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Methods for Small-Angle Scattering Measurements on Peptiplexes of DNA with Cell-Penetrating Peptides. Methods Mol Biol 2021. [PMID: 34766290 DOI: 10.1007/978-1-0716-1752-6_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/05/2023]
Abstract
Peptiplexes are soft biomaterials formed through the noncovalent association between cell-penetrating peptides and nucleic acids. Although internalization often involves electrostatic anchoring followed by endocytosis, the mode of action of these transporters remains elusive in many cases, and proper understanding of mechanisms behind their penetrating capabilities necessarily entails structural data at the nanoscopic scale. In this chapter, we examine the structural landscape of peptiplexes, emphasizing the complex behavior of these polyelectrolyte self-assemblies and how supramolecular order impacts their translocation efficiency. We discuss experimental tools commonly used to investigate the structure of peptiplexes and pay special attention to small-angle X-ray scattering (SAXS) as a suitable method for unveiling their nanoscale organization. A roadmap for standard SAXS measurements in CPP/DNA samples is presented alongside a selection of observations from our own experience dealing with SAXS applied to the investigation of CPPs.
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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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Szpryngiel S, Mäler L. Insights into the Membrane Interacting Properties of the C-Terminal Domain of the Monotopic Glycosyltransferase DGD2 in Arabidopsis thaliana. Biochemistry 2016; 55:6776-6786. [PMID: 27951648 DOI: 10.1021/acs.biochem.6b00559] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Glycosyltransferases (GTs) are responsible for regulating the membrane composition of plants. The synthesis of one of the main lipids in the membrane, the galactolipid digalactosyldiacylglycerol, is regulated by the enzyme digalactosyldiacylglycerol synthase 2 (atDGD2) under starving conditions, such as phosphate shortage. The enzyme belongs to the GT-B fold, characterized by two β/α/β Rossmann domains that are connected by a flexible linker. atDGD2 has previously been shown to attach to lipid membranes by the N-terminal domain via interactions with negatively charged lipids. The role of the C-terminal domain in the membrane interaction is, however, not known. Here we have used a combination of in silico prediction methods and biophysical experimental techniques to shed light on the membrane interacting properties of the C-terminal domain. Our results demonstrate that there is an amphipathic sequence, corresponding to residues V240-E258, that interacts with lipids in a charge-dependent way. A second sequence was identified as being potentially important, with a high charge density, but no amphipathic character. The features of the plant atDGD2 observed here are similar in prokaryotic glycosyltransferases. On the basis of our results, and by analogy to other glycosyltransferases, we propose that atDGD2 interacts with the membrane through the N-terminus and with parts of the C-terminus acting as a switch, allowing for a dynamic interaction with the membrane.
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Affiliation(s)
- Scarlett Szpryngiel
- Department of Biochemistry and Biophysics, Center for Biomembrane Research, The Arrhenius Laboratory, Stockholm University , 10691 Stockholm, Sweden
| | - Lena Mäler
- Department of Biochemistry and Biophysics, Center for Biomembrane Research, The Arrhenius Laboratory, Stockholm University , 10691 Stockholm, Sweden
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Bera S, Kar RK, Mondal S, Pahan K, Bhunia A. Structural Elucidation of the Cell-Penetrating Penetratin Peptide in Model Membranes at the Atomic Level: Probing Hydrophobic Interactions in the Blood-Brain Barrier. Biochemistry 2016; 55:4982-96. [PMID: 27532224 PMCID: PMC5014585 DOI: 10.1021/acs.biochem.6b00518] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Cell-penetrating peptides (CPPs) have shown promise in nonpermeable therapeutic drug delivery, because of their ability to transport a variety of cargo molecules across the cell membranes and their noncytotoxicity. Drosophila antennapedia homeodomain-derived CPP penetratin (RQIKIWFQNRRMKWKK), being rich in positively charged residues, has been increasingly used as a potential drug carrier for various purposes. Penetratin can breach the tight endothelial network known as the blood-brain barrier (BBB), permitting treatment of several neurodegenerative maladies, including Alzheimer's disease, Parkinson's disease, and Huntington's disease. However, a detailed structural understanding of penetratin and its mechanism of action is lacking. This study defines structural features of the penetratin-derived peptide, DK17 (DRQIKIWFQNRRMKWKK), in several model membranes and describes a membrane-induced conformational transition of the DK17 peptide in these environments. A series of biophysical experiments, including high-resolution nuclear magnetic resonance spectroscopy, provides the three-dimensional structure of DK17 in different membranes mimicking the BBB or total brain lipid extract. Molecular dynamics simulations support the experimental results showing preferential binding of DK17 to particular lipids at atomic resolution. The peptide conserves the structure of the subdomain spanning residues Ile6-Arg11, despite considerable conformational variation in different membrane models. In vivo data suggest that the wild type, not a mutated sequence, enters the central nervous system. Together, these data highlight important structural and functional attributes of DK17 that could be utilized in drug delivery for neurodegenerative disorders.
