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Madsen M, Prestel A, Madland E, Westh P, Tøndervik A, Sletta H, Peters GHJ, Aachmann FL, Kragelund BB, Svensson B. Molecular insights into alginate β-lactoglobulin A multivalencies-The foundation for their amorphous aggregates and coacervation. Protein Sci 2023; 32:e4556. [PMID: 36571497 PMCID: PMC9847093 DOI: 10.1002/pro.4556] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 12/06/2022] [Accepted: 12/22/2022] [Indexed: 12/27/2022]
Abstract
For improved control of biomaterial property design, a better understanding of complex coacervation involving anionic polysaccharides and proteins is needed. Here, we address the initial steps in condensate formation of β-lactoglobulin A (β-LgA) with nine defined alginate oligosaccharides (AOSs) and describe their multivalent interactions in structural detail. Binding of AOSs containing four, five, or six uronic acid residues (UARs), either all mannuronate (M), all guluronate (G), or alternating M and G embodying the block structural components of alginates, was characterized by isothermal titration calorimetry, nuclear magnetic resonance spectroscopy (NMR), and molecular docking. β-LgA was highly multivalent exhibiting binding stoichiometries decreasing from five to two AOSs with increasing degree of polymerization (DP) and similar affinities in the mid micromolar range. The different AOS binding sites on β-LgA were identified by NMR chemical shift perturbation analyses and showed diverse compositions of charged, polar and hydrophobic residues. Distinct sites for the shorter AOSs merged to accommodate longer AOSs. The AOSs bound dynamically to β-LgA, as concluded from saturation transfer difference and 1 H-ligand-targeted NMR analyses. Molecular docking using Glide within the Schrödinger suite 2016-1 revealed the orientation of AOSs to only vary slightly at the preferred β-LgA binding site resulting in similar XP glide scores. The multivalency coupled with highly dynamic AOS binding with lack of confined conformations in the β-LgA complexes may help explain the first steps toward disordered β-LgA alginate coacervate structures.
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Affiliation(s)
- Mikkel Madsen
- Enzyme and Protein Chemistry, Department of Biotechnology and BiomedicineTechnical University of DenmarkKgs. LyngbyDenmark
| | - Andreas Prestel
- Structural Biology and NMR Laboratory, Department of BiologyUniversity of CopenhagenCopenhagen NDenmark
| | - Eva Madland
- Norwegian Biopolymer Laboratory (NOBIPOL), Department of Biotechnology and Food ScienceNTNU Norwegian University of Science and TechnologyTrondheimNorway
| | - Peter Westh
- Interfacial Enzymology, Department of Biotechnology and BiomedicineTechnical University of DenmarkKgs. LyngbyDenmark
| | - Anne Tøndervik
- Department of Biotechnology and Nanomedicine, SINTEF IndustryTrondheimNorway
| | - Håvard Sletta
- Department of Biotechnology and Nanomedicine, SINTEF IndustryTrondheimNorway
| | - Günther H. J. Peters
- Biophysical and Biomedicinal Chemistry, Department of ChemistryTechnical University of DenmarkKgs. LyngbyDenmark
| | - Finn L. Aachmann
- Norwegian Biopolymer Laboratory (NOBIPOL), Department of Biotechnology and Food ScienceNTNU Norwegian University of Science and TechnologyTrondheimNorway
| | - Birthe B. Kragelund
- Structural Biology and NMR Laboratory, Department of BiologyUniversity of CopenhagenCopenhagen NDenmark
| | - Birte Svensson
- Enzyme and Protein Chemistry, Department of Biotechnology and BiomedicineTechnical University of DenmarkKgs. LyngbyDenmark
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Koga T, Kingetsu S, Higashi N. Supramolecular Nanofibers from Collagen-Mimetic Peptides Bearing Various Aromatic Groups at N-Termini via Hierarchical Self-Assembly. Int J Mol Sci 2021; 22:4533. [PMID: 33926094 PMCID: PMC8123610 DOI: 10.3390/ijms22094533] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2021] [Revised: 04/23/2021] [Accepted: 04/23/2021] [Indexed: 11/17/2022] Open
Abstract
Self-assembly of artificial peptides has been widely studied for constructing nanostructured materials, with numerous potential applications in the nanobiotechnology field. Herein, we report the synthesis and hierarchical self-assembly of collagen-mimetic peptides (CMPs) bearing various aromatic groups at the N-termini, including 2-naphthyl, 1-naphtyl, anthracenyl, and pyrenyl groups, into nanofibers. The CMPs (R-(GPO)n: n > 4) formed a triple helix structure in water at 4 °C, as confirmed via CD analyses, and their conformations were more stable with increasing hydrophobicity of the terminal aromatic group and peptide chain length. The resulting pre-organized triple helical CMPs showed diverse self-assembly into highly ordered nanofibers, reflecting their slight differences in hydrophobic/hydrophilic balance and configuration of aromatic templates. TEM analysis demonstrated that 2Np-CMPn (n = 6 and 7) and Py-CMP6 provided well-developed natural collagen-like nanofibers and An-CMPn (n = 5-7) self-assembled into rod-like micelle fibers. On the other hand, 2Np-CMP5 and 1Np-CMP6 were unable to form nanofibers under the same conditions. Furthermore, the Py-CMP6 nanofiber was found to encapsulate a guest hydrophobic molecule, Nile red, and exhibited unique emission behavior based on the specific nanostructure. In addition to the ability of CMPs to bind small molecules, their controlled self-assembly enables their versatile utilization in drug delivery and wavelength-conversion nanomaterials.
