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Bali AP, Sahu ID, Craig AF, Clark EE, Burridge KM, Dolan MT, Dabney-Smith C, Konkolewicz D, Lorigan GA. Structural characterization of styrene-maleic acid copolymer-lipid nanoparticles (SMALPs) using EPR spectroscopy. Chem Phys Lipids 2019; 220:6-13. [PMID: 30796886 DOI: 10.1016/j.chemphyslip.2019.02.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Revised: 01/29/2019] [Accepted: 02/18/2019] [Indexed: 12/31/2022]
Abstract
Spectroscopic studies of membrane proteins (MPs) are challenging due to difficulties in preparing homogenous and functional lipid membrane mimetic systems into which membrane proteins can properly fold and function. It has recently been shown that styrene-maleic acid (SMA) copolymers act as a macromolecular surfactant and therefore facilitate the formation of disk-shaped lipid bilayer nanoparticles (styrene-maleic acid copolymer-lipid nanoparticles (SMALPs)) that retain structural characteristics of native lipid membranes. We have previously reported controlled synthesis of SMA block copolymers using reversible addition-fragmentation chain transfer (RAFT) polymerization, and that alteration of the weight ratio of styrene to maleic acid affects nanoparticle size. RAFT-synthesis offers superior control over SMA polymer architecture compared to conventional radical polymerization techniques used for commercially available SMA. However, the interactions between the lipid bilayer and the solubilized RAFT-synthesized SMA polymer are currently not fully understood. In this study, EPR spectroscopy was used to detect the perturbation on the acyl chain upon introduction of the RAFT-synthesized SMA polymer by attaching PC-based nitroxide spin labels to the 5th, 12th, and 16th positions along the acyl chain of the lipid bilayer. EPR spectra showed high rigidity at the 12th position compared to the other two regions, displaying similar qualities to commercially available polymers synthesized via conventional methods. In addition, central EPR linewidths and correlation time data were obtained that are consistent with previous findings.
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Affiliation(s)
- Avnika P Bali
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH, 45056, USA
| | - Indra D Sahu
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH, 45056, USA
| | - Andrew F Craig
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH, 45056, USA
| | - Emily E Clark
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH, 45056, USA
| | - Kevin M Burridge
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH, 45056, USA
| | - Madison T Dolan
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH, 45056, USA
| | - Carole Dabney-Smith
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH, 45056, USA
| | - Dominik Konkolewicz
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH, 45056, USA.
| | - Gary A Lorigan
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH, 45056, USA.
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Sahu ID, Craig AF, Dunagum MM, McCarrick RM, Lorigan GA. Characterization of Bifunctional Spin Labels for Investigating the Structural and Dynamic Properties of Membrane Proteins Using EPR Spectroscopy. J Phys Chem B 2017; 121:9185-9195. [PMID: 28877443 DOI: 10.1021/acs.jpcb.7b07631] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Site-directed spin labeling (SDSL) coupled with electron paramagnetic resonance (EPR) spectroscopy is a very powerful technique to study structural and dynamic properties of membrane proteins. The most widely used spin label is methanthiosulfonate (MTSL). However, the flexibility of this spin label introduces greater uncertainties in EPR measurements obtained for determining structures, side-chain dynamics, and backbone motion of membrane protein systems. Recently, a newer bifunctional spin label (BSL), 3,4-bis(methanethiosulfonylmethyl)-2,2,5,5-tetramethyl-2,5-dihydro-1H-pyrrol-1-yloxy, has been introduced to overcome the dynamic limitations associated with the MTSL spin label and has been invaluable in determining protein backbone dynamics and inter-residue distances due to its restricted internal motion and fewer size restrictions. While BSL has been successful in providing more accurate information about the structure and dynamics of several proteins, a detailed characterization of the spin label is still lacking. In this study, we characterized BSLs by performing CW-EPR spectral line shape analysis as a function of temperature on spin-labeled sites inside and outside of the membrane for the integral membrane protein KCNE1 in POPC/POPG lipid bilayers and POPC/POPG lipodisq nanoparticles. The experimental data revealed a powder pattern spectral line shape for all of the KCNE1-BSL samples at 296 K, suggesting the motion of BSLs approaches the rigid limit regime for these series of samples. BSLs were further utilized to report for the first time the distance measurement between two BSLs attached on an integral membrane protein KCNE1 in POPC/POPG lipid bilayers at room temperature using dipolar line broadening CW-EPR spectroscopy. The CW dipolar line broadening EPR data revealed a 15 ± 2 Å distance between doubly attached BSLs on KCNE1 (53/57-63/67) which is consistent with molecular dynamics modeling and the solution NMR structure of KCNE1 which yielded a distance of 17 Å. This study demonstrates the utility of investigating the structural and dynamic properties of membrane proteins in physiologically relevant membrane mimetics using BSLs.
