1
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Baudrexl M, Fida T, Berk B, Schwarz WH, Zverlov VV, Groll M, Liebl W. Biochemical and Structural Characterization of Thermostable GH159 Glycoside Hydrolases Exhibiting α-L-Arabinofuranosidase Activity. Front Mol Biosci 2022; 9:907439. [PMID: 35847984 PMCID: PMC9278983 DOI: 10.3389/fmolb.2022.907439] [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: 03/29/2022] [Accepted: 06/06/2022] [Indexed: 11/13/2022] Open
Abstract
Functional, biochemical, and preliminary structural properties are reported for three glycoside hydrolases of the recently described glycoside hydrolase (GH) family 159. The genes were cloned from the genomic sequences of different Caldicellulosiruptor strains. This study extends the spectrum of functions of GH159 enzymes. The only activity previously reported for GH159 was hydrolytic activity on β-galactofuranosides. Activity screening using a set of para-nitrophenyl (pNP) glycosides suggested additional arabinosidase activity on substrates with arabinosyl residues, which has not been previously reported for members of GH159. Even though the thermophilic enzymes investigated-Cs_Gaf159A, Ch_Gaf159A, and Ck_Gaf159A-cleaved pNP-α-l-arabinofuranoside, they were only weakly active on arabinogalactan, and they did not cleave arabinose from arabinan, arabinoxylan, or gum arabic. However, the enzymes were able to hydrolyze the α-1,3-linkage in different arabinoxylan-derived oligosaccharides (AXOS) with arabinosylated xylose at the non-reducing end (A3X, A2,3XX), suggesting their role in the intracellular hydrolysis of oligosaccharides. Crystallization and structural analysis of the apo form of one of the Caldicellulosiruptor enzymes, Ch_Gaf159A, enabled the elucidation of the first 3D structure of a GH159 member. This work revealed a five-bladed β-propeller structure for GH159 enzymes. The 3D structure and its substrate-binding pocket also provides an explanation at the molecular level for the observed exo-activity of the enzyme. Furthermore, the structural data enabled the prediction of the catalytic amino acids. This was supported by the complete inactivation by mutation of residues D19, D142, and E190 of Ch_Gaf159A.
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Affiliation(s)
- Melanie Baudrexl
- Chair of Microbiology, Technical University of Munich, Freising, Germany
| | - Tarik Fida
- Chair of Microbiology, Technical University of Munich, Freising, Germany
| | - Berkay Berk
- Chair of Microbiology, Technical University of Munich, Freising, Germany
| | | | - Vladimir V. Zverlov
- Chair of Microbiology, Technical University of Munich, Freising, Germany
- Institute of Molecular Genetics, Russian Academy of Science, Moscow, Russia
| | - Michael Groll
- Chair of Biochemistry, Center for Protein Assemblies, Technical University of Munich, Garching, Germany
| | - Wolfgang Liebl
- Chair of Microbiology, Technical University of Munich, Freising, Germany
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2
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Kuepper A, McLoughlin NM, Neubacher S, Yeste-Vázquez A, Collado Camps E, Nithin C, Mukherjee S, Bethge L, Bujnicki JM, Brock R, Heinrichs S, Grossmann TN. Constrained peptides mimic a viral suppressor of RNA silencing. Nucleic Acids Res 2021; 49:12622-12633. [PMID: 34871435 PMCID: PMC8682738 DOI: 10.1093/nar/gkab1149] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Revised: 10/01/2021] [Accepted: 11/03/2021] [Indexed: 12/26/2022] Open
Abstract
The design of high-affinity, RNA-binding ligands has proven very challenging. This is due to the unique structural properties of RNA, often characterized by polar surfaces and high flexibility. In addition, the frequent lack of well-defined binding pockets complicates the development of small molecule binders. This has triggered the search for alternative scaffolds of intermediate size. Among these, peptide-derived molecules represent appealing entities as they can mimic structural features also present in RNA-binding proteins. However, the application of peptidic RNA-targeting ligands is hampered by a lack of design principles and their inherently low bio-stability. Here, the structure-based design of constrained α-helical peptides derived from the viral suppressor of RNA silencing, TAV2b, is described. We observe that the introduction of two inter-side chain crosslinks provides peptides with increased α-helicity and protease stability. One of these modified peptides (B3) shows high affinity for double-stranded RNA structures including a palindromic siRNA as well as microRNA-21 and its precursor pre-miR-21. Notably, B3 binding to pre-miR-21 inhibits Dicer processing in a biochemical assay. As a further characteristic this peptide also exhibits cellular entry. Our findings show that constrained peptides can efficiently mimic RNA-binding proteins rendering them potentially useful for the design of bioactive RNA-targeting ligands.
