1
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Miura Y. The conformational properties of alamethicin in ethanol studied by NMR. EUROPEAN BIOPHYSICS JOURNAL : EBJ 2024:10.1007/s00249-024-01711-1. [PMID: 38849514 DOI: 10.1007/s00249-024-01711-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Revised: 04/02/2024] [Accepted: 05/10/2024] [Indexed: 06/09/2024]
Abstract
Alamethicin, a peptide consisted of 20 amino acid residues, has been known to function as an antibiotic. The peptides self-associate in biological membranes, form an ion channel, and then induce cell death by leaking intracellular contents through a transmembrane pore of an ion channel. We investigated conformation and its thermal stability of alamethicin-A6 and -U6 in ethanol using proton nuclear magnetic resonance (NMR) spectroscopy; alamethicin-A6 and -U6 have the amino acid sequences of UPUAUAQUVUGLUPVUUQQO and UPUAUUQUVUGLUPVUUQQO, respectively, where U and O represent α-aminoisobutyric acid and phenylalaninol, respectively. As indicated by the under bars in the sequences, only the residue 6 differs between the alamethicins. We show that the alamethicins in ethanol form helix conformation in the region of the residues 2-11 and a non-regular conformation in the regions of the N- and C-termini, and that the helices are maintained up to 66 °C at least. Conformations in the region of the residues 12-18 of the alamethicins, however, are not well identified due to the lack of NMR data. In addition, we demonstrate that the amide proton chemical shift temperature coefficients' method, which is known as an indicator for intramolecular hydrogen bonds in peptides and proteins in aqueous solutions, can be also applied to the alamethicins in ethanol. Further, we show that the conformation around the C-terminus of alamethicin-A6 is restrained by intramolecular hydrogen bonds, whereas that of alamethicin-U6 is either restrained or unrestrained by intramolecular hydrogen bonds; the alamethicin-U6 molecules having the restrained and unrestrained conformations coexist in ethanol. We discuss the two types of conformations using a model chain consisting of particles linked by rigid bonds called as the free jointed chain.
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Affiliation(s)
- Yoshinori Miura
- Center for Advanced Instrumental Analysis, Kyushu University, Kasuga, 816-8580, Japan.
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2
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Herrera-León C, Ramos-Martín F, Antonietti V, Sonnet P, D'Amelio N. The impact of phosphatidylserine exposure on cancer cell membranes on the activity of the anticancer peptide HB43. FEBS J 2021; 289:1984-2003. [PMID: 34767285 DOI: 10.1111/febs.16276] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Revised: 10/19/2021] [Accepted: 11/10/2021] [Indexed: 02/04/2023]
Abstract
HB43 (FAKLLAKLAKKLL) is a synthetic peptide active against cell lines derived from breast, colon, melanoma, lung, prostate, and cervical cancers. Despite its remarkable spectrum of activity, the mechanism of action at the molecular level has never been investigated, preventing further optimization of its selectivity. The alternation of charged and hydrophobic residues suggests amphipathicity, but the formation of alpha-helical structure seems discouraged by its short length and the large number of positively charged residues. Using different biophysical and in silico approaches we show that HB43 is completely unstructured in solution but assumes alpha-helical conformation in the presence of DPC micelles and liposomes exposing phosphatidylserine (PS) used as mimics of cancer cell membranes. Membrane permeabilization assays demonstrate that the interaction leads to the preferential destabilization of PS-containing vesicles with respect to PC-containing ones, here used as noncancerous cell mimics. ssNMR reveals that HB43 is able to fluidify the internal structure of cancer-cell mimicking liposomes while MD simulations show its internalization in such bilayers. This is achieved by the formation of specific interactions between the lysine side chains and the carboxylate group of phosphatidylserine and/or the phosphate oxygen atoms of targeted phospholipids, which could catalyze the formation of the alpha helix required for internalization. With the aim of better understanding the peptide biocompatibility and the additional antibacterial activity, the interaction with noncancerous cell mimicking liposomes exposing phosphatidylcholine (PC) and bacterial mimicking bilayers exposing phosphatidylglycerol (PG) is also described.
