2024; 19:e0300453. [PMID: 38683783 PMCID: PMC11057775 DOI: 10.1371/journal.pone.0300453] [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: 11/03/2023] [Accepted: 02/27/2024] [Indexed: 05/02/2024] Open
Abstract
The activity-regulated cytoskeleton-associated protein (Arc) is a complex regulator of synaptic plasticity in glutamatergic neurons. Understanding its molecular function is key to elucidate the neurobiology of memory and learning, stress regulation, and multiple neurological and psychiatric diseases. The recent development of anti-Arc nanobodies has promoted the characterization of the molecular structure and function of Arc. This study aimed to validate two anti-Arc nanobodies, E5 and H11, as selective modulators of the human Arc N-lobe (Arc-NL), a domain that mediates several molecular functions of Arc through its peptide ligand binding site. The structural characteristics of recombinant Arc-NL-nanobody complexes were solved at atomic resolution using X-ray crystallography. Both anti-Arc nanobodies bind specifically to the multi-peptide binding site of Arc-NL. Isothermal titration calorimetry showed that the Arc-NL-nanobody interactions occur at nanomolar affinity, and that the nanobodies can displace a TARPγ2-derived peptide from the binding site. Thus, both anti-Arc-NL nanobodies could be used as competitive inhibitors of endogenous Arc ligands. Differences in the CDR3 loops between the two nanobodies indicate that the spectrum of short linear motifs recognized by the Arc-NL should be expanded. We provide a robust biochemical background to support the use of anti-Arc nanobodies in attempts to target Arc-dependent synaptic plasticity. Function-blocking anti-Arc nanobodies could eventually help unravel the complex neurobiology of synaptic plasticity and allow to develop diagnostic and treatment tools.
Collapse
Affiliation(s)
| | - Lasse Neset
- Department of Biomedicine, University of Bergen, Bergen, Norway
| | | | - Sarah Weber
- Department of Biomedicine, University of Bergen, Bergen, Norway
| | | | - Aleksi Sutinen
- Faculty of Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, Oulu, Finland
| | | | - Andrea J. Lopez
- Department of Biomedicine, University of Bergen, Bergen, Norway
| | | | - Petri Kursula
- Department of Biomedicine, University of Bergen, Bergen, Norway
- Faculty of Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, Oulu, Finland
| |
Collapse
|
5
|
Pennington H, Birtles D, Shi ZW, Lee J. A Salt Bridge and Disulfide Bond within the Lassa Virus Fusion Domain Are Required for the Initiation of Membrane Fusion. ACS OMEGA 2024; 9:4920-4930. [PMID: 38313535 PMCID: PMC10831964 DOI: 10.1021/acsomega.3c08632] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 12/13/2023] [Accepted: 12/28/2023] [Indexed: 02/06/2024]
Abstract
Infection with Lassa virus (LASV), an Old-World arenavirus that is endemic to West Africa, causes Lassa fever, a lethal hemorrhagic fever. Delivery of LASV's genetic material into the host cell is an integral component of its lifecycle. This is accomplished via membrane fusion, a process initiated by a hydrophobic sequence known as the fusion domain (FD). The LASV FD (G260-N295) consists of two structurally distinct regions: an N-terminal fusion peptide (FP: G260-T274) and an internal fusion loop (FL: C279-N295) that is connected by a short linker region (P275-Y278). However, the molecular mechanisms behind how the LASV FD initiates fusion remain unclear. Here, we demonstrate that the LASV FD adopts a fusogenic, helical conformation at a pH akin to that of the lysosomal compartment. Additionally, we identified a conserved disulfide bond (C279 and C292) and salt bridge (R282 and E289) within the FL that are pertinent to fusion. We found that the disulfide bond must be present so that the FD can bind to the lipid bilayer and subsequently initiate fusion. Moreover, the salt bridge is essential for the secondary structure of the FD such that it can associate with the lipid bilayer in the proper orientation for full functionality. In conclusion, our findings indicate that the LASV FD preferentially initiates fusion at a pH akin to that of the lysosome through a mechanism that requires a conserved salt bridge and, to a lesser extent, an intact disulfide bond within the internal FL.
Collapse
Affiliation(s)
- Hallie
N. Pennington
- Department of Chemistry and
Biochemistry, College of Computer, Mathematics, and Natural Science, University of Maryland College Park, College Park, Maryland 20740, United States
| | - Daniel Birtles
- Department of Chemistry and
Biochemistry, College of Computer, Mathematics, and Natural Science, University of Maryland College Park, College Park, Maryland 20740, United States
| | - Zoe W. Shi
- Department of Chemistry and
Biochemistry, College of Computer, Mathematics, and Natural Science, University of Maryland College Park, College Park, Maryland 20740, United States
| | - Jinwoo Lee
- Department of Chemistry and
Biochemistry, College of Computer, Mathematics, and Natural Science, University of Maryland College Park, College Park, Maryland 20740, United States
| |
Collapse
|
6
|
Miranda MCR, Nunes CM, Santos LF, da Silva LB, de Jesus VR, Filho NA, Pedro JAF, Lopes JLS, Oliveira CLP, Fantini MCA, Cardoso JS, Trezena AG, Ribeiro OG, Sant'Anna OA, Tino-De-Franco M, Martins TS. Ordered mesoporous silicas for potential applications in solid vaccine formulations. Vaccine 2024; 42:689-700. [PMID: 38145911 DOI: 10.1016/j.vaccine.2023.12.032] [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: 09/02/2023] [Revised: 12/06/2023] [Accepted: 12/08/2023] [Indexed: 12/27/2023]
Abstract
In an effort to develop efficient vaccine formulations, the use of ordered mesoporous silica (SBA-15) as an antigen carrier has been investigated. SBA-15 has required properties such as high surface area and pore volume, including narrow pore size distribution to protect antigens inside its matrix. This study aimed to examine the impact of solvent removal methods, specifically freeze-drying and evaporation on the intrinsic properties of an immunogenic complex. The immunogenic complexes, synthesized and incorporated with BSA, were characterized by various physicochemical techniques. Small Angle X-ray Scattering measurements revealed the characteristic reflections associated to pure SBA-15, indicating the preservation of the silica mesostructured following BSA incorporation and the formation of BSA aggregates within the macropore region. Nitrogen Adsorption Isotherm measurements demonstrated a decrease in surface area and pore volume for all samples, indicating that the BSA was incorporated into the SBA-15 matrix. Fluorescence spectroscopy evidenced that the tryptophan residues in BSA inside SBA-15 or in solution displayed similar spectra, showing the preservation of the aromatic residues' environment. The Circular Dichroism spectra of BSA in both conditions suggest the preservation of its native secondary structure after the encapsulation process. The immunogenic analysis with the detection of anti-BSA IgG did not give any significant difference between the non-dried, freeze-dried or evaporated groups. However, all groups containing BSA and SBA-15 showed results almost three times higher than the groups with pure BSA (control group). These facts indicate that none of the BSA incorporation methods interfered with the immunogenicity of the complex. In particular, the freeze-dried process is regularly used in the pharmaceutical industry, therefore its adequacy to produce immunogenic complexes was proved Furthermore, the results showed that SBA-15 increased the immunogenic activity of BSA.
Collapse
Affiliation(s)
- Matheus C R Miranda
- Instituto de Ciências Ambientais, Químicas e Farmacêuticas, Universidade Federal de São Paulo, Diadema, SP, Brazil
| | - Carmen M Nunes
- Instituto de Ciências Ambientais, Químicas e Farmacêuticas, Universidade Federal de São Paulo, Diadema, SP, Brazil
| | - Luana F Santos
- Instituto de Ciências Ambientais, Químicas e Farmacêuticas, Universidade Federal de São Paulo, Diadema, SP, Brazil
| | - Leonardo B da Silva
- Instituto de Ciências Ambientais, Químicas e Farmacêuticas, Universidade Federal de São Paulo, Diadema, SP, Brazil
| | - Vinicius R de Jesus
- Instituto de Ciências Ambientais, Químicas e Farmacêuticas, Universidade Federal de São Paulo, Diadema, SP, Brazil
| | - Newton Andréo Filho
- Instituto de Ciências Ambientais, Químicas e Farmacêuticas, Universidade Federal de São Paulo, Diadema, SP, Brazil
| | - Jéssica A F Pedro
- Instituto de Física, Universidade de São Paulo, São Paulo, SP, Brazil
| | - José L S Lopes
- Departamento de Física, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP, Brazil
| | | | | | | | | | | | | | | | - Tereza S Martins
- Instituto de Ciências Ambientais, Químicas e Farmacêuticas, Universidade Federal de São Paulo, Diadema, SP, Brazil.
| |
Collapse
|
7
|
Turbant F, Machiels Q, Waeytens J, Wien F, Arluison V. The Amyloid Assembly of the Bacterial Hfq Is Lipid-Driven and Lipid-Specific. Int J Mol Sci 2024; 25:1434. [PMID: 38338713 PMCID: PMC10855545 DOI: 10.3390/ijms25031434] [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: 12/27/2023] [Revised: 01/20/2024] [Accepted: 01/22/2024] [Indexed: 02/12/2024] Open
Abstract
Under specific conditions, some proteins can self-assemble into fibrillar structures called amyloids. Initially, these proteins were associated with neurodegenerative diseases in eucaryotes. Nevertheless, they have now been identified in the three domains of life. In bacteria, they are involved in diverse biological processes and are usually useful for the cell. For this reason, they are classified as "functional amyloids". In this work, we focus our analysis on a bacterial functional amyloid called Hfq. Hfq is a pleiotropic regulator that mediates several aspects of genetic expression, mainly via the use of small noncoding RNAs. Our previous work showed that Hfq amyloid-fibrils interact with membranes. This interaction influences Hfq amyloid structure formation and stability, but the specifics of the lipid on the dynamics of this process is unknown. Here, we show, using spectroscopic methods, how lipids specifically drive and modulate Hfq amyloid assembly or, conversely, its disassembly. The reported effects are discussed in light of the consequences for bacterial cell life.
Collapse
Affiliation(s)
- Florian Turbant
- Laboratoire Léon Brillouin LLB, CEA, CNRS UMR12, CEA Saclay, 91191 Gif-sur-Yvette, France;
- Synchrotron SOLEIL, L’Orme des Merisiers, Saint Aubin BP48, 91192 Gif-sur-Yvette, France;
- Department of Molecular Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland
| | - Quentin Machiels
- Structure et Fonction des Membranes Biologiques, Université Libre de Bruxelles, 1050 Bruxelles, Belgium; (Q.M.); (J.W.)
| | - Jehan Waeytens
- Structure et Fonction des Membranes Biologiques, Université Libre de Bruxelles, 1050 Bruxelles, Belgium; (Q.M.); (J.W.)
- Unit of Pharmacognosy, Bioanalysis and Drug Discovery, Université Libre de Bruxelles, 1050 Bruxelles, Belgium
| | - Frank Wien
- Synchrotron SOLEIL, L’Orme des Merisiers, Saint Aubin BP48, 91192 Gif-sur-Yvette, France;
| | - Véronique Arluison
- Laboratoire Léon Brillouin LLB, CEA, CNRS UMR12, CEA Saclay, 91191 Gif-sur-Yvette, France;
- SDV Department, Université Paris Cité, 75006 Paris, France
| |
Collapse
|
8
|
Turbant F, Mosca K, Busi F, Arluison V, Wien F. Circular and Linear Dichroism for the Analysis of Small Noncoding RNA Properties. Methods Mol Biol 2024; 2741:399-416. [PMID: 38217665 DOI: 10.1007/978-1-0716-3565-0_21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2024]
Abstract
Useful structural information about the conformation of nucleic acids can be quickly acquired by circular and linear dichroism (CD/LD) spectroscopy. These techniques, rely on the differential absorption of polarised light and are indeed extremely sensitive to subtle changes in the structure of chiral biomolecules. Many CD analyses of DNA or DNA:protein complexes have been conducted with substantial data acquisitions. Conversely, CD RNA analysis are still scarce, despite the fact that RNA plays a wide cellular function. This chapter seeks to introduce the reader to the use of circular, linear dichroism and in particular the use of Synchrotron Radiation for such samples. The use of these techniques on small noncoding RNA (sRNA) will be exemplified by analyzing changes in base stacking and/or helical parameters for the understanding of sRNA structure and function, especially by translating the dynamics of RNA:RNA annealing but also to access RNA stability or RNA:RNA alignment. The effect of RNA remodeling proteins will also be addressed. These analyses are especially useful to decipher the mechanisms by which sRNA will adopt the proper conformation thanks to the action of proteins such as Hfq or ProQ in the regulation of the expression of their target mRNAs.
Collapse
Affiliation(s)
- Florian Turbant
- Laboratoire Léon Brillouin LLB, CEA, CNRS UMR 12, CEA Saclay, Gif-sur-Yvette, France
- Synchrotron SOLEIL, L'Orme des Merisiers Saint Aubin, Gif-sur-Yvette, France
| | - Kevin Mosca
- Laboratoire Léon Brillouin LLB, CEA, CNRS UMR 12, CEA Saclay, Gif-sur-Yvette, France
- Synchrotron SOLEIL, L'Orme des Merisiers Saint Aubin, Gif-sur-Yvette, France
- SANOFI, Marcy-l'Etoile, France
| | - Florent Busi
- Université Paris Cité, Paris, France
- BFA, UMR 8251, Université Paris cité, CNRS, Paris, France
| | - Véronique Arluison
- CEA Saclay, Laboratoire LeÇon Brillouin LLB, CEA/CNRS, Gif-sur-Yvette, France
- Université Paris Cité, Paris, France
| | - Frank Wien
- Laboratoire Léon Brillouin LLB, CEA, CNRS UMR 12, CEA Saclay, Gif-sur-Yvette, France.
| |
Collapse
|
9
|
Turbant F, Blache A, Węgrzyn G, Achouak W, Wien F, Arluison V. Use of Synchrotron Radiation Circular Dichroism to Analyze the Interaction and Insertion of Proteins into Bacterial Outer Membrane Vesicles. Methods Mol Biol 2024; 2843:73-94. [PMID: 39141295 DOI: 10.1007/978-1-0716-4055-5_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/15/2024]
Abstract
Circular dichroism (CD) is a spectroscopic technique commonly used for the analysis of proteins. Particularly, it allows the determination of protein secondary structure content in various media, including the membrane environment. In this chapter, we present how CD applications can be used to analyze the interaction of proteins with bacterial outer membrane vesicles (OMVs). Most CD studies characterizing the structure of proteins inserted into membranes rely on artificial lipid bilayers, mimicking natural membranes. Nevertheless, these artificial models lack the important features of the true membrane, especially for the outer membrane of Gram-negative bacteria. These features include lipid diversity, glycosylation, and asymmetry. Here, we show how to analyze the interactions of proteins, either integral or peripheral, with OMVs in solution and with supported membranes of OMVs, using conventional CD and orientated circular dichroism (OCD). We explain how to decipher the spectroscopic signals to obtain information on the molecular structure of the protein upon its interaction with an OMV and through its potential insertion into an OMV membrane.