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Affiliation(s)
- Arne Kuepper
- Chemical Genomics Centre of the Max Planck Society, Dortmund 44227, Germany
- Department of Chemistry and Chemical Biology, Technical University Dortmund, Dortmund 44227, Germany
| | - Niall M McLoughlin
- Department of Chemistry and Pharmaceutical Sciences, Vrije Universiteit Amsterdam, Amsterdam 1081 HZ, The Netherlands
- Amsterdam Institute of Molecular and Life Sciences (AIMMS), Vrije Universiteit Amsterdam, Amsterdam 1081 HZ, The Netherlands
| | - Saskia Neubacher
- Department of Chemistry and Pharmaceutical Sciences, Vrije Universiteit Amsterdam, Amsterdam 1081 HZ, The Netherlands
- Amsterdam Institute of Molecular and Life Sciences (AIMMS), Vrije Universiteit Amsterdam, Amsterdam 1081 HZ, The Netherlands
| | - Alejandro Yeste-Vázquez
- Department of Chemistry and Pharmaceutical Sciences, Vrije Universiteit Amsterdam, Amsterdam 1081 HZ, The Netherlands
- Amsterdam Institute of Molecular and Life Sciences (AIMMS), Vrije Universiteit Amsterdam, Amsterdam 1081 HZ, The Netherlands
| | - Estel Collado Camps
- Department of Biochemistry, Radboud Institute for Molecular Life Sciences, Radboud University, Nijmegen Medical Center, Nijmegen 6525 GA, The Netherlands
| | - Chandran Nithin
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, Warsaw 02-109, Poland
| | - Sunandan Mukherjee
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, Warsaw 02-109, Poland
| | - Lucas Bethge
- Silence Therapeutics GmbH, Robert-Rössle-Str. 10, 13125 Berlin, Germany
| | - Janusz M Bujnicki
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, Warsaw 02-109, Poland
| | - Roland Brock
- Department of Biochemistry, Radboud Institute for Molecular Life Sciences, Radboud University, Nijmegen Medical Center, Nijmegen 6525 GA, The Netherlands
- Department of Medical Biochemistry, College of Medicine and Medical Sciences, Arabian Gulf University, Manama 293, Bahrain
| | - Stefan Heinrichs
- University Hospital Essen, Institute for Transfusion Medicine, Essen 45147, Germany
| | - Tom N Grossmann
- Chemical Genomics Centre of the Max Planck Society, Dortmund 44227, Germany
- Department of Chemistry and Chemical Biology, Technical University Dortmund, Dortmund 44227, Germany
- Department of Chemistry and Pharmaceutical Sciences, Vrije Universiteit Amsterdam, Amsterdam 1081 HZ, The Netherlands
- Amsterdam Institute of Molecular and Life Sciences (AIMMS), Vrije Universiteit Amsterdam, Amsterdam 1081 HZ, The Netherlands
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3
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Adihou H, Gopalakrishnan R, Förster T, Guéret SM, Gasper R, Geschwindner S, Carrillo García C, Karatas H, Pobbati AV, Vazquez-Chantada M, Davey P, Wassvik CM, Pang JKS, Soh BS, Hong W, Chiarparin E, Schade D, Plowright AT, Valeur E, Lemurell M, Grossmann TN, Waldmann H. A protein tertiary structure mimetic modulator of the Hippo signalling pathway. Nat Commun 2020; 11:5425. [PMID: 33110077 PMCID: PMC7591920 DOI: 10.1038/s41467-020-19224-8] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Accepted: 09/28/2020] [Indexed: 11/21/2022] Open
Abstract
Transcription factors are key protein effectors in the regulation of gene transcription, and in many cases their activity is regulated via a complex network of protein–protein interactions (PPI). The chemical modulation of transcription factor activity is a long-standing goal in drug discovery but hampered by the difficulties associated with the targeting of PPIs, in particular when extended and flat protein interfaces are involved. Peptidomimetics have been applied to inhibit PPIs, however with variable success, as for certain interfaces the mimicry of a single secondary structure element is insufficient to obtain high binding affinities. Here, we describe the design and characterization of a stabilized protein tertiary structure that acts as an inhibitor of the interaction between the transcription factor TEAD and its co-repressor VGL4, both playing a central role in the Hippo signalling pathway. Modification of the inhibitor with a cell-penetrating entity yielded a cell-permeable proteomimetic that activates cell proliferation via regulation of the Hippo pathway, highlighting the potential of protein tertiary structure mimetics as an emerging class of PPI modulators. Targeting the interaction between transcription factor TEAD and its co-repressor VGL4 is an attractive strategy to chemically modulate Hippo signaling. Here, the authors develop a proteomimetic with stabilized tertiary structure that inhibits the TEAD:VGL4 interaction in vitro and in cells.
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Affiliation(s)
- Hélène Adihou
- Medicinal Chemistry, Research and Early Development Cardiovascular, Renal and Metabolism, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden.,AstraZeneca-MPI Satellite Unit, Dortmund, Germany
| | - Ranganath Gopalakrishnan
- Medicinal Chemistry, Research and Early Development Cardiovascular, Renal and Metabolism, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden.,AstraZeneca-MPI Satellite Unit, Dortmund, Germany
| | - Tim Förster
- AstraZeneca-MPI Satellite Unit, Dortmund, Germany
| | - Stéphanie M Guéret
- Medicinal Chemistry, Research and Early Development Cardiovascular, Renal and Metabolism, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden.,AstraZeneca-MPI Satellite Unit, Dortmund, Germany
| | - Raphael Gasper
- Max Planck Institute for Molecular Physiology, Dortmund, Germany
| | - Stefan Geschwindner
- Structure & Biophysics, Discovery Sciences, R&D, AstraZeneca, Gothenburg, Sweden
| | - Carmen Carrillo García
- Department of Pharmaceutical and Medicinal Chemistry, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Hacer Karatas
- Max Planck Institute for Molecular Physiology, Dortmund, Germany
| | - Ajaybabu V Pobbati
- Department of Multi-Modal Molecular (M3) Biology, A*STAR Institute of Molecular and Cell Biology, Singapore, Singapore
| | | | - Paul Davey
- Medicinal Chemistry, Oncology R&D, AstraZeneca, Cambridge, UK
| | - Carola M Wassvik
- Medicinal Chemistry, Research and Early Development Cardiovascular, Renal and Metabolism, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Jeremy Kah Sheng Pang
- Disease Modelling and Therapeutics Laboratory, A*STAR Institute of Molecular and Cell Biology, Singapore, Singapore.,Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Boon Seng Soh
- Disease Modelling and Therapeutics Laboratory, A*STAR Institute of Molecular and Cell Biology, Singapore, Singapore.,Department of Biological Sciences, National University of Singapore, Singapore, Singapore.,Key Laboratory for Major Obstetric Diseases of Guangdong Province, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Wanjin Hong
- Department of Multi-Modal Molecular (M3) Biology, A*STAR Institute of Molecular and Cell Biology, Singapore, Singapore
| | | | - Dennis Schade
- Department of Pharmaceutical and Medicinal Chemistry, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Alleyn T Plowright
- Medicinal Chemistry, Research and Early Development Cardiovascular, Renal and Metabolism, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Eric Valeur
- Medicinal Chemistry, Research and Early Development Cardiovascular, Renal and Metabolism, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Malin Lemurell
- Medicinal Chemistry, Research and Early Development Cardiovascular, Renal and Metabolism, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Tom N Grossmann
- Department of Chemistry and Pharmaceutical Sciences, VU University Amsterdam, Amsterdam, Netherlands. .,Amsterdam Institute of Molecular and Life Sciences (AIMMS), VU University Amsterdam, Amsterdam, Netherlands.
| | - Herbert Waldmann
- Max Planck Institute for Molecular Physiology, Dortmund, Germany. .,Department of Chemistry and Chemical Biology, Technical University Dortmund, Dortmund, Germany.
