101
|
Oliver RC, Pingali SV, Urban VS. Designing Mixed Detergent Micelles for Uniform Neutron Contrast. J Phys Chem Lett 2017; 8:5041-5046. [PMID: 28960995 DOI: 10.1021/acs.jpclett.7b02149] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Micelle-forming detergents provide an amphipathic environment that mimics lipid bilayers and are important tools used to solubilize and stabilize membrane proteins in solution for in vitro structural investigations. Small-angle neutron scattering (SANS) at the neutron contrast match point of detergent molecules allows observing the signal from membrane proteins unobstructed by contributions from the detergent. However, we show that even for a perfectly average-contrast matched detergent there arises significant core-shell scattering from the contrast difference between aliphatic detergent tails and hydrophilic head groups. This residual signal interferes with interpreting structural data of membrane proteins. This complication is often made worse by the presence of excess empty (protein-free) micelles. We present an approach for the rational design of mixed micelles containing a deuterated detergent analog, which eliminates neutron contrast between core and shell and allows the micelle scattering to be fully contrast-matched to unambiguously resolve membrane protein structure using solution SANS.
Collapse
Affiliation(s)
- Ryan C Oliver
- Center for Structural Molecular Biology and Biology and Soft Matter Division, Oak Ridge National Laboratory , P.O. Box 2008, MS 6475, Oak Ridge, Tennessee 37831, United States
| | - Sai Venkatesh Pingali
- Center for Structural Molecular Biology and Biology and Soft Matter Division, Oak Ridge National Laboratory , P.O. Box 2008, MS 6475, Oak Ridge, Tennessee 37831, United States
| | - Volker S Urban
- Center for Structural Molecular Biology and Biology and Soft Matter Division, Oak Ridge National Laboratory , P.O. Box 2008, MS 6475, Oak Ridge, Tennessee 37831, United States
| |
Collapse
|
102
|
Hutchison JM, Lu Z, Li G, Travis B, Mittal R, Deatherage CL, Sanders CR. Dodecyl-β-melibioside Detergent Micelles as a Medium for Membrane Proteins. Biochemistry 2017; 56:5481-5484. [PMID: 28980804 PMCID: PMC5685800 DOI: 10.1021/acs.biochem.7b00810] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
There remains a need for new non-ionic detergents that are suitable for use in biochemical and biophysical studies of membrane proteins. Here we explore the properties of n-dodecyl-β-melibioside (β-DDMB) micelles as a medium for membrane proteins. Melibiose is d-galactose-α(1→6)-d-glucose. Light scattering showed the β-DDMB micelle to be roughly 30 kDa smaller than micelles formed by the commonly used n-dodecyl-β-maltoside (β-DDM). β-DDMB stabilized diacylglycerol kinase (DAGK) against thermal inactivation. Moreover, activity assays conducted using aliquots of DAGK purified into β-DDMB yielded activities that were 40% higher than those of DAGK purified into β-DDM. β-DDMB yielded similar or better TROSY-HSQC NMR spectra for two single-pass membrane proteins and the tetraspan membrane protein peripheral myelin protein 22. β-DDMB appears be a useful addition to the toolbox of non-ionic detergents available for membrane protein research.
Collapse
Affiliation(s)
- James M. Hutchison
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-8725, United States
| | - Zhenwei Lu
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-8725, United States
| | - Geoffrey Li
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-8725, United States
| | - Ben Travis
- Anatrace, 434 W. Dussel Dr., Maumee, OH 43537
| | | | - Catherine L. Deatherage
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-8725, United States
| | - Charles R. Sanders
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-8725, United States
| |
Collapse
|
103
|
Faramarzi S, Bonnett B, Scaggs CA, Hoffmaster A, Grodi D, Harvey E, Mertz B. Molecular Dynamics Simulations as a Tool for Accurate Determination of Surfactant Micelle Properties. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2017; 33:9934-9943. [PMID: 28836794 DOI: 10.1021/acs.langmuir.7b02666] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Molecular dynamics (MD) simulations were used to characterize the equilibrium size, shape, hydration, and self-assembly of dodecylphosphocholine (DPC) and dodecyl-β-D-maltoside (DDM) micelles. We show that DPC molecules self-assemble to form micelles with sizes within the range reported in the experimental literature. The equilibrium shape of DPC and DDM micelles as well as associated micellar radii are in agreement with small-angle X-ray scattering (SAXS) experiments and theoretical packing parameters. In addition, we show that hydration of the micelle interior is limited; however, flexibility of the acyl chains leads to dynamic encounters with the solvated outer shell of the micelle, providing an explanation for long-standing differences in models of micelle hydration. Altogether, our results provide fundamental understanding of physical characteristics of micelles that can be utilized to study other types of detergents and proteomicelle complexes.
Collapse
Affiliation(s)
- Sadegh Faramarzi
- C. Eugene Bennett Department of Chemistry, West Virginia University , 217 Clark Hall, Morgantown, West Virginia 26506, United States
| | - Brittany Bonnett
- Biology, Chemistry, and Geoscience Department, Fairmont State University , 1201 Locust Avenue, Fairmont, West Virginia 26554, United States
| | - Carl A Scaggs
- Biology, Chemistry, and Geoscience Department, Fairmont State University , 1201 Locust Avenue, Fairmont, West Virginia 26554, United States
| | - Ashley Hoffmaster
- Biology, Chemistry, and Geoscience Department, Fairmont State University , 1201 Locust Avenue, Fairmont, West Virginia 26554, United States
| | - Danielle Grodi
- Biology, Chemistry, and Geoscience Department, Fairmont State University , 1201 Locust Avenue, Fairmont, West Virginia 26554, United States
| | - Erica Harvey
- Biology, Chemistry, and Geoscience Department, Fairmont State University , 1201 Locust Avenue, Fairmont, West Virginia 26554, United States
| | - Blake Mertz
- C. Eugene Bennett Department of Chemistry, West Virginia University , 217 Clark Hall, Morgantown, West Virginia 26506, United States
| |
Collapse
|
104
|
Counterion-Induced Cationic Flexible Nanoparticle Catalytic of Piperidinolysis of Phenyl Salicylate. J SURFACTANTS DETERG 2017. [DOI: 10.1007/s11743-017-1975-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
|
105
|
Smułek W, Kaczorek E, Hricovíniová Z. Alkyl Xylosides: Physico-Chemical Properties and Influence on Environmental Bacteria Cells. J SURFACTANTS DETERG 2017; 20:1269-1279. [PMID: 29200811 PMCID: PMC5686273 DOI: 10.1007/s11743-017-2012-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2016] [Accepted: 08/18/2017] [Indexed: 12/03/2022]
Abstract
A group of four selected non-ionic surfactants based on carbohydrates, namely octyl d-xyloside (C8X), nonyl d-xyloside (C9X), decyl d-xyloside (C10X) and dodecyl d-xyloside (C12X), have been investigated to accomplish a better understanding of their physico-chemical properties as well as biological activities. The surface-active properties, such as critical micelle concentration (CMC), emulsion and foam stability, the impact of the compounds on cell surface hydrophobicity and cell membrane permeability together with their toxicity on the selected bacterial strains have been determined as well. The studied group of surfactants showed high surface-active properties allowing a decrease in the surface tension to values below 25 mN m-1 for dodecyl d-xyloside at the CMC. The investigated compounds did not have any toxic influence on two Pseudomonas bacterial strains at concentrations below 25 mg L-1. The studied long-chain alkyl xylosides influenced both the cell inner membrane permeability and the cell surface hydrophobicity. Furthermore, the alkyl chain length, as well as the surfactant concentration, had a significant impact on the modifications of the cell surface properties. The tested non-ionic surfactants exhibited strong surface-active properties accompanied by the significant influence on growth and properties of Pseudomonas bacteria cells.
Collapse
Affiliation(s)
- Wojciech Smułek
- Institute of Chemical Technology and Engineering, Poznan University of Technology, Berdychowo 4, 60-965 Poznan, Poland
| | - Ewa Kaczorek
- Institute of Chemical Technology and Engineering, Poznan University of Technology, Berdychowo 4, 60-965 Poznan, Poland
| | - Zuzana Hricovíniová
- Institute of Chemistry, Slovak Academy of Sciences, Dúbravská cesta 9, 845 38 Bratislava, Slovakia
| |
Collapse
|
106
|
Krüger D, Kamerlin SCL. Micelle Maker: An Online Tool for Generating Equilibrated Micelles as Direct Input for Molecular Dynamics Simulations. ACS OMEGA 2017; 2:4524-4530. [PMID: 28884160 PMCID: PMC5579539 DOI: 10.1021/acsomega.7b00820] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Accepted: 08/01/2017] [Indexed: 06/07/2023]
Abstract
Micelles play an important role in both experimental and computational studies of the effect of lipid interactions on biological systems. The spherical geometry and the dynamical behavior of micelles makes generating micelle structures for use in molecular simulations challenging. An easy tool for generating simulation-ready micelle models, covering a broad range of lipids, is highly desirable. Here, we present a new Web server, Micelle Maker, which can provide equilibrated micelle models as a direct input for subsequent molecular dynamics simulations from a broad range of lipids (currently 25 lipid types, including 24 glycolipids). The Web server, which is available at http://www.micellemaker.net, uses error checking routines to prevent clashes during the initial placement of the lipids and uses AMBER's GLYCAM library for generating minimized or equilibrated micelle models, but the resulting structures can be used as starting points for simulations with any force field or simulation package. Extensive validation simulations with an overall simulation time of 12 μs using eight micelle models where assembly information is available show that all of the micelles remain very stable over the whole simulation time. Finally, we discuss the advantages of Micelle Maker relative to other approaches in the field.