Collapse
Affiliation(s)
- Florian Turbant
- Laboratoire Léon Brillouin LLB, UMR12 CEA/CNRS, CEA Saclay, Gif-sur-Yvette, France
- Synchrotron SOLEIL, L'Orme des Merisiers, Saint Aubin BP48, Gif-sur-Yvette, France
- Department of Molecular Biology, University of Gdansk, Gdansk, Poland
| | - Anais Blache
- Lab of Microbial Ecology of the Rhizosphere, (LEMiRE), Aix Marseille University, CEA, CNRS, BIAM, Saint Paul Lez Durance, France
| | - Grzegorz Węgrzyn
- Department of Molecular Biology, University of Gdansk, Gdansk, Poland
| | - Wafa Achouak
- Lab of Microbial Ecology of the Rhizosphere, (LEMiRE), Aix Marseille University, CEA, CNRS, BIAM, Saint Paul Lez Durance, France
| | - Frank Wien
- Synchrotron SOLEIL, L'Orme des Merisiers, Saint Aubin BP48, Gif-sur-Yvette, France
| | - Véronique Arluison
- Laboratoire Léon Brillouin LLB, UMR12 CEA/CNRS, CEA Saclay, Gif-sur-Yvette, France
- Université Paris Cité, UFR Sciences du Vivant, Paris, France
| |
Collapse
|
10
|
Sutinen A, Jones NC, Hoffmann SV, Ruskamo S, Kursula P. Conformational analysis of membrane-proximal segments of GDAP1 in a lipidic environment using synchrotron radiation suggests a mode of assembly at the mitochondrial outer membrane. Biophys Chem 2023; 303:107113. [PMID: 37778197 DOI: 10.1016/j.bpc.2023.107113] [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: 07/10/2023] [Revised: 09/19/2023] [Accepted: 09/24/2023] [Indexed: 10/03/2023]
Abstract
The mitochondrial outer membrane creates a diffusion barrier between the cytosol and the mitochondrial intermembrane space, allowing the exchange of metabolic products, important for efficient mitochondrial function in neurons. The ganglioside-induced differentiation-associated protein 1 (GDAP1) is a mitochondrial outer membrane protein with a critical role in mitochondrial dynamics and metabolic balance in neurons. Missense mutations in the GDAP1 gene are linked to the most common human peripheral neuropathy, Charcot-Marie-Tooth disease (CMT). GDAP1 is a distant member of the glutathione-S-transferase (GST) superfamily, with unknown enzymatic properties or functions at the molecular level. The structure of the cytosol-facing GST-like domain has been described, but there is no consensus on how the protein interacts with the mitochondrial outer membrane. Here, we describe a model for GDAP1 assembly on the membrane using peptides vicinal to the GDAP1 transmembrane domain. We used oriented circular dichroism spectroscopy (OCD) with synchrotron radiation to study the secondary structure and orientation of GDAP1 segments at the outer and inner surfaces of the outer mitochondrial membrane. These experiments were complemented by small-angle X-ray scattering, providing the first experimental structural models for full-length human GDAP1. The results indicate that GDAP1 is bound into the membrane via a single transmembrane helix, flanked by two peripheral helices interacting with the outer and inner leaflets of the mitochondrial outer membrane in different orientations. Impairment of these interactions could be a mechanism for CMT in the case of missense mutations affecting these segments instead of the GST-like domain.
Collapse
Affiliation(s)
- Aleksi Sutinen
- Faculty of Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Nykola C Jones
- ISA, Department of Physics and Astronomy, Aarhus University, Aarhus, Denmark
| | | | - Salla Ruskamo
- Faculty of Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Petri Kursula
- Faculty of Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, Oulu, Finland; Department of Biomedicine, University of Bergen, Bergen, Norway.
| |
Collapse
|
11
|
Janes RW, Wallace BA. DichroPipeline: A suite of online and downloadable tools and resources for protein circular dichroism spectroscopic data analyses, interpretations, and their interoperability with other bioinformatics tools and resources. Protein Sci 2023; 32:e4817. [PMID: 37881887 PMCID: PMC10680340 DOI: 10.1002/pro.4817] [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: 09/01/2023] [Accepted: 09/30/2023] [Indexed: 10/27/2023]
Abstract
Circular Dichroism (CD) spectroscopy is a widely-used method for characterizing individual protein structures in solutions, membranes, films and macromolecular complexes, as well as for probing macromolecular interactions, conformational changes associated with binding substrates, and in different functionally-related environments. This paper describes a series of related computational and display tools that have been developed over many years to aid in those characterizations and functional interpretations. The new DichroPipeline described herein links a series of format-compatible data processing, analysis, and display tools to enable users to facilely produce the spectra, which can then be made available in the Protein Circular Dichroism Data Bank (https://pcddb.cryst.bbk.ac.uk/) resource, in which the CD spectral and associated metadata for each entry are linked to other structural and functional data bases including the Protein Data Bank (PDB), and the UniProt sequence data base, amongst others. These tools and resources thus provide the basis for a wide range of traceable structural characterizations of soluble, membrane and intrinsically-disordered proteins.
Collapse
Affiliation(s)
- Robert W. Janes
- School of Biological and Behavioural SciencesQueen Mary University of LondonLondonUK
| | - B. A. Wallace
- School of Biological SciencesBirkbeck University of LondonLondonUK
| |
Collapse
|
12
|
Kim H, Okada K, Chae I, Lim B, Ji S, Kwon Y, Lee SW. Virus-Based Pyroelectricity. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2023; 35:e2305503. [PMID: 37611920 DOI: 10.1002/adma.202305503] [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: 06/08/2023] [Revised: 08/07/2023] [Indexed: 08/25/2023]
Abstract
The first observation of heat-induced electrical potential generation on a virus and its detection through pyroelectricity are presented. Specifically, the authors investigate the pyroelectric properties of the M13 phage, which possesses inherent dipole structures derived from the noncentrosymmetric arrangement of the major coat protein (pVIII) with an α-helical conformation. Unidirectional polarization of the phage is achieved through genetic engineering of the tail protein (pIII) and template-assisted self-assembly techniques. By modifying the pVIII proteins with varying numbers of glutamate residues, the structure-dependent tunable pyroelectric properties of the phage are explored. The most polarized phage exhibits a pyroelectric coefficient of 0.13 µC m-2 °C-1 . Computational modeling and circular dichroism (CD) spectroscopy analysis confirm that the unfolding of α-helices within the pVIII proteins leads to changes in phage polarization upon heating. Moreover, the phage is genetically modified to enable its pyroelectric function in diverse chemical environments. This phage-based approach not only provides valuable insights into bio-pyroelectricity but also opens up new opportunities for the detection of various viral particles. Furthermore, it holds great potential for the development of novel biomaterials for future applications in biosensors and bioelectric materials.
Collapse
Affiliation(s)
- Han Kim
- Department of Applied Science and Technology, University of California, Berkeley, CA, 94720, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Kento Okada
- Department of Bioengineering, University of California, Berkeley, CA, 94720, USA
- Department of Materials Science and Engineering, University of California, Berkeley, CA, 94720, USA
| | - Inseok Chae
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- Department of Bioengineering, University of California, Berkeley, CA, 94720, USA
| | - Butaek Lim
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- Department of Bioengineering, University of California, Berkeley, CA, 94720, USA
| | - Seungwook Ji
- Department of Applied Science and Technology, University of California, Berkeley, CA, 94720, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Yoonji Kwon
- Department of Bioengineering, University of California, Berkeley, CA, 94720, USA
| | - Seung-Wuk Lee
- Department of Applied Science and Technology, University of California, Berkeley, CA, 94720, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- Department of Bioengineering, University of California, Berkeley, CA, 94720, USA
| |
Collapse
|
13
|
Hasan MM, Polino AJ, Mukherjee S, Vaupel B, Goldberg DE. The mature N-termini of Plasmodium effector proteins confer specificity of export. mBio 2023; 14:e0121523. [PMID: 37646514 PMCID: PMC10653839 DOI: 10.1128/mbio.01215-23] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Accepted: 07/10/2023] [Indexed: 09/01/2023] Open
Abstract
IMPORTANCE Malaria parasites export hundreds of proteins to the cytoplasm of the host red blood cells for their survival. A five amino acid sequence, called the PEXEL motif, is conserved among many exported proteins and is thought to be a signal for export. However, the motif is cleaved inside the endoplasmic reticulum of the parasite, and mature proteins starting from the fourth PEXEL residue travel to the parasite periphery for export. We showed that the PEXEL motif is dispensable for export as long as identical mature proteins can be efficiently produced via alternative means in the ER. We also showed that the exported and non-exported proteins are differentiated at the parasite periphery based on their mature N-termini; however, any discernible export signal within that region remained cryptic. Our study resolves a longstanding paradox in PEXEL protein trafficking.
Collapse
Affiliation(s)
- Muhammad M. Hasan
- Division of Infectious Diseases, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri, USA
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Alexander J. Polino
- Division of Infectious Diseases, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri, USA
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Sumit Mukherjee
- Division of Infectious Diseases, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri, USA
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Barbara Vaupel
- Division of Infectious Diseases, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri, USA
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Daniel E. Goldberg
- Division of Infectious Diseases, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri, USA
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, USA
| |
Collapse
|
14
|
Aguilera P, Berríos-Pastén C, Veloso M, Gálvez-Silva M, Turbant F, Lagos R, Wien F, Arluison V, Marcoleta AE. The Green Tea Polyphenol Epigallocatechin-Gallate (EGCG) Interferes with Microcin E492 Amyloid Formation. Molecules 2023; 28:7262. [PMID: 37959682 PMCID: PMC10648153 DOI: 10.3390/molecules28217262] [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: 09/22/2023] [Revised: 10/09/2023] [Accepted: 10/17/2023] [Indexed: 11/15/2023] Open
Abstract
Microcin E492 (MccE492) is an antimicrobial peptide and proposed virulence factor produced by some Klebsiella pneumoniae strains, which, under certain conditions, form amyloid fibers, leading to the loss of its antibacterial activity. Although this protein has been characterized as a model functional amyloid, the secondary structure transitions behind its formation, and the possible effect of molecules that inhibit this process, have not been investigated. In this study, we examined the ability of the green tea flavonoid epigallocatechin gallate (EGCG) to interfere with MccE492 amyloid formation. Aggregation kinetics followed by thioflavin T binding were used to monitor amyloid formation in the presence or absence of EGCG. Additionally, synchrotron radiation circular dichroism (SRCD) and transmission electron microscopy (TEM) were used to study the secondary structure, thermal stability, and morphology of microcin E492 fibers. Our results showed that EGCG significantly inhibited the formation of the MccE492 amyloid, resulting in mainly amorphous aggregates and small oligomers. However, these aggregates retained part of the β-sheet SRCD signal and a high resistance to heat denaturation, suggesting that the aggregation process is sequestered or deviated at some stage but not completely prevented. Thus, EGCG is an interesting inhibitor of the amyloid formation of MccE492 and other bacterial amyloids.
Collapse
Affiliation(s)
- Paulina Aguilera
- Grupo de Microbiología Integrativa, Laboratorio de Biología Estructural y Molecular BEM, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425 Ñuñoa, Santiago 7800003, Chile; (P.A.); (C.B.-P.); (M.V.); (M.G.-S.); (R.L.)
| | - Camilo Berríos-Pastén
- Grupo de Microbiología Integrativa, Laboratorio de Biología Estructural y Molecular BEM, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425 Ñuñoa, Santiago 7800003, Chile; (P.A.); (C.B.-P.); (M.V.); (M.G.-S.); (R.L.)
| | - Marcelo Veloso
- Grupo de Microbiología Integrativa, Laboratorio de Biología Estructural y Molecular BEM, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425 Ñuñoa, Santiago 7800003, Chile; (P.A.); (C.B.-P.); (M.V.); (M.G.-S.); (R.L.)
| | - Matías Gálvez-Silva
- Grupo de Microbiología Integrativa, Laboratorio de Biología Estructural y Molecular BEM, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425 Ñuñoa, Santiago 7800003, Chile; (P.A.); (C.B.-P.); (M.V.); (M.G.-S.); (R.L.)
| | - Florian Turbant
- Synchrotron SOLEIL, L’Orme des Merisiers, Saint Aubin BP48, 91192 Gif-sur-Yvette, France; (F.T.); (F.W.)