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4
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Xi J, Xiao J, Perez-Aguilar JM, Ping J, Johnson ATC, Saven JG, Liu R. Characterization of an engineered water-soluble variant of the full-length human mu opioid receptor. J Biomol Struct Dyn 2019; 38:4364-4370. [PMID: 31588852 DOI: 10.1080/07391102.2019.1677502] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
A water-soluble variant of the transmembrane domain of the human mu opioid receptor (wsMOR-TM) was previously characterized. This study explored whether the full-length version of the engineered water-soluble receptor, (wsMOR-FL), could be overexpressed in Escherichia coli and if it would retain water solubility, binding capability and thermostability. wsMOR was over-expressed and purified in E. coli BL21(DE3) cells (EMD/Novagen) as we reported previously for the wsMOR-TM. Both native N and C termini were added back to the highly engineered wsMOR-TM. Six His-tag was added in the N terminus for purification purposes. The wsMOR-FL was characterized using atomic force microscope for its monomeric state, circular dichroism for its secondary structure and thermostability. Its binding with naltrexone is also determined. Compared to the native human MOR, wsMOR-FL displays similar helical secondary structure content and comparable affinity (nM) for the antagonist naltrexone. The secondary structure of the receptor remains stable within a wide range of pH (6-9). In contrast to the transmembrane portion, the secondary structure of full-length receptor tolerated a wide range of temperature (10-90 °C). The receptor remains predominantly as a monomer in solution, as directly imaged using atomic force microscopy. This study demonstrated that functional full-length water-soluble variant of human mu receptor can be over-expressed and purified using an E. coli over-expression system. This provides a novel tool for the investigation of structural and functional properties of the human MOR. N- and C-termini strengthened the thermostability of the protein in this specific water soluble variant. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Jin Xi
- Department of Anesthesiology and Critical Care, University of Pennsylvania, Philadelphia, PA, USA
| | - Jie Xiao
- Department of Anesthesiology and Critical Care, University of Pennsylvania, Philadelphia, PA, USA
| | - Jose Manuel Perez-Aguilar
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA, USA.,School of Chemical Sciences, Meritorious Autonomous University of Puebla (BUAP), Puebla, Puebla, Mexico
| | - Jinglei Ping
- Department of Physics and Astronomy, University of Pennsylvania, Philadelphia, PA, USA
| | - A T Charlie Johnson
- Department of Physics and Astronomy, University of Pennsylvania, Philadelphia, PA, USA
| | - Jeffery G Saven
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA, USA
| | - Renyu Liu
- Department of Anesthesiology and Critical Care, University of Pennsylvania, Philadelphia, PA, USA
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5
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Nagati V, Nakkka S, Yeggoni DP, Subramanyam R. Forskolin-loaded human serum albumin nanoparticles and its biological importance. J Biomol Struct Dyn 2019; 38:1539-1550. [PMID: 31057091 DOI: 10.1080/07391102.2019.1614481] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
In this study, forskolin-loaded human serum albumin nanoparticles (FR-HSANPs) were successfully prepared by incorporation and affinity-binding methods. FR-HSANPs were characterized by transmission electron microscope that most of them are circular in shape and size is around 340 nm. The drug loading was more than 88% and further sustained release profiles were observed as it is 77.5% in 24 h time. Additionally, the cytotoxicity results with HepG2 cells indicated that FR-HSANPs showed significantly higher cytotoxicity and lower cell viability as compared to free forskolin (FR). Furthermore, to understand the binding mechanism of human serum albumin (HSA) with forskolin resulted from fluorescence quenching as a static mechanism and the binding constant is 6.26 ± 0.1 × 104 M-1, indicating a strong binding affinity. Further, association and dissociation kinetics of forskolin-HSA was calculated from surface plasmon resonance spectroscopy and the binding constant found to be Kforskolin = 3.4 ± 0.24 × 104 M-1 and also fast dissociation was observed. Further, we used circular dichroism and molecular dynamics simulations to elucidate the possible structural changes including local conformational changes and rigidity of the residues of both HSA and HSA-forskolin complexes.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Veerababu Nagati
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad, India
| | - Sailaja Nakkka
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad, India
| | | | - Rajagopal Subramanyam
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad, India
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6
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Ros U, Carretero GPB, Paulino J, Crusca E, Pazos F, Cilli EM, Lanio ME, Schreier S, Alvarez C. Self-association and folding in membrane determine the mode of action of peptides from the lytic segment of sticholysins. Biochimie 2018; 156:109-117. [PMID: 30326255 DOI: 10.1016/j.biochi.2018.10.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Accepted: 10/11/2018] [Indexed: 01/09/2023]
Abstract
Sticholysin I and II (Sts: St I and St II) are proteins of biomedical interest that form pores upon the insertion of their N-terminus in the plasma membrane. Peptides spanning the N-terminal residues of StI (StI1-31) or StII (StII1-30) can mimic the permeabilizing ability of these toxins, emerging as candidates to rationalize their potential biomedical applications. These peptides have different activities that correlate with their hydrophobicity. However, it is not clear how this property contributes to peptide folding in solution or upon binding to membranes. Here we compared the conformational properties of these peptides and shorter versions lacking the hydrophobic segment 1-11 of StI (StI12-31) or 1-10 of StII (StII11-30). Folding of peptides was assessed in solution and in membrane mimetic systems and related with their ability to bind to membranes and to permeabilize lipid vesicles. Our results suggest that the differences in activity among peptides could be ascribed to their different folding propensity and different membrane binding properties. In solution, StII1-30 tends to acquire α-helical conformation coexisting with self-associated structures, while StI1-31 remains structureless. Both peptides fold as α-helix in membrane; but StII1-30 also self-associates in the lipid environment, a process that is favored by its higher affinity for membrane. We stress the contribution of the non-polar/polar balance of the 1-10 amino acid sequence of the peptides as a determining factor for different self-association capabilities. Such difference in hydrophobicity seems to determine the molecular path of peptides folding upon binding to membranes, with an impact in their permeabilizing activity. This study contributes to a better understanding of the molecular mechanisms underlying the permeabilizing activity of Sts N-terminal derived peptides, with connotation for the exploitation of these small molecules as alternative of the full-length toxins in clinical settings.