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Affiliation(s)
- Claudia Herrera-León
- Unité de Génie Enzymatique et Cellulaire, UMR 7025, CNRS, Université de Picardie Jules Verne, Amiens, France
| | - Francisco Ramos-Martín
- Unité de Génie Enzymatique et Cellulaire, UMR 7025, CNRS, Université de Picardie Jules Verne, Amiens, France
| | - Viviane Antonietti
- Agents Infectieux, Résistance et Chimiothérapie, UFR de Pharmacie, AGIR UR 4294, Université de Picardie Jules Verne, Amiens, France
| | - Pascal Sonnet
- Agents Infectieux, Résistance et Chimiothérapie, UFR de Pharmacie, AGIR UR 4294, Université de Picardie Jules Verne, Amiens, France
| | - Nicola D'Amelio
- Unité de Génie Enzymatique et Cellulaire, UMR 7025, CNRS, Université de Picardie Jules Verne, Amiens, France
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3
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Majeed S, Ahmad AB, Sehar U, Georgieva ER. Lipid Membrane Mimetics in Functional and Structural Studies of Integral Membrane Proteins. MEMBRANES 2021; 11:685. [PMID: 34564502 PMCID: PMC8470526 DOI: 10.3390/membranes11090685] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 08/18/2021] [Accepted: 08/30/2021] [Indexed: 12/12/2022]
Abstract
Integral membrane proteins (IMPs) fulfill important physiological functions by providing cell-environment, cell-cell and virus-host communication; nutrients intake; export of toxic compounds out of cells; and more. However, some IMPs have obliterated functions due to polypeptide mutations, modifications in membrane properties and/or other environmental factors-resulting in damaged binding to ligands and the adoption of non-physiological conformations that prevent the protein from returning to its physiological state. Thus, elucidating IMPs' mechanisms of function and malfunction at the molecular level is important for enhancing our understanding of cell and organism physiology. This understanding also helps pharmaceutical developments for restoring or inhibiting protein activity. To this end, in vitro studies provide invaluable information about IMPs' structure and the relation between structural dynamics and function. Typically, these studies are conducted on transferred from native membranes to membrane-mimicking nano-platforms (membrane mimetics) purified IMPs. Here, we review the most widely used membrane mimetics in structural and functional studies of IMPs. These membrane mimetics are detergents, liposomes, bicelles, nanodiscs/Lipodisqs, amphipols, and lipidic cubic phases. We also discuss the protocols for IMPs reconstitution in membrane mimetics as well as the applicability of these membrane mimetic-IMP complexes in studies via a variety of biochemical, biophysical, and structural biology techniques.
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Affiliation(s)
- Saman Majeed
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79409, USA
| | - Akram Bani Ahmad
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79409, USA
| | - Ujala Sehar
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79409, USA
| | - Elka R Georgieva
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79409, USA
- Department of Cell Physiology and Molecular Biophysics, Texas Tech University Health Science Center, Lubbock, TX 79409, USA
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4
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Chang Z, Deng J, Zhao W, Yang J. Exploring interactions between lipids and amyloid-forming proteins: A review on applying fluorescence and NMR techniques. Chem Phys Lipids 2021; 236:105062. [PMID: 33600803 DOI: 10.1016/j.chemphyslip.2021.105062] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 01/27/2021] [Accepted: 02/12/2021] [Indexed: 12/13/2022]
Abstract
A hallmark of Alzheimer's, Parkinson's, and other amyloid diseases is the assembly of amyloid proteins into amyloid aggregates or fibrils. In many cases, the formation and cytotoxicity of amyloid assemblies are associated with their interaction with cell membranes. Despite studied for many years, the characterization of the interaction is challenged for reasons on the multiple aggregation states of amyloid-forming proteins, transient and weak interactions in the complex system. Although several strategies such as computation biology, spectroscopy, and imaging methods have been performed, there is an urgent need to detail the molecular mechanism in different time scales and high resolutions. This review highlighted the recent applications of fluorescence, solution and solid-state NMR in exploring the interactions between amyloid protein and membranes attributing to their advantages of high sensitivity and atomic resolution.
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Affiliation(s)
- Ziwei Chang
- National Center for Magnetic Resonance in Wuhan, Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan, 430071, PR China
| | - Jing Deng
- National Center for Magnetic Resonance in Wuhan, Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan, 430071, PR China; University of Chinese Academy of Sciences, Beijing, 100049, PR China
| | - Weijing Zhao
- National Center for Magnetic Resonance in Wuhan, Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan, 430071, PR China
| | - Jun Yang
- National Center for Magnetic Resonance in Wuhan, Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan, 430071, PR China; Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, 430074, PR China.
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5
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Zhou S, Pettersson P, Huang J, Brzezinski P, Pomès R, Mäler L, Ädelroth P. NMR Structure and Dynamics Studies of Yeast Respiratory Supercomplex Factor 2. Structure 2020; 29:275-283.e4. [PMID: 32905793 DOI: 10.1016/j.str.2020.08.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Revised: 08/12/2020] [Accepted: 08/19/2020] [Indexed: 12/22/2022]
Abstract
The Saccharomyces cerevisiae respiratory supercomplex factor 2 (Rcf2) is a 224-residue protein located in the mitochondrial inner membrane where it is involved in the formation of supercomplexes composed of cytochrome bc1 and cytochrome c oxidase. We previously demonstrated that Rcf2 forms a dimer in dodecylphosphocholine micelles, and here we report the solution NMR structure of this Rcf2 dimer. Each Rcf2 monomer has two soluble α helices and five putative transmembrane (TM) α helices, including an unexpectedly charged TM helix at the C terminus, which mediates dimer formation. The NOE contacts indicate the presence of inter-monomer salt bridges and hydrogen bonds at the dimer interface, which stabilize the Rcf2 dimer structure. Moreover, NMR chemical shift change mapping upon lipid titrations as well as molecular dynamics analysis reveal possible structural changes upon embedding Rcf2 into a native lipid environment. Our results contribute to the understanding of respiratory supercomplex formation and regulation.