- Laboratoire Léon Brillouin LLB, CEA, CNRS UMR12, Université Paris-Saclay, CEA Saclay, 91191 Gif-sur-Yvette, France
| | - Rosalba Lagos
- Grupo de Microbiología Integrativa, Laboratorio de Biología Estructural y Molecular BEM, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425 Ñuñoa, Santiago 7800003, Chile; (P.A.); (C.B.-P.); (M.V.); (M.G.-S.); (R.L.)
| | - Frank Wien
- Synchrotron SOLEIL, L’Orme des Merisiers, Saint Aubin BP48, 91192 Gif-sur-Yvette, France; (F.T.); (F.W.)
| | - Veronique Arluison
- Laboratoire Léon Brillouin LLB, CEA, CNRS UMR12, Université Paris-Saclay, CEA Saclay, 91191 Gif-sur-Yvette, France
- UFR Sciences du Vivant, Université Paris Cité, 75006 Paris, France
| | - Andrés E. Marcoleta
- Grupo de Microbiología Integrativa, Laboratorio de Biología Estructural y Molecular BEM, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425 Ñuñoa, Santiago 7800003, Chile; (P.A.); (C.B.-P.); (M.V.); (M.G.-S.); (R.L.)
| |
Collapse
|
15
|
Kind L, Driver M, Raasakka A, Onck PR, Njølstad PR, Arnesen T, Kursula P. Structural properties of the HNF-1A transactivation domain. Front Mol Biosci 2023; 10:1249939. [PMID: 37908230 PMCID: PMC10613711 DOI: 10.3389/fmolb.2023.1249939] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 09/26/2023] [Indexed: 11/02/2023] Open
Abstract
Hepatocyte nuclear factor 1α (HNF-1A) is a transcription factor with important gene regulatory roles in pancreatic β-cells. HNF1A gene variants are associated with a monogenic form of diabetes (HNF1A-MODY) or an increased risk for type 2 diabetes. While several pancreatic target genes of HNF-1A have been described, a lack of knowledge regarding the structure-function relationships in HNF-1A prohibits a detailed understanding of HNF-1A-mediated gene transcription, which is important for precision medicine and improved patient care. Therefore, we aimed to characterize the understudied transactivation domain (TAD) of HNF-1A in vitro. We present a bioinformatic approach to dissect the TAD sequence, analyzing protein structure, sequence composition, sequence conservation, and the existence of protein interaction motifs. Moreover, we developed the first protocol for the recombinant expression and purification of the HNF-1A TAD. Small-angle X-ray scattering and synchrotron radiation circular dichroism suggested a disordered conformation for the TAD. Furthermore, we present functional data on HNF-1A undergoing liquid-liquid phase separation, which is in line with in silico predictions and may be of biological relevance for gene transcriptional processes in pancreatic β-cells.
Collapse
Affiliation(s)
- Laura Kind
- Department of Biomedicine, University of Bergen, Bergen, Norway
| | - Mark Driver
- Zernike Institute for Advanced Materials, University of Groningen, Groningen, Netherlands
| | - Arne Raasakka
- Department of Biomedicine, University of Bergen, Bergen, Norway
| | - Patrick R. Onck
- Zernike Institute for Advanced Materials, University of Groningen, Groningen, Netherlands
| | - Pål Rasmus Njølstad
- Mohn Center for Diabetes Precision Medicine, Department of Clinical Science, University of Bergen, Bergen, Norway
- Section of Endocrinology and Metabolism, Children and Youth Clinic, Haukeland University Hospital, Bergen, Norway
| | - Thomas Arnesen
- Department of Biomedicine, University of Bergen, Bergen, Norway
- Department of Surgery, Haukeland University Hospital, Bergen, Norway
| | - Petri Kursula
- Department of Biomedicine, University of Bergen, Bergen, Norway
- Faculty of Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, Oulu, Finland
| |
Collapse
|
16
|
Miles AJ, Drew ED, Wallace BA. DichroIDP: a method for analyses of intrinsically disordered proteins using circular dichroism spectroscopy. Commun Biol 2023; 6:823. [PMID: 37553525 PMCID: PMC10409736 DOI: 10.1038/s42003-023-05178-2] [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: 09/09/2022] [Accepted: 07/25/2023] [Indexed: 08/10/2023] Open
Abstract
Intrinsically disordered proteins (IDPs) are comprised of significant numbers of residues that form neither helix, sheet, nor any other canonical type of secondary structure. They play important roles in a broad range of biological processes, such as molecular recognition and signalling, largely due to their chameleon-like ability to change structure from unordered when free in solution to ordered when bound to partner molecules. Circular dichroism (CD) spectroscopy is a widely-used method for characterising protein secondary structures, but analyses of IDPs using CD spectroscopy have suffered because the methods and reference datasets used for the empirical determination of secondary structures do not contain adequate representations of unordered structures. This work describes the creation, validation and testing of a standalone Windows-based application, DichroIDP, and a new reference dataset, IDP175, which is suitable for analyses of proteins containing significant amounts of disordered structure. DichroIDP enables secondary structure determinations of IDPs and proteins containing intrinsically disordered regions.
Collapse
Affiliation(s)
- Andrew J Miles
- Institute of Structural and Molecular Biology, Birkbeck University of London, London, WC1E 7HX, UK
| | - Elliot D Drew
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London, E1 4NS, UK
- Zappi, London, NW1 7JN, UK
| | - B A Wallace
- Institute of Structural and Molecular Biology, Birkbeck University of London, London, WC1E 7HX, UK.
| |
Collapse
|
17
|
Turbant F, Waeytens J, Blache A, Esnouf E, Raussens V, Węgrzyn G, Achouak W, Wien F, Arluison V. Interactions and Insertion of Escherichia coli Hfq into Outer Membrane Vesicles as Revealed by Infrared and Orientated Circular Dichroism Spectroscopies. Int J Mol Sci 2023; 24:11424. [PMID: 37511182 PMCID: PMC10379585 DOI: 10.3390/ijms241411424] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 07/10/2023] [Accepted: 07/11/2023] [Indexed: 07/30/2023] Open
Abstract
The possible carrier role of Outer Membrane Vesicles (OMVs) for small regulatory noncoding RNAs (sRNAs) has recently been demonstrated. Nevertheless, to perform their function, these sRNAs usually need a protein cofactor called Hfq. In this work we show, by using a combination of infrared and circular dichroism spectroscopies, that Hfq, after interacting with the inner membrane, can be translocated into the periplasm, and then be exported in OMVs, with the possibility to be bound to sRNAs. Moreover, we provide evidence that Hfq interacts with and is inserted into OMV membranes, suggesting a role for this protein in the release of sRNA outside the vesicle. These findings provide clues to the mechanism of host-bacteria interactions which may not be defined solely by protein-protein and protein-outer membrane contacts, but also by the exchange of RNAs, and in particular sRNAs.
Collapse
Affiliation(s)
- Florian Turbant
- Laboratoire Léon Brillouin LLB, CEA, CNRS UMR12, Université Paris Saclay, CEA Saclay, 91191 Gif-sur-Yvette, France
- Synchrotron SOLEIL, L'Orme des Merisiers, Saint Aubin BP48, 91192 Gif-sur-Yvette, France
- Department of Molecular Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland
| | - Jehan Waeytens
- Structure et Fonction des Membranes Biologiques, Université libre de Bruxelles, 1050 Bruxelles, Belgium
| | - Anaïs Blache
- Lab of Microbial Ecology of the Rhizosphere, (LEMiRE), BIAM, CEA, CNRS, Aix Marseille University, 13115 Saint Paul Lez Durance, France
| | - Emeline Esnouf
- Laboratoire Léon Brillouin LLB, CEA, CNRS UMR12, Université Paris Saclay, CEA Saclay, 91191 Gif-sur-Yvette, France
| | - Vincent Raussens
- Structure et Fonction des Membranes Biologiques, Université libre de Bruxelles, 1050 Bruxelles, Belgium
| | - Grzegorz Węgrzyn
- Department of Molecular Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland
| | - Wafa Achouak
- Lab of Microbial Ecology of the Rhizosphere, (LEMiRE), BIAM, CEA, CNRS, Aix Marseille University, 13115 Saint Paul Lez Durance, France
| | - Frank Wien
- Synchrotron SOLEIL, L'Orme des Merisiers, Saint Aubin BP48, 91192 Gif-sur-Yvette, France
| | - Véronique Arluison
- Laboratoire Léon Brillouin LLB, CEA, CNRS UMR12, Université Paris Saclay, CEA Saclay, 91191 Gif-sur-Yvette, France
- UFR Sciences du Vivant, Université Paris Cité, 75006 Paris, France
| |
Collapse
|
18
|
Liu C, Pfister B, Osman R, Ritter M, Heutinck A, Sharma M, Eicke S, Fischer-Stettler M, Seung D, Bompard C, Abt MR, Zeeman SC. LIKE EARLY STARVATION 1 and EARLY STARVATION 1 promote and stabilize amylopectin phase transition in starch biosynthesis. SCIENCE ADVANCES 2023; 9:eadg7448. [PMID: 37235646 DOI: 10.1126/sciadv.adg7448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Accepted: 04/19/2023] [Indexed: 05/28/2023]
Abstract
Starch, the most abundant carbohydrate reserve in plants, primarily consists of the branched glucan amylopectin, which forms semi-crystalline granules. Phase transition from a soluble to an insoluble form depends on amylopectin architecture, requiring a compatible distribution of glucan chain lengths and a branch-point distribution. Here, we show that two starch-bound proteins, LIKE EARLY STARVATION 1 (LESV) and EARLY STARVATION 1 (ESV1), which have unusual carbohydrate-binding surfaces, promote the phase transition of amylopectin-like glucans, both in a heterologous yeast system expressing the starch biosynthetic machinery and in Arabidopsis plants. We propose a model wherein LESV serves as a nucleating role, with its carbohydrate-binding surfaces helping align glucan double helices to promote their phase transition into semi-crystalline lamellae, which are then stabilized by ESV1. Because both proteins are widely conserved, we suggest that protein-facilitated glucan crystallization may be a general and previously unrecognized feature of starch biosynthesis.
Collapse
Affiliation(s)
- Chun Liu
- Institute of Molecular Plant Biology, ETH Zurich, Universitätstrasse 2, 8092 Zurich, Switzerland
| | - Barbara Pfister
- Institute of Molecular Plant Biology, ETH Zurich, Universitätstrasse 2, 8092 Zurich, Switzerland
| | - Rayan Osman
- Université de Lille, CNRS, UMR 8576-UGSF-Unité de Glycobiologie Structurale et Fonctionnelle, Lille, France
| | - Maximilian Ritter
- Institute for Building Materials, ETH Zurich, Stefano-Franscini-Platz 3, 8093 Zurich, Switzerland
| | - Arvid Heutinck
- Institute of Molecular Plant Biology, ETH Zurich, Universitätstrasse 2, 8092 Zurich, Switzerland
| | - Mayank Sharma
- Institute of Molecular Plant Biology, ETH Zurich, Universitätstrasse 2, 8092 Zurich, Switzerland
| | - Simona Eicke
- Institute of Molecular Plant Biology, ETH Zurich, Universitätstrasse 2, 8092 Zurich, Switzerland
| | | | - David Seung
- Institute of Molecular Plant Biology, ETH Zurich, Universitätstrasse 2, 8092 Zurich, Switzerland
| | - Coralie Bompard
- Université de Lille, CNRS, UMR 8576-UGSF-Unité de Glycobiologie Structurale et Fonctionnelle, Lille, France
| | - Melanie R Abt
- Institute of Molecular Plant Biology, ETH Zurich, Universitätstrasse 2, 8092 Zurich, Switzerland
| | - Samuel C Zeeman
- Institute of Molecular Plant Biology, ETH Zurich, Universitätstrasse 2, 8092 Zurich, Switzerland
| |
Collapse
|
19
|
Ma J, Yang B, Hu X, Gao Y, Qin C. The binding mechanism of benzophenone-type UV filters and human serum albumin: The role of site, number, and type of functional group substitutions. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2023; 324:121342. [PMID: 36828352 DOI: 10.1016/j.envpol.2023.121342] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 02/17/2023] [Accepted: 02/21/2023] [Indexed: 06/18/2023]
Abstract
Benzophenone-type UV filters (BPs) are common in natural aquatic environments. They can cause endocrine disruption or other adverse effects once they enter the human body via the food chain or drinking water. The primary cause of BPs accumulation and toxicity is the transport of BPs into the human body. Functional group substitutions can have a significant impact on the interactions of BPs and transporters, resulting in a variety of impact effects. Therefore, we explored the interaction between human serum albumin (HSA, a typical transporter) and ten typical BPs [benzophenone (BP1), 2-hydroxybenzophenone (BP2), 4-hydroxybenzophenone (BP3), 2,2'-dihydroxybenzophenone (BP4), 2,4-dihydroxybenzophenone (BP5), 4,4'-dihydroxybenzophenone (BP6), 2,4,4'-trihydroxybenzophenone (BP7), 2,2',4,4'-tetrahydroxybenzophenone (BP8), 2-hydroxy-4-methoxybenzophenone (BP9), and 2,2'-dihydroxy-4-methoxybenzophenone (BP10)] to study the role of functional group substitutions in binding. The results showed that BPs could bind to HSA at site 2, with binding constants ranging from 2.01 × 103 to 4.57 × 105 L/mol. Compared to BP1, hydroxyl and methoxy substitutions enhanced the BPs-HSA binding. The combined effect of the number and site of hydroxyl substitution at BPs determined the binding strength between BPs and HSA. It was more accessible to bind HSA when BPs were substituted with para-hydroxyl (4-hydroxyl) groups than with ortho-hydroxyl (2-hydroxyl) groups. Moreover, the additional para-methoxy (4-methoxy) group increased the BP-HSA binding strength by approximately 47 times under the same hydroxyl substitution conditions. Theoretical calculations revealed that functional group substitutions increased the intermolecular binding force by increasing the negative electrostatic potential surface area of BPs, which significantly increased the electrostatic and dispersion forces between the BPs and HSA. This BPs-HSA binding decreased the α-helix of HSA and influenced the ratio of other secondary structures, including β-sheet, β-turn, and random coil of HSA. This study provides a theoretical and experimental foundation for understanding the human health risks associated with BPs.