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Affiliation(s)
- Indra D Sahu
- Department of Chemistry and Biochemistry, Miami University , Oxford, Ohio 45056, United States
| | - Andrew F Craig
- Department of Chemistry and Biochemistry, Miami University , Oxford, Ohio 45056, United States
| | - Megan M Dunagum
- Department of Chemistry and Biochemistry, Miami University , Oxford, Ohio 45056, United States
| | - Robert M McCarrick
- Department of Chemistry and Biochemistry, Miami University , Oxford, Ohio 45056, United States
| | - Gary A Lorigan
- Department of Chemistry and Biochemistry, Miami University , Oxford, Ohio 45056, United States
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Sahu ID, Zhang R, Dunagan MM, Craig AF, Lorigan GA. Characterization of KCNE1 inside Lipodisq Nanoparticles for EPR Spectroscopic Studies of Membrane Proteins. J Phys Chem B 2017; 121:5312-5321. [DOI: 10.1021/acs.jpcb.7b01705] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Affiliation(s)
- Indra D. Sahu
- Department of Chemistry and
Biochemistry, Miami University, Oxford, Ohio 45056, United States
| | - Rongfu Zhang
- Department of Chemistry and
Biochemistry, Miami University, Oxford, Ohio 45056, United States
| | - Megan M. Dunagan
- Department of Chemistry and
Biochemistry, Miami University, Oxford, Ohio 45056, United States
| | - Andrew F. Craig
- Department of Chemistry and
Biochemistry, Miami University, Oxford, Ohio 45056, United States
| | - Gary A. Lorigan
- Department of Chemistry and
Biochemistry, Miami University, Oxford, Ohio 45056, United States
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Craig AF, Clark EE, Sahu ID, Zhang R, Frantz ND, Al-Abdul-Wahid MS, Dabney-Smith C, Konkolewicz D, Lorigan GA. Tuning the size of styrene-maleic acid copolymer-lipid nanoparticles (SMALPs) using RAFT polymerization for biophysical studies. Biochim Biophys Acta 2016; 1858:2931-2939. [PMID: 27539205 DOI: 10.1016/j.bbamem.2016.08.004] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2016] [Revised: 07/15/2016] [Accepted: 08/07/2016] [Indexed: 11/29/2022]
Abstract
Characterization of membrane proteins is challenging due to the difficulty in mimicking the native lipid bilayer with properly folded and functional membrane proteins. Recently, styrene-maleic acid (StMA) copolymers have been shown to facilitate the formation of disc-like lipid bilayer mimetics that maintain the structural and dynamic integrity of membrane proteins. Here we report the controlled synthesis and characterization of StMA containing block copolymers. StMA polymers with different compositions and molecular weights were synthesized and characterized by size exclusion chromatography (SEC). These polymers act as macromolecular surfactants for 1-Palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC)/1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-(1'-rac-glycerol (POPG) lipids, forming disc like structures of the lipids with the polymer wrapping around the hydrophobic lipid edge. A combination of dynamic light scattering (DLS), solid-state nuclear magnetic resonance (SSNMR) spectroscopy, and transmission electron microscopy (TEM) was used to characterize the size of the nanoparticles created using these StMA polymers. At a weight ratio of 1.25:1 StMA to lipid, the nanoparticle size created is 28+1nm for a 2:1 ratio, 10+1nm for a 3:1 StMA ratio and 32+1nm for a 4:1 StMA ratio independent of the molecular weight of the polymer. Due to the polymer acting as a surfactant that forms disc like nanoparticles, we term these StMA based block copolymers "RAFT SMALPs". RAFT SMALPs show promise as a new membrane mimetic with different nanoscale sizes, which can be used for a wide variety of biophysical studies of membrane proteins.