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Affiliation(s)
- Shu Zhou
- Department of Biochemistry and Biophysics, Stockholm University, 10691 Stockholm, Sweden; High Magnetic Field Laboratory, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230031, China
| | - Pontus Pettersson
- Department of Biochemistry and Biophysics, Stockholm University, 10691 Stockholm, Sweden
| | - Jingjing Huang
- Molecular Medicine, The Hospital for Sick Children, Toronto, Department of Biochemistry, University of Toronto, Toronto, Ontario M5G 0A4, Canada
| | - Peter Brzezinski
- Department of Biochemistry and Biophysics, Stockholm University, 10691 Stockholm, Sweden
| | - Régis Pomès
- Molecular Medicine, The Hospital for Sick Children, Toronto, Department of Biochemistry, University of Toronto, Toronto, Ontario M5G 0A4, Canada
| | - Lena Mäler
- Department of Biochemistry and Biophysics, Stockholm University, 10691 Stockholm, Sweden.
| | - Pia Ädelroth
- Department of Biochemistry and Biophysics, Stockholm University, 10691 Stockholm, Sweden.
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6
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Geudens N, Kovács B, Sinnaeve D, Oni FE, Höfte M, Martins JC. Conformation and Dynamics of the Cyclic Lipopeptide Viscosinamide at the Water-Lipid Interface. Molecules 2019; 24:E2257. [PMID: 31213011 PMCID: PMC6630293 DOI: 10.3390/molecules24122257] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2019] [Revised: 06/11/2019] [Accepted: 06/13/2019] [Indexed: 12/19/2022] Open
Abstract
Cyclic lipodepsipeptides or CLiPs from Pseudomonas are secondary metabolites that mediate a wide range of biological functions for their producers, and display antimicrobial and anticancer activities. Direct interaction of CLiPs with the cellular membranes is presumed to be essential in causing these. To understand the processes involved at the molecular level, knowledge of the conformation and dynamics of CLiPs at the water-lipid interface is required to guide the interpretation of biophysical investigations in model membrane systems. We used NMR and molecular dynamics to study the conformation, location and orientation of the Pseudomonas CLiP viscosinamide in a water/dodecylphosphocholine solution. In the process, we demonstrate the strong added value of combining uniform, isotope-enriched viscosinamide and protein NMR methods. In particular, the use of techniques to determine backbone dihedral angles and detect and identify long-lived hydrogen bonds, establishes that the solution conformation previously determined in acetonitrile is maintained in water/dodecylphosphocholine solution. Paramagnetic relaxation enhancements pinpoint viscosinamide near the water-lipid interface, with its orientation dictated by the amphipathic distribution of hydrophobic and hydrophilic residues. Finally, the experimental observations are supported by molecular dynamics simulations. Thus a firm structural basis is now available for interpreting biophysical and bioactivity data relating to this class of compounds.
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Affiliation(s)
- Niels Geudens
- NMR and Structural Analysis Unit, Department of Organic and Macromolecular Chemistry, GhentUniversity, Campus Sterre, S4, Krijgslaan 281, B-9000 Gent, Belgium.
| | - Benjámin Kovács
- NMR and Structural Analysis Unit, Department of Organic and Macromolecular Chemistry, GhentUniversity, Campus Sterre, S4, Krijgslaan 281, B-9000 Gent, Belgium.
| | - Davy Sinnaeve
- NMR and Structural Analysis Unit, Department of Organic and Macromolecular Chemistry, GhentUniversity, Campus Sterre, S4, Krijgslaan 281, B-9000 Gent, Belgium.
| | - Feyisara Eyiwumi Oni
- Laboratory of Phytopathology, Department of Plants and Crops, Ghent University, Coupure Links 653, B-9000 Gent, Belgium.
| | - Monica Höfte
- Laboratory of Phytopathology, Department of Plants and Crops, Ghent University, Coupure Links 653, B-9000 Gent, Belgium.
| | - José C Martins
- NMR and Structural Analysis Unit, Department of Organic and Macromolecular Chemistry, GhentUniversity, Campus Sterre, S4, Krijgslaan 281, B-9000 Gent, Belgium.