Collapse
Affiliation(s)
- Junchao Ma
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, PR China
| | - Bing Yang
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, PR China
| | - Xiaojie Hu
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, PR China
| | - Yanzheng Gao
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, PR China
| | - Chao Qin
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, PR China.
| |
Collapse
|
20
|
Walsemann T, Böttger M, Traidl S, Schwager C, Gülsen A, Freimooser S, Roesner LM, Werfel T, Jappe U. Specific IgE against the house dust mite allergens Der p 5, 20 and 21 influences the phenotype and severity of atopic diseases. Allergy 2023; 78:731-742. [PMID: 36239002 DOI: 10.1111/all.15553] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 09/12/2022] [Accepted: 09/23/2022] [Indexed: 11/30/2022]
Abstract
BACKGROUND House dust mites (HDM) are among the most important sources for airborne allergens with high relevance for atopic diseases. Routine tests contain only 4 of 32 registered allergens of Dermatophagoides pteronyssinus. Clinical relevance and pathomechanistic properties of many allergens are not well understood. OBJECTIVE The association of several HDM allergens with allergic rhinitis, allergic asthma, and atopic dermatitis was investigated to identify allergens with biomarker potential and to transfer them into diagnostics. METHODS Eight out of nine D. pteronyssinus allergens (nDer p 1, rDer p 2, rDer p 5, rDer p 7, rDer p 10, rDer p 13, rDer p 20, rDer p 21, rDer p 23) were recombinantly expressed and purified. Sensitization patterns of 384 HDM-allergic individuals exhibiting different clinical phenotypes were analyzed with a serum-saving multiplex array. RESULTS Sensitization to more than three mite allergens (sensitization count) was associated with allergic asthma and/or atopic dermatitis. Reactions to Der p 5 and Der p 21 were more frequent in allergic asthma compared to allergic rhinitis. Atopic dermatitis patients were more often sensitized to Der p 5, Der p 20, and Der p 21 among others. Der p 20-IgE > 80 kU/L was associated with severe atopic dermatitis in 75% of patients. CONCLUSION This study demonstrates the clinical importance of the sensitization count and of certain allergens (Der p 5, Der p 20, and Der p 21) not available for routine diagnostics yet. Implementing them as well as the sensitization count in diagnostic measures will improve diagnosis and risk assessment of HDM-allergic patients.
Collapse
Affiliation(s)
- Theresa Walsemann
- Division of Clinical and Molecular Allergology, Priority Area Asthma and Allergy, Research Center Borstel, German Center for Lung Research (DZL) Airway Research Center North (ARCN), Borstel, Germany
| | - Marisa Böttger
- Division of Clinical and Molecular Allergology, Priority Area Asthma and Allergy, Research Center Borstel, German Center for Lung Research (DZL) Airway Research Center North (ARCN), Borstel, Germany
| | - Stephan Traidl
- Division of Immunodermatology and Allergy Research, Department of Dermatology and Allergy, Hannover Medical School, Hannover, Germany
| | - Christian Schwager
- Division of Clinical and Molecular Allergology, Priority Area Asthma and Allergy, Research Center Borstel, German Center for Lung Research (DZL) Airway Research Center North (ARCN), Borstel, Germany
| | - Askin Gülsen
- Interdisciplinary Allergy Outpatient Clinic, Department of Pneumology, University of Luebeck, Luebeck, Germany
| | - Sina Freimooser
- Division of Immunodermatology and Allergy Research, Department of Dermatology and Allergy, Hannover Medical School, Hannover, Germany
| | - Lennart Matthias Roesner
- Division of Immunodermatology and Allergy Research, Department of Dermatology and Allergy, Hannover Medical School, Hannover, Germany.,Cluster of Excellence RESIST (EXC 2155), Hannover Medical School, Hannover, Germany
| | - Thomas Werfel
- Division of Immunodermatology and Allergy Research, Department of Dermatology and Allergy, Hannover Medical School, Hannover, Germany.,Cluster of Excellence RESIST (EXC 2155), Hannover Medical School, Hannover, Germany
| | - Uta Jappe
- Division of Clinical and Molecular Allergology, Priority Area Asthma and Allergy, Research Center Borstel, German Center for Lung Research (DZL) Airway Research Center North (ARCN), Borstel, Germany.,Interdisciplinary Allergy Outpatient Clinic, Department of Pneumology, University of Luebeck, Luebeck, Germany
| |
Collapse
|
21
|
Righetto GM, Lopes JLDS, Bispo PJM, André C, Souza JM, Andricopulo AD, Beltramini LM, Camargo ILBDC. Antimicrobial Activity of an Fmoc-Plantaricin 149 Derivative Peptide against Multidrug-Resistant Bacteria. Antibiotics (Basel) 2023; 12:antibiotics12020391. [PMID: 36830301 PMCID: PMC9952790 DOI: 10.3390/antibiotics12020391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 02/07/2023] [Accepted: 02/09/2023] [Indexed: 02/17/2023] Open
Abstract
Antimicrobial resistance poses a major threat to public health. Given the paucity of novel antimicrobials to treat resistant infections, the emergence of multidrug-resistant bacteria renewed interest in antimicrobial peptides as potential therapeutics. This study designed a new analog of the antimicrobial peptide Plantaricin 149 (Pln149-PEP20) based on previous Fmoc-peptides. The minimal inhibitory concentrations of Pln149-PEP20 were determined for 60 bacteria of different species and resistance profiles, ranging from 1 mg/L to 128 mg/L for Gram-positive bacteria and 16 to 512 mg/L for Gram-negative. Furthermore, Pln149-PEP20 demonstrated excellent bactericidal activity within one hour. To determine the propensity to develop resistance to Pln149-PEP20, a directed-evolution in vitro experiment was performed. Whole-genome sequencing of selected mutants with increased MICs and wild-type isolates revealed that most mutations were concentrated in genes associated with membrane metabolism, indicating the most likely target of Pln149-PEP20. Synchrotron radiation circular dichroism showed how this molecule disturbs the membranes, suggesting a carpet mode of interaction. Membrane depolarization and transmission electron microscopy assays supported these two hypotheses, although a secondary intracellular mechanism of action is possible. The molecule studied in this research has the potential to be used as a novel antimicrobial therapy, although further modifications and optimization remain possible.
Collapse
Affiliation(s)
- Gabriela Marinho Righetto
- Laboratory of Molecular Epidemiology and Microbiology, Department of Physics and Interdisciplinary Science, São Carlos Institute of Physics, University of São Paulo, São Carlos 13563-120, Brazil
| | - José Luiz de Souza Lopes
- Laboratory of Applied Biophysics, Department of Applied Physics, Institute of Physics, University of São Paulo, São Paulo 05315-970, Brazil
| | - Paulo José Martins Bispo
- Department of Ophthalmology, Infectious Disease Institute, Massachusetts Eye and Ear, Harvard Medical School, Boston, MA 02115, USA
| | - Camille André
- Department of Ophthalmology, Infectious Disease Institute, Massachusetts Eye and Ear, Harvard Medical School, Boston, MA 02115, USA
| | - Julia Medeiros Souza
- Laboratory of Medicinal and Computational Chemistry, Department of Physics and Interdisciplinary Science, São Carlos Institute of Physics, University of São Paulo, São Carlos 13563-120, Brazil
| | - Adriano Defini Andricopulo
- Laboratory of Medicinal and Computational Chemistry, Department of Physics and Interdisciplinary Science, São Carlos Institute of Physics, University of São Paulo, São Carlos 13563-120, Brazil
| | - Leila Maria Beltramini
- Group of Biophysics and Structural Biology “Sérgio Mascarenhas”, Department of Physics and Interdisciplinary Science, São Carlos Institute of Physics, University of São Paulo, São Carlos 13563-120, Brazil
| | - Ilana Lopes Baratella da Cunha Camargo
- Laboratory of Molecular Epidemiology and Microbiology, Department of Physics and Interdisciplinary Science, São Carlos Institute of Physics, University of São Paulo, São Carlos 13563-120, Brazil
- Correspondence: ; Tel.: +55-(16)-3373-8654
| |
Collapse
|
22
|
Liu L, Zhang J, Wang P, Tong Y, Li Y, Chen H. Functional Properties of Corn Byproduct-Based Emulsifier Prepared by Hydrothermal-Alkaline. Molecules 2023; 28:molecules28020665. [PMID: 36677721 PMCID: PMC9865437 DOI: 10.3390/molecules28020665] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2022] [Revised: 12/30/2022] [Accepted: 01/02/2023] [Indexed: 01/11/2023] Open
Abstract
As consumers' interest in nature-sourced additives has increased, zein has been treated hydrothermally under alkaline conditions to prepare a nature-sourced emulsifier. The effects of mild hydrothermal-alkaline treatment with different temperatures or alkaline concentrations on the emulsifying properties of zein were investigated. The emulsification activity and stability index of zein hydrolysates increased by 39% and 164%, respectively. The optimal simple stabilized emulsion was uniform and stable against heat treatment up to 90 °C, sodium chloride up to 200 mmol/L, and pH values ranging from 6 to 9. Moreover, it presented excellent storage stability compared to commonly used food emulsifiers. The surface hydrophobicity caused the depolymerization of the tertiary structure of zein and the dissociation of subunits along with exposure of hydrophilic groups. The amino acid composition and circular dichroism results reveal that the treatment dissociated protein subunits and transformed α-helices into anti-parallel β-sheets and random coil. In conclusion, mild hydrothermal-alkaline treatment may well contribute to the extended functional properties of zein as a nature-sourced emulsifier.
Collapse
Affiliation(s)
- Lu Liu
- Department of Nutrition and Health, China Agricultural University, Beijing 100083, China
| | - Jijun Zhang
- National Engineering Research Center for Corn Deep Processing, Changchun 130000, China
- Nutrition & Health Research Institute, China Oil and Foodstuffs Corporation, Beijing 102200, China
| | - Pengjie Wang
- Department of Nutrition and Health, China Agricultural University, Beijing 100083, China
| | - Yi Tong
- China Oil and Foodstuffs Biotechnology Corporation, Changchun 130000, China
| | - Yi Li
- China Oil and Foodstuffs Biotechnology Corporation, Changchun 130000, China
| | - Han Chen
- Department of Nutrition and Health, China Agricultural University, Beijing 100083, China
- Correspondence:
| |
Collapse
|
23
|
FtsEX-independent control of RipA-mediated cell separation in Corynebacteriales. Proc Natl Acad Sci U S A 2022; 119:e2214599119. [PMID: 36469781 PMCID: PMC9897464 DOI: 10.1073/pnas.2214599119] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The bacterial cell wall is a multi-layered mesh, whose major component is peptidoglycan (PG), a sugar polymer cross-linked by short peptide stems. During cell division, a careful balance of PG synthesis and degradation, precisely coordinated both in time and space, is necessary to prevent uncontrolled destruction of the cell wall. In Corynebacteriales, the D,L endopeptidase RipA has emerged as a major PG hydrolase for cell separation, and RipA defaults have major implications for virulence of the human pathogens Mycobacterium tuberculosis and Corynebacterium diphtheriae. However, the precise mechanisms by which RipA mediates cell separation remain elusive. Here we report phylogenetic, biochemical, and structural analysis of the Corynebacterium glutamicum homologue of RipA, Cg1735. The crystal structures of full-length Cg1735 in two different crystal forms revealed the C-terminal NlpC/P60 catalytic domain obtruded by its N-terminal conserved coiled-coil domain, which locks the enzyme in an autoinhibited state. We show that this autoinhibition is relieved by the extracellular core domain of the transmembrane septal protein Cg1604. The crystal structure of Cg1604 revealed a (β/α) protein with an overall topology similar to that of receiver domains from response regulator proteins. The atomic model of the Cg1735-Cg1604 complex, based on bioinformatical and mutational analysis, indicates that a conserved, distal-membrane helical insertion in Cg1604 is responsible for Cg1735 activation. The reported data provide important insights into how intracellular cell division signal(s), yet to be identified, control PG hydrolysis during RipA-mediated cell separation in Corynebacteriales.
Collapse
|
24
|
Adjuvant effect of mesoporous silica SBA-15 on anti-diphtheria and anti-tetanus humoral immune response. Biologicals 2022; 80:18-26. [DOI: 10.1016/j.biologicals.2022.10.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 07/25/2022] [Accepted: 10/25/2022] [Indexed: 11/21/2022] Open
|
25
|
Cappannini A, Mosca K, Mukherjee S, Moafinejad S, Sinden R, Arluison V, Bujnicki J, Wien F. NACDDB: Nucleic Acid Circular Dichroism Database. Nucleic Acids Res 2022; 51:D226-D231. [PMID: 36280237 PMCID: PMC9825466 DOI: 10.1093/nar/gkac829] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Accepted: 09/15/2022] [Indexed: 01/29/2023] Open
Abstract
The Nucleic Acid Circular Dichroism Database (NACDDB) is a public repository that archives and freely distributes circular dichroism (CD) and synchrotron radiation CD (SRCD) spectral data about nucleic acids, and the associated experimental metadata, structural models, and links to literature. NACDDB covers CD data for various nucleic acid molecules, including DNA, RNA, DNA/RNA hybrids, and various nucleic acid derivatives. The entries are linked to primary sequence and experimental structural data, as well as to the literature. Additionally, for all entries, 3D structure models are provided. All entries undergo expert validation and curation procedures to ensure completeness, consistency, and quality of the data included. The NACDDB is open for submission of the CD data for nucleic acids. NACDDB is available at: https://genesilico.pl/nacddb/.
Collapse
Affiliation(s)
| | | | - Sunandan Mukherjee
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, ul. Ks. Trojdena 4, PL-02-109 Warsaw, Poland
| | - S Naeim Moafinejad
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, ul. Ks. Trojdena 4, PL-02-109 Warsaw, Poland
| | - Richard R Sinden
- Department of Chemistry, Biology, and Health Sciences, South Dakota School of Mines and Technology, Rapid City, SD 57701, USA
| | | | | | - Frank Wien
- To whom correspondence should be addressed. Tel: +33 169359695;
| |
Collapse
|
26
|
Self-assembly and Hydrogelation Properties of Peptides Derived from Peptic Cleavage of Aggregation-prone Regions of Ovalbumin. Gels 2022; 8:gels8100641. [PMID: 36286142 PMCID: PMC9601990 DOI: 10.3390/gels8100641] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2022] [Revised: 09/15/2022] [Accepted: 10/01/2022] [Indexed: 11/04/2022] Open
Abstract
Egg white protein hydrolysate generated with pepsin was investigated for the presence of peptides with self-assembly and hydrogelation properties. Incubation of the hydrolysates for 16 h resulted in aggregates with significantly (p < 0.05) lower free amino nitrogen and sulfhydryl contents, and higher particle diameter and surface hydrophobicity compared to the hydrolysates. LC-MS/MS analysis of the aggregates resulted in identification of 429 ovalbumin-derived peptides, among which the top-six aggregation-prone peptides IFYCPIAIM, NIFYCPIAIM, VLVNAIVFKGL, YCPIAIMSA, MMYQIGLF, and VYSFSLASRL were predicted using AGGRESCAN by analysis of the aggregation “Hot Spots”. NIFYCPIAIM had the highest thioflavin T fluorescence intensity, particle diameter (5611.3 nm), and polydispersity index (1.0) after 24 h, suggesting the formation of β-sheet structures with heterogeneous particle size distribution. Transmission electron microscopy of MMYQIGLF, and VYSFSLASRL demonstrated the most favorable peptide self-assembly, based on the formation of densely packed, intertwined fibrils. Rheological studies confirmed the viscoelastic and mechanical properties of the hydrogels, with IFYCPIAIM, NIFYCPIAIM, VLVNAIVFKGL, and VYSFSLASRL forming elastic solid hydrogels (tan δ < 1), while YCPIAIMSA and MMYQIGLF formed viscous liquid-like hydrogels (tan δ > 1). The results provide valuable insight into the influence of peptide sequence on hydrogelation and self-assembly progression, and prospects of food peptides in biomaterial applications.