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Affiliation(s)
- Uris Ros
- Center for Protein Studies, Biology Faculty, University of Havana, Havana, Cuba
| | - Gustavo P B Carretero
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo, Brazil
| | - Joana Paulino
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo, Brazil
| | - Edson Crusca
- Department of Biochemistry, Institute of Chemistry, São Paulo State University, Araraquara, São Paulo, Brazil
| | - Fabiola Pazos
- Center for Protein Studies, Biology Faculty, University of Havana, Havana, Cuba
| | - Eduardo M Cilli
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo, Brazil
| | - Maria E Lanio
- Center for Protein Studies, Biology Faculty, University of Havana, Havana, Cuba
| | - Shirley Schreier
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo, Brazil
| | - Carlos Alvarez
- Center for Protein Studies, Biology Faculty, University of Havana, Havana, Cuba.
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7
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Stelzer W, Scharnagl C, Leurs U, Rand KD, Langosch D. The Impact of the ‘Austrian’ Mutation of the Amyloid Precursor Protein Transmembrane Helix is Communicated to the Hinge Region. ChemistrySelect 2016. [DOI: 10.1002/slct.201601090] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Walter Stelzer
- Lehrstuhl Chemie der Biopolymere; Technical University of Munich and Munich Center for Integrated Protein Science (CIPS ); Weihenstephaner Berg 3 85354 Freising Germany
| | - Christina Scharnagl
- Fakultät für Physik E14; Technical University of Munich; Maximus-von-Imhof-Forum 4 85354 Freising Germany
| | - Ulrike Leurs
- Department of Pharmacy; University of Copenhagen; Universitetsparken 2 2100 Copenhagen Denmark
| | - Kasper D. Rand
- Department of Pharmacy; University of Copenhagen; Universitetsparken 2 2100 Copenhagen Denmark
| | - Dieter Langosch
- Lehrstuhl Chemie der Biopolymere; Technical University of Munich and Munich Center for Integrated Protein Science (CIPS ); Weihenstephaner Berg 3 85354 Freising Germany
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8
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Scharnagl C, Pester O, Hornburg P, Hornburg D, Götz A, Langosch D. Side-chain to main-chain hydrogen bonding controls the intrinsic backbone dynamics of the amyloid precursor protein transmembrane helix. Biophys J 2014; 106:1318-26. [PMID: 24655507 DOI: 10.1016/j.bpj.2014.02.013] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2013] [Revised: 01/28/2014] [Accepted: 02/07/2014] [Indexed: 01/19/2023] Open
Abstract
Many transmembrane helices contain serine and/or threonine residues whose side chains form intrahelical H-bonds with upstream carbonyl oxygens. Here, we investigated the impact of threonine side-chain/main-chain backbonding on the backbone dynamics of the amyloid precursor protein transmembrane helix. This helix consists of a N-terminal dimerization region and a C-terminal cleavage region, which is processed by γ-secretase to a series of products. Threonine mutations within this transmembrane helix are known to alter the cleavage pattern, which can lead to early-onset Alzheimer's disease. Circular dichroism spectroscopy and amide exchange experiments of synthetic transmembrane domain peptides reveal that mutating threonine enhances the flexibility of this helix. Molecular dynamics simulations show that the mutations reduce intrahelical amide H-bonding and H-bond lifetimes. In addition, the removal of side-chain/main-chain backbonding distorts the helix, which alters bending and rotation at a diglycine hinge connecting the dimerization and cleavage regions. We propose that the backbone dynamics of the substrate profoundly affects the way by which the substrate is presented to the catalytic site within the enzyme. Changing this conformational flexibility may thus change the pattern of proteolytic processing.
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Affiliation(s)
| | - Oxana Pester
- Munich Center for Integrated Protein Science (CIPS(M)) at Lehrstuhl Chemie der Biopolymere, Technische Universität München, Freising, Germany
| | - Philipp Hornburg
- Fakultät für Physik E14, Technische Universität München, Freising, Germany
| | - Daniel Hornburg
- Fakultät für Physik E14, Technische Universität München, Freising, Germany
| | - Alexander Götz
- Munich Center for Integrated Protein Science (CIPS(M)) at Lehrstuhl Chemie der Biopolymere, Technische Universität München, Freising, Germany
| | - Dieter Langosch
- Munich Center for Integrated Protein Science (CIPS(M)) at Lehrstuhl Chemie der Biopolymere, Technische Universität München, Freising, Germany
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9
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Characterization of a computationally designed water-soluble human μ-opioid receptor variant using available structural information. Anesthesiology 2014; 121:866-75. [PMID: 24835677 DOI: 10.1097/aln.0000000000000308] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
BACKGROUND The recent X-ray crystal structure of the murine μ-opioid receptor (MUR) allowed the authors to reengineer a previously designed water-soluble variant of the transmembrane portion of the human MUR (wsMUR-TM). METHODS The new variant of water-soluble MUR (wsMUR-TM_v2) was engineered based on the murine MUR crystal structure. This novel variant was expressed in Escherichia coli and purified. The properties of the receptor were characterized and compared with those of wsMUR-TM. RESULTS Seven residues originally included for mutation in the design of the wsMUR-TM were reverted to their native identities. wsMUR-TM_v2 contains 16% mutations of the total sequence. It was overexpressed and purified with high yield. Although dimers and higher oligomers were observed to form over time, the wsMUR-TM_v2 stayed predominantly monomeric at concentrations as high as 7.5 mg/ml in buffer within a 2-month period. Its secondary structure was predominantly helical and comparable with those of both the original wsMUR-TM variant and the native MUR. The binding affinity of wsMUR-TM_v2 for naltrexone (K(d) approximately 70 nM) was in close agreement with that for wsMUR-TM. The helical content of wsMUR-TM_v2 decreased cooperatively with increasing temperature, and the introduction of sucrose was able to stabilize the protein. CONCLUSIONS A novel functional wsMUR-TM_v2 with only 16% mutations was successfully engineered, expressed in E. coli, and purified based on information from the crystal structure of murine MUR. This not only provides a novel alternative tool for MUR studies in solution conditions but also offers valuable information for protein engineering and structure-function relations.