Collapse
Affiliation(s)
- Dennis
M. Krüger
- Science for Life Laboratory,
Department of Cell and Molecular Biology, Uppsala Biomedical Center, Uppsala University, Box 596, S-754 21 Uppsala, Sweden
| | - Shina C. L. Kamerlin
- Science for Life Laboratory,
Department of Cell and Molecular Biology, Uppsala Biomedical Center, Uppsala University, Box 596, S-754 21 Uppsala, Sweden
| |
Collapse
|
107
|
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
| |
Collapse
|
108
|
Chakraborty G, Chowdhury MP, Saha SK. Solvent-Induced Molecular Folding and Self-Assembled Nanostructures of Tyrosine and Tryptophan Analogues in Aqueous Solution: Fascinating Morphology of High Order. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2017; 33:6581-6594. [PMID: 28595386 DOI: 10.1021/acs.langmuir.7b01651] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Hydrophobic derivatives of tyrosine and tryptophan, viz. octyl and dodecyl esters of tyrosine and octyl ester of tryptophan, are synthesized, and the interfacial and bulk properties in aqueous media are investigated as models for the membrane proteins. Molecular modeling by the density functional theory method is carried out to understand the molecular conformation and geometry for the purpose of determining the packing parameters. Water-induced molecular folding of the esters of both tyrosine and tryptophan, as observed using rotating frame nuclear Overhauser effect spectroscopy, indicates that the segregation of the hydrophobic and hydrophilic blocks in water is the key to the development of fascinating interfacial property displayed by the aromatic amino acid esters. The unusually high-order morphology of the aggregates, as observed using high-resolution transmission electron microscopy, is highly uncommon for single-chain amphiphiles and points to the fact that the self-assembly behavior of the present systems resembles that of block copolymers. The study of the growth of mesosized hollow aggregates with internal bilayer structures from tyrosine and tryptophan-based model systems would add to the understanding of biochemistry and biotechnology relevant to the cell membrane. The potential of biocompatible nanostructured motifs as the drug carriers is discussed. The highly functional role played by the aromatic amino acids at the membrane-water interface will be considered with the present amphiphilic models for future perspective.
Collapse
Affiliation(s)
- Gulmi Chakraborty
- Department of Chemistry, University of North Bengal , Darjeeling 734 013, India
| | | | - Swapan K Saha
- Department of Chemistry, University of North Bengal , Darjeeling 734 013, India
| |
Collapse
|
109
|
Structural and Dynamic Insights of the Interaction between Tritrpticin and Micelles: An NMR Study. Biophys J 2017; 111:2676-2688. [PMID: 28002744 DOI: 10.1016/j.bpj.2016.10.034] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Revised: 10/14/2016] [Accepted: 10/27/2016] [Indexed: 01/02/2023] Open
Abstract
A large number of antimicrobial peptides (AMPs) acts with high selectivity and specificity through interactions with membrane lipid components. These peptides undergo complex conformational changes in solution; upon binding to an interface, one major conformation is stabilized. Here we describe a study of the interaction between tritrpticin (TRP3), a cathelicidin AMP, and micelles of different chemical composition. The peptide's structure and dynamics were examined using one-dimensional and two-dimensional NMR. Our data showed that the interaction occurred by conformational selection and the peptide acquired similar structures in all systems studied, despite differences in detergent headgroup charge or dipole orientation. Fluorescence and paramagnetic relaxation enhancement experiments showed that the peptide is located in the interface region and is slightly more deeply inserted in 1-myristoyl-2-hydroxy-sn-glycero-3-phospho-1'-rac-glycerol (LMPG, anionic) than in 1-lauroyl-2-hydroxy-sn-glycero-3-phosphocholine (LLPC, zwitterionic) micelles. Moreover, the tilt angle of an assumed helical portion of the peptide is similar in both systems. In previous work we proposed that TRP3 acts by a toroidal pore mechanism. In view of the high hydrophobic core exposure, hydration, and curvature presented by micelles, the conformation of TRP3 in these systems could be related to the peptide's conformation in the toroidal pore.
Collapse
|
110
|
Abdalla S, Al-Marzouki F, Obaid A, Bahabri F. Controlled Light Cross-Linking Technique to Prepare Healable Materials. Polymers (Basel) 2017; 9:polym9060241. [PMID: 30970918 PMCID: PMC7934017 DOI: 10.3390/polym9060241] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2017] [Revised: 06/19/2017] [Accepted: 06/19/2017] [Indexed: 11/23/2022] Open
Abstract
Detection of defects, damages and cracks in structural polymers is very difficult, and even if they are detected, they will be very hard to be repaired. This is because different kinds of stress can reduce the mechanical efficiency of structural and functional thermosetting composite materials and they can damage the polymer matrix, thus reducing the purposed properties. General healing processes use thermal energy “alone” to heal these materials, thus impairing the intended properties of the materials. Therefore, we present a thermal healing ability that can be switched-on and/or -off at desire using illumination by photon energy (visible and ultra violet). By this technique, one can control local heal while keeping the efficiency of the material nearly unchanged. Furan-based cross-linker chemically reacts (forward- and reverse-reaction) with short-chains of maleimide-substituted poly(lauryl methacrylate) to form robust chemical bonds. This permits us to perform local control over thermally induced de- and/or re-cross-linking techniques. One can extend and apply this technique to cover micro-devices, coating-techniques, fine lithography, micro- and nano-fabrication processes, etc. Therefore, the present work developed a suitable technology with structural polymeric material, which has the ability to self-heal cracks (and damages) and recover structural function.
Collapse
Affiliation(s)
- Soliman Abdalla
- Department of Physics, Faculty of Science, King Abdulaziz University Jeddah, P.O. Box 80203, Jeddah 21589, Saudi Arabia.
| | - Fahad Al-Marzouki
- Department of Physics, Faculty of Science, King Abdulaziz University Jeddah, P.O. Box 80203, Jeddah 21589, Saudi Arabia.
| | - Abdullah Obaid
- Department of Physics, Faculty of Science, King Abdulaziz University Jeddah, P.O. Box 80203, Jeddah 21589, Saudi Arabia.
| | - Fatma Bahabri
- Department of Physics, Faculty of Science, King Abdulaziz University Jeddah, P.O. Box 80203, Jeddah 21589, Saudi Arabia.
| |
Collapse
|
111
|
Langelaan DN, Pandey A, Sarker M, Rainey JK. Preserved Transmembrane Segment Topology, Structure, and Dynamics in Disparate Micellar Environments. J Phys Chem Lett 2017; 8:2381-2386. [PMID: 28492329 PMCID: PMC5770213 DOI: 10.1021/acs.jpclett.7b00867] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Detergent micelles are frequently employed as membrane mimetics for solution-state membrane protein nuclear magnetic resonance spectroscopy. Here we compare topology, structure, ps-ns time-scale dynamics, and hydrodynamics of a model protein with one transmembrane (TM) segment (residues 1-55 of the apelin receptor, APJ, a G-protein-coupled receptor) in three distinct, commonly used micellar environments. In each environment, two solvent-protected helical segments connected by a solvent-exposed kink were observed. The break in helical character at the kink was maintained in a helix-stabilizing fluorinated alcohol environment, implying that this structural feature is inherent. Molecular dynamics simulations also substantiate favorable self-assembly of compact protein-micelle complexes with a more dynamic, solvent-exposed kink. Despite the observed similarity in TM segment behavior, micelle-dependent differences were clear in the structure, dynamics, and compactness of the 30-residue, extramembrane N-terminal tail of the protein. This would affect intermolecular interactions and, correspondingly, the functional state of the membrane protein.
Collapse
Affiliation(s)
- David N. Langelaan
- Department of Biochemistry & Molecular Biology, Dalhousie University, Halifax NS B3H 4R2, Canada
| | - Aditya Pandey
- Department of Biochemistry & Molecular Biology, Dalhousie University, Halifax NS B3H 4R2, Canada
| | - Muzaddid Sarker
- Department of Biochemistry & Molecular Biology, Dalhousie University, Halifax NS B3H 4R2, Canada
| | - Jan K. Rainey
- Department of Biochemistry & Molecular Biology, Dalhousie University, Halifax NS B3H 4R2, Canada
- Department of Chemistry, Dalhousie University, Halifax NS B3H 4R2, Canada
- Corresponding author:
| |
Collapse
|
112
|
Abney CW, Do C, Luo H, Wright J, He L, Dai S. Controlling the Intermediate Structure of an Ionic Liquid for f-Block Element Separations. J Phys Chem Lett 2017; 8:2049-2054. [PMID: 28423277 DOI: 10.1021/acs.jpclett.7b00755] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Recent research has revealed molecular structure beyond the inner coordination sphere is essential in defining the performance of separation processes; nevertheless, such structure remains largely unexplored. Here we apply small-angle neutron scattering (SANS) and X-ray absorption fine structure (XAFS) spectroscopy to investigate the structure of an ionic liquid system studied for f-block element separations. SANS data reveal dramatic changes in the ionic liquid microstructure (∼150 Å) which we demonstrate can be controlled by judicious selection of counterion. Mesoscale structural features (>500 Å) are also observed as a function of metal concentration. XAFS analysis supports formation of extended aggregate structures, similar to those observed in traditional solvent extraction processes, and suggests additional parallels may be drawn from further study. Achieving precise tunability over the intermediate features is an important development in controlling mesoscale structure and realizing advanced new forms of soft matter.