Collapse
|
27
|
Circular dichroism of biopharmaceutical proteins in a quality-regulated environment. J Pharm Biomed Anal 2022; 219:114945. [DOI: 10.1016/j.jpba.2022.114945] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 07/12/2022] [Accepted: 07/13/2022] [Indexed: 11/18/2022]
|
28
|
Birtles D, Oh AE, Lee J. Exploring the
pH
dependence of the
SARS‐CoV
‐2 complete fusion domain and the role of its unique structural features. Protein Sci 2022. [PMCID: PMC9538437 DOI: 10.1002/pro.4390] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
Abstract
SARS‐CoV‐2 may enter target cells through the process of membrane fusion at either the plasma (~pH 7.4–7.0) or endosomal (~pH 6.5–5.0) membrane in order to deliver its genetic information. The fusion domain (FD) of the spike glycoprotein is responsible for initiating fusion and is thus integral to the viral life cycle. The FD of SARS‐CoV‐2 is unique in that it consists of two structurally distinctive regions referred to as the fusion peptide (FP) and the fusion loop (FL); yet the molecular mechanisms behind how this FD perturbs the membrane to initiate fusion remains unclear. In this study via solution NMR, we witnessed only a slight conformational change in the FD between pH 7.4 and pH 5.0, resulting in a minor elongation of helix 1. However, we found that the FD's ability to mediate membrane fusion has a large and significant pH dependence, with fusion events being more readily induced at low pH. Interestingly, a biphasic relationship between the environmental pH and fusogenicity was discovered, suggesting a preference for the FD to initiate fusion at the late endosomal membrane. Furthermore, the conserved disulfide bond and hydrophobic motif “LLF” were found to be critical for the function of the complete FD, with minimal activity witnessed when either was perturbed. In conclusion, these findings indicate that the SARS‐CoV‐2 FD preferably initiates fusion at a pH similar to the late endosome through a mechanism that heavily relies on the internal disulfide bond of the FL and hydrophobic LLF motif within the FP.
Collapse
Affiliation(s)
- Daniel Birtles
- Department of Chemistry and Biochemistry University of Maryland College Park Maryland USA
| | - Anna E. Oh
- Department of Chemistry and Biochemistry University of Maryland College Park Maryland USA
| | - Jinwoo Lee
- Department of Chemistry and Biochemistry University of Maryland College Park Maryland USA
| |
Collapse
|
29
|
Lopes JLS, Araujo CCF, Neves RC, Bürck J, Couto SG. Structural analysis of the peptides temporin-Ra and temporin-Rb and interactions with model membranes. EUROPEAN BIOPHYSICS JOURNAL : EBJ 2022; 51:493-502. [PMID: 35978176 DOI: 10.1007/s00249-022-01615-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 07/27/2022] [Accepted: 07/31/2022] [Indexed: 06/15/2023]
Abstract
The skin of amphibians is widely exploited as rich sources of membrane active peptides that differ in chain size, polypeptide net charge, secondary structure, target selectivity and toxicity. In this study, two small antimicrobial peptides, temporin-Ra and temporin-Rb, originally isolated from the skin of the European marsh frog (Rana ridibunda), described as active against pathogen bacteria and presenting low toxicity to eukaryotic cells were synthesized and had their physicochemical properties and mechanism of action investigated. The temporin peptides were examined in aqueous solution and in the presence of membrane models (lipid monolayers, micelles, lipid bilayers and vesicles). A combined approach of bioinformatics analyses, biological activity assays, surface pressure measurements, synchrotron radiation circular dichroism spectroscopy, and oriented circular dichroism spectroscopy were employed. Both peptides were able to adsorb at a lipid-air interface with a negative surface charge density, and efficiently disturb the lipid surface packing. A disorder-to-helix transition was observed on the secondary structure of both peptides when either in a non-polar environment or interacting with model membranes containing a negative net charge density. The binding of both temporin-Ra and temporin-Rb to membrane models is modulated by the presence of negatively charged lipids in the membrane. The amphipathic helix induced in temporin-Ra is oriented parallel to the membrane surface in negatively charged or in zwitterionic lipid bilayers, with no tendency for realignment after binding. Temporin-Rb, instead, assumes a β-sheet conformation when deposited into oriented stacked lipid bilayers. Due to their short size and simple composition, both peptides are quite attractive for the development of new classes of peptide-based anti-infective drugs.
Collapse
Affiliation(s)
- José L S Lopes
- Instituto de Física, Universidade de São Paulo, São Paulo, SP, 05080-900, Brazil
| | - Caio C F Araujo
- Faculdade de Medicina, Universidade Federal de Goiás, Goiânia, GO, 74690-900, Brazil
| | - Rogério C Neves
- Instituto de Patologia Tropical E Saúde Pública, Universidade Federal de Goiás, Goiânia, GO, 74605050, Brazil
| | - Jochen Bürck
- Institute of Biological Interfaces (IBG-2), Karlsruhe Institute of Technology (KIT), POB 3640, 76021, Karlsruhe, Germany
| | - Sheila G Couto
- Instituto de Física, Universidade Federal de Goiás, Av. Esperança, s/n - Campus Samambaia, Goiânia, GO, 74690-900, Brazil.
| |
Collapse
|
30
|
Turbant F, Waeytens J, Campidelli C, Bombled M, Martinez D, Grélard A, Habenstein B, Raussens V, Velez M, Wien F, Arluison V. Unraveling Membrane Perturbations Caused by the Bacterial Riboregulator Hfq. Int J Mol Sci 2022; 23:ijms23158739. [PMID: 35955871 PMCID: PMC9369112 DOI: 10.3390/ijms23158739] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 08/01/2022] [Accepted: 08/02/2022] [Indexed: 12/02/2022] Open
Abstract
Hfq is a pleiotropic regulator that mediates several aspects of bacterial RNA metabolism. The protein notably regulates translation efficiency and RNA decay in Gram-negative bacteria, usually via its interaction with small regulatory RNAs. Previously, we showed that the Hfq C-terminal region forms an amyloid-like structure and that these fibrils interact with membranes. The immediate consequence of this interaction is a disruption of the membrane, but the effect on Hfq structure was unknown. To investigate details of the mechanism of interaction, the present work uses different in vitro biophysical approaches. We show that the Hfq C-terminal region influences membrane integrity and, conversely, that the membrane specifically affects the amyloid assembly. The reported effect of this bacterial master regulator on membrane integrity is discussed in light of the possible consequence on small regulatory RNA-based regulation.
Collapse
Affiliation(s)
- Florian Turbant
- Laboratoire Léon Brillouin LLB, CEA, CNRS UMR12, Université Paris Saclay, CEA Saclay, 91191 Gif-sur-Yvette, France
- Department of Molecular Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland
| | - Jehan Waeytens
- Structure et Fonction des Membranes Biologiques, Université Libre de Bruxelles, 1050 Bruxelles, Belgium
- Institut de Chimie Physique, CNRS UMR8000, Université Paris-Sud, Université Paris-Saclay, 91400 Orsay, France
| | - Camille Campidelli
- Laboratoire Léon Brillouin LLB, CEA, CNRS UMR12, Université Paris Saclay, CEA Saclay, 91191 Gif-sur-Yvette, France
| | - Marianne Bombled
- Laboratoire Léon Brillouin LLB, CEA, CNRS UMR12, Université Paris Saclay, CEA Saclay, 91191 Gif-sur-Yvette, France
| | - Denis Martinez
- Institute of Chemistry & Biology of Membranes & Nanoobjects (UMR5248 CBMN), University of Bordeaux, CNRS, Bordeaux INP, 33600 Pessac, France
| | - Axelle Grélard
- Institute of Chemistry & Biology of Membranes & Nanoobjects (UMR5248 CBMN), University of Bordeaux, CNRS, Bordeaux INP, 33600 Pessac, France
| | - Birgit Habenstein
- Institute of Chemistry & Biology of Membranes & Nanoobjects (UMR5248 CBMN), University of Bordeaux, CNRS, Bordeaux INP, 33600 Pessac, France
| | - Vincent Raussens
- Structure et Fonction des Membranes Biologiques, Université Libre de Bruxelles, 1050 Bruxelles, Belgium
| | - Marisela Velez
- Instituto de Catálisis y Petroleoquímica, CSIC, c/Marie Curie, 2, Cantoblanco, E-28049 Madrid, Spain
| | - Frank Wien
- Synchrotron SOLEIL, L’Orme des Merisiers, Saint Aubin BP48, 91192 Gif-sur-Yvette, France
- Correspondence: (F.W.); (V.A.)
| | - Véronique Arluison
- Laboratoire Léon Brillouin LLB, CEA, CNRS UMR12, Université Paris Saclay, CEA Saclay, 91191 Gif-sur-Yvette, France
- UFR SDV, Université Paris Cité, 75006 Paris, France
- Correspondence: (F.W.); (V.A.)
| |
Collapse
|
31
|
Renault JP, Huart L, Milosavljević AR, Bozek JD, Palaudoux J, Guigner JM, Marichal L, Leroy J, Wien F, Hervé Du Penhoat MA, Nicolas C. Electronic Structure and Solvation Effects from Core and Valence Photoelectron Spectroscopy of Serum Albumin. Int J Mol Sci 2022; 23:ijms23158227. [PMID: 35897833 PMCID: PMC9331649 DOI: 10.3390/ijms23158227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 07/20/2022] [Accepted: 07/21/2022] [Indexed: 12/07/2022] Open
Abstract
X-ray photoelectron spectroscopy of bovine serum albumin (BSA) in a liquid jet is used to investigate the electronic structure of a solvated protein, yielding insight into charge transfer mechanisms in biological systems in their natural environment. No structural damage was observed in BSA following X-ray photoelectron spectroscopy in a liquid jet sample environment. Carbon and nitrogen atoms in different chemical environments were resolved in the X-ray photoelectron spectra of both solid and solvated BSA. The calculations of charge distributions demonstrate the difficulty of assigning chemical contributions in complex systems in an aqueous environment. The high-resolution X-ray core electron spectra recorded are unchanged upon solvation. A comparison of the valence bands of BSA in both phases is also presented. These bands display a higher sensitivity to solvation effects. The ionization energy of the solvated BSA is determined at 5.7 ± 0.3 eV. Experimental results are compared with theoretical calculations to distinguish the contributions of various molecular components to the electronic structure. This comparison points towards the role of water in hole delocalization in proteins.
Collapse
Affiliation(s)
- Jean-Philippe Renault
- Université Paris-Saclay, CEA, CNRS, NIMBE, CEA Saclay, 91191 Gif-sur-Yvette, France; (L.H.); (L.M.); (J.L.)
- Correspondence: (J.-P.R.); (C.N.)
| | - Lucie Huart
- Université Paris-Saclay, CEA, CNRS, NIMBE, CEA Saclay, 91191 Gif-sur-Yvette, France; (L.H.); (L.M.); (J.L.)
- Synchrotron SOLEIL, 91192 Saint Aubin, France; (A.R.M.); (J.D.B.); (F.W.)
- Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, Sorbonne Université, UMR CNRS 7590, MNHN, 75252 Paris, France; (J.-M.G.); (M.-A.H.D.P.)
| | | | - John D. Bozek
- Synchrotron SOLEIL, 91192 Saint Aubin, France; (A.R.M.); (J.D.B.); (F.W.)
| | - Jerôme Palaudoux
- Laboratoire de Chimie Physique-Matière et Rayonnement, Sorbonne Université, UMR CNRS 7614, 75252 Paris, France;
| | - Jean-Michel Guigner
- Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, Sorbonne Université, UMR CNRS 7590, MNHN, 75252 Paris, France; (J.-M.G.); (M.-A.H.D.P.)
| | - Laurent Marichal
- Université Paris-Saclay, CEA, CNRS, NIMBE, CEA Saclay, 91191 Gif-sur-Yvette, France; (L.H.); (L.M.); (J.L.)
| | - Jocelyne Leroy
- Université Paris-Saclay, CEA, CNRS, NIMBE, CEA Saclay, 91191 Gif-sur-Yvette, France; (L.H.); (L.M.); (J.L.)
| | - Frank Wien
- Synchrotron SOLEIL, 91192 Saint Aubin, France; (A.R.M.); (J.D.B.); (F.W.)
| | - Marie-Anne Hervé Du Penhoat
- Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, Sorbonne Université, UMR CNRS 7590, MNHN, 75252 Paris, France; (J.-M.G.); (M.-A.H.D.P.)
| | - Christophe Nicolas
- Synchrotron SOLEIL, 91192 Saint Aubin, France; (A.R.M.); (J.D.B.); (F.W.)