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Affiliation(s)
- Tomoyuki Koga
- Department of Molecular Chemistry and Biochemistry, Faculty of Science and Engineering, Doshisha University, Kyotanabe, Kyoto 610-0321, Japan;
| | | | - Nobuyuki Higashi
- Department of Molecular Chemistry and Biochemistry, Faculty of Science and Engineering, Doshisha University, Kyotanabe, Kyoto 610-0321, Japan;
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Williams C, Fernández-Calvo P, Colinas M, Pauwels L, Goossens A. Jasmonate and auxin perception: how plants keep F-boxes in check. J Exp Bot 2019; 70:3401-3414. [PMID: 31173086 DOI: 10.1093/jxb/erz272] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Accepted: 05/29/2019] [Indexed: 05/24/2023]
Abstract
Phytohormones regulate the plasticity of plant growth and development, and responses to biotic and abiotic stresses. Many hormone signal transduction cascades involve ubiquitination and subsequent degradation of proteins by the 26S proteasome. The conjugation of ubiquitin to a substrate is facilitated by the E1 activating, E2 conjugating, and the substrate-specifying E3 ligating enzymes. The most prevalent type of E3 ligase in plants is the Cullin-RING ligase (CRL)-type, with F-box proteins (FBPs) as the substrate recognition component. The activity of these SKP-Cullin-F-box (SCF) complexes needs to be tightly regulated in time and place. Here, we review the regulation of SCF function in plants on multiple levels, with a focus on the auxin and jasmonate SCF-type receptor complexes. We discuss in particular the relevance of protein-protein interactions and post-translational modifications as mechanisms to keep SCF functioning under control. Additionally, we highlight the unique property of SCFTIR1/AFB and SCFCOI1 to recognize substrates by forming co-receptor complexes. Finally, we explore how engineered selective agonists can be used to study and uncouple the outcomes of the complex auxin and jasmonate signaling networks that are governed by these FBPs.
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Affiliation(s)
- Clara Williams
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Patricia Fernández-Calvo
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
- Centre for Plant Biotechnology and Genomics, Parque Cientifico y Tecnologico, UPM Campus de Montegancedo, Madrid, Spain
| | - Maite Colinas
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Laurens Pauwels
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Alain Goossens
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
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Wang L, Samigullin K, Wagner M, McQuilken AC, Warren TH, Daniliuc CG, Kehr G, Erker G. An Ethylene-Bridged Phosphane/Borane Frustrated Lewis Pair Featuring the -B(Fxyl)2 Lewis Acid Component. Chemistry 2016; 22:11015-21. [PMID: 27355412 DOI: 10.1002/chem.201601583] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2016] [Indexed: 11/07/2022]
Abstract
Hydroboration of dimesitylvinylphosphane with bis[3,5-bis(trifluoromethyl)phenyl]borane [HB(Fxyl)2 ] gave the intramolecular ethylene-bridged P/B frustrated Lewis pair (FLP) Mes2 PCH2 CH2 B(Fxyl)2 . The new compound underwent a variety of typical FLP reactions such as P/B-addition to the carbonyl group of p-chloro-benzaldehyde. Cooperative N,N-addition to nitric oxide gave the respective persistent P/B FLPNO(.) radical, which readily reacted with 1,4-cyclohexadiene by H-atom abstraction to yield the corresponding P/B FLPNOH product. The B(Fxyl)2 -containing FLP reacted as a template for the HB(C6 F5 )2 reduction of carbon monoxide to the formyl stage to give the respective FLP(η(2) -formylborane) product. Most products were characterized by single-crystal X-ray crystal structure analysis.