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7
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Mandaliti W, Nepravishta R, Pica F, Vallebona PS, Garaci E, Paci M. Potential mechanism of thymosin-α1-membrane interactions leading to pleiotropy: experimental evidence and hypotheses. Expert Opin Biol Ther 2018; 18:33-42. [DOI: 10.1080/14712598.2018.1456527] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Walter Mandaliti
- Department of Chemical Sciences and Technologies, University of Rome “Tor Vergata”, Rome, Italy
| | - Ridvan Nepravishta
- Department of Chemical Sciences and Technologies, University of Rome “Tor Vergata”, Rome, Italy
- School of Pharmacy, East Anglia University, Norwich, UK
| | - Francesca Pica
- Department of Experimental Medicine and Surgery, University of Rome “Tor Vergata”, Rome, Italy
| | | | - Enrico Garaci
- San Raffaele Pisana Scientific Institute for Research, Hospitalization and Health Care, Rome, Italy
| | - Maurizio Paci
- Department of Chemical Sciences and Technologies, University of Rome “Tor Vergata”, Rome, Italy
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8
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Pettersson P, Ye W, Jakob M, Tannert F, Klösgen RB, Mäler L. Structure and dynamics of plant TatA in micelles and lipid bilayers studied by solution NMR. FEBS J 2018; 285:1886-1906. [PMID: 29654717 DOI: 10.1111/febs.14452] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Revised: 03/09/2018] [Accepted: 03/27/2018] [Indexed: 12/21/2022]
Abstract
The twin-arginine translocase (Tat) transports folded proteins across the cytoplasmic membrane of prokaryotes and the thylakoid membrane of plant chloroplasts. In Gram-negative bacteria and chloroplasts, the translocon consists of three subunits, TatA, TatB, and TatC, of which TatA is responsible for the actual membrane translocation of the substrate. Herein we report on the structure, dynamics, and lipid interactions of a fully functional C-terminally truncated 'core TatA' from Arabidopsis thaliana using solution-state NMR. Our results show that TatA consists of a short N-terminal transmembrane helix (TMH), a short connecting linker (hinge) and a long region with propensity to form an amphiphilic helix (APH). The dynamics of TatA were characterized using 15 N relaxation NMR in combination with model-free analysis. The TMH has order parameters characteristic of a well-structured helix, the hinge is somewhat less rigid, while the APH has lower order parameters indicating structural flexibility. The TMH is short with a surprisingly low protection from solvent, and only the first part of the APH is protected to some extent. In order to uncover possible differences in TatA's structure and dynamics in detergent compared to in a lipid bilayer, fast-tumbling bicelles and large unilamellar vesicles were used. Results indicate that the helicity of TatA increases in both the TMH and APH in the presence of lipids, and that the N-terminal part of the TMH is significantly more rigid. The results indicate that plant TatA has a significant structural plasticity and a capability to adapt to local environments.
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Affiliation(s)
- Pontus Pettersson
- Department of Biochemistry and Biophysics, Stockholm University, Sweden
| | - Weihua Ye
- Department of Biochemistry and Biophysics, Stockholm University, Sweden
| | - Mario Jakob
- Institut für Biologie, Institutsbereich Pflanzenphysiologie, Martin-Luther University, Halle, Germany
| | - Franzisca Tannert
- Institut für Biologie, Institutsbereich Pflanzenphysiologie, Martin-Luther University, Halle, Germany
| | - Ralf Bernd Klösgen
- Institut für Biologie, Institutsbereich Pflanzenphysiologie, Martin-Luther University, Halle, Germany
| | - Lena Mäler
- Department of Biochemistry and Biophysics, Stockholm University, Sweden
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9
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Solution NMR structure of yeast Rcf1, a protein involved in respiratory supercomplex formation. Proc Natl Acad Sci U S A 2018; 115:3048-3053. [PMID: 29507228 DOI: 10.1073/pnas.1712061115] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
The Saccharomyces cerevisiae respiratory supercomplex factor 1 (Rcf1) protein is located in the mitochondrial inner membrane where it is involved in formation of supercomplexes composed of respiratory complexes III and IV. We report the solution structure of Rcf1, which forms a dimer in dodecylphosphocholine (DPC) micelles, where each monomer consists of a bundle of five transmembrane (TM) helices and a short flexible soluble helix (SH). Three TM helices are unusually charged and provide the dimerization interface consisting of 10 putative salt bridges, defining a "charge zipper" motif. The dimer structure is supported by molecular dynamics (MD) simulations in DPC, although the simulations show a more dynamic dimer interface than the NMR data. Furthermore, CD and NMR data indicate that Rcf1 undergoes a structural change when reconstituted in liposomes, which is supported by MD data, suggesting that the dimer structure is unstable in a planar membrane environment. Collectively, these data indicate a dynamic monomer-dimer equilibrium. Furthermore, the Rcf1 dimer interacts with cytochrome c, suggesting a role as an electron-transfer bridge between complexes III and IV. The Rcf1 structure will help in understanding its functional roles at a molecular level.
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10
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Loffredo MR, Ghosh A, Harmouche N, Casciaro B, Luca V, Bortolotti A, Cappiello F, Stella L, Bhunia A, Bechinger B, Mangoni ML. Membrane perturbing activities and structural properties of the frog-skin derived peptide Esculentin-1a(1-21)NH2 and its Diastereomer Esc(1-21)-1c: Correlation with their antipseudomonal and cytotoxic activity. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2017; 1859:2327-2339. [DOI: 10.1016/j.bbamem.2017.09.009] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Revised: 08/21/2017] [Accepted: 09/08/2017] [Indexed: 01/21/2023]
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11