Collapse
Affiliation(s)
- Carter W Abney
- Oak Ridge National Laboratory , One Bethel Valley Road, P.O. Box 2008, Oak Ridge, Tennessee 37831, United States
| | - Changwoo Do
- Biology and Soft Matter Division, Neutron Sciences Directorate, Oak Ridge National Laboratory , P.O. Box 2008, Oak Ridge, Tennessee 37831, United States
| | - Huimin Luo
- Oak Ridge National Laboratory , One Bethel Valley Road, P.O. Box 2008, Oak Ridge, Tennessee 37831, United States
| | - Joshua Wright
- Advanced Photon Source, Argonne National Laboratory , 9700 Cass Avenue, Lemont, Illinois 60439, United States
- Illinois Institute of Technology , 3300 South Federal Street, Chicago, Illinois 60616, United States
| | - Lilin He
- Biology and Soft Matter Division, Neutron Sciences Directorate, Oak Ridge National Laboratory , P.O. Box 2008, Oak Ridge, Tennessee 37831, United States
| | - Sheng Dai
- Oak Ridge National Laboratory , One Bethel Valley Road, P.O. Box 2008, Oak Ridge, Tennessee 37831, United States
- Department of Chemistry, University of Tennessee , Knoxville, Tennessee 37966, United States
| |
Collapse
|
113
|
Patterson RE, Weatherbee-Martin N, Rainey JK. Pyrene-Apelin Conjugation Modulates Fluorophore- and Peptide-Micelle Interactions. J Phys Chem B 2017; 121:4768-4777. [PMID: 28414462 DOI: 10.1021/acs.jpcb.7b02376] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Bioactive apelin peptide forms ranging in length from 12 to 55 amino acids bind to and activate the apelin receptor (AR or APJ), a class A G-protein coupled receptor. Apelin-12, -17, and -36 isoforms, named according to length, with an additional N-terminal cysteine residue allowed for regiospecific and efficient conjugation of pyrene maleimide. Through steady-state fluorescence spectroscopy, the emission properties of pyrene in aqueous buffer were compared to those of the pyrene-apelin conjugates both without and with zwitterionic or anionic micelles. Pyrene photophysics are consistent with an expected partitioning into the hydrophobic micellar cores, while pyrene-apelin conjugation prevented this partitioning. Apelin, conversely, is expected to preferentially interact with anionic micelles; pyrene-apelin conjugates appear to lose preferential interaction. Finally, Förster resonance energy transfer between pyrene and tryptophan residues in the N-terminal tail and first transmembrane segment (the AR55 construct, comprising residues 1-55 of the AR) was consistent with efficient nonspecific pyrene-apelin conjugate binding to micelles rather than direct, specific apelin-AR55 binding. This approach provides a versatile fluorophore conjugation strategy for apelin, particularly valuable given that even a highly hydrophobic fluorophore is not deleterious to peptide behavior in membrane-mimetic micellar systems.
Collapse
Affiliation(s)
- Robin E Patterson
- Departments of †Biochemistry & Molecular Biology and ‡Chemistry, Dalhousie University , Halifax, Nova Scotia B3H 4R2, Canada
| | - Nathan Weatherbee-Martin
- Departments of †Biochemistry & Molecular Biology and ‡Chemistry, Dalhousie University , Halifax, Nova Scotia B3H 4R2, Canada
| | - Jan K Rainey
- Departments of †Biochemistry & Molecular Biology and ‡Chemistry, Dalhousie University , Halifax, Nova Scotia B3H 4R2, Canada
| |
Collapse
|
114
|
Abstract
Aqueous-based synthesis is one of the most popular methods to prepare nanoparticles. In these procedures, surfactants are needed to regulate the growth and final particle size. While there are numerous evidence on the decisive role of surfactants, a quantitative description remains elusive. This study develops a theoretical model to correlate the surfactant activities to particle growth. In the model, the "penetrability" of ions within surfactant layer is used to combine surface reaction and adsorption/desorption processes. The penetrability was then directly correlated to surfactant size. The theory was verified by synthesis of iron oxide nanoparticles with series of cationic surfactants. Eight surfactants, with same headgroup and increasing hydrocarbon tail, were employed. The experimental data showed a deterministic correlation between surfactant tails and particle size. The experimental correlation between surfactant length and particle size was predicted by the model. The modeling results verify the role of surfactant as capping agent during particle growth. More importantly, it provides a theoretical framework to control particle size in wet synthesis.
Collapse
Affiliation(s)
- Chi M Phan
- Nanochemistry Research Institute and Department of Chemical Engineering, Curtin University , GPO Box U1987, Perth, Western Australia 6845, Australia
| | - Hoang M Nguyen
- Nanochemistry Research Institute and Department of Chemical Engineering, Curtin University , GPO Box U1987, Perth, Western Australia 6845, Australia.,The University of Da Nang-University of Science and Technology , Da Nang 59000, Vietnam
| |
Collapse
|
115
|
Palos Pacheco R, Eismin RJ, Coss CS, Wang H, Maier RM, Polt R, Pemberton JE. Synthesis and Characterization of Four Diastereomers of Monorhamnolipids. J Am Chem Soc 2017; 139:5125-5132. [DOI: 10.1021/jacs.7b00427] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Ricardo Palos Pacheco
- Department
of Chemistry and Biochemistry and ‡Department of Soil, Water and Environmental
Science, University of Arizona, Tucson, Arizona 85721, United States
| | - Ryan J. Eismin
- Department
of Chemistry and Biochemistry and ‡Department of Soil, Water and Environmental
Science, University of Arizona, Tucson, Arizona 85721, United States
| | - Clifford S. Coss
- Department
of Chemistry and Biochemistry and ‡Department of Soil, Water and Environmental
Science, University of Arizona, Tucson, Arizona 85721, United States
| | - Hui Wang
- Department
of Chemistry and Biochemistry and ‡Department of Soil, Water and Environmental
Science, University of Arizona, Tucson, Arizona 85721, United States
| | - Raina M. Maier
- Department
of Chemistry and Biochemistry and ‡Department of Soil, Water and Environmental
Science, University of Arizona, Tucson, Arizona 85721, United States
| | - Robin Polt
- Department
of Chemistry and Biochemistry and ‡Department of Soil, Water and Environmental
Science, University of Arizona, Tucson, Arizona 85721, United States
| | - Jeanne E. Pemberton
- Department
of Chemistry and Biochemistry and ‡Department of Soil, Water and Environmental
Science, University of Arizona, Tucson, Arizona 85721, United States
| |
Collapse
|
116
|
Investigation of aqueous foam stability containing pigment colorant using polyoxyethylene nonionic surfactant. CHEMICAL PAPERS 2017. [DOI: 10.1007/s11696-017-0157-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
|
117
|
Lebecque S, Crowet J, Nasir M, Deleu M, Lins L. Molecular dynamics study of micelles properties according to their size. J Mol Graph Model 2017; 72:6-15. [DOI: 10.1016/j.jmgm.2016.12.007] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2016] [Revised: 12/07/2016] [Accepted: 12/09/2016] [Indexed: 11/26/2022]
|
118
|
Quantification of Detergents Complexed with Membrane Proteins. Sci Rep 2017; 7:41751. [PMID: 28176812 PMCID: PMC5297245 DOI: 10.1038/srep41751] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Accepted: 12/23/2016] [Indexed: 01/20/2023] Open
Abstract
Most membrane proteins studies require the use of detergents, but because of the lack of a general, accurate and rapid method to quantify them, many uncertainties remain that hamper proper functional and structural data analyses. To solve this problem, we propose a method based on matrix-assisted laser desorption/ionization mass spectrometry (MALDI-TOF MS) that allows quantification of pure or mixed detergents in complex with membrane proteins. We validated the method with a wide variety of detergents and membrane proteins. We automated the process, thereby allowing routine quantification for a broad spectrum of usage. As a first illustration, we show how to obtain information of the amount of detergent in complex with a membrane protein, essential for liposome or nanodiscs reconstitutions. Thanks to the method, we also show how to reliably and easily estimate the detergent corona diameter and select the smallest size, critical for favoring protein-protein contacts and triggering/promoting membrane protein crystallization, and to visualize the detergent belt for Cryo-EM studies.
Collapse
|
119
|
Sakuragi M, Zushi T, Seguchi R, Arai T, Taguchi K, Kusakabe K. Locational Analysis of Glutathione in Liposomes by Using Small-angle X-ray Scattering. CHEM LETT 2017. [DOI: 10.1246/cl.160932] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
|
120
|
Gabel F. Applications of SANS to Study Membrane Protein Systems. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 1009:201-214. [DOI: 10.1007/978-981-10-6038-0_12] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
|
121
|
Lee S, Mao A, Bhattacharya S, Robertson N, Grisshammer R, Tate CG, Vaidehi N. How Do Short Chain Nonionic Detergents Destabilize G-Protein-Coupled Receptors? J Am Chem Soc 2016; 138:15425-15433. [PMID: 27792324 PMCID: PMC5148649 DOI: 10.1021/jacs.6b08742] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Stability of detergent-solubilized G-protein-coupled receptors (GPCRs) is crucial for their purification in a biologically relevant state, and it is well-known that short chain detergents such as octylglucoside are more denaturing than long chain detergents such as dodecylmaltoside. However, the molecular basis for this phenomenon is poorly understood. To gain insights into the mechanism of detergent destabilization of GPCRs, we used atomistic molecular dynamics simulations of thermostabilized adenosine receptor (A2AR) mutants embedded in either a lipid bilayer or detergent micelles of alkylmaltosides and alkylglucosides. A2AR mutants in dodecylmaltoside or phospholipid showed low flexibility and good interhelical packing. In contrast, A2AR mutants in either octylglucoside or nonylglucoside showed decreased α-helicity in transmembrane regions, decreased α-helical packing, and the interpenetration of detergent molecules between transmembrane α-helices. This was not observed in octylglucoside containing phospholipid. Cholesteryl hemisuccinate in dodecylmaltoside increased the energetic stability of the receptor by wedging into crevices on the hydrophobic surface of A2AR, increasing packing interactions within the receptor and stiffening the detergent micelle. The data suggest a three-stage process for the initial events in the destabilization of GPCRs by octylglucoside: (i) highly mobile detergent molecules form small micelles around the receptor; (ii) loss of α-helicity and decreased interhelical packing interactions in transmembrane regions are promoted by increased receptor thermal motion; (iii) transient separation of transmembrane helices allowed penetration of detergent molecules into the core of the receptor. The relative hydration of the headgroup and alkyl chain correlates with detergent harshness and suggests new avenues to develop milder versions of octylglucoside for receptor crystallization.