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10
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The Cleavage Domain of the Amyloid Precursor Protein Transmembrane Helix Does Not Exhibit Above-Average Backbone Dynamics. Chembiochem 2013; 14:1943-8. [DOI: 10.1002/cbic.201300322] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2013] [Indexed: 11/07/2022]
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11
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Langer M, Sah R, Veser A, Gütlich M, Langosch D. Structural properties of model phosphatidylcholine flippases. ACTA ACUST UNITED AC 2013; 20:63-72. [PMID: 23352140 DOI: 10.1016/j.chembiol.2012.11.006] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2011] [Revised: 11/13/2012] [Accepted: 11/20/2012] [Indexed: 11/28/2022]
Abstract
Lipid translocation from one lipid bilayer leaflet to the other, termed flip-flop, is required for the distribution of newly synthesized phospholipids during membrane biogenesis. However, a dedicated biogenic lipid flippase has not yet been identified. Here, we show that the efficiency by which model transmembrane peptides facilitate flip of reporter lipids with different headgroups critically depends on their content of helix-destabilizing residues, the charge state of polar flanking residues, and the composition of the host membrane. In particular, increased backbone dynamics of the transmembrane helix relates to its increased ability to flip lipids with phosphatidylcholine and phosphatidylserine headgroups, whereas a more rigid helix favors phosphatidylethanolamine flip. Further, the transmembrane domains of many SNARE protein subtypes share essential features with the dynamic model peptides. Indeed, recombinant SNAREs possess significant lipid flippase activity.
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Affiliation(s)
- Marcella Langer
- Lehrstuhl für Chemie der Biopolymere, Department für biowissenschaftliche Grundlagen, Technische Universität München, Weihenstephaner Berg 3, 85354 Freising and Munich Center For Integrated Protein Science (CIPS(M)), Germany
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12
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Perez-Aguilar JM, Xi J, Matsunaga F, Cui X, Selling B, Saven JG, Liu R. A computationally designed water-soluble variant of a G-protein-coupled receptor: the human mu opioid receptor. PLoS One 2013; 8:e66009. [PMID: 23799068 PMCID: PMC3682944 DOI: 10.1371/journal.pone.0066009] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2013] [Accepted: 04/30/2013] [Indexed: 11/19/2022] Open
Abstract
G-protein-coupled receptors (GPCRs) play essential roles in various physiological processes, and are widely targeted by pharmaceutical drugs. Despite their importance, studying GPCRs has been problematic due to difficulties in isolating large quantities of these membrane proteins in forms that retain their ligand binding capabilities. Creating water-soluble variants of GPCRs by mutating the exterior, transmembrane residues provides a potential method to overcome these difficulties. Here we present the first study involving the computational design, expression and characterization of water-soluble variant of a human GPCR, the human mu opioid receptor (MUR), which is involved in pain and addiction. An atomistic structure of the transmembrane domain was built using comparative (homology) modeling and known GPCR structures. This structure was highly similar to the subsequently determined structure of the murine receptor and was used to computationally design 53 mutations of exterior residues in the transmembrane region, yielding a variant intended to be soluble in aqueous media. The designed variant expressed in high yield in Escherichia coli and was water soluble. The variant shared structural and functionally related features with the native human MUR, including helical secondary structure and comparable affinity for the antagonist naltrexone (Kd = 65 nM). The roles of cholesterol and disulfide bonds on the stability of the receptor variant were also investigated. This study exemplifies the potential of the computational approach to produce water-soluble variants of GPCRs amenable for structural and functionally related characterization in aqueous solution.
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Affiliation(s)
- Jose Manuel Perez-Aguilar
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Jin Xi
- Department of Anesthesiology and Critical Care, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Felipe Matsunaga
- Department of Anesthesiology and Critical Care, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Xu Cui
- Department of Anesthesiology and Critical Care, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- Department of Anesthesiology, Beijing Tongren Hospital, Capital Medical University, Beijing, China
| | - Bernard Selling
- Impact Biologicals Inc., Swarthmore, Pennsylvania, United States of America
| | - Jeffery G. Saven
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- * E-mail: (RL); (JGS)
| | - Renyu Liu
- Department of Anesthesiology and Critical Care, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- * E-mail: (RL); (JGS)
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Pester O, Barrett PJ, Hornburg D, Hornburg P, Pröbstle R, Widmaier S, Kutzner C, Dürrbaum M, Kapurniotu A, Sanders CR, Scharnagl C, Langosch D. The backbone dynamics of the amyloid precursor protein transmembrane helix provides a rationale for the sequential cleavage mechanism of γ-secretase. J Am Chem Soc 2013; 135:1317-29. [PMID: 23265086 PMCID: PMC3560327 DOI: 10.1021/ja3112093] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
The etiology of Alzheimer's disease depends on the relative abundance of different amyloid-β (Aβ) peptide species. These peptides are produced by sequential proteolytic cleavage within the transmembrane helix of the 99 residue C-terminal fragment of the amyloid precursor protein (C99) by the intramembrane protease γ-secretase. Intramembrane proteolysis is thought to require local unfolding of the substrate helix, which has been proposed to be cleaved as a homodimer. Here, we investigated the backbone dynamics of the substrate helix. Amide exchange experiments of monomeric recombinant C99 and of synthetic transmembrane domain peptides reveal that the N-terminal Gly-rich homodimerization domain exchanges much faster than the C-terminal cleavage region. MD simulations corroborate the differential backbone dynamics, indicate a bending motion at a diglycine motif connecting dimerization and cleavage regions, and detect significantly different H-bond stabilities at the initial cleavage sites. Our results are consistent with the following hypotheses about cleavage of the substrate: First, the GlyGly hinge may precisely position the substrate within γ-secretase such that its catalytic center must start proteolysis at the known initial cleavage sites. Second, the ratio of cleavage products formed by subsequent sequential proteolysis could be influenced by differential extents of solvation and by the stabilities of H-bonds at alternate initial sites. Third, the flexibility of the Gly-rich domain may facilitate substrate movement within the enzyme during sequential proteolysis. Fourth, dimerization may affect substrate processing by decreasing the dynamics of the dimerization region and by increasing that of the C-terminal part of the cleavage region.