- Correspondence: (J.-P.R.); (C.N.)
| |
Collapse
|
32
|
A new bioinspired peptide on defensin from C. annuum fruits: Antimicrobial activity, mechanisms of action and therapeutical potential. Biochim Biophys Acta Gen Subj 2022; 1866:130218. [PMID: 35905923 DOI: 10.1016/j.bbagen.2022.130218] [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: 04/26/2022] [Revised: 07/12/2022] [Accepted: 07/22/2022] [Indexed: 11/22/2022]
Abstract
BACKGROUND Antimicrobial peptides, natural or synthetic, appear as promising molecules for antimicrobial therapy because of their both broad antimicrobial activity and mechanism of action. Herein, we determine the anti-Candida and antimycobacterial activities, mechanism of action on yeasts, and cytotoxicity on mammalian cells in the presence of the bioinspired peptide CaDef2.1G27-K44. METHODS CaDef2.1G27-K44 was designed to attain the following criteria: high positive net charge; low molecular weight (<3000 Da); Boman index ≤2.5; and total hydrophobic ratio ≥ 40%. The mechanism of action was studied by growth inhibition, plasma membrane permeabilization, ROS induction, mitochondrial functionality, and metacaspase activity assays. The cytotoxicity on macrophages, monocytes, and erythrocytes were also determined. RESULTS CaDef2.1G27-K44 showed inhibitory activity against Candida spp. with MIC100 values ranging from 25 to 50 μM and the standard and clinical isolate of Mycobacterium tuberculosis with MIC50 of 33.2 and 55.4 μM, respectively. We demonstrate that CaDef2.1G27-K44 is active against yeasts at different salt concentrations, induced morphological alterations, caused membrane permeabilization, increased ROS, causes loss of mitochondrial functionality, and activation of metacaspases. CaDef2.1G27-K44 has low cytotoxicity against mammalian cells. CONCLUSIONS The results obtained showed that CaDef2.1G27-K44 has great antimicrobial activity against Candida spp. and M. tuberculosis with low toxicity to host cells. For Candida spp., the treatment with CaDef2.1G27-K44 induces a process of regulated cell death with apoptosis-like features. GENERAL SIGNIFICANCE We show a new AMP bioinspired with physicochemical characteristics important for selectivity and antimicrobial activity, which is a promising candidate for drug development, mainly to control Candida infections.
Collapse
|
33
|
Mameri H, Gaudin JC, Lollier V, Tranquet O, Brossard C, Pietri M, Marion D, Codreanu-Morel F, Beaudouin E, Wien F, Gohon Y, Briozzo P, Denery-Papini S. Critical structural elements for the antigenicity of wheat allergen LTP1 (Tri a 14) revealed by site-directed mutagenesis. Sci Rep 2022; 12:12253. [PMID: 35851276 PMCID: PMC9293932 DOI: 10.1038/s41598-022-15811-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Accepted: 06/29/2022] [Indexed: 11/09/2022] Open
Abstract
Lipid transfer proteins (LTPs) were identified as allergens in a large variety of pollens and foods, including cereals. LTPs belong to the prolamin superfamily and display an α-helical fold, with a bundle of four α-helices held together by four disulfide bonds. Wheat LTP1 is involved in allergic reactions to food. To identify critical structural elements of antibody binding to wheat LTP1, we used site-directed mutagenesis on wheat recombinant LTP1 to target: (i) sequence conservation and/or structure flexibility or (ii) each disulfide bond. We evaluated the modifications induced by these mutations on LTP1 secondary structure by synchrotron radiation circular dichroism and on its antigenicity with patient's sera and with mouse monoclonal antibodies. Disruption of the C28-C73 disulfide bond significantly affected IgE-binding and caused protein denaturation, while removing C13-C27 bond decreased LTP1 antigenicity and slightly modified LTP1 overall folding. In addition, we showed Lys72 to be a key residue; the K72A mutation did not affect global folding but modified the local 3D structure of LTP1 and strongly reduced IgE-binding. This work revealed a cluster of residues (C13, C27, C28, C73 and K72), four of which embedded in disulfide bonds, which play a critical role in LTP1 antigenicity.
Collapse
Affiliation(s)
- Hamza Mameri
- INRAE, UR 1268 Biopolymères Interactions Assemblages (BIA), 44316, Nantes, France. .,UMR 1208 IATE, Univ Montpellier, INRAE, L'Institut-Agro Montpellier, 34060, Montpellier, France.
| | - Jean-Charles Gaudin
- INRAE, UR 1268 Biopolymères Interactions Assemblages (BIA), 44316, Nantes, France.,INRAE, UMR 0588 Biologie intégrée pour la valorisation de la diversité des arbres et de la forêt (BIOFORA), 45075, Orléans, France
| | - Virginie Lollier
- INRAE, UR 1268 Biopolymères Interactions Assemblages (BIA), 44316, Nantes, France.,INRAE, UR BIA, 44316, Nantes, France.,INRAE, PROBE Research Infrastructure, BIBS Facility, 44316, Nantes, France
| | - Olivier Tranquet
- INRAE, UR 1268 Biopolymères Interactions Assemblages (BIA), 44316, Nantes, France.,INRAE UMR 1163 Biodiversité et Biotechnologie Fongiques (BBF), 13288, Marseille, France
| | - Chantal Brossard
- INRAE, UR 1268 Biopolymères Interactions Assemblages (BIA), 44316, Nantes, France
| | - Manon Pietri
- INRAE, UR 1268 Biopolymères Interactions Assemblages (BIA), 44316, Nantes, France.,Institut de Cancérologie de l'Ouest, Centre René Gauducheau, 44805, Saint Herblain Cedex, France
| | - Didier Marion
- INRAE, UR 1268 Biopolymères Interactions Assemblages (BIA), 44316, Nantes, France
| | - Fanny Codreanu-Morel
- CHU Luxembourg, Centre Hospitalier de Luxembourg, Kanner Klinik, 1210, Luxembourg, Luxembourg
| | - Etienne Beaudouin
- Service d'Allergologie, Hôpital de Mercy, CHR Metz, 57000, Metz, France
| | - Frank Wien
- Synchrotron Soleil, Saint-Aubin, 91192, Gif-sur-Yvette, France
| | - Yann Gohon
- INRAE, UMR 1318 Institut Jean-Pierre Bourgin, 78026, Versailles, France
| | - Pierre Briozzo
- INRAE, UMR 1318 Institut Jean-Pierre Bourgin, 78026, Versailles, France
| | - Sandra Denery-Papini
- INRAE, UR 1268 Biopolymères Interactions Assemblages (BIA), 44316, Nantes, France.
| |
Collapse
|
34
|
A “traffic jam” of (+)-catechin caused by hyperglycemia — The interaction between (+)-catechin and human serum albumin (HSA) in high glucose environment. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.118975] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
|
35
|
Sutinen A, Nguyen GTT, Raasakka A, Muruganandam G, Loris R, Ylikallio E, Tyynismaa H, Bartesaghi L, Ruskamo S, Kursula P. Structural insights into Charcot-Marie-Tooth disease-linked mutations in human GDAP1. FEBS Open Bio 2022; 12:1306-1324. [PMID: 35509130 PMCID: PMC9249340 DOI: 10.1002/2211-5463.13422] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 04/25/2022] [Accepted: 05/03/2022] [Indexed: 11/11/2022] Open
Abstract
Charcot-Marie-Tooth disease (CMT) is the most common inherited peripheral polyneuropathy in humans, and its different subtypes are linked to mutations in dozens of different genes. Mutations in ganglioside-induced differentiation-associated protein 1 (GDAP1) cause two types of CMT, demyelinating CMT4A and axonal CMT2K. The GDAP1-linked CMT genotypes are mainly missense point mutations. Despite clinical profiling and in vivo studies on the mutations, the etiology of GDAP1-linked CMT is poorly understood. Here, we describe the biochemical and structural properties of the Finnish founding CMT2K mutation H123R as well as CMT2K-linked R120W, both of which are autosomal dominant mutations. The disease variant proteins retain close to normal structure and solution behaviour, but both present a significant decrease in thermal stability. Using GDAP1 variant crystal structures, we identify a side chain interaction network between helices ⍺3, ⍺6, and ⍺7, which is affected by CMT mutations, as well as a hinge in the long helix ⍺6, which is linked to structural flexibility. Structural analysis of GDAP1 indicates that CMT may arise from disruption of specific intra- and intermolecular interaction networks, leading to alterations in GDAP1 structure and stability, and eventually, insufficient motor and sensory neuron function.
Collapse
Affiliation(s)
- Aleksi Sutinen
- Faculty of Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, Finland
| | - Giang Thi Tuyet Nguyen
- Faculty of Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, Finland
| | - Arne Raasakka
- Department of Biomedicine, University of Bergen, Norway
| | - Gopinath Muruganandam
- VIB-VUB Center for Structural Biology, Vlaams Instituut voor Biotechnologie, Brussels, Belgium.,Structural Biology Brussels, Department of Bioengineering Sciences, Vrije Universiteit Brussel, Belgium
| | - Remy Loris
- VIB-VUB Center for Structural Biology, Vlaams Instituut voor Biotechnologie, Brussels, Belgium.,Structural Biology Brussels, Department of Bioengineering Sciences, Vrije Universiteit Brussel, Belgium
| | - Emil Ylikallio
- Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, Finland.,Clinical Neurosciences, Helsinki University Hospital, Neurology, Finland
| | - Henna Tyynismaa
- Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, Finland
| | | | - Salla Ruskamo
- Faculty of Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, Finland
| | - Petri Kursula
- Faculty of Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, Finland.,Department of Biomedicine, University of Bergen, Norway
| |
Collapse
|
36
|
Kind L, Raasakka A, Molnes J, Aukrust I, Bjørkhaug L, Njølstad PR, Kursula P, Arnesen T. Structural and biophysical characterization of transcription factor HNF-1A as a tool to study MODY3 diabetes variants. J Biol Chem 2022; 298:101803. [PMID: 35257744 PMCID: PMC8988010 DOI: 10.1016/j.jbc.2022.101803] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 02/15/2022] [Accepted: 02/20/2022] [Indexed: 11/05/2022] Open
Abstract
Hepatocyte nuclear factor 1A (HNF-1A) is a transcription factor expressed in several embryonic and adult tissues, modulating the expression of numerous target genes. Pathogenic variants in the HNF1A gene are known to cause maturity-onset diabetes of the young 3 (MODY3 or HNF1A MODY), a disease characterized by dominant inheritance, age of onset before 25 to 35 years of age, and pancreatic β-cell dysfunction. A precise diagnosis can alter management of this disease, as insulin can be exchanged with sulfonylurea tablets and genetic counseling differs from polygenic forms of diabetes. Therefore, more knowledge on the mechanisms of HNF-1A function and the level of pathogenicity of the numerous HNF1A variants is required for precise diagnostics. Here, we structurally and biophysically characterized an HNF-1A protein containing both the DNA-binding domain and the dimerization domain, and determined the folding and DNA-binding capacity of two established MODY3 HNF-1A variant proteins (P112L, R263C) and one variant of unknown significance (N266S). All three variants showed reduced functionality compared to the WT protein. Furthermore, while the R263C and N266S variants displayed reduced binding to an HNF-1A target promoter, we found the P112L variant was unstable in vitro and in cells. Our results support and mechanistically explain disease causality for these investigated variants and present a novel approach for the dissection of structurally unstable and DNA-binding defective variants. This study indicates that structural and biochemical investigation of HNF-1A is a valuable tool in reliable variant classification needed for precision diabetes diagnostics and management.
Collapse
Affiliation(s)
- Laura Kind
- Department of Biomedicine, University of Bergen, Bergen, Norway.
| | - Arne Raasakka
- Department of Biomedicine, University of Bergen, Bergen, Norway
| | - Janne Molnes
- Center for Diabetes Research, Department of Clinical Science, University of Bergen, Bergen, Norway; Department of Medical Genetics, Haukeland University Hospital, Bergen, Norway
| | - Ingvild Aukrust
- Center for Diabetes Research, Department of Clinical Science, University of Bergen, Bergen, Norway; Department of Medical Genetics, Haukeland University Hospital, Bergen, Norway
| | - Lise Bjørkhaug
- Department of Safety, Chemistry, and Biomedical Laboratory Sciences, Western Norway University of Applied Sciences, Bergen, Norway
| | - Pål Rasmus Njølstad
- Center for Diabetes Research, Department of Clinical Science, University of Bergen, Bergen, Norway; Section of Endocrinology and Metabolism, Children and Youth Clinic, Haukeland University Hospital, Bergen, Norway.
| | - Petri Kursula
- Department of Biomedicine, University of Bergen, Bergen, Norway; Faculty of Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Thomas Arnesen
- Department of Biomedicine, University of Bergen, Bergen, Norway; Department of Biological Sciences, University of Bergen, Bergen, Norway; Department of Surgery, Haukeland University Hospital, Bergen, Norway.
| |
Collapse
|
37
|
Synchrotron Radiation Circular Dichroism, a New Tool to Probe Interactions between Nucleic Acids Involved in the Control of ColE1-Type Plasmid Replication. APPLIED SCIENCES-BASEL 2022. [DOI: 10.3390/app12052639] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/10/2022]
Abstract
Hfq is a bacterial master regulator which promotes the pairing of nucleic acids. Due to the high molecular weight of the complexes formed between nucleic acids and the amyloid form of the protein, it is difficult to analyze solely by a gel shift assay the complexes formed, as they all migrate at the same position in the gel. In addition, precise kinetics measurements are not possible using a gel shift assay. Here, we used a synchrotron-based biophysical approach, synchrotron radiation circular dichroism (SRCD), to probe the interaction of the Escherichia coli Hfq C-terminal amyloid region with nucleic acids involved in the control of ColE1-like plasmid replication. We observed that this C-terminal region of Hfq has an unexpected and significant effect on the annealing of nucleic acids involved in this process and, more importantly, on their alignment. Functional consequences of this newly discovered property of the Hfq amyloid region are discussed in terms of the biological significance of Hfq in the ColE1-type plasmid replication process and antibiotic resistance.
Collapse
|
38
|
Disaggregation of Islet Amyloid Polypeptide Fibrils as a Potential Anti-Fibrillation Mechanism of Tetrapeptide TNGQ. Int J Mol Sci 2022; 23:ijms23041972. [PMID: 35216095 PMCID: PMC8876742 DOI: 10.3390/ijms23041972] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 02/04/2022] [Accepted: 02/08/2022] [Indexed: 11/17/2022] Open
Abstract
Islet amyloid polypeptide (IAPP) fibrillation has been commonly associated with the exacerbation of type 2 diabetes prognosis. Consequently, inhibition of IAPP fibrillation to minimize β-cell cytotoxicity is an important approach towards β-cell preservation and type 2 diabetes management. In this study, we identified three tetrapeptides, TNGQ, MANT, and YMSV, that inhibited IAPP fibrillation. Using thioflavin T (ThT) fluorescence assay, circular dichroism (CD) spectroscopy, dynamic light scattering (DLS), and molecular docking, we evaluated the potential anti-fibrillation mechanism of the tetrapeptides. ThT fluorescence kinetics and microscopy as well as transmission electron microscopy showed that TNGQ was the most effective inhibitor based on the absence of normal IAPP fibrillar morphology. CD spectroscopy showed that TNGQ maintained the α-helical conformation of monomeric IAPP, while DLS confirmed the presence of varying fibrillation species. Molecular docking showed that TNGQ and MANT interact with monomeric IAPP mainly by hydrogen bonding and electrostatic interaction, with TNGQ binding at IAPP surface compared to YMSV, which had the highest docking score, but interact mainly through hydrophobic interaction in IAPP core. The highly polar TNGQ was the most active and appeared to inhibit IAPP fibrillation by disaggregation of preformed IAPP fibrils. These findings indicate the potential of TNGQ in the development of peptide-based anti-fibrillation and antidiabetic nutraceuticals.