Collapse
Affiliation(s)
- Sangbae Lee
- Department of Molecular Immunology, Beckman Research Institute of the City of Hope, 1500 E. Duarte Road, Duarte, California 91010, USA
| | - Allen Mao
- Department of Molecular Immunology, Beckman Research Institute of the City of Hope, 1500 E. Duarte Road, Duarte, California 91010, USA
| | - Supriyo Bhattacharya
- Department of Molecular Immunology, Beckman Research Institute of the City of Hope, 1500 E. Duarte Road, Duarte, California 91010, USA
| | - Nathan Robertson
- Heptares Therapeutics Ltd, BioPark, Broadwater Road, Welwyn Garden City, AL7 3AX, UK
| | - Reinhard Grisshammer
- Membrane Protein Structure Function Unit, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Department of Health and Human Services, Rockville, Maryland 20852, USA
| | - Christopher G. Tate
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Nagarajan Vaidehi
- Department of Molecular Immunology, Beckman Research Institute of the City of Hope, 1500 E. Duarte Road, Duarte, California 91010, USA
| |
Collapse
|
122
|
Iadanza MG, Higgins AJ, Schiffrin B, Calabrese AN, Brockwell DJ, Ashcroft AE, Radford SE, Ranson NA. Lateral opening in the intact β-barrel assembly machinery captured by cryo-EM. Nat Commun 2016; 7:12865. [PMID: 27686148 PMCID: PMC5056442 DOI: 10.1038/ncomms12865] [Citation(s) in RCA: 138] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Accepted: 08/04/2016] [Indexed: 02/06/2023] Open
Abstract
The β-barrel assembly machinery (BAM) is a ∼203 kDa complex of five proteins (BamA-E), which is essential for viability in E. coli. BAM promotes the folding and insertion of β-barrel proteins into the outer membrane via a poorly understood mechanism. Several current models suggest that BAM functions through a 'lateral gating' motion of the β-barrel of BamA. Here we present a cryo-EM structure of the BamABCDE complex, at 4.9 Å resolution. The structure is in a laterally open conformation showing that gating is independent of BamB binding. We describe conformational changes throughout the complex and interactions between BamA, B, D and E, and the detergent micelle that suggest communication between BAM and the lipid bilayer. Finally, using an enhanced reconstitution protocol and functional assays, we show that for the outer membrane protein OmpT, efficient folding in vitro requires lateral gating in BAM.
Collapse
Affiliation(s)
- Matthew G. Iadanza
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, University of Leeds, Mount Preston Street, Leeds LS2 9JT, UK
| | - Anna J. Higgins
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, University of Leeds, Mount Preston Street, Leeds LS2 9JT, UK
| | - Bob Schiffrin
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, University of Leeds, Mount Preston Street, Leeds LS2 9JT, UK
| | - Antonio N. Calabrese
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, University of Leeds, Mount Preston Street, Leeds LS2 9JT, UK
| | - David J. Brockwell
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, University of Leeds, Mount Preston Street, Leeds LS2 9JT, UK
| | - Alison E. Ashcroft
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, University of Leeds, Mount Preston Street, Leeds LS2 9JT, UK
| | - Sheena E. Radford
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, University of Leeds, Mount Preston Street, Leeds LS2 9JT, UK
| | - Neil A. Ranson
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, University of Leeds, Mount Preston Street, Leeds LS2 9JT, UK
| |
Collapse
|
123
|
Ryzhakov A, Do Thi T, Stappaerts J, Bertoletti L, Kimpe K, Sá Couto AR, Saokham P, Van den Mooter G, Augustijns P, Somsen GW, Kurkov S, Inghelbrecht S, Arien A, Jimidar MI, Schrijnemakers K, Loftsson T. Self-Assembly of Cyclodextrins and Their Complexes in Aqueous Solutions. J Pharm Sci 2016; 105:2556-2569. [DOI: 10.1016/j.xphs.2016.01.019] [Citation(s) in RCA: 85] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2015] [Revised: 01/19/2016] [Accepted: 01/21/2016] [Indexed: 12/12/2022]
|
124
|
Michaux C, Roussel G, Lopes-Rodrigues M, Matagne A, Perpète E. Unravelling the mechanisms of a protein refolding process based on the association of detergents and co-solvents. J Pept Sci 2016; 22:485-91. [DOI: 10.1002/psc.2893] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2016] [Revised: 03/30/2016] [Accepted: 04/05/2016] [Indexed: 02/03/2023]
Affiliation(s)
- C. Michaux
- Laboratory of Physical Chemistry of Biomolecules, Chemistry Department; University of Namur; 61 rue de Bruxelles 5000 Namur Belgium
| | - G. Roussel
- Laboratory of Physical Chemistry of Biomolecules, Chemistry Department; University of Namur; 61 rue de Bruxelles 5000 Namur Belgium
| | - M. Lopes-Rodrigues
- Laboratory of Physical Chemistry of Biomolecules, Chemistry Department; University of Namur; 61 rue de Bruxelles 5000 Namur Belgium
| | - A. Matagne
- Laboratory of Enzymology and Protein Folding, Centre for Protein Engineering, Institut de Chimie B6; University of Liège; 7 Place du 20 août 4000 Liège Belgium
| | - E.A. Perpète
- Laboratory of Physical Chemistry of Biomolecules, Chemistry Department; University of Namur; 61 rue de Bruxelles 5000 Namur Belgium
| |
Collapse
|
125
|
Garrido PF, Brocos P, Amigo A, García-Río L, Gracia-Fadrique J, Piñeiro Á. STAND: Surface Tension for Aggregation Number Determination. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2016; 32:3917-3925. [PMID: 27048988 DOI: 10.1021/acs.langmuir.6b00477] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Taking advantage of the extremely high dependence of surface tension on the concentration of amphiphilic molecules in aqueous solution, a new model based on the double equilibrium between free and aggregated molecules in the liquid phase and between free molecules in the liquid phase and those adsorbed at the air/liquid interface is presented and validated using literature data and fluorescence measurements. A key point of the model is the use of both the Langmuir isotherm and the Gibbs adsorption equation in terms of free molecules instead of the nominal concentration of the solute. The application of the model should be limited to non ionic compounds since it does not consider the presence of counterions. It requires several coupled nonlinear fittings for which we developed a software that is publicly available in our server as a web application. Using this tool, it is straightforward to get the average aggregation number of an amphiphile, the micellization free energy, the adsorption constant, the maximum surface excess (and so the minimum area per molecule), the distribution of solute in the liquid phase between free and aggregate species, and the surface coverage in only a couple of seconds, just by uploading a text file with surface tension vs concentration data and the corresponding uncertainties.
Collapse
Affiliation(s)
- Pablo F Garrido
- Departamento de Física Aplicada, Facultade de Física, Universidade de Santiago de Compostela , 15782 Santiago de Compostela, Spain
| | - Pilar Brocos
- Departamento de Física Aplicada, Facultade de Física, Universidade de Santiago de Compostela , 15782 Santiago de Compostela, Spain
| | - Alfredo Amigo
- Departamento de Física Aplicada, Facultade de Física, Universidade de Santiago de Compostela , 15782 Santiago de Compostela, Spain
| | - Luis García-Río
- Departamento de Química Física, Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS), Facultade de Química, Universidade de Santiago de Compostela , 15782 Santiago de Compostela, Spain
| | - Jesús Gracia-Fadrique
- Departamento de Fisicoquímica, Facultad de Química, Universidad Nacional Autónoma de México, Ciudad Universitaria , 04510 México D.F., Mexico
| | - Ángel Piñeiro
- Departamento de Física Aplicada, Facultade de Física, Universidade de Santiago de Compostela , 15782 Santiago de Compostela, Spain
| |
Collapse
|
126
|
Frislev HS, Jessen CM, Oliveira CLP, Pedersen JS, Otzen DE. Liprotides made of α-lactalbumin and cis fatty acids form core-shell and multi-layer structures with a common membrane-targeting mechanism. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2016; 1864:847-59. [PMID: 27068540 DOI: 10.1016/j.bbapap.2016.04.003] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2016] [Revised: 04/05/2016] [Accepted: 04/07/2016] [Indexed: 10/22/2022]
Abstract
α-Lactalbumin (aLA) has been shown to form complexes with oleic acid (OA), which may target cancer cells. We recently showed that aLA and several other proteins all form protein-OA complexes called liprotides with a generic structure consisting of a micellar OA core surrounded by a shell of partially denatured protein. Here we report that a heat treatment and an alkaline treatment method both allow us to prepare liprotide complexes composed of aLA and a range of unsaturated fatty acids (FA), provided the FAs contain cis (but not trans) double bonds. All liprotides containing cis-FA form both small and large species, which all consist of partially denatured aLA, though the overall shape of the species differs. Small liprotides have a simple core-shell structure while the larger liprotides are multi-layered, i.e. they have an additional layer of both FA and aLA surrounding the outside of the core-shell structure. All liprotides can transfer their entire FA content to vesicles, releasing aLA as monomers and softening the lipid membrane. The more similar to OA, the more efficiently the different FAs induce hemolysis. We conclude that aLA can take up and transfer a wide variety of FA to membranes, provided they contain a cis-bond. This highlights liprotides as a general class of complexes where both protein and cis-FA component can be varied without departing from a generic (though sometimes multi-layered) core-shell structure.