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Pérez Y, Gómara MJ, Yuste E, Gómez-Gutierrez P, Pérez JJ, Haro I. Structural Study of a New HIV-1 Entry Inhibitor and Interaction with the HIV-1 Fusion Peptide in Dodecylphosphocholine Micelles. Chemistry 2017; 23:11703-11713. [DOI: 10.1002/chem.201702531] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2017] [Indexed: 11/07/2022]
Affiliation(s)
- Yolanda Pérez
- Nuclear Magnetic Resonance Facility; IQAC-CSIC; Jordi Girona, 18-26 08034 Barcelona Spain
| | - Maria José Gómara
- Unit of Synthesis and Biomedical Applications of Peptides; IQAC-CSIC; Jordi Girona, 18-26 08034 Barcelona Spain
| | - Eloísa Yuste
- Department of Chemical Engineering (ETSEIB); Universitat Politecnica de Catalunya; 08034 Barcelona Spain
- Present address: AIDS Immunopathology Unit; Centro Nacional Microbiología; Instituto de Salud Carlos III; 28029 Madrid Spain
| | | | | | - Isabel Haro
- Unit of Synthesis and Biomedical Applications of Peptides; IQAC-CSIC; Jordi Girona, 18-26 08034 Barcelona Spain
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12
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Liebau J, Mäler L. Immersion Depths of Lipid Carbons in Bicelles Measured by Paramagnetic Relaxation Enhancement. J Phys Chem B 2017; 121:7660-7670. [DOI: 10.1021/acs.jpcb.7b05822] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Jobst Liebau
- Department of Biochemistry
and Biophysics, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Lena Mäler
- Department of Biochemistry
and Biophysics, Stockholm University, SE-106 91 Stockholm, Sweden
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13
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Liebau J, Ye W, Mäler L. Characterization of fast-tumbling isotropic bicelles by PFG diffusion NMR. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2017; 55:395-404. [PMID: 26662467 DOI: 10.1002/mrc.4399] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2015] [Revised: 11/12/2015] [Accepted: 11/17/2015] [Indexed: 06/05/2023]
Abstract
Small isotropic bicelles are versatile membrane mimetics, which, in contrast to micelles, provide a lipid bilayer and are at the same time suitable for solution-state NMR studies. The lipid composition of the bilayer is flexible allowing for incorporation of various head groups and acyl chain types. In bicelles, lipids are solubilized by detergents, which are localized in the rim of the disk-shaped lipid bilayer. Bicelles have been characterized by a broad array of biophysical methods, pulsed-field gradient NMR (PFG NMR) being one of them. PFG NMR can readily be used to measure diffusion coefficients of macromolecules. It is thus employed to characterize bicelle size and morphology. Even more importantly, PFG NMR can be used to study the degree of protein association to membranes. Here, we present the advances that have been made in producing small, fast-tumbling isotropic bicelles from a variety of lipids and detergents, together with insights on the morphology of such mixtures gained from PFG NMR. Furthermore, we review approaches to study protein-membrane interaction by PFG NMR. Copyright © 2015 John Wiley & Sons, Ltd.
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Affiliation(s)
- Jobst Liebau
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Weihua Ye
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Lena Mäler
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
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14
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Mukherjee J, Gupta MN. Protein aggregates: Forms, functions and applications. Int J Biol Macromol 2017; 97:778-789. [DOI: 10.1016/j.ijbiomac.2016.11.014] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2015] [Revised: 11/02/2016] [Accepted: 11/05/2016] [Indexed: 11/15/2022]
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15
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Abstract
Membrane proteins play a most important part in metabolism, signaling, cell motility, transport, development, and many other biochemical and biophysical processes which constitute fundamentals of life on the molecular level. Detailed understanding of these processes is necessary for the progress of life sciences and biomedical applications. Nanodiscs provide a new and powerful tool for a broad spectrum of biochemical and biophysical studies of membrane proteins and are commonly acknowledged as an optimal membrane mimetic system that provides control over size, composition, and specific functional modifications on the nanometer scale. In this review we attempted to combine a comprehensive list of various applications of nanodisc technology with systematic analysis of the most attractive features of this system and advantages provided by nanodiscs for structural and mechanistic studies of membrane proteins.
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Affiliation(s)
- Ilia G Denisov
- Department of Biochemistry and Department of Chemistry, University of Illinois , Urbana, Illinois 61801, United States
| | - Stephen G Sligar
- Department of Biochemistry and Department of Chemistry, University of Illinois , Urbana, Illinois 61801, United States
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16
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Wimmer R, Uggerhøj LE. Determination of Structure and Micellar Interactions of Small Antimicrobial Peptides by Solution-State NMR. Methods Mol Biol 2017; 1548:73-88. [PMID: 28013498 DOI: 10.1007/978-1-4939-6737-7_6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
NMR spectroscopy is a well-established technique to determine the structure of peptides and small proteins in solution, also when bound to detergent micelles or phospholipid bicelles. The structure of the peptide alone is, however, not conveying the full picture, if the peptide is bound to a micelle, since it does not tell anything about the orientation of the peptide in the micelle. This article describes how to obtain that information together with information on peptide structure.
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Affiliation(s)
- Reinhard Wimmer
- Department of Chemistry and Bioscience, University of Aalborg, Frederik Bajers vej 7H, 9220, Aalborg, Denmark.