Collapse
|
39
|
Gomes Ramalli S, John Miles A, Janes RW, Wallace BA. The PCDDB (Protein Circular Dichroism Data Bank): A Bioinformatics Resource for Protein Characterisations and Methods Development. J Mol Biol 2022; 434:167441. [PMID: 34999124 DOI: 10.1016/j.jmb.2022.167441] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2021] [Revised: 12/19/2021] [Accepted: 01/01/2022] [Indexed: 12/20/2022]
Abstract
The Protein Circular Dichroism Data Bank (PCDDB) [https://pcddb.cryst.bbk.ac.uk] is an established resource for the biological, biophysical, chemical, bioinformatics, and molecular biology communities. It is a freely-accessible repository of validated protein circular dichroism (CD) spectra and associated sample and other metadata, with entries having links to other bioinformatics resources including, amongst others, structure (PDB) and sequence (UniProt) databases, as well as to published papers which produced the data and cite the database entries. It includes primary (unprocessed) and final (processed) spectral data, which are available in both text and pictorial formats, as well as detailed sample and validation information produced for each of the entries. Recently the metadata content associated with each of the entries, as well as the number and structural breadth of the protein components included, have been expanded. The PCDDB includes data on both wild-type and mutant proteins, and because CD studies primarily examine proteins in solution, it also contains examples of the effects of different environments on their structures, plus thermal unfolding/folding series. Methods for both sequence and spectral comparisons are included. The data included in the PCDDB complement results from crystal, cryo-electron microscopy, NMR spectroscopy, bioinformatics characterisations and classifications, and other structural information available for the proteins via links to other databases. The entries in the PCDDB have been used for the development of new analytical methodologies, for interpreting spectral and other biophysical data, and for providing insight into structures and functions of individual soluble and membrane proteins and protein complexes.
Collapse
Affiliation(s)
- Sergio Gomes Ramalli
- Institute of Structural and Molecular Biology, Birkbeck, University of London, Malet Street, London WC1E 7HX, UK
| | - Andrew John Miles
- Institute of Structural and Molecular Biology, Birkbeck, University of London, Malet Street, London WC1E 7HX, UK
| | - Robert W Janes
- School of Biological and Behavioural Sciences, Queen Mary University of London, London E1 4NS, UK.
| | - B A Wallace
- Institute of Structural and Molecular Biology, Birkbeck, University of London, Malet Street, London WC1E 7HX, UK.
| |
Collapse
|
40
|
Waeytens J, Turbant F, Arluison V, Raussens V, Wien F. Analysis of Bacterial Amyloid Interaction with Lipidic Membrane by Orientated Circular Dichroism and Infrared Spectroscopies. Methods Mol Biol 2022; 2538:217-234. [PMID: 35951303 DOI: 10.1007/978-1-0716-2529-3_15] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Fourier transform infrared spectroscopy (FTIR), circular dichroism (CD), and orientated circular dichroism (OCD) are complementary spectroscopies widely used for the analysis of protein samples such as the amyloids commonly renowned as neurodegenerative agents. Determining the secondary structure content of proteins, such as aggregated β-sheets inside the amyloids and in various environments, including membranes and lipids, has made these techniques very valuable and complemental to high-resolution techniques such as nuclear magnetic resonance (NMR), X-ray crystallography, and cryo-electron microscopy. FTIR and CD are extremely sensitive to structural changes of proteins due to environmental changes. Furthermore, FTIR provides information on lipid modifications upon protein binding, whereas synchrotron radiation CD (SRCD) and OCD are sensitive to the subtle structural changes occurring in β-sheet-rich proteins and their orientation or alignment with lipid bilayers. FTIR and CD techniques allow the identification of parallel and antiparallel β-sheet content and are therefore complementary. In this chapter, we present FTIR and CD/OCD applications to study the interactions of bacterial amyloids with membranes and lipids. Moreover, we show how to decipher the spectroscopic signals to obtain information on the molecular structure of amyloids and their interaction with lipids, addressing potential amyloid insertion into membranes and the lipid bilayer adjustments observed.
Collapse
Affiliation(s)
- Jehan Waeytens
- Centre de Biologie structurale et de Bioinformatique, Structure et Fonction des Membranes Biologiques, Université libre de Bruxelles, Bruxelles, Belgium
- Institut de Chimie Physique, CNRS UMR8000, Université Paris-Sud, Université Paris-Saclay, Orsay, France
| | - Florian Turbant
- Laboratoire Léon Brillouin LLB, CEA, CNRS UMR12, Université Paris Saclay, Gif-sur-Yvette, France
| | - Véronique Arluison
- Laboratoire Léon Brillouin LLB, CEA, CNRS UMR12, Université Paris Saclay, Gif-sur-Yvette, France
- Université de Paris Cité, Paris, France
| | - Vincent Raussens
- Centre de Biologie structurale et de Bioinformatique, Structure et Fonction des Membranes Biologiques, Université libre de Bruxelles, Bruxelles, Belgium.
| | - Frank Wien
- Synchrotron SOLEIL, L'Orme des Merisiers, Gif-sur-Yvette, France.
| |
Collapse
|
41
|
Busi F, Turbant F, Waeytens J, El Hamoui O, Wien F, Arluison V. Evaluation of Amyloid Inhibitor Efficiency to Block Bacterial Survival. Methods Mol Biol 2022; 2538:145-163. [PMID: 35951299 DOI: 10.1007/978-1-0716-2529-3_11] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Amyloid inhibitors, such as the green tea compound epigallocatechin gallate EGCG, apomorphine or curlicide, have antibacterial properties. Conversely, antibiotics such as tetracycline derivatives or rifampicin also affect eukaryotic amyloids formation and may be used to treat neurodegenerative diseases. This opens the possibility for existing drugs to be repurposed in view of new therapy, targeting amyloid-like proteins from eukaryotes to prokaryotes and conversely. Here we present how to evaluate the effect of these amyloid-forming inhibitors on bacterial amyloid self-assemblies in vitro and on bacterial survival. The different approaches possible are presented.
Collapse
Affiliation(s)
- Florent Busi
- Université Paris Cité, BFA, UMR 8251, CNRS, Paris, France.
- Université Paris Cité, Paris, France.
| | - Florian Turbant
- Laboratoire Léon Brillouin LLB, CEA, CNRS UMR 12, Université Paris Saclay, CEA Saclay, Gif-sur-Yvette, France
| | - Jehan Waeytens
- Structure et Fonction des Membranes Biologiques, Université libre de Bruxelles, Bruxelles, Belgium
- Institut de Chimie Physique, CNRS UMR8000, Université Paris-Sud, Université Paris-Saclay, Orsay, France
| | - Omar El Hamoui
- DISCO Beamline, Synchrotron SOLEIL, L'Orme des Merisiers Saint Aubin, Gif-sur-Yvette, France
| | - Frank Wien
- DISCO Beamline, Synchrotron SOLEIL, L'Orme des Merisiers Saint Aubin, Gif-sur-Yvette, France
| | - Véronique Arluison
- Université Paris Cité, Paris, France
- Laboratoire Léon Brillouin LLB, CEA, CNRS UMR 12, Université Paris Saclay, CEA Saclay, Gif-sur-Yvette, France
| |
Collapse
|
42
|
Caillaud M, Gobeaux F, Hémadi M, Boutary S, Guenoun P, Desmaële D, Couvreur P, Wien F, Testard F, Massaad-Massade L. Supramolecular organization and biological interaction of squalenoyl siRNA nanoparticles. Int J Pharm 2021; 609:121117. [PMID: 34562556 DOI: 10.1016/j.ijpharm.2021.121117] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Revised: 09/15/2021] [Accepted: 09/16/2021] [Indexed: 12/14/2022]
Abstract
Small interfering RNAs (siRNA) are attractive and powerful tools to inhibit the expression of a targeted gene. However, their extreme hydrophilicities combined with a negative charge and short plasma half-life counteract their use as therapeutics. Previously, we chemically linked siRNA to squalene (SQ) which self-assembled as nanoparticles (NPs) with pharmacological efficiency in cancers and recently in a hereditary neuropathy. In order to understand the siRNA-SQ NP assembly and fate once intravenously injected, the present study detailed characterization of siRNA-SQ NP structure and its interaction with serum components. From SAXS and SANS analysis, we propose that the siRNA-SQ bioconjugate self-assembled as 11-nm diameter supramolecular assemblies, which are connected one to another to form spherical nanoparticles of around 130-nm diameter. The siRNA-SQ NPs were stable in biological media and interacted with serum components, notably with albumin and LDL. The high specificity of siRNA to decrease or normalize gene expression and the high colloidal stability when encapsulated into squalene nanoparticles offer promising targeted therapy with wide applications for pathologies with gene expression dysregulation.
Collapse
Affiliation(s)
- Marie Caillaud
- U1195 Diseases and Hormones of the Nervous System, INSERM U1195 and University Paris-Saclay, 94276 Le Kremlin-Bicêtre, France
| | - Frédéric Gobeaux
- Université Paris-Saclay, CEA, CNRS, NIMBE, LIONS, 91191 Gif-sur-Yvette, France
| | - Miryana Hémadi
- Université de Paris, CNRS-UMR 7086, Interfaces, Traitements, Organisation et DYnamique des Systèmes (ITODYS), UFR de Chimie, 75013 Paris, France
| | - Suzan Boutary
- U1195 Diseases and Hormones of the Nervous System, INSERM U1195 and University Paris-Saclay, 94276 Le Kremlin-Bicêtre, France
| | - Patrick Guenoun
- Université Paris-Saclay, CEA, CNRS, NIMBE, LIONS, 91191 Gif-sur-Yvette, France
| | - Didier Desmaële
- Institut Galien Paris-Saclay, CNRS UMR 8612, Université Paris-Saclay, 92290 Châtenay-Malabry, France
| | - Patrick Couvreur
- Institut Galien Paris-Saclay, CNRS UMR 8612, Université Paris-Saclay, 92290 Châtenay-Malabry, France
| | | | - Fabienne Testard
- Université Paris-Saclay, CEA, CNRS, NIMBE, LIONS, 91191 Gif-sur-Yvette, France
| | - Liliane Massaad-Massade
- U1195 Diseases and Hormones of the Nervous System, INSERM U1195 and University Paris-Saclay, 94276 Le Kremlin-Bicêtre, France.
| |
Collapse
|
43
|
Moro-Pérez L, Lozada-Chang SL, Rivas-García G, Álvarez C, Rojas-Pérez L, Boggiano-Ayo T, González-González Y. Purification and Conformational Characterization of a Novel Interleukin-2 Mutein. Protein J 2021; 40:917-928. [PMID: 34643845 DOI: 10.1007/s10930-021-10025-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/01/2021] [Indexed: 11/29/2022]
Abstract
Toxicity of high-dose IL-2-based therapies have motivated the development of the IL-2 mutein, which has low expansion properties for regulatory T lymphocytes. The development of two variants (A and B) for the IL-2 mutein purification as well as a conformational comparative study by Circular dichroism (CD) and fluorescence spectroscopy of these products were evaluated. For the first time, in our center, were used of DTT and 2% SDS in the solubilization step to decrease the aggregates on intermediate product, which favors that disulfide bridges are correctly formed during re-folding. A molecular weight of 18 kDa to the monomeric form and of 25-37 kDa to the oligomeric species were estimated by SDS-PAGE. IL-2 mutein showed similar far-UV CD spectral characteristic typical of cytokines with 41% of α-helix content. Batches obtained by Process B showed similar conformational features according near-UV CD and FS studies. However, those obtained by Process A differed in their folding. IL-2 mutein showed that conformational features by near-UV CD were affected by 2% SDS, no variations on secondary structure were observed. Melting temperature values by far-UV CD were higher than 95 °C, indicating a high thermal stability. Finally, the drug product obtained by Process B showed similar conformational characteristics by near-UV CD and FS, and higher biological activity values (7.0 × 103 ng/mL) in the cell proliferation assay with respect to Process A. Also, the recovery was 15% higher than in the Process A and exhibited a 78.48% of purity. Indeed, Process B was selected for the purification.