Collapse
Affiliation(s)
- Henriette S Frislev
- Interdisciplinary Nanoscience Center (iNANO), Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 14, DK-8000 Aarhus C, Denmark
| | - Christian M Jessen
- Department of Chemistry and Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Gustav Wieds Vej 14, DK-8000 Aarhus C, Denmark
| | - Cristiano L P Oliveira
- Department of Chemistry and Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Gustav Wieds Vej 14, DK-8000 Aarhus C, Denmark; Institute of Physics, University of São Paulo, Rua do Matão, 187, São Paulo, São Paulo, 05314-970, Brazil
| | - Jan Skov Pedersen
- Department of Chemistry and Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Gustav Wieds Vej 14, DK-8000 Aarhus C, Denmark
| | - Daniel E Otzen
- Interdisciplinary Nanoscience Center (iNANO), Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 14, DK-8000 Aarhus C, Denmark.
| |
Collapse
|
127
|
Pollock NL, Satriano L, Zegarra-Moran O, Ford RC, Moran O. Structure of wild type and mutant F508del CFTR: A small-angle X-ray scattering study of the protein–detergent complexes. J Struct Biol 2016; 194:102-11. [DOI: 10.1016/j.jsb.2016.02.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2015] [Revised: 02/01/2016] [Accepted: 02/02/2016] [Indexed: 10/22/2022]
|
128
|
Hiruma-Shimizu K, Shimizu H, Thompson GS, Kalverda AP, Patching SG. Deuterated detergents for structural and functional studies of membrane proteins: Properties, chemical synthesis and applications. Mol Membr Biol 2016; 32:139-55. [DOI: 10.3109/09687688.2015.1125536] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Affiliation(s)
| | - Hiroki Shimizu
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, Hokkaido, Japan,
| | - Gary S. Thompson
- School of Molecular and Cellular Biology, University of Leeds, Leeds, UK,
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, UK, and
| | - Arnout P. Kalverda
- School of Molecular and Cellular Biology, University of Leeds, Leeds, UK,
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, UK, and
| | | |
Collapse
|
129
|
Burdíková J, Mravec F, Pekař M. The formation of mixed micelles of sugar surfactants and phospholipids and their interactions with hyaluronan. Colloid Polym Sci 2016. [DOI: 10.1007/s00396-016-3840-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
|
130
|
Bruetzel LK, Fischer S, Salditt A, Sedlak SM, Nickel B, Lipfert J. A Mo-anode-based in-house source for small-angle X-ray scattering measurements of biological macromolecules. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2016; 87:025103. [PMID: 26931887 DOI: 10.1063/1.4940936] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
We demonstrate the use of a molybdenum-anode-based in-house small-angle X-ray scattering (SAXS) setup to study biological macromolecules in solution. Our system consists of a microfocus X-ray tube delivering a highly collimated flux of 2.5 × 10(6) photons/s at a beam size of 1.2 × 1.2 mm(2) at the collimation path exit and a maximum beam divergence of 0.16 mrad. The resulting observable scattering vectors q are in the range of 0.38 Å(-1) down to 0.009 Å(-1) in SAXS configuration and of 0.26 Å(-1) up to 5.7 Å(-1) in wide-angle X-ray scattering (WAXS) mode. To determine the capabilities of the instrument, we collected SAXS data on weakly scattering biological macromolecules including proteins and a nucleic acid sample with molecular weights varying from ∼12 to 69 kDa and concentrations of 1.5-24 mg/ml. The measured scattering data display a high signal-to-noise ratio up to q-values of ∼0.2 Å(-1) allowing for an accurate structural characterization of the samples. Moreover, the in-house source data are of sufficient quality to perform ab initio 3D structure reconstructions that are in excellent agreement with the available crystallographic structures. In addition, measurements for the detergent decyl-maltoside show that the setup can be used to determine the size, shape, and interactions (as characterized by the second virial coefficient) of detergent micelles. This demonstrates that the use of a Mo-anode based in-house source is sufficient to determine basic geometric parameters and 3D shapes of biomolecules and presents a viable alternative to valuable beam time at third generation synchrotron sources.
Collapse
Affiliation(s)
- Linda K Bruetzel
- Department of Physics, Nanosystems Initiative Munich, and Center for Nanoscience, Ludwig-Maximilians-University Munich, Amalienstr. 54, 80799 Munich, Germany and Geschwister-Scholl Platz 1, 80539 Munich, Germany
| | - Stefan Fischer
- Department of Physics, Nanosystems Initiative Munich, and Center for Nanoscience, Ludwig-Maximilians-University Munich, Amalienstr. 54, 80799 Munich, Germany and Geschwister-Scholl Platz 1, 80539 Munich, Germany
| | - Annalena Salditt
- Department of Physics, Nanosystems Initiative Munich, and Center for Nanoscience, Ludwig-Maximilians-University Munich, Amalienstr. 54, 80799 Munich, Germany and Geschwister-Scholl Platz 1, 80539 Munich, Germany
| | - Steffen M Sedlak
- Department of Physics, Nanosystems Initiative Munich, and Center for Nanoscience, Ludwig-Maximilians-University Munich, Amalienstr. 54, 80799 Munich, Germany and Geschwister-Scholl Platz 1, 80539 Munich, Germany
| | - Bert Nickel
- Department of Physics, Nanosystems Initiative Munich, and Center for Nanoscience, Ludwig-Maximilians-University Munich, Amalienstr. 54, 80799 Munich, Germany and Geschwister-Scholl Platz 1, 80539 Munich, Germany
| | - Jan Lipfert
- Department of Physics, Nanosystems Initiative Munich, and Center for Nanoscience, Ludwig-Maximilians-University Munich, Amalienstr. 54, 80799 Munich, Germany and Geschwister-Scholl Platz 1, 80539 Munich, Germany
| |
Collapse
|
131
|
Srinivasan P. Multifunctional-layered materials for creating membrane-restricted nanodomains and nanoscale imaging. APPLIED PHYSICS LETTERS 2016; 108:033702. [PMID: 26869725 PMCID: PMC4723406 DOI: 10.1063/1.4940388] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2015] [Accepted: 01/11/2016] [Indexed: 06/05/2023]
Abstract
Experimental platform that allows precise spatial positioning of biomolecules with an exquisite control at nanometer length scales is a valuable tool to study the molecular mechanisms of membrane bound signaling. Using micromachined thin film gold (Au) in layered architecture, it is possible to add both optical and biochemical functionalities in in vitro. Towards this goal, here, I show that docking of complementary DNA tethered giant phospholiposomes on Au surface can create membrane-restricted nanodomains. These nanodomains are critical features to dissect molecular choreography of membrane signaling complexes. The excited surface plasmon resonance modes of Au allow label-free imaging at diffraction-limited resolution of stably docked DNA tethered phospholiposomes, and lipid-detergent bicelle structures. Such multifunctional building block enables realizing rigorously controlled in vitro set-up to model membrane anchored biological signaling, besides serving as an optical tool for nanoscale imaging.
Collapse
Affiliation(s)
- P Srinivasan
- Department of Electrical and Computer Engineering, University of California , Santa Barbara, California 93106, USA and Neuroscience Research Institute, University of California , Santa Barbara, California 93106, USA
| |
Collapse
|
132
|
Ryan TM, Griffin MDW, McGillivray DJ, Knott RB, Wood K, Masters CL, Kirby N, Curtain CC. Apolipoprotein C-II Adopts Distinct Structures in Complex with Micellar and Submicellar Forms of the Amyloid-Inhibiting Lipid-Mimetic Dodecylphosphocholine. Biophys J 2016; 110:85-94. [PMID: 26745412 PMCID: PMC4805880 DOI: 10.1016/j.bpj.2015.11.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2015] [Revised: 11/03/2015] [Accepted: 11/09/2015] [Indexed: 01/21/2023] Open
Abstract
The formation of amyloid deposits is a common feature of a broad range of diseases, including atherosclerosis, Alzheimer's disease, and Parkinson's disease. The basis and role of amyloid deposition in the pathogenesis of these diseases is still being defined, however an interesting feature of amyloidogenic proteins is that the majority of the pathologically associated proteins are involved in lipid homeostasis, be it in lipid transport, incorporation into membranes, or the regulation of lipid pathways. Thus, amyloid-forming proteins commonly bind lipids, and lipids are generally involved in the proper folding of these proteins. However, understanding of the basis for these lipid-related aspects of amyloidogenesis is lacking. Thus, we have used the apolipoprotein C-II amyloid model system in conjunction with x-ray and neutron scattering analyses to address this problem. Apolipoprotein C-II is a well-studied model system of systemic amyloid fibril formation, with a clear and well-defined pathway for fibril formation, where the effects of lipid interaction are characterized, particularly for the lipid mimetic dodecylphosphocholine. We show that the micellar state of an inhibitory lipid can have a very significant effect on protein conformation, with micelles stabilizing a particular α-helical structure, whereas submicellar lipids stabilize a very different dimeric, α-helical structure. These results indicate that lipids may have an important role in the development and progression of amyloid-related diseases.
Collapse
Affiliation(s)
- Timothy M Ryan
- Australian Synchrotron, Clayton, Victoria, Australia; The Florey Institute, The University of Melbourne, Parkville, Victoria, Australia; The MacDiarmid Institute of Advanced Materials and Nanotechnology, Wellington, New Zealand.
| | - Michael D W Griffin
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, Victoria, Australia
| | - Duncan J McGillivray
- School of Chemical Science, The University of Auckland, Auckland, New Zealand; The MacDiarmid Institute of Advanced Materials and Nanotechnology, Wellington, New Zealand
| | - Robert B Knott
- Australian Nuclear Science and Technology Organisation, New South Wales, Australia
| | - Kathleen Wood
- Australian Nuclear Science and Technology Organisation, New South Wales, Australia
| | - Colin L Masters
- The Florey Institute, The University of Melbourne, Parkville, Victoria, Australia
| | - Nigel Kirby
- Australian Synchrotron, Clayton, Victoria, Australia
| | - Cyril C Curtain
- The Florey Institute, The University of Melbourne, Parkville, Victoria, Australia
| |
Collapse
|
133
|
Polidori A, Raynal S, Barret LA, Dahani M, Barrot-Ivolot C, Jungas C, Frotscher E, Keller S, Ebel C, Breyton C, Bonneté F. Sparingly fluorinated maltoside-based surfactants for membrane-protein stabilization. NEW J CHEM 2016. [DOI: 10.1039/c5nj03502c] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
|
134
|
Detergents in Membrane Protein Purification and Crystallisation. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 922:13-28. [PMID: 27553232 DOI: 10.1007/978-3-319-35072-1_2] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Detergents play a significant role in structural and functional characterisation of integral membrane proteins (IMPs). IMPs reside in the biological membranes and exhibit a great variation in their structural and physical properties. For in vitro biophysical studies, structural and functional analyses, IMPs need to be extracted from the membrane lipid bilayer environment in which they are found and purified to homogeneity while maintaining a folded and functionally active state. Detergents are capable of successfully solubilising and extracting the IMPs from the membrane bilayers. A number of detergents with varying structure and physicochemical properties are commercially available and can be applied for this purpose. Nevertheless, it is important to choose a detergent that is not only able to extract the membrane protein but also provide an optimal environment while retaining the correct structural and physical properties of the protein molecule. Choosing the best detergent for this task can be made possible by understanding the physical and chemical properties of the different detergents and their interaction with the IMPs. In addition, understanding the mechanism of membrane solubilisation and protein extraction along with crystallisation requirements, if crystallographic studies are going to be undertaken, can help in choosing the best detergent for the purpose. This chapter aims to present the fundamental properties of detergents and highlight information relevant to IMP crystallisation. The first section of the chapter reviews the physicochemical properties of detergents and parameters essential for predicting their behaviour in solution. The second section covers the interaction of detergents with the biologic membranes and proteins followed by their role in membrane protein crystallisation. The last section will briefly cover the types of detergent and their properties focusing on custom designed detergents for membrane protein studies.