| | - Lars Erik Uggerhøj
- Department of Chemistry and Bioscience, University of Aalborg, Frederik Bajers vej 7H, 9220, Aalborg, Denmark
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17
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Fast-tumbling bicelles constructed from native Escherichia coli lipids. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2016; 1858:2097-2105. [DOI: 10.1016/j.bbamem.2016.06.008] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Revised: 06/09/2016] [Accepted: 06/10/2016] [Indexed: 11/20/2022]
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18
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Naranjo AN, McNeely PM, Katsaras J, Robinson AS. Impact of purification conditions and history on A2A adenosine receptor activity: The role of CHAPS and lipids. Protein Expr Purif 2016; 124:62-7. [PMID: 27241126 DOI: 10.1016/j.pep.2016.05.015] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2016] [Revised: 05/23/2016] [Accepted: 05/26/2016] [Indexed: 02/08/2023]
Abstract
The adenosine A2A receptor (A2AR) is a much-studied class A G protein-coupled receptor (GPCR). For biophysical studies, A2AR is commonly purified in a detergent mixture of dodecylmaltoside (DDM), 3-(3-cholamidopropyl) dimethylammoniopropane sulfonate (CHAPS), and cholesteryl hemisuccinate (CHS). Here we studied the effects of CHAPS on the ligand binding activity and stability of wild type, full-length human A2AR. We also tested the cholesterol requirement for maintaining the active conformation of the receptor when solubilized in detergent micelles. To this end, the receptor was purified using DDM, DDM/CHAPS, or the short hydrocarbon chain lipid 1,2-dihexanoyl-sn-glycero-3-phosphocholine (DHPC, di-6:0PC). After solubilization in DDM, DDM/CHAPS, or DHPC micelles, although A2AR was found to retain its native-like fold, its binding ability was significantly compromised compared to DDM or DDM/CHAPS with CHS. It therefore appears that although cholesterol is not needed for A2AR to retain a native-like, α-helical conformation, it may be a critical component for high affinity ligand binding. Further, this result suggests that the conformational differences between the active and inactive protein may be so subtle that commonly used spectroscopic methods are unable to differentiate between the two forms, highlighting the need for activity measurements. The studies presented in this paper also underline the importance of the protein's purification history; i.e., detergents that interact with the protein during purification affect the ligand binding properties of the receptor in an irreversible manner.
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Affiliation(s)
- Andrea N Naranjo
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE 19711, United States
| | - Patrick M McNeely
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE 19711, United States
| | - John Katsaras
- Biology and Soft Matter Division, Neutron Sciences Directorate, Oak Ridge National Laboratory, Oak Ridge, TN 37831-6100, United States; Department of Physics and Astronomy, The University of Tennessee, Knoxville, TN 37996-1200, United States; Joint Institute for Neutron Sciences, Oak Ridge National Laboratory, Oak Ridge, TN 37831-6453, United States
| | - Anne Skaja Robinson
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE 19711, United States; Department of Chemical and Biomolecular Engineering, 300 Lindy Boggs Laboratory, Tulane University, New Orleans, LA 70118, United States.
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19
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Nepravishta R, Mandaliti W, Vallebona PS, Pica F, Garaci E, Paci M. Mechanism of Action of Thymosinα1: Does It Interact with Membrane by Recognition of Exposed Phosphatidylserine on Cell Surface? A Structural Approach. VITAMINS AND HORMONES 2016; 102:101-19. [PMID: 27450732 DOI: 10.1016/bs.vh.2016.04.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Thymosinα1 is a peptidic hormone with pleiotropic activity, which is used in the therapy of several diseases. It is unstructured in water solution and interacts with negative regions of micelles and vesicles assuming two tracts of helical conformation with a structural flexible break in between. The studies of the interaction of Thymosinα1 with micelles of mixed dipalmitoylphosphatidylcholine and sodium dodecylsulfate and vesicles with mixed dipalmitoylphosphatidylcholine/dipalmitoylphosphatidylserine, the latter the negative component of the membranes, by (1)H and natural abundance (15)N NMR are herewith reported, reviewed, and discussed. The results indicate that the preferred interactions are those where the surface is negatively charged due to sodium dodecylsulfate or due to the presence of dipalmitoylphosphatidylserine exposed on the surface. In fact the unbalance of dipalmitoylphosphatidylserine on the cellular surface is an important phenomenon present in pathological conditions of cells. Moreover, the direct interaction of Thymosinα1 with K562 cells presenting an overexposure of phosphatidylserine as a consequence of resveratrol-induced apoptosis was carried out.
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Affiliation(s)
- R Nepravishta
- University of Rome "Tor Vergata", Rome, Italy; Faculty of Pharmacy Catholic University "Our Lady of Good Counsel", Tirane, Albania
| | - W Mandaliti
- University of Rome "Tor Vergata", Rome, Italy
| | | | - F Pica
- University of Rome "Tor Vergata", Rome, Italy
| | - E Garaci
- University of Rome "Tor Vergata", Rome, Italy; San Raffaele Pisana Scientific Institute for Research, Hospitalization and Health Care, Rome, Italy
| | - M Paci
- University of Rome "Tor Vergata", Rome, Italy.
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20
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Liebau J, Pettersson P, Szpryngiel S, Mäler L. Membrane Interaction of the Glycosyltransferase WaaG. Biophys J 2016; 109:552-63. [PMID: 26244737 DOI: 10.1016/j.bpj.2015.06.036] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2015] [Revised: 06/17/2015] [Accepted: 06/19/2015] [Indexed: 11/30/2022] Open
Abstract
The glycosyltransferase WaaG is involved in the synthesis of lipopolysaccharides that constitute the outer leaflet of the outer membrane in Gram-negative bacteria such as Escherichia coli. WaaG has been identified as a potential antibiotic target, and inhibitor scaffolds have previously been investigated. WaaG is located at the cytosolic side of the inner membrane, where the enzyme catalyzes the transfer of the first outer-core glucose to the inner core of nascent lipopolysaccharides. Here, we characterized the binding of WaaG to membrane models designed to mimic the inner membrane of E. coli. Based on the crystal structure, we identified an exposed and largely α-helical 30-residue sequence, with a net positive charge and several aromatic amino acids, as a putative membrane-interacting region of WaaG (MIR-WaaG). We studied the peptide corresponding to this sequence, along with its bilayer interactions, using circular dichroism, fluorescence quenching, fluorescence anisotropy, and NMR. In the presence of dodecylphosphocholine, MIR-WaaG was observed to adopt a three-dimensional structure remarkably similar to the segment in the crystal structure. We found that the membrane interaction of WaaG is conferred at least in part by MIR-WaaG and that electrostatic interactions play a key role in binding. Moreover, we propose a mechanism of anchoring WaaG to the inner membrane of E. coli, where the central part of MIR-WaaG inserts into one leaflet of the bilayer. In this model, electrostatic interactions as well as surface-exposed Tyr residues bind WaaG to the membrane.