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Affiliation(s)
- Long Wang
- Organisch-Chemisches Institut, Universität Münster, Corrensstraße 40, 48149, Münster, Germany
| | - Kamil Samigullin
- Institut für Anorganische und Analytische Chemie, Goethe-Universität Frankfurt, Max-von-Laue-Straße 7, 60438, Frankfurt (Main), Germany
| | - Matthias Wagner
- Institut für Anorganische und Analytische Chemie, Goethe-Universität Frankfurt, Max-von-Laue-Straße 7, 60438, Frankfurt (Main), Germany
| | - Alison C McQuilken
- Department of Chemistry, Georgetown University, Box 571557, Washington DC, 20057-1227, USA
| | - Timothy H Warren
- Department of Chemistry, Georgetown University, Box 571557, Washington DC, 20057-1227, USA
| | - Constantin G Daniliuc
- Organisch-Chemisches Institut, Universität Münster, Corrensstraße 40, 48149, Münster, Germany
| | - Gerald Kehr
- Organisch-Chemisches Institut, Universität Münster, Corrensstraße 40, 48149, Münster, Germany
| | - Gerhard Erker
- Organisch-Chemisches Institut, Universität Münster, Corrensstraße 40, 48149, Münster, Germany.
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Lisowiec J, Magner D, Kierzek E, Lenartowicz E, Kierzek R. Structural determinants for alternative splicing regulation of the MAPT pre-mRNA. RNA Biol 2015; 12:330-42. [PMID: 25826665 DOI: 10.1080/15476286.2015.1017214] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Alternative splicing at the MAPT gene exon 10 yields similar levels of the 3R and 4R tau protein isoforms. (1) The presence of mutations, particularly in exon 10 and intron 10-11, changes the quantity of tau isoforms. Domination each of the isoform yields tau protein aggregation and frontotemporal dementia and Parkinsonism linked to chromosome 17 (FTDP-17). Here, we report for the first time the secondary structure of the 194/195 nucleotide region for the wild type (WT) and 10 mutants of the MAPT gene pre-mRNA determined using both chemical and microarray mapping. Thermodynamic analyses indicate that single nucleotide mutations in the splicing regulatory element (SRE) that form a hairpin affect its stability by up to 4 and 7 kcal/mol. Moreover, binding the regulatory hairpin of small molecule ligands (neomycin, kanamycin, tobramycin and mitoxantrone) enhance its stability depending on the nature of the ligands and the RNA mutations. Experiments using the cos-7 cell line indicate that the presence of ligands and modified antisense oligonucleotides affect the quantity of 3R and 4R isoforms. This finding correlates with the thermodynamic stability of the regulatory hairpin. An alternative splicing regulation mechanism for exon 10 is postulated based on our experimental data and on published data.
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Key Words
- AD, Alzheimer disease
- DMS, dimethyl sulfide
- ESE, exonic splicing enhancer
- ESS, exonic splicing silencer
- FTD, frontotemporal dementia
- FTDP-17, frontotemporal dementia and Parkinsonism linked to chromosome 17
- ISM, intronic splicing modulator
- ISS, intronic splicing silencer
- MAPT, microtubule-associated protein tau
- NMIA, N-methylisotoic anhydride
- NMR, nuclear magnetic resonance
- PPE, polypurine enhancer
- RNA structure
- RNA thermodynamics
- RT-PCR, reverse transcription polymerase chain reaction
- SHAPE, selective 2′-hydroxyl acylation analyzed by primer extension
- SMA, spinal muscular atrophy
- SRE, splicing regulatory element
- U1 snRNP, U1 small nuclear ribonucleoprotein
- WT, wild type
- alternative splicing regulation
- antisense oligonucleotides
- neurodegradation
- pre-mRNA, pre-messenger RNA
- small molecule binding
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Affiliation(s)
- Jolanta Lisowiec
- a Institute of Bioorganic Chemistry; Polish Academy of Sciences ; Noskowskiego, Poland
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