Collapse
|
135
|
Abstract
In experimental studies of solubilized membrane proteins, the detergent corona influences the protein behavior and the resulting measurement. Thus, combinations of experimental techniques with atomistic modeling have been used to resolve corona structural parameters and distributions. Here, we used small-angle X-ray scattering (SAXS) data and molecular dynamics simulations to study a model protein-detergent complex (PDC) consisting of aquaporin-0 and dodecyl-β-maltoside molecules (βDDM). The corona morphology of single snapshots was found to be rough, but it is smooth and compacted in 100-ns-scale ensemble averages. Individual snapshots therefore were unable to accurately represent the ensemble information as captured by experimental SAXS. Mimicking of annular lipids by detergent was also observed. SAXS prediction using different published methods was used to identify optimal βDDM numbers. Explicit-solvent methods predicted best agreement using 290-βDDM PDCs, but implicit-solvent methods gave unclear predictions due to overcompensation by free solvation-layer density parameters. Thus, ensemble-based approaches and physically motivated constraints will help to extract structural information from SAXS data.
Collapse
Affiliation(s)
- Po-Chia Chen
- Institute for Microbiology and Genetics, Georg-August-University Göttingen , Justus-von-Liebig weg 11, 37077 Göttingen, Germany
| | - Jochen S Hub
- Institute for Microbiology and Genetics, Georg-August-University Göttingen , Justus-von-Liebig weg 11, 37077 Göttingen, Germany
| |
Collapse
|
136
|
Maurya SR, Mahalakshmi R. N-helix and Cysteines Inter-regulate Human Mitochondrial VDAC-2 Function and Biochemistry. J Biol Chem 2015; 290:30240-52. [PMID: 26487717 PMCID: PMC4683249 DOI: 10.1074/jbc.m115.693978] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2015] [Indexed: 12/25/2022] Open
Abstract
Human voltage-dependent anion channel-2 (hVDAC-2) functions primarily as the crucial anti-apoptotic protein in the outer mitochondrial membrane, and additionally as a gated bidirectional metabolite transporter. The N-terminal helix (NTH), involved in voltage sensing, bears an additional 11-residue extension (NTE) only in hVDAC-2. In this study, we assign a unique role for the NTE as influencing the chaperone-independent refolding kinetics and overall thermodynamic stability of hVDAC-2. Our electrophysiology data shows that the N-helix is crucial for channel activity, whereas NTE sensitizes this isoform to voltage gating. Additionally, hVDAC-2 possesses the highest cysteine content, possibly for regulating reactive oxygen species content. We identify interdependent contributions of the N-helix and cysteines to channel function, and the measured stability in micellar environments with differing physicochemical properties. The evolutionary demand for the NTE in the presence of cysteines clearly emerges from our biochemical and functional studies, providing insight into factors that functionally demarcate hVDAC-2 from the other VDACs.
Collapse
Affiliation(s)
- Svetlana Rajkumar Maurya
- From the Department of Biological Sciences, Molecular Biophysics Laboratory, Indian Institute of Science Education and Research, Bhopal 462023, India
| | - Radhakrishnan Mahalakshmi
- From the Department of Biological Sciences, Molecular Biophysics Laboratory, Indian Institute of Science Education and Research, Bhopal 462023, India
| |
Collapse
|
137
|
Routledge SJ, Mikaliunaite L, Patel A, Clare M, Cartwright SP, Bawa Z, Wilks MDB, Low F, Hardy D, Rothnie AJ, Bill RM. The synthesis of recombinant membrane proteins in yeast for structural studies. Methods 2015; 95:26-37. [PMID: 26431670 DOI: 10.1016/j.ymeth.2015.09.027] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2015] [Revised: 09/28/2015] [Accepted: 09/29/2015] [Indexed: 12/22/2022] Open
Abstract
Historically, recombinant membrane protein production has been a major challenge meaning that many fewer membrane protein structures have been published than those of soluble proteins. However, there has been a recent, almost exponential increase in the number of membrane protein structures being deposited in the Protein Data Bank. This suggests that empirical methods are now available that can ensure the required protein supply for these difficult targets. This review focuses on methods that are available for protein production in yeast, which is an important source of recombinant eukaryotic membrane proteins. We provide an overview of approaches to optimize the expression plasmid, host cell and culture conditions, as well as the extraction and purification of functional protein for crystallization trials in preparation for structural studies.
Collapse
Affiliation(s)
- Sarah J Routledge
- Department of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge CB2 1PD, UK; School of Life & Health Sciences, Aston University, Aston Triangle, Birmingham B4 7ET, UK
| | - Lina Mikaliunaite
- School of Life & Health Sciences, Aston University, Aston Triangle, Birmingham B4 7ET, UK
| | - Anjana Patel
- School of Life & Health Sciences, Aston University, Aston Triangle, Birmingham B4 7ET, UK
| | - Michelle Clare
- School of Life & Health Sciences, Aston University, Aston Triangle, Birmingham B4 7ET, UK
| | - Stephanie P Cartwright
- School of Life & Health Sciences, Aston University, Aston Triangle, Birmingham B4 7ET, UK
| | - Zharain Bawa
- School of Life & Health Sciences, Aston University, Aston Triangle, Birmingham B4 7ET, UK
| | - Martin D B Wilks
- Smallpeice Enterprises Ltd, 27 Newbold Terrace East, Leamington Spa, Warwickshire CV32 4ES, UK
| | - Floren Low
- School of Life & Health Sciences, Aston University, Aston Triangle, Birmingham B4 7ET, UK
| | - David Hardy
- School of Life & Health Sciences, Aston University, Aston Triangle, Birmingham B4 7ET, UK
| | - Alice J Rothnie
- School of Life & Health Sciences, Aston University, Aston Triangle, Birmingham B4 7ET, UK
| | - Roslyn M Bill
- School of Life & Health Sciences, Aston University, Aston Triangle, Birmingham B4 7ET, UK.
| |
Collapse
|
138
|
Dahani M, Barret LA, Raynal S, Jungas C, Pernot P, Polidori A, Bonneté F. Use of dynamic light scattering and small-angle X-ray scattering to characterize new surfactants in solution conditions for membrane-protein crystallization. Acta Crystallogr F Struct Biol Commun 2015; 71:838-46. [PMID: 26144228 PMCID: PMC4498704 DOI: 10.1107/s2053230x15009516] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2015] [Accepted: 05/18/2015] [Indexed: 11/11/2022] Open
Abstract
The structural and interactive properties of two novel hemifluorinated surfactants, F2H9-β-M and F4H5-β-M, the syntheses of which were based on the structure and hydrophobicity of the well known dodecyl-β-maltoside (DD-β-M), are described. The shape of their micellar assemblies was characterized by small-angle X-ray scattering and their intermicellar interactions in crystallizing conditions were measured by dynamic light scattering. Such information is essential for surfactant phase-diagram determination and membrane-protein crystallization.
Collapse
Affiliation(s)
- Mohamed Dahani
- Institut des Biomolécules Max Mousseron/CBSA, UMR 5247, Avignon University, 33 Rue Louis Pasteur, 84000 Avignon,France
| | - Laurie-Anne Barret
- Institut des Biomolécules Max Mousseron/CBSA, UMR 5247, Avignon University, 33 Rue Louis Pasteur, 84000 Avignon,France
- Laboratoire de Bioénergétique Cellulaire/Biologie Végétale et Microbiologie Environnementales, UMR 7265, 13108 Saint-Paul-lez-Durance, France
| | - Simon Raynal
- Institut des Biomolécules Max Mousseron/CBSA, UMR 5247, Avignon University, 33 Rue Louis Pasteur, 84000 Avignon,France
| | - Colette Jungas
- Laboratoire de Bioénergétique Cellulaire/Biologie Végétale et Microbiologie Environnementales, UMR 7265, 13108 Saint-Paul-lez-Durance, France
| | - Pétra Pernot
- European Synchrotron Radiation Facility, 71 Avenue des Martyrs, 38000 Grenoble, France
| | - Ange Polidori
- Institut des Biomolécules Max Mousseron/CBSA, UMR 5247, Avignon University, 33 Rue Louis Pasteur, 84000 Avignon,France
| | - Françoise Bonneté
- Institut des Biomolécules Max Mousseron/CBSA, UMR 5247, Avignon University, 33 Rue Louis Pasteur, 84000 Avignon,France
| |
Collapse
|
139
|
Jaber R, Wasbrough MJ, Holdaway JA, Edler KJ. Interactions between quaternary ammonium surfactants and polyethylenimine at high pH in film forming systems. J Colloid Interface Sci 2015; 449:286-96. [DOI: 10.1016/j.jcis.2015.01.034] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2014] [Revised: 01/14/2015] [Accepted: 01/14/2015] [Indexed: 10/24/2022]
|
140
|
Abla M, Unger S, Keller S, Bonneté F, Ebel C, Pucci B, Breyton C, Durand G. Micellar and biochemical properties of a propyl-ended fluorinated surfactant designed for membrane–protein study. J Colloid Interface Sci 2015; 445:127-136. [DOI: 10.1016/j.jcis.2014.12.066] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2014] [Revised: 12/19/2014] [Accepted: 12/19/2014] [Indexed: 01/21/2023]
|
141
|
Troutman JM, Erickson KM, Scott PM, Hazel JM, Martinez CD, Dodbele S. Tuning the production of variable length, fluorescent polyisoprenoids using surfactant-controlled enzymatic synthesis. Biochemistry 2015; 54:2817-27. [PMID: 25897619 DOI: 10.1021/acs.biochem.5b00310] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Bactoprenyl diphosphate (BPP), a two-E eight-Z configuration C55 isoprenoid, serves as a critical anchor for the biosynthesis of complex glycans central to bacterial survival and pathogenesis. BPP is formed by the polymerase undecaprenyl pyrophosphate synthase (UppS), which catalyzes the elongation of a single farnesyl diphosphate (FPP) with eight Z-configuration isoprene units from eight isopentenyl diphosphates. In vitro analysis of UppS and other polyprenyl diphosphate synthases requires the addition of a surfactant such as Triton X-100 to stimulate the release of the hydrophobic product from the enzyme for effective and efficient turnover. Here using a fluorescent 2-nitrileanilinogeranyl diphosphate analogue of FPP, we have found that a wide range of surfactants can stimulate release of product from UppS and that the structure of the surfactant has a major impact on the lengths of products produced by the protein. Of particular importance, shorter chain surfactants promote the release of isoprenoids with four to six Z-configuration isoprene additions, while larger chain surfactants promote the formation of natural isoprenoid lengths (8Z) and larger. We have found that the product chain lengths can be readily controlled and coarsely tuned by adjusting surfactant identity, concentration, and reaction time. We have also found that binary mixtures of just two surfactants can be used to fine-tune isoprenoid lengths. The surfactant effects discovered do not appear to be significantly altered with an alternative isoprenoid substrate. However, the surfactant effects do appear to be dependent on differences in UppS between bacterial species. This work provides new insights into surfactant effects in enzymology and highlights how these effects can be leveraged for the chemoenzymatic synthesis of otherwise difficult to obtain glycan biosynthesis probes. This work also provides key reagents for the systematic analysis of structure-activity relationships between glycan biosynthesis enzymes and isoprenoid structure.