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Affiliation(s)
- Jobst Liebau
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Pontus Pettersson
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Scarlett Szpryngiel
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Lena Mäler
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden.
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21
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Mandaliti W, Nepravishta R, Sinibaldi Vallebona P, Pica F, Garaci E, Paci M. Thymosin α1 Interacts with Exposed Phosphatidylserine in Membrane Models and in Cells and Uses Serum Albumin as a Carrier. Biochemistry 2016; 55:1462-72. [DOI: 10.1021/acs.biochem.5b01345] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Walter Mandaliti
- Department
of Chemical Sciences and Technologies, University of Rome “Tor Vergata”, Via della Ricerca Scientifica 1, 00133 Rome, Italy
| | - Ridvan Nepravishta
- Department
of Chemical Sciences and Technologies, University of Rome “Tor Vergata”, Via della Ricerca Scientifica 1, 00133 Rome, Italy
- Department
of Chemical Pharmaceutical and Biomolecular Technologies, Faculty of Pharmacy Catholic University “Our Lady of Good Counsel”, Rr. D.
Hoxha, Tirane, Albania
| | - Paola Sinibaldi Vallebona
- Department
of Experimental Medicine and Surgery, University of Rome “Tor Vergata”, Via Montpellier 1, 00133 Rome, Italy
| | - Francesca Pica
- Department
of Experimental Medicine and Surgery, University of Rome “Tor Vergata”, Via Montpellier 1, 00133 Rome, Italy
| | - Enrico Garaci
- Department
of Experimental Medicine and Surgery, University of Rome “Tor Vergata”, Via Montpellier 1, 00133 Rome, Italy
- San
Raffaele Pisana Scientific Institute for Research, Hospitalization and Health Care, 00163 Rome, Italy
| | - Maurizio Paci
- Department
of Chemical Sciences and Technologies, University of Rome “Tor Vergata”, Via della Ricerca Scientifica 1, 00133 Rome, Italy
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22
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Analysing DHPC/DMPC bicelles by diffusion NMR and multivariate decomposition. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2015; 1848:2910-7. [DOI: 10.1016/j.bbamem.2015.09.002] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2015] [Revised: 08/06/2015] [Accepted: 09/01/2015] [Indexed: 12/16/2022]
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23
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Misiewicz J, Afonin S, Grage SL, van den Berg J, Strandberg E, Wadhwani P, Ulrich AS. Action of the multifunctional peptide BP100 on native biomembranes examined by solid-state NMR. JOURNAL OF BIOMOLECULAR NMR 2015; 61:287-98. [PMID: 25616492 DOI: 10.1007/s10858-015-9897-8] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2014] [Accepted: 01/10/2015] [Indexed: 05/22/2023]
Abstract
Membrane composition is a key factor that regulates the destructive activity of antimicrobial peptides and the non-leaky permeation of cell penetrating peptides in vivo. Hence, the choice of model membrane is a crucial aspect in NMR studies and should reflect the biological situation as closely as possible. Here, we explore the structure and dynamics of the short multifunctional peptide BP100 using a multinuclear solid-state NMR approach. The membrane alignment and mobility of this 11 amino acid peptide was studied in various synthetic lipid bilayers with different net charge, fluidity, and thickness, as well as in native biomembranes harvested from prokaryotic and eukaryotic cells. (19)F-NMR provided the high sensitivity and lack of natural abundance background that are necessary to observe a labelled peptide even in protoplast membranes from Micrococcus luteus and in erythrocyte ghosts. Six selectively (19)F-labeled BP100 analogues gave remarkably similar spectra in all of the macroscopically oriented membrane systems, which were studied under quasi-native conditions of ambient temperature and full hydration. This similarity suggests that BP100 has the same surface-bound helical structure and high mobility in the different biomembranes and model membranes alike, independent of charge, thickness or cholesterol content of the system. (31)P-NMR spectra of the phospholipid components did not indicate any bilayer perturbation, so the formation of toroidal wormholes or micellarization can be excluded as a mechanism of its antimicrobial or cell penetrating action. However, (2)H-NMR analysis of the acyl chain order parameter profiles showed that BP100 leads to considerable membrane thinning and thereby local destabilization.