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Affiliation(s)
- Oxana Pester
- Lehrstuhl Chemie der Biopolymere, Technische Universität München, Weihenstephaner Berg 3, 85354 Freising, and Munich Center For Integrated Protein Science (CIPS), Germany
| | - Paul J. Barrett
- Department of Biochemistry and Center for Structural Biology, Vanderbilt University School of Medicine, Nashville, Tennessee USA 37232-8725
| | - Daniel Hornburg
- Lehrstuhl Chemie der Biopolymere, Technische Universität München, Weihenstephaner Berg 3, 85354 Freising, and Munich Center For Integrated Protein Science (CIPS), Germany
| | - Philipp Hornburg
- Lehrstuhl Chemie der Biopolymere, Technische Universität München, Weihenstephaner Berg 3, 85354 Freising, and Munich Center For Integrated Protein Science (CIPS), Germany
| | - Rasmus Pröbstle
- Lehrstuhl Chemie der Biopolymere, Technische Universität München, Weihenstephaner Berg 3, 85354 Freising, and Munich Center For Integrated Protein Science (CIPS), Germany
| | - Simon Widmaier
- Lehrstuhl Chemie der Biopolymere, Technische Universität München, Weihenstephaner Berg 3, 85354 Freising, and Munich Center For Integrated Protein Science (CIPS), Germany
| | - Christoph Kutzner
- Lehrstuhl Chemie der Biopolymere, Technische Universität München, Weihenstephaner Berg 3, 85354 Freising, and Munich Center For Integrated Protein Science (CIPS), Germany
| | - Milena Dürrbaum
- Lehrstuhl Chemie der Biopolymere, Technische Universität München, Weihenstephaner Berg 3, 85354 Freising, and Munich Center For Integrated Protein Science (CIPS), Germany
| | - Aphrodite Kapurniotu
- Fachgebiet Peptidbiochemie, Technische Universität München, Emil-Erlenmeyer-Forum 5, 85354 Freising, Germany
| | - Charles R. Sanders
- Department of Biochemistry and Center for Structural Biology, Vanderbilt University School of Medicine, Nashville, Tennessee USA 37232-8725
| | - Christina Scharnagl
- Fakultät für Physik E14, Technische Universität München, Maximus-von-Imhof-Forum 4, 85354 Freising, Germany
| | - Dieter Langosch
- Lehrstuhl Chemie der Biopolymere, Technische Universität München, Weihenstephaner Berg 3, 85354 Freising, and Munich Center For Integrated Protein Science (CIPS), Germany
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14
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Chen WW, Sing Tay DK, Leong SSJ, Kwak SK. Three-dimensional structure of human β-defensin 28 via homology modelling and molecular dynamics. MOLECULAR SIMULATION 2012. [DOI: 10.1080/08927022.2011.604854] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
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15
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Tay DKS, Rajagopalan G, Li X, Chen Y, Lua LH, Leong SSJ. A new bioproduction route for a novel antimicrobial peptide. Biotechnol Bioeng 2010; 108:572-81. [DOI: 10.1002/bit.22970] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2010] [Revised: 08/31/2010] [Accepted: 09/30/2010] [Indexed: 11/07/2022]
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16
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Poschner BC, Fischer K, Herrmann JR, Hofmann MW, Langosch D. Structural features of fusogenic model transmembrane domains that differentially regulate inner and outer leaflet mixing in membrane fusion. Mol Membr Biol 2010; 27:1-10. [PMID: 19939203 DOI: 10.3109/09687680903362044] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
The transmembrane domains of fusion proteins are known to be important for their fusogenic activity. In an effort to systematically investigate the structure/function relationships of transmembrane domains we had previously designed LV-peptides that mimic natural fusion protein TMDs in their ability to drive fusion after incorporation into liposomal membranes. Here, we investigate the impact of different structural features of LV-peptide TMDs on inner and outer leaflet mixing. We find that fusion driven by the helical peptides involves a hemifusion intermediate as previously seen for natural fusion proteins. Helix backbone dynamics enhances fusion by selectively promoting outer leaflet mixing. Furthermore, the hydrophobic length of the peptides as well as covalent attachment of long acyl chains affects outer and inner leaflet mixing to different extents. Different structural features of transmembrane domains thus appear to differentially influence the rearrangements of lipids in fusion initiation and the hemifusion-to-fusion transition. The relevance of these findings in respect to the function of natural fusion proteins is discussed.