Collapse
Affiliation(s)
- Jerry M Troutman
- †Department of Chemistry, ‡Nanoscale Science Program, and §The Center for Biomedical Engineering and Science, University of North Carolina at Charlotte, 9201 University City Boulevard, Charlotte, North Carolina 28223, United States
| | - Katelyn M Erickson
- †Department of Chemistry, ‡Nanoscale Science Program, and §The Center for Biomedical Engineering and Science, University of North Carolina at Charlotte, 9201 University City Boulevard, Charlotte, North Carolina 28223, United States
| | - Phillip M Scott
- †Department of Chemistry, ‡Nanoscale Science Program, and §The Center for Biomedical Engineering and Science, University of North Carolina at Charlotte, 9201 University City Boulevard, Charlotte, North Carolina 28223, United States
| | - Joseph M Hazel
- †Department of Chemistry, ‡Nanoscale Science Program, and §The Center for Biomedical Engineering and Science, University of North Carolina at Charlotte, 9201 University City Boulevard, Charlotte, North Carolina 28223, United States
| | - Christina D Martinez
- †Department of Chemistry, ‡Nanoscale Science Program, and §The Center for Biomedical Engineering and Science, University of North Carolina at Charlotte, 9201 University City Boulevard, Charlotte, North Carolina 28223, United States
| | - Samantha Dodbele
- †Department of Chemistry, ‡Nanoscale Science Program, and §The Center for Biomedical Engineering and Science, University of North Carolina at Charlotte, 9201 University City Boulevard, Charlotte, North Carolina 28223, United States
| |
Collapse
|
142
|
Purification of a Multidrug Resistance Transporter for Crystallization Studies. Antibiotics (Basel) 2015; 4:113-35. [PMID: 27025617 PMCID: PMC4790320 DOI: 10.3390/antibiotics4010113] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2015] [Revised: 02/23/2015] [Accepted: 02/25/2015] [Indexed: 01/12/2023] Open
Abstract
Crystallization of integral membrane proteins is a challenging field and much effort has been invested in optimizing the overexpression and purification steps needed to obtain milligram amounts of pure, stable, monodisperse protein sample for crystallography studies. Our current work involves the structural and functional characterization of the Escherichia coli multidrug resistance transporter MdtM, a member of the major facilitator superfamily (MFS). Here we present a protocol for isolation of MdtM to increase yields of recombinant protein to the milligram quantities necessary for pursuit of structural studies using X-ray crystallography. Purification of MdtM was enhanced by introduction of an elongated His-tag, followed by identification and subsequent removal of chaperonin contamination. For crystallization trials of MdtM, detergent screening using size exclusion chromatography determined that decylmaltoside (DM) was the shortest-chain detergent that maintained the protein in a stable, monodispersed state. Crystallization trials of MdtM performed using the hanging-drop diffusion method with commercially available crystallization screens yielded 3D protein crystals under several different conditions. We contend that the purification protocol described here may be employed for production of high-quality protein of other multidrug efflux members of the MFS, a ubiquitous, physiologically and clinically important class of membrane transporters.
Collapse
|
143
|
Määttä J, Vierros S, Sammalkorpi M. Controlling Carbon-Nanotube—Phospholipid Solubility by Curvature-Dependent Self-Assembly. J Phys Chem B 2015; 119:4020-32. [DOI: 10.1021/jp5128173] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Jukka Määttä
- Department of Chemistry, Aalto University School of Chemical Technology, 02150 Espoo, Finland
| | - Sampsa Vierros
- Department of Chemistry, Aalto University School of Chemical Technology, 02150 Espoo, Finland
| | - Maria Sammalkorpi
- Department of Chemistry, Aalto University School of Chemical Technology, 02150 Espoo, Finland
| |
Collapse
|
144
|
Georgieva ER, Xiao S, Borbat PP, Freed JH, Eliezer D. Tau binds to lipid membrane surfaces via short amphipathic helices located in its microtubule-binding repeats. Biophys J 2015; 107:1441-52. [PMID: 25229151 DOI: 10.1016/j.bpj.2014.07.046] [Citation(s) in RCA: 81] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2014] [Revised: 07/18/2014] [Accepted: 07/24/2014] [Indexed: 11/16/2022] Open
Abstract
Tau is a microtubule-associated protein that is genetically linked to dementia and linked to Alzheimer's disease via its presence in intraneuronal neurofibrillary tangle deposits, where it takes the form of aggregated paired helical and straight filaments. Although the precise mechanisms by which tau contributes to neurodegeneration remain unclear, tau aggregation is commonly considered to be a critical component of tau-mediated pathogenicity. Nevertheless, the context in which tau aggregation begins in vivo is unknown. Tau is enriched in membrane-rich neuronal structures such as axons and growth cones, and can interact with membranes both via intermediary proteins and directly via its microtubule-binding domain (MBD). Membranes efficiently facilitate tau aggregation in vitro, and may therefore provide a physiologically relevant context for nucleating tau aggregation in vivo. Furthermore, tau-membrane interactions may potentially play a role in tau's poorly understood normal physiological functions. Despite the potential importance of direct tau-membrane interactions for tau pathology and physiology, the structural mechanisms that underlie such interactions remain to be elucidated. Here, we employ electron spin resonance spectroscopy to investigate the secondary and long-range structural properties of the MBD of three-repeat tau isoforms when bound to lipid vesicles and membrane mimetics. We show that the membrane interactions of the tau MBD are mediated by short amphipathic helices formed within each of the MBD repeats in the membrane-bound state. To our knowledge, this is the first detailed elucidation of helical tau structure in the context of intact lipid bilayers. We further show, for the first time (to our knowledge), that these individual helical regions behave as independent membrane-binding sites linked by flexible connecting regions. These results represent the first (to our knowledge) detailed structural view of membrane-bound tau and provide insights into potential mechanisms for membrane-mediated tau aggregation. Furthermore, the results may have implications for the structural basis of tau-microtubule interactions and microtubule-mediated tau aggregation.
Collapse
Affiliation(s)
- Elka R Georgieva
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York; National Biomedical Center for Advanced ESR Technology, Cornell University, Ithaca, New York
| | - Shifeng Xiao
- Department of Biochemistry, Weill Cornell Medical College, New York, New York; Program in Structural Biology, Weill Cornell Medical College, New York, New York
| | - Peter P Borbat
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York; National Biomedical Center for Advanced ESR Technology, Cornell University, Ithaca, New York
| | - Jack H Freed
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York; National Biomedical Center for Advanced ESR Technology, Cornell University, Ithaca, New York.
| | - David Eliezer
- Department of Biochemistry, Weill Cornell Medical College, New York, New York; Program in Structural Biology, Weill Cornell Medical College, New York, New York.
| |
Collapse
|
145
|
Functional consequences of the oligomeric assembly of proteorhodopsin. J Mol Biol 2015; 427:1278-1290. [PMID: 25597999 PMCID: PMC4374980 DOI: 10.1016/j.jmb.2015.01.004] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2014] [Revised: 12/21/2014] [Accepted: 01/08/2015] [Indexed: 11/24/2022]
Abstract
The plasma membrane is the crucial interface between the cell and its exterior, packed with embedded proteins experiencing simultaneous protein-protein and protein-membrane interactions. A prominent example of cell membrane complexity is the assembly of transmembrane proteins into oligomeric structures, with potential functional consequences that are not well understood. From the study of proteorhodopsin (PR), a prototypical seven-transmembrane light-driven bacterial proton pump, we find evidence that the inter-protein interaction modulated by self-association yields functional changes observable from the protein interior. We also demonstrate that the oligomer is likely a physiologically relevant form of PR, as crosslinking of recombinantly expressed PR reveals an oligomeric population within the Escherichia coli membrane (putatively hexameric). Upon chromatographic isolation of oligomeric and monomeric PR in surfactant micelles, the oligomer exhibits distinctly different optical absorption properties from monomeric PR, as reflected in a prominent decrease in the pKa of the primary proton acceptor residue (D97) and slowing of the light-driven conformational change. These functional effects are predominantly determined by specific PR-PR contacts over nonspecific surfactant interactions. Interestingly, varying the surfactant type alters the population of oligomeric states and the proximity of proteins within an oligomer, as determined by sparse electron paramagnetic resonance distance measurements. Nevertheless, the dynamic surfactant environment retains the key function-tuning property exerted by oligomeric contacts. A potentially general design principle for transmembrane protein function emerges from this work, one that hinges on specific oligomeric contacts that can be modulated by protein expression or membrane composition.