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Affiliation(s)
- Swapna Bera
- Department of Biophysics, Bose Institute, P-1/12 CIT Scheme VII(M), Kolkata 700054, India
| | - Rajiv K Kar
- Department of Biophysics, Bose Institute, P-1/12 CIT Scheme VII(M), Kolkata 700054, India
| | - Susanta Mondal
- Department of Neurological Sciences, Rush University Medical Center, Chicago, IL, USA
| | - Kalipada Pahan
- Department of Neurological Sciences, Rush University Medical Center, Chicago, IL, USA
- Division of Research and Development, Jesse Brown Veterans Affairs Medical Center, 820 South Damen Avenue, Chicago, IL, USA
| | - Anirban Bhunia
- Department of Biophysics, Bose Institute, P-1/12 CIT Scheme VII(M), Kolkata 700054, India
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Bodor A, Kövér KE, Mäler L. Membrane interactions in small fast-tumbling bicelles as studied by 31P NMR. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2014; 1848:760-6. [PMID: 25497765 DOI: 10.1016/j.bbamem.2014.12.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2014] [Revised: 11/11/2014] [Accepted: 12/01/2014] [Indexed: 01/02/2023]
Abstract
Small fast-tumbling bicelles are ideal for studies of membrane interactions at molecular level; they allow analysis of lipid properties using solution-state NMR. In the present study we used 31P NMR relaxation to obtain detailed information on lipid head-group dynamics. We explored the effect of two topologically different membrane-interacting peptides on bicelles containing either dimyristoylphosphocholine (DMPC), or a mixture of DMPC and dimyristoylphosphoglycerol (DMPG), and dihexanoylphosphocholine (DHPC). KALP21 is a model transmembrane peptide, designed to span a DMPC bilayer and dynorphin B is a membrane surface active neuropeptide. KALP21 causes significant increase in bicelle size, as evidenced by both dynamic light scattering and 31P T2 relaxation measurements. The effect of dynorphin B on bicelle size is more modest, although significant effects on T2 relaxation are observed at higher temperatures. A comparison of 31P T1 values for the lipids with and without the peptides showed that dynorphin B has a greater effect on lipid head-group dynamics than KALP21, especially at elevated temperatures. From the field-dependence of T1 relaxation data, a correlation time describing the overall lipid motion was derived. Results indicate that the positively charged dynorphin B decreases the mobility of the lipid molecules--in particular for the negatively charged DMPG--while KALP21 has a more modest influence. Our results demonstrate that while a transmembrane peptide has severe effects on overall bilayer properties, the surface bound peptide has a more dramatic effect in reducing lipid head-group mobility. These observations may be of general importance for understanding peptide-membrane interactions.
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Affiliation(s)
- Andrea Bodor
- Laboratory of Structural Chemistry and Biology, Institute of Chemistry, Eötvös Loránd University, H-1117 Budapest, Hungary.
| | - Katalin E Kövér
- Department of Inorganic and Analytical Chemistry, University of Debrecen, H-4032 Debrecen, Hungary
| | - Lena Mäler
- Department of Biochemistry and Biophysics, Stockholm University, 10691 Stockholm Sweden.
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Ye W, Lind J, Eriksson J, Mäler L. Characterization of the morphology of fast-tumbling bicelles with varying composition. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2014; 30:5488-5496. [PMID: 24785902 DOI: 10.1021/la500231z] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Small, fast-tumbling bicelles are frequently used in solution NMR studies of protein-lipid interactions. For this purpose it is critical to have information about the organization of the lipids within the bicelle structure. We have studied the morphology of small, fast-tumbling bicelles containing DMPC and DHPC as a function of temperature, lipid concentration, and the relative ratio (q value) of lipid (DMPC) to detergent (DHPC) amounts. Dynamic light scattering and cryo-transmission electron microscopy techniques were used to measure the size of the bicelles and to monitor the shape and dispersity of the particles in the samples. The stability and size of DMPC-containing bicelle mixtures were found to be highly dependent on temperature and the total lipid concentration for mixtures with q = 1 and q = 1.5. Stable DMPC/DHPC bicelles are only formed at low q values (0.5). Bicelle mixtures with q > 0.5 appear to be multidisperse containing more than one component, one with r(H) around 2.5 nm and one with r(H) of 6-8 nm. This is interpreted as a coexistence of small (possibly mixed micelles) bicelles and much larger bicelles. Incubating the sample at 37 °C increases the phase separation. Moreover, low total amphiphile concentrations and low q values lead to the formation of a temperature-independent morphology, interpreted as the formation of small particles in which the DHPC and DMPC are more mixed. On the basis of these results, we propose the existence of a critical bicelle concentration, a parameter that determines the existence of bilayered bicelles, which varies with q value. This polymorphism was not observed at any concentrations for q = 0.5 bicelles, for which a small but detectable temperature dependence was observed at high concentrations. The results demonstrate that q = 0.5 mixtures predominantly form "classical" bicelles, but that caution is needed when using fast-tumbling mixtures with q values higher than 0.5.