Collapse
Affiliation(s)
- Leina Moro-Pérez
- Bioprocess R&D Department, Center of Molecular Immunology, 216 Street and 15 Avenue, Atabey, Playa, P.O. Box 16040, 11600, Havana, Cuba.
| | - Sum Lai Lozada-Chang
- Bioprocess R&D Department, Center of Molecular Immunology, 216 Street and 15 Avenue, Atabey, Playa, P.O. Box 16040, 11600, Havana, Cuba
| | - Gabriela Rivas-García
- Center of Molecular Immunology, Quality Control Direction, 216 Street and 15 Avenue, Atabey, Playa, P.O. Box 16040, 11600, Havana, Cuba
| | - Carlos Álvarez
- Biology Faculty, Center for Protein Studies, University of Havana, 25 St. No. 455, Vedado, 10400, Havana, Cuba
| | - Laritza Rojas-Pérez
- Biology Faculty, Center for Protein Studies, University of Havana, 25 St. No. 455, Vedado, 10400, Havana, Cuba
| | - Tammy Boggiano-Ayo
- Bioprocess R&D Department, Center of Molecular Immunology, 216 Street and 15 Avenue, Atabey, Playa, P.O. Box 16040, 11600, Havana, Cuba
| | - Yamile González-González
- Center of Molecular Immunology, EPOVAC Facility, 216 Street and 15 Avenue, Atabey, Playa, P.O. Box 16040, 11600, Havana, Cuba
| |
Collapse
|
44
|
Banerjee R, Sheet T, Banerjee S, Biondi B, Formaggio F, Toniolo C, Peggion C. C α-Methyl-l-valine: A Preferential Choice over α-Aminoisobutyric Acid for Designing Right-Handed α-Helical Scaffolds. Biochemistry 2021; 60:2704-2714. [PMID: 34463474 DOI: 10.1021/acs.biochem.1c00340] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
In synthetic peptides containing Gly and coded α-amino acids, one of the most common practices to enhance their helical extent is to incorporate a large number of l-Ala residues along with noncoded, strongly foldameric α-aminoisobutyric acid (Aib) units. Earlier studies have established that Aib-based peptides, with propensity for both the 310- and α-helices, have a tendency to form ordered three-dimensional structure that is much stronger than that exhibited by their l-Ala rich counterparts. However, the achiral nature of Aib induces an inherent, equal preference for the right- and left-handed helical conformations as found in Aib homopeptide stretches. This property poses challenges in the analysis of a model peptide helical conformation based on chirospectroscopic techniques like electronic circular dichroism (ECD), a very important tool for assigning secondary structures. To overcome such ambiguity, we have synthesized and investigated a thermally stable 14-mer peptide in which each of the Aib residues of our previously designed and reported analogue ABGY (where B stands for Aib) is replaced by Cα-methyl-l-valine (L-AMV). Analysis of the results described here from complementary ECD and 1H nuclear magnetic resonance spectroscopic techniques in a variety of environments firmly establishes that the L-AMV-containing peptide exhibits a significantly stronger preference compared to that of its Aib parent in terms of conferring α-helical character. Furthermore, being a chiral α-amino acid, L-AMV shows an intrinsic, extremely strong bias for a quite specific (right-handed) screw sense. These findings emphasize the relevance of L-AMV as a more appropriate unit for the design of right-handed α-helical peptide models that may be utilized as conformationally constrained scaffolds.
Collapse
Affiliation(s)
| | | | | | - Barbara Biondi
- Department of Chemical Sciences, University of Padova, 35131 Padova, Italy.,Institute of Biomolecular Chemistry, Padova Unit, CNR, 35131 Padova, Italy
| | - Fernando Formaggio
- Department of Chemical Sciences, University of Padova, 35131 Padova, Italy.,Institute of Biomolecular Chemistry, Padova Unit, CNR, 35131 Padova, Italy
| | - Claudio Toniolo
- Department of Chemical Sciences, University of Padova, 35131 Padova, Italy.,Institute of Biomolecular Chemistry, Padova Unit, CNR, 35131 Padova, Italy
| | - Cristina Peggion
- Department of Chemical Sciences, University of Padova, 35131 Padova, Italy.,Institute of Biomolecular Chemistry, Padova Unit, CNR, 35131 Padova, Italy
| |
Collapse
|
45
|
Turbant F, Wu P, Wien F, Arluison V. The Amyloid Region of Hfq Riboregulator Promotes DsrA: rpoS RNAs Annealing. BIOLOGY 2021; 10:biology10090900. [PMID: 34571778 PMCID: PMC8468756 DOI: 10.3390/biology10090900] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 08/30/2021] [Accepted: 09/05/2021] [Indexed: 11/16/2022]
Abstract
Hfq is a bacterial RNA chaperone which promotes the pairing of small noncoding RNAs to target mRNAs, allowing post-transcriptional regulation. This RNA annealing activity has been attributed for years to the N-terminal region of the protein that forms a toroidal structure with a typical Sm-fold. Nevertheless, many Hfqs, including that of Escherichia coli, have a C-terminal region with unclear functions. Here we use a biophysical approach, Synchrotron Radiation Circular Dichroism (SRCD), to probe the interaction of the E. coli Hfq C-terminal amyloid region with RNA and its effect on RNA annealing. This C-terminal region of Hfq, which has been described to be dispensable for sRNA:mRNA annealing, has an unexpected and significant effect on this activity. The functional consequences of this novel property of the amyloid region of Hfq in relation to physiological stress are discussed.
Collapse
Affiliation(s)
- Florian Turbant
- Laboratoire Léon Brillouin LLB, CEA, CNRS UMR12, Université Paris Saclay, CEA Saclay, 91191 Gif-sur-Yvette, France;
| | - Pengzhi Wu
- Department of Biology, ETH Zürich, 8093 Zürich, Switzerland;
| | - Frank Wien
- Synchrotron SOLEIL, L’Orme des Merisiers, Saint Aubin BP48, 91192 Gif-sur-Yvette, France
- Correspondence: (F.W.); or (V.A.); Tel.: +33-(0)169359665 (F.W.); +33-(0)169083282 (V.A.)
| | - Véronique Arluison
- Laboratoire Léon Brillouin LLB, CEA, CNRS UMR12, Université Paris Saclay, CEA Saclay, 91191 Gif-sur-Yvette, France;
- UFR Sciences du Vivant, Université de Paris, 75006 Paris, France
- Correspondence: (F.W.); or (V.A.); Tel.: +33-(0)169359665 (F.W.); +33-(0)169083282 (V.A.)
| |
Collapse
|
46
|
Chen G, Zhou J, Zuo Y, Huo W, Peng J, Li M, Zhang Y, Wang T, Zhang L, Zhang L, Liang H. Structural basis for diguanylate cyclase activation by its binding partner in Pseudomonas aeruginosa. eLife 2021; 10:67289. [PMID: 34498587 PMCID: PMC8457831 DOI: 10.7554/elife.67289] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2021] [Accepted: 09/08/2021] [Indexed: 12/21/2022] Open
Abstract
Cyclic-di-guanosine monophosphate (c-di-GMP) is an important effector associated with acute-chronic infection transition in Pseudomonas aeruginosa. Previously, we reported a signaling network SiaABCD, which regulates biofilm formation by modulating c-di-GMP level. However, the mechanism for SiaD activation by SiaC remains elusive. Here we determine the crystal structure of SiaC-SiaD-GpCpp complex and revealed a unique mirror symmetric conformation: two SiaD form a dimer with long stalk domains, while four SiaC bind to the conserved motifs on the stalks of SiaD and stabilize the conformation for further enzymatic catalysis. Furthermore, SiaD alone exhibits an inactive pentamer conformation in solution, demonstrating that SiaC activates SiaD through a dynamic mechanism of promoting the formation of active SiaD dimers. Mutagenesis assay confirmed that the stalks of SiaD are necessary for its activation. Together, we reveal a novel mechanism for DGC activation, which clarifies the regulatory networks of c-di-GMP signaling.
Collapse
Affiliation(s)
- Gukui Chen
- Key Laboratory of Resources Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, ShaanXi, China
| | - Jiashen Zhou
- Department of Pharmacology and Chemical Biology, Shanghai Jiao Tong University, School of Medicine, Shanghai, China
| | - Yili Zuo
- Key Laboratory of Resources Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, ShaanXi, China
| | - Weiping Huo
- Key Laboratory of Resources Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, ShaanXi, China
| | - Juan Peng
- Key Laboratory of Resources Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, ShaanXi, China
| | - Meng Li
- Key Laboratory of Resources Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, ShaanXi, China
| | - Yani Zhang
- Key Laboratory of Resources Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, ShaanXi, China
| | - Tietao Wang
- Key Laboratory of Resources Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, ShaanXi, China
| | - Lin Zhang
- Department of Pharmacology and Chemical Biology, Shanghai Jiao Tong University, School of Medicine, Shanghai, China
| | - Liang Zhang
- Department of Pharmacology and Chemical Biology, Shanghai Jiao Tong University, School of Medicine, Shanghai, China
| | - Haihua Liang
- Key Laboratory of Resources Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, ShaanXi, China.,School of Medicine, Southern University of Science and Technology, Shenzhen, China
| |
Collapse
|
47
|
Miles AJ, Janes RW, Wallace BA. Tools and methods for circular dichroism spectroscopy of proteins: a tutorial review. Chem Soc Rev 2021; 50:8400-8413. [PMID: 34132259 PMCID: PMC8328188 DOI: 10.1039/d0cs00558d] [Citation(s) in RCA: 96] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Indexed: 12/31/2022]
Abstract
Circular dichroism (CD) spectroscopy is a widely-used method in biochemistry, structural biology and pharmaceutical chemistry. More than 24 000 papers published in the past decade have included CD characterisations of proteins; many of those studies have also included other complementary chemical, biophysical, and computational chemistry methods. This tutorial review describes the background to the technique of CD spectroscopy and good practice methods for high quality data collection. It specifically focuses on both established and new methods and tools available for experimental design and interpretation, data processing, visualisation, analysis, validation, archiving, and accession, including tools developed to enhance the complementarity of this method with other structural and chemical biology studies.
Collapse
Affiliation(s)
- A. J. Miles
- Institute of Structural and Molecular Biology, Birkbeck University of LondonLondon WC1E 7HXUK
| | - Robert W. Janes
- School of Biological and Chemical Sciences, Queen Mary University of LondonLondon E1 4NSUK
| | - B. A. Wallace
- Institute of Structural and Molecular Biology, Birkbeck University of LondonLondon WC1E 7HXUK
| |
Collapse
|
48
|
Miles AJ, Ramalli SG, Wallace BA. DichroWeb, a website for calculating protein secondary structure from circular dichroism spectroscopic data. Protein Sci 2021; 31:37-46. [PMID: 34216059 PMCID: PMC8740839 DOI: 10.1002/pro.4153] [Citation(s) in RCA: 197] [Impact Index Per Article: 65.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 06/17/2021] [Accepted: 06/22/2021] [Indexed: 11/06/2022]
Abstract
Circular dichroism (CD) spectroscopy is a widely‐used method for characterizing the secondary structures of proteins. The well‐established and highly used analysis website, DichroWeb (located at: http://dichroweb.cryst.bbk.ac.uk/html/home.shtml) enables the facile quantitative determination of helix, sheet, and other secondary structure contents of proteins based on their CD spectra. DichroWeb includes a range of reference datasets and algorithms, plus graphical and quantitative methods for determining the quality of the analyses produced. This article describes the current website content, usage and accessibility, as well as the many upgraded features now present in this highly popular tool that was originally created nearly two decades ago.
Collapse
Affiliation(s)
- Andrew J Miles
- Institute of Structural and Molecular Biology, Birkbeck University of London, London, UK
| | - Sergio G Ramalli
- Institute of Structural and Molecular Biology, Birkbeck University of London, London, UK
| | - B A Wallace
- Institute of Structural and Molecular Biology, Birkbeck University of London, London, UK
| |
Collapse
|
49
|
Effect of setting data collection parameters on the reliability of a circular dichroism spectrum. EUROPEAN BIOPHYSICS JOURNAL : EBJ 2021; 50:687-697. [PMID: 33538870 DOI: 10.1007/s00249-021-01499-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Revised: 11/12/2020] [Accepted: 01/13/2021] [Indexed: 10/22/2022]
Abstract
Circular dichroism (CD) spectroscopy is a well-established biophysical technique used to investigate the structure of molecules. The analysis of a protein CD spectrum depends on the quality of the original CD data, which can be affected by the sample purity, background absorption of the additives/solvent/buffer, the choice of the parameters used for data collection, etc. In this paper, the CD spectrum of myoglobin was used as a model to exploit how variations on each data collection parameter could affect the final protein CD spectrum and, the subsequent effect of them on the quantitative analysis of protein secondary structure. Bioinformatics analysis carried out with SESCA package and PDBMD2CD server predicted a theoretical myoglobin CD spectrum, and a Monte Carlo-like model was implemented to estimate the uncertainty in secondary structure predictions performed with CDSSTR, Selcon 3 and ContinLL algorithms. An inappropriate choice of data collection parameters can lead to a misinterpretation of the CD data in terms of the protein structural content.
Collapse
|
50
|
Dilworth MV, Findlay HE, Booth PJ. Detergent-free purification and reconstitution of functional human serotonin transporter (SERT) using diisobutylene maleic acid (DIBMA) copolymer. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2021; 1863:183602. [PMID: 33744253 PMCID: PMC8111416 DOI: 10.1016/j.bbamem.2021.183602] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 03/02/2021] [Accepted: 03/03/2021] [Indexed: 12/17/2022]
Abstract
Structure and function analysis of human membrane proteins in lipid bilayer environments is acutely lacking despite the fundame1ntal cellular importance of these proteins and their dominance of drug targets. An underlying reason is that detailed study usually requires a potentially destabilising detergent purification of the proteins from their host membranes prior to subsequent reconstitution in a membrane mimic; a situation that is exacerbated for human membrane proteins due to the inherent difficulties in overexpressing suitable quantities of the proteins. We advance the promising styrene maleic acid polymer (SMA) extraction approach to introduce a detergent-free method of obtaining stable, functional human membrane transporters in bilayer nanodiscs directly from yeast cells. We purify the human serotonin transporter (hSERT) following overexpression in Pichia pastoris using diisobutylene maleic acid (DIBMA) as a superior method to traditional detergents or the more established styrene maleic acid polymer. hSERT plays a pivotal role in neurotransmitter regulation being responsible for the transport of the neurotransmitter 5-hydroxytryptamine (5-HT or serotonin). It is representative of the neurotransmitter sodium symporter (NSS) family, whose importance is underscored by the numerous diseases attributed to their malfunction. We gain insight into hSERT activity through an in vitro transport assay and find that DIBMA extraction improves the thermostability and activity of hSERT over the conventional detergent method. The non-aromatic amphipathic polymer DIBMA can be successfully employed to purify human membrane proteins. DIBMA solubilisation of hSERT from yeast membranes and resultant nanodisc thermostability is comparable to SMA. DIBMA and SMA encapsulated hSERT lipid-nanodiscs exhibit higher binding activity than hSERT DDMCHS micelles. Proteoliposomes reconstituted with hSERT-DIBMALPs possess higher transport activity than comparable DDMCHS reconstitutions.
Collapse
Affiliation(s)
- Marvin V Dilworth
- Department of Chemistry, King's College London, London SE1 1DB, United Kingdom.
| | - Heather E Findlay
- Department of Chemistry, King's College London, London SE1 1DB, United Kingdom.
| | - Paula J Booth
- Department of Chemistry, King's College London, London SE1 1DB, United Kingdom.
| |
Collapse
|