Collapse
|
146
|
Meyer A, Dierks K, Hussein R, Brillet K, Brognaro H, Betzel C. Systematic analysis of protein-detergent complexes applying dynamic light scattering to optimize solutions for crystallization trials. Acta Crystallogr F Struct Biol Commun 2015; 71:75-81. [PMID: 25615974 PMCID: PMC4304753 DOI: 10.1107/s2053230x14027149] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2014] [Accepted: 12/11/2014] [Indexed: 11/12/2022] Open
Abstract
Detergents are widely used for the isolation and solubilization of membrane proteins to support crystallization and structure determination. Detergents are amphiphilic molecules that form micelles once the characteristic critical micelle concentration (CMC) is achieved and can solubilize membrane proteins by the formation of micelles around them. The results are presented of a study of micelle formation observed by in situ dynamic light-scattering (DLS) analyses performed on selected detergent solutions using a newly designed advanced hardware device. DLS was initially applied in situ to detergent samples with a total volume of approximately 2 µl. When measured with DLS, pure detergents show a monodisperse radial distribution in water at concentrations exceeding the CMC. A series of all-trans n-alkyl-β-D-maltopyranosides, from n-hexyl to n-tetradecyl, were used in the investigations. The results obtained verify that the application of DLS in situ is capable of distinguishing differences in the hydrodynamic radii of micelles formed by detergents differing in length by only a single CH2 group in their aliphatic tails. Subsequently, DLS was applied to investigate the distribution of hydrodynamic radii of membrane proteins and selected water-insoluble proteins in presence of detergent micelles. The results confirm that stable protein-detergent complexes were prepared for (i) bacteriorhodopsin and (ii) FetA in complex with a ligand as examples of transmembrane proteins. A fusion of maltose-binding protein and the Duck hepatitis B virus X protein was added to this investigation as an example of a non-membrane-associated protein with low water solubility. The increased solubility of this protein in the presence of detergent could be monitored, as well as the progress of proteolytic cleavage to separate the fusion partners. This study demonstrates the potential of in situ DLS to optimize solutions of protein-detergent complexes for crystallization applications.
Collapse
Affiliation(s)
- Arne Meyer
- Institute of Biochemistry and Molecular Biology, Laboratory for Structural Biology of Infection and Inflammation, University of Hamburg, c/o DESY, Building 22a, Notkestrasse 85, 22603 Hamburg, Germany
| | - Karsten Dierks
- Institute of Biochemistry and Molecular Biology, Laboratory for Structural Biology of Infection and Inflammation, University of Hamburg, c/o DESY, Building 22a, Notkestrasse 85, 22603 Hamburg, Germany
- XtalConcepts, Marlowring 19, 22525 Hamburg, Germany
| | - Rana Hussein
- Institute of Biochemistry and Molecular Biology, Laboratory for Structural Biology of Infection and Inflammation, University of Hamburg, c/o DESY, Building 22a, Notkestrasse 85, 22603 Hamburg, Germany
| | - Karl Brillet
- UMR 7242–IMPReSs Platform, ESBS, Pôle API, 300 Boulevard Sébastien Brant, CS10413, 67412 Illkirch CEDEX, France
| | - Hevila Brognaro
- Multi User Center for Biomolecular Innovation, Department of Physics, São Paulo State University, UNESP/IBILCE, Caixa Postal 136, São José do Rio Preto-SP, 15054, Brazil
| | - Christian Betzel
- Institute of Biochemistry and Molecular Biology, Laboratory for Structural Biology of Infection and Inflammation, University of Hamburg, c/o DESY, Building 22a, Notkestrasse 85, 22603 Hamburg, Germany
| |
Collapse
|
147
|
Schonenbach NS, Hussain S, O'Malley MA. Structure and function of G protein‐coupled receptor oligomers: implications for drug discovery. WILEY INTERDISCIPLINARY REVIEWS-NANOMEDICINE AND NANOBIOTECHNOLOGY 2014; 7:408-27. [DOI: 10.1002/wnan.1319] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2014] [Revised: 09/26/2014] [Accepted: 10/11/2014] [Indexed: 12/21/2022]
Affiliation(s)
- Nicole S. Schonenbach
- Department of Chemical EngineeringUniversity of California Santa BarbaraSanta BarbaraCAUSA
| | - Sunyia Hussain
- Department of Chemical EngineeringUniversity of California Santa BarbaraSanta BarbaraCAUSA
| | - Michelle A. O'Malley
- Department of Chemical EngineeringUniversity of California Santa BarbaraSanta BarbaraCAUSA
| |
Collapse
|
148
|
Oliver RC, Lipfert J, Fox DA, Lo RH, Kim JJ, Doniach S, Columbus L. Tuning micelle dimensions and properties with binary surfactant mixtures. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2014; 30:13353-13361. [PMID: 25312254 DOI: 10.1021/la503458n] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Detergent micelles are used in many areas of research and technology, in particular, as mimics of the cellular membranes in the purification and biochemical and structural characterization of membrane proteins. Applications of detergent micelles are often hindered by the limited set of properties of commercially available detergents. Mixtures of micelle-forming detergents provide a means to systematically obtain additional micellar properties and expand the repertoire of micelle features available; however, our understanding of the properties of detergent mixtures is still limited. In this study, the shape and size of binary mixtures of seven different detergents commonly used in molecular host-guest systems and membrane protein research were investigated. The data suggests that the detergents form ideally mixed micelles with sizes and shapes different from those of pure individual micelles. For most measurements of size, the mixtures varied linearly with detergent mole fraction and therefore can be calculated from the values of the pure detergents. We propose that properties such as the geometry, size, and surface charge can be systematically and predictably tuned for specific applications.
Collapse
Affiliation(s)
- Ryan C Oliver
- Department of Chemistry, University of Virginia , Charlottesville, Virginia 22904, United States
| | | | | | | | | | | | | |
Collapse
|
149
|
Foo ACY, Harvey BGR, Metz JJ, Goto NK. Influence of hydrophobic mismatch on the catalytic activity of Escherichia coli GlpG rhomboid protease. Protein Sci 2014; 24:464-73. [PMID: 25307614 DOI: 10.1002/pro.2585] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2014] [Accepted: 10/09/2014] [Indexed: 12/21/2022]
Abstract
Rhomboids comprise a broad family of intramembrane serine proteases that are found in a wide range of organisms and participate in a diverse array of biological processes. High-resolution structures of the catalytic transmembrane domain of the Escherichia coli GlpG rhomboid have provided numerous insights that help explain how hydrolytic cleavage can be achieved below the membrane surface. Key to this are observations that GlpG hydrophobic domain dimensions may not be sufficient to completely span the native lipid bilayer. This formed the basis for a model where hydrophobic mismatch Induces thinning of the local membrane environment to promote access to transmembrane substrates. However, hydrophobic mismatch also has the potential to alter the functional properties of the rhomboid, a possibility we explore in the current work. For this purpose, we purified the catalytic transmembrane domain of GlpG into phosphocholine or maltoside detergent micelles of varying alkyl chain lengths, and assessed proteolytic function with a model water-soluble substrate. Catalytic turnover numbers were found to depend on detergent alkyl chain length, with saturated chains containing 10-12 carbon atoms supporting maximal activity. Similar results were obtained in phospholipid bicelles, with no proteolytic activity being detected in longer-chain lipids. Although differences in thermal stability and GlpG oligomerization could not explain these activity differences, circular dichroism spectra suggest that mismatch gives rise to a small change in structure. Overall, these results demonstrate that hydrophobic mismatch can exert an inhibitory effect on rhomboid activity, with the potential for changes in local membrane environment to regulate activity in vivo.
Collapse
Affiliation(s)
- Alexander C Y Foo
- Department of Chemistry, University of Ottawa, Ottawa, Ontario, Canada, K1N 6N5
| | | | | | | |
Collapse
|
150
|
Baturin S, Galka JJ, Piyadasa H, Gajjeraman S, O'Neil JD. The effects of a protein osmolyte on the stability of the integral membrane protein glycerol facilitator. Biochem Cell Biol 2014; 92:564-75. [PMID: 25387032 DOI: 10.1139/bcb-2014-0076] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Osmolytes are naturally occurring molecules used by a wide variety of organisms to stabilize proteins under extreme conditions of temperature, salinity, hydrostatic pressure, denaturant concentration, and desiccation. The effects of the osmolyte trimethylamine N-oxide (TMAO) as well as the influence of detergent head group and acyl chain length on the stability of the Escherichia coli integral membrane protein glycerol facilitator (GF) tetramer to thermal and chemical denaturation by sodium dodecyl sulphate (SDS) are reported. TMAO promotes the association of the normally tetrameric α-helical protein into higher order oligomers in dodecyl-maltoside (DDM), but not in tetradecyl-maltoside (TDM), lyso-lauroylphosphatidyl choline (LLPC), or lyso-myristoylphosphatidyl choline (LMPC), as determined by dynamic light scattering (DLS); an octameric complex is particularly stable as indicated by SDS polyacrylamide gel electrophoresis. TMAO increases the heat stability of the GF tetramer an average of 10 °C in the 4 detergents and also protects the protein from denaturation by SDS. However, it did not promote re-association to the tetramer when added to SDS-dissociated protein. TMAO also promotes the formation of rod-like detergent micelles, and DLS was found to be useful for monitoring the structure of the protein and the redistribution of detergent during thermal dissociation of the protein. The protein is more thermally stable in detergents with the phosphatidylcholine head group (LLPC and LMPC) than in the maltoside detergents. The implications of the results for osmolyte mechanism, membrane protein stability, and protein-protein interactions are discussed.
Collapse
Affiliation(s)
- Simon Baturin
- Department of Chemistry, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
| | | | | | | | | |
Collapse
|