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Affiliation(s)
- Bernhard C Poschner
- Lehrstuhl Chemie der Biopolymere, Technische Universität München, Weihenstephaner Berg 3, 85354 Freising, and Munich Center for Integrated Protein Science (CIPSM), Germany
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17
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Jákli I, Perczel A. The inherent flexibility of peptides and protein fragments quantitized by CD in conjunction with CCA+. J Pept Sci 2009; 15:738-52. [PMID: 19768692 DOI: 10.1002/psc.1169] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
ECD spectroscopy is traditionally used for rapid, non-atomic level structure analysis of natural products such as peptides and proteins. Unlike globular proteins, peptides less frequently adopt a single 3D-fold in a time average manner. Moreover, they exhibit an ensemble of conformers composed of a multitude of substantially different structures. In principle, both ECD- and vibrational circular dichroism (VCD)-spectroscopy are sensitive enough to pick up structural information on these dynamic ensembles. However, the interpretation of the raw spectral data of these highly dynamic molecular systems can be cumbersome. The herein presented Convex Constraint Analysis Plus method, or CCA+ for short (http://www.chem.elte.hu/departments/protnmr/cca/), provides a unique opportunity for spectral ensemble analysis of peptides, glycopeptides, peptidomimetics, and other foldamers. The precision and accuracy of the approach is presented here through different peptide model systems. An interesting temperature and pH dependent folding and unfolding of a miniprotein (e.g. Tc5b variant) is also described. Analysis of CD spectra sets strongly affected by solvent and ion type is also introduced to account for severe environmental-induced structure influencing effect(s). The deconvolution makes always possible the quantitative data analysis even when the interpretation of the deconvolution resulted in pure CD curves is complex.
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Affiliation(s)
- Imre Jákli
- Laboratory of Structural Chemistry and Biology, Institute of Chemistry, Eötvös Loránd University, Pázmány Péter sétány 1/A, H-1117, Budapest, Hungary
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18
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Poschner BC, Langosch D. Stabilization of conformationally dynamic helices by covalently attached acyl chains. Protein Sci 2009; 18:1801-5. [PMID: 19569191 DOI: 10.1002/pro.155] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Acylation of proteins is known to mediate membrane attachment and to influence subcellular sorting. Here, we report that acylation can stabilize secondary structure. Circular dichroism spectroscopy showed that N-terminal attachment of acyl chains decreases the ability of an intrinsically flexible hydrophobic model peptide to refold from an alpha-helical state to beta-sheet in response to changing solvent conditions. Acylation also stabilized the membrane-embedded alpha-helix. This increase of global helix stability did not result from decreased local conformational dynamics of the helix backbone as assessed by deuterium/hydrogen-exchange experiments. We concluded that acylation can stabilize the structure of intrinsically dynamic helices and may thus prevent misfolding.
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Affiliation(s)
- Bernhard C Poschner
- Lehrstuhl Chemie der Biopolymere, Technische Universität München, 85354 Freising, Germany
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19
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Gössler-Schöfberger R, Hesser G, Muik M, Wechselberger C, Jilek A. An orphan dermaseptin from frog skin reversibly assembles to amyloid-like aggregates in a pH-dependent fashion. FEBS J 2009; 276:5849-59. [PMID: 19765079 DOI: 10.1111/j.1742-4658.2009.07266.x] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Dermaseptin PD-3-7 (aDrs) from frog skin contains three aspartic acid residues resulting in a negative net charge at neutral pH, as opposed to numerous other dermaseptins which are cationic helical antimicrobial peptides. Still, this peptide can be fitted into an amphipathic alpha helix by an Edmundson wheel projection. However, folding to the proposed helix was induced to only a low extent by zwitterionic vesicles or even detergents. Furthermore, no evidence of antibacterial or cytotoxic activity from soluble aDrs could be obtained. The peptide has an inherent propensity to an extended conformation in aqueous solution and self-assembles into amyloid fibrils in a reversible pH-controlled fashion, which was studied in some detail; above pH 5, the amyloid fibrils disassemble in a cooperative manner. This is probably caused by deprotonation of both side chain and terminal carboxyl groups, which results in intermolecular electrostatic repulsion. At neutral pH, this process proceeds instantaneously to the soluble form. Within the transition interval (pH 5-6.5), however, 'backward' granular aggregates, 10-500 nm in size, are formed. Such metastable amorphous aggregates, which are quickly released from an amyloid depot by a shift in pH, can mediate a strong cytotoxic effect. This activity does not involve lysis or interference with the cellular redox status, but apparently acts via an as yet unidentified mechanism. In this study, we present a new member of an emerging class of self-assembling frog skin peptides with extraordinary self-aggregation properties, which may potentially be relevant for biological processes. Structured digital abstract: * MINT-7256467: Dermaseptin (uniprotkb:O93455) and Dermaseptin (uniprotkb:O93455) bind (MI:0407) by circular dichroism (MI:0016) * MINT-7255686: Dermaseptin (uniprotkb:O93455) and Dermaseptin (uniprotkb:O93455) bind (MI:0407) by biophysical (MI:0013) * MINT-7256439: Dermaseptin (uniprotkb:O93455) and Dermaseptin (uniprotkb:O93455) bind (MI:0407) by fluorescence microscopy (MI:0416) * MINT-7256449: Dermaseptin (uniprotkb:O93455) and Dermaseptin (uniprotkb:O93455) bind (MI:0407) by electron microscopy (MI:0040) * MINT-7256430: Dermaseptin (uniprotkb:O93455) and Dermaseptin (uniprotkb:O93455) bind (MI:0407) by fluorescence technologies (MI:0051).
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20
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Poschner BC, Quint S, Hofmann MW, Langosch D. Sequence-specific conformational dynamics of model transmembrane domains determines their membrane fusogenic function. J Mol Biol 2009; 386:733-41. [PMID: 19154744 DOI: 10.1016/j.jmb.2008.12.077] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2008] [Accepted: 12/29/2008] [Indexed: 10/21/2022]
Abstract
The transmembrane domains of fusion proteins are known to be functionally important and display an overabundance of helix-destabilizing Ile and Val residues. In an effort to systematically study the relationship of fusogenicity and helix stability, we previously designed LV peptides, a low-complexity model system whose hydrophobic core consists of Leu and Val residues at different ratios. The ability of LV peptides to fuse membranes increases with the content of helix-destabilizing residues. Here, we monitored the kinetics of amide deuterium/hydrogen exchange of LV-peptide helices to probe their conformational dynamics. The kinetics indeed increases strongly with the content of helix-destabilizing residues and is likely to reflect local fluctuations of the helix backbones as all peptides exhibit uncorrelated exchange and contain subpopulations of amide deuterium atoms that exchange with different velocities. Interestingly, helices whose amide deuterium atoms are shifted from slower to faster subpopulations are more fusogenic. Novel peptide variants in which Val residues are concentrated at peripheral or central domains of the hydrophobic core were designed to map functionally relevant helix subdomains. Their structural and functional analysis suggests that dynamic domains close to the helix termini are more relevant for fusogenicity than central domains but cooperate with the latter to achieve strong fusogenicity.