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Affiliation(s)
- Weihua Ye
- Department of Biochemistry and Biophysics, Center for Biomembrane Research, The Arrhenius Laboratory, Stockholm University , SE-10691 Stockholm, Sweden
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Mäler L. Solution NMR studies of cell-penetrating peptides in model membrane systems. Adv Drug Deliv Rev 2013; 65:1002-11. [PMID: 23137785 DOI: 10.1016/j.addr.2012.10.011] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2012] [Revised: 10/17/2012] [Accepted: 10/22/2012] [Indexed: 12/29/2022]
Abstract
Cell-penetrating peptides (CPPs) are a class of short, often cationic peptides that have the capability to translocate across cellular membranes, and although the translocation most likely involves several pathways, they interact directly with membranes, as well as with model bilayers. Most CPPs attain a three-dimensional structure when interacting with bilayers, while they are more or less unstructured in aqueous solution. To understand the relationship between structure and the effect that CPPs have on membranes it is of great importance to investigate CPPs at atomic resolution in a suitable membrane model. Moreover, the location in bilayers is likely to be correlated with the translocation mechanism. Solution-state NMR offers a unique possibility to investigate structure, dynamics and location of proteins and peptides in bilayers. This review focuses on solution NMR as a tool for investigating CPP-lipid interactions. Structural propensities and cell-penetrating capabilities can be derived from a combination of CPP solution structures and studies of the effect that the peptides have on bilayers and the localization in a bilayer.
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Affiliation(s)
- Lena Mäler
- Department of Biochemistry and Biophysics, The Arrhenius Laboratory, Stockholm University, Stockholm, Sweden.
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Björnerås J, Gräslund A, Mäler L. Membrane Interaction of Disease-Related Dynorphin A Variants. Biochemistry 2013; 52:4157-67. [DOI: 10.1021/bi4004205] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Johannes Björnerås
- Department of Biochemistry
and Biophysics, The Arrhenius
Laboratory, Stockholm University, 10691
Stockholm, Sweden
| | - Astrid Gräslund
- Department of Biochemistry
and Biophysics, The Arrhenius
Laboratory, Stockholm University, 10691
Stockholm, Sweden
| | - Lena Mäler
- Department of Biochemistry
and Biophysics, The Arrhenius
Laboratory, Stockholm University, 10691
Stockholm, Sweden
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Marbella LE, Cho HS, Spence MM. Observing the translocation of a mitochondria-penetrating peptide with solid-state NMR. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2013; 1828:1674-82. [PMID: 23567916 DOI: 10.1016/j.bbamem.2013.03.027] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2013] [Revised: 03/25/2013] [Accepted: 03/29/2013] [Indexed: 12/18/2022]
Abstract
A new class of penetrating peptides that can target the mitochondria with high specificity was recently discovered. In this work, we developed a model inner mitochondrial membrane, equipped with a transmembrane gradient, suitable for solid-state NMR experiments. Using solid-state NMR, we observed a mitochondria-penetrating peptide interacting with the model inner mitochondrial membrane to gain insight into the mechanism of translocation. The paramagnetic relaxation effect due to Mn(2+) ions on (13)C magic angle spinning NMR was used to measure the insertion depth of the peptide and its distribution in each monolayer of the membrane. We found that at low peptide concentration the peptide binds to the outer leaflet and at high concentration, it crosses the hydrophobic bilayer core and is distributed in both leaflets. In both concentration regimes, the peptide binds at the C2 position on the lipid acyl chain. The mitochondria-penetrating peptide crossed to the inner leaflet of the model membranes without disrupting the lamellarity. These results provide evidence that supports the electroporation model of translocation. We estimated the energy associated with crossing the inner mitochondrial membrane. We found that the transmembrane potential provides sufficient energy for the peptide to cross the hydrophobic core, which is the most unfavorable step in translocation.
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Affiliation(s)
- Lauren E Marbella
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260, USA.
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Aisenbrey C, Pendem N, Guichard G, Bechinger B. Solid state NMR studies of oligourea foldamers: Interaction of 15N-labelled amphiphilic helices with oriented lipid membranes. Org Biomol Chem 2012; 10:1440-7. [DOI: 10.1039/c1ob06278f] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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