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Affiliation(s)
- Julia Misiewicz
- Institute of Organic Chemistry, Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg 6, 76131, Karlsruhe, Germany
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24
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Usachev K, Filippov A, Khairutdinov B, Antzutkin O, Klochkov V. NMR structure of the Arctic mutation of the Alzheimer’s Aβ(1–40) peptide docked to SDS micelles. J Mol Struct 2014. [DOI: 10.1016/j.molstruc.2014.08.030] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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25
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Ariöz C, Ye W, Bakali A, Ge C, Liebau J, Götzke H, Barth A, Wieslander Å, Mäler L. Anionic Lipid Binding to the Foreign Protein MGS Provides a Tight Coupling between Phospholipid Synthesis and Protein Overexpression in Escherichia coli. Biochemistry 2013; 52:5533-44. [DOI: 10.1021/bi400616n] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Candan Ariöz
- Center for Biomembrane
Research, Department of Biochemistry
and Biophysics, Stockholm University, SE-106
91 Stockholm, Sweden
| | - Weihua Ye
- Center for Biomembrane
Research, Department of Biochemistry
and Biophysics, Stockholm University, SE-106
91 Stockholm, Sweden
| | - Amin Bakali
- Center for Biomembrane
Research, Department of Biochemistry
and Biophysics, Stockholm University, SE-106
91 Stockholm, Sweden
| | - Changrong Ge
- Center for Biomembrane
Research, Department of Biochemistry
and Biophysics, Stockholm University, SE-106
91 Stockholm, Sweden
| | - Jobst Liebau
- Center for Biomembrane
Research, Department of Biochemistry
and Biophysics, Stockholm University, SE-106
91 Stockholm, Sweden
| | - Hansjörg Götzke
- Center for Biomembrane
Research, Department of Biochemistry
and Biophysics, Stockholm University, SE-106
91 Stockholm, Sweden
| | - Andreas Barth
- Center for Biomembrane
Research, Department of Biochemistry
and Biophysics, Stockholm University, SE-106
91 Stockholm, Sweden
| | - Åke Wieslander
- Center for Biomembrane
Research, Department of Biochemistry
and Biophysics, Stockholm University, SE-106
91 Stockholm, Sweden
| | - Lena Mäler
- Center for Biomembrane
Research, Department of Biochemistry
and Biophysics, Stockholm University, SE-106
91 Stockholm, Sweden
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26
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Song J. Why do proteins aggregate? "Intrinsically insoluble proteins" and "dark mediators" revealed by studies on "insoluble proteins" solubilized in pure water. F1000Res 2013; 2:94. [PMID: 24555050 PMCID: PMC3869494 DOI: 10.12688/f1000research.2-94.v1] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 03/20/2013] [Indexed: 12/22/2022] Open
Abstract
In 2008, I reviewed and proposed a model for our discovery in 2005 that unrefoldable and insoluble proteins could in fact be solubilized in unsalted water. Since then, this discovery has offered us and other groups a powerful tool to characterize insoluble proteins, and we have further addressed several fundamental and disease-relevant issues associated with this discovery. Here I review these results, which are conceptualized into several novel scenarios. 1) Unlike 'misfolded proteins', which still retain the capacity to fold into well-defined structures but are misled to 'off-pathway' aggregation, unrefoldable and insoluble proteins completely lack this ability and will unavoidably aggregate in vivo with ~150 mM ions, thus designated as 'intrinsically insoluble proteins (IIPs)' here. IIPs may largely account for the 'wastefully synthesized' DRiPs identified in human cells. 2) The fact that IIPs including membrane proteins are all soluble in unsalted water, but get aggregated upon being exposed to ions, logically suggests that ions existing in the background play a central role in mediating protein aggregation, thus acting as 'dark mediators'. Our study with 14 salts confirms that IIPs lack the capacity to fold into any well-defined structures. We uncover that salts modulate protein dynamics and anions bind proteins with high selectivity and affinity, which is surprisingly masked by pre-existing ions. Accordingly, I modified my previous model. 3) Insoluble proteins interact with lipids to different degrees. Remarkably, an ALS-causing P56S mutation transforms the β-sandwich MSP domain into a helical integral membrane protein. Consequently, the number of membrane-interacting proteins might be much larger than currently recognized. To attack biological membranes may represent a common mechanism by which aggregated proteins initiate human diseases. 4) Our discovery also implies a solution to the 'chicken-and-egg paradox' for the origin of primitive membranes embedded with integral membrane proteins, if proteins originally emerged in unsalted prebiotic media.
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Affiliation(s)
- Jianxing Song
- Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore, 119260, Singapore ; Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 119260, Singapore
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27
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Ye W, Liebau J, Mäler L. New Membrane Mimetics with Galactolipids: Lipid Properties in Fast-Tumbling Bicelles. J Phys Chem B 2013; 117:1044-50. [DOI: 10.1021/jp311093p] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Weihua Ye
- Department
of Biochemistry and Biophysics, The Arrhenius
Laboratory, Stockholm University, 106 91
Stockholm, Sweden
| | - Jobst Liebau
- Department
of Biochemistry and Biophysics, The Arrhenius
Laboratory, Stockholm University, 106 91
Stockholm, Sweden
| | - Lena Mäler
- Department
of Biochemistry and Biophysics, The Arrhenius
Laboratory, Stockholm University, 106 91
Stockholm, Sweden
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