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Affiliation(s)
- Bernhard C Poschner
- Lehrstuhl für Chemie der Biopolymere, Technische Universität München, Weihenstephaner Berg 3, 85354 Freising, Germany
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21
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Weigang LMM, Langosch D, Letzel T. Gas-phase behavior of noncovalent transmembrane segment complexes. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2008; 22:4089-4097. [PMID: 19025888 DOI: 10.1002/rcm.3843] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Specific helix oligomerization between transmembrane segments (TMSs) is often promoted by motifs like GxxxG. Disruption of this motif in the transmembrane segments of vesicular stomatitis virus G-protein and of glycophorin A results in a reduced dimerization level studied by in vivo systems like ToxR. This paper reports the influence of sequence motifs like GxxxG in solution and the gas phase.The transmembrane segments may behave differently in the gas and liquid phase, because of the absence of surrounding solvent molecules in the gas phase. Comparison of experiments depending on peptide properties performed in the gas and liquid phase discloses that the peptides retain 'some memory' of their liquid-phase structure in the gas phase. A direct correlation has been found between helicity in solution as determined by circular dichroism and dimerization in the gas phase monitored by electrospray mass spectrometry. These results show that a proper folding in solution is required for oligomerization.On the other hand, sequence-specific oligomerization depending on the GxxxG motif was not observed with the mass spectrometric detection. Further on, neither concentration-dependent complex studies nor studies regarding complex stability in the gas phase - via collision-induced dissociation (CID) - led to sequence-specific differences.Finally, the findings show that in mass spectrometric measurements noncovalent interactions of studied TMSs is rather more dependent on the secondary structure and proper folding than on their primary structure.
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Affiliation(s)
- Linda M M Weigang
- Lehrstuhl für Chemie der Biopolymere, Department für Biowissenschaftliche Grundlagen, Technische Universität München, Weihenstephaner Berg 3, 85354 Freising - Weihenstephan, Germany
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22
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Rocha S, Thünemann AF, Pereira MDC, Coelho M, Möhwald H, Brezesinski G. Influence of fluorinated and hydrogenated nanoparticles on the structure and fibrillogenesis of amyloid beta-peptide. Biophys Chem 2008; 137:35-42. [PMID: 18625543 DOI: 10.1016/j.bpc.2008.06.010] [Citation(s) in RCA: 95] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2008] [Revised: 06/21/2008] [Accepted: 06/23/2008] [Indexed: 12/20/2022]
Abstract
Peptide aggregation in amyloid fibrils is implicated in the pathogenesis of several diseases such as Alzheimer's disease. There is a strong correlation between amyloid fibril formation and a decrease in conformational stability of the native state. Amyloid-beta peptide (Abeta), the aggregating peptide in Alzheimer's disease, is natively unfolded. The deposits found in Alzheimer's disease are composed of Abeta fibrillar aggregates rich in beta-sheet structure. The influence of fluorinated complexes on the secondary structure and fibrillogenesis of Abeta peptide was studied by circular dichroism (CD) spectroscopy and transmission electron microscopy (TEM). CD spectra show that complexes of polyampholyte and fluorinated dodecanoic acid induce alpha-helix structure in Abeta, but their hydrogenated analogous lead to beta-sheet formation and aggregation. The fluorinated nanoparticles with highly negative zeta potential and hydrophobic fluorinated core have the fundamental characteristics to prevent Abeta fibrillogenesis.
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Affiliation(s)
- Sandra Rocha
- LEPAE, Dept. of Chemical Engineering, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal.
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23
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Meinke G, Ezeokonkwo C, Balbo P, Stafford W, Moore C, Bohm A. Structure of yeast poly(A) polymerase in complex with a peptide from Fip1, an intrinsically disordered protein. Biochemistry 2008; 47:6859-69. [PMID: 18537269 DOI: 10.1021/bi800204k] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In yeast, the mRNA processing enzyme poly(A) polymerase is tethered to the much larger 3'-end processing complex via Fip1, a 36 kDa protein of unknown structure. We report the 2.6 A crystal structure of yeast poly(A) polymerase in complex with a peptide containing residues 80-105 of Fip1. The Fip1 peptide binds to the outside surface of the C-terminal domain of the polymerase. On the basis of this structure, we designed a mutant of the polymerase (V498Y, C485R) that is lethal to yeast. The mutant is unable to bind Fip1 but retains full polymerase activity. Fip1 is found in all eukaryotes and serves to connect poly(A) polymerase to pre-mRNA processing complexes in yeast, plants, and mammals. However, the Fip1 sequence is highly divergent, and residues on both Pap1 and Fip1 at the observed interaction surface are poorly conserved. Herein we demonstrate using analytical ultracentrifugation, circular dichroism, proteolytic studies, and other techniques that, in the absence of Pap1, Fip1 is largely, if not completely, unfolded. We speculate that flexibility may be important for Fip1's function as a molecular scaffold.
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Affiliation(s)
- Gretchen Meinke
- Department of Biochemistry, Tufts University, 136 Harrison Avenue, Boston, Massachusetts 02111, USA
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24
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Secondary structure and distribution of fusogenic LV-peptides in lipid membranes. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2007; 37:435-45. [DOI: 10.1007/s00249-007-0233-4] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2007] [Revised: 10/11/2007] [Accepted: 10/28/2007] [Indexed: 11/26/2022]
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