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Affiliation(s)
- Andrew F Craig
- Department of Chemistry and Biochemistry, Miami University, 651 E. High Street, Oxford, OH 45056, United States
| | - Emily E Clark
- Department of Chemistry and Biochemistry, Miami University, 651 E. High Street, Oxford, OH 45056, United States
| | - Indra D Sahu
- Department of Chemistry and Biochemistry, Miami University, 651 E. High Street, Oxford, OH 45056, United States
| | - Rongfu Zhang
- Department of Chemistry and Biochemistry, Miami University, 651 E. High Street, Oxford, OH 45056, United States
| | - Nick D Frantz
- Department of Chemistry and Biochemistry, Miami University, 651 E. High Street, Oxford, OH 45056, United States
| | - M Sameer Al-Abdul-Wahid
- Department of Chemistry and Biochemistry, Miami University, 651 E. High Street, Oxford, OH 45056, United States
| | - Carole Dabney-Smith
- Department of Chemistry and Biochemistry, Miami University, 651 E. High Street, Oxford, OH 45056, United States
| | - Dominik Konkolewicz
- Department of Chemistry and Biochemistry, Miami University, 651 E. High Street, Oxford, OH 45056, United States
| | - Gary A Lorigan
- Department of Chemistry and Biochemistry, Miami University, 651 E. High Street, Oxford, OH 45056, United States.
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Sahu ID, Craig AF, Rongfu Z, Dixit G, McCarrick RM, Lorigan GA. Investigation of the Binding of the Human KCNE1 Protein with the Voltage Gated Potassium Channel KCNQ1 using DEER EPR Spectroscopy. Biophys J 2016. [DOI: 10.1016/j.bpj.2015.11.850] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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Sahu ID, Craig AF, Dunagan MM, Troxel KR, Zhang R, Meiberg AG, Harmon CN, McCarrick RM, Kroncke BM, Sanders CR, Lorigan GA. Probing Structural Dynamics and Topology of the KCNE1 Membrane Protein in Lipid Bilayers via Site-Directed Spin Labeling and Electron Paramagnetic Resonance Spectroscopy. Biochemistry 2015; 54:6402-12. [PMID: 26418890 DOI: 10.1021/acs.biochem.5b00505] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
KCNE1 is a single transmembrane protein that modulates the function of voltage-gated potassium channels, including KCNQ1. Hereditary mutations in the genes encoding either protein can result in diseases such as congenital deafness, long QT syndrome, ventricular tachyarrhythmia, syncope, and sudden cardiac death. Despite the biological significance of KCNE1, the structure and dynamic properties of its physiologically relevant native membrane-bound state are not fully understood. In this study, the structural dynamics and topology of KCNE1 in bilayered lipid vesicles was investigated using site-directed spin labeling (SDSL) and electron paramagnetic resonance (EPR) spectroscopy. A 53-residue nitroxide EPR scan of the KCNE1 protein sequence including all 27 residues of the transmembrane domain (45-71) and 26 residues of the N- and C-termini of KCNE1 in lipid bilayered vesicles was analyzed in terms of nitroxide side-chain motion. Continuous wave-EPR spectral line shape analysis indicated the nitroxide spin label side-chains located in the KCNE1 TMD are less mobile when compared to the extracellular region of KCNE1. The EPR data also revealed that the C-terminus of KCNE1 is more mobile when compared to the N-terminus. EPR power saturation experiments were performed on 41 sites including 18 residues previously proposed to reside in the transmembrane domain (TMD) and 23 residues of the N- and C-termini to determine the topology of KCNE1 with respect to the 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC)/1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-(1'-rac-glycerol) (POPG) lipid bilayers. The results indicated that the transmembrane domain is indeed buried within the membrane, spanning the width of the lipid bilayer. Power saturation data also revealed that the extracellular region of KCNE1 is solvent-exposed with some of the portions partially or weakly interacting with the membrane surface. These results are consistent with the previously published solution NMR structure of KCNE1 in micelles.
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Affiliation(s)
- Indra D Sahu
- Department of Chemistry and Biochemistry, Miami University , Oxford, Ohio 45056, United States
| | - Andrew F Craig
- Department of Chemistry and Biochemistry, Miami University , Oxford, Ohio 45056, United States
| | - Megan M Dunagan
- Department of Chemistry and Biochemistry, Miami University , Oxford, Ohio 45056, United States
| | - Kaylee R Troxel
- Department of Chemistry and Biochemistry, Miami University , Oxford, Ohio 45056, United States
| | - Rongfu Zhang
- Department of Chemistry and Biochemistry, Miami University , Oxford, Ohio 45056, United States
| | - Andrew G Meiberg
- Department of Chemistry and Biochemistry, Miami University , Oxford, Ohio 45056, United States
| | - Corrinne N Harmon
- Department of Chemistry and Biochemistry, Miami University , Oxford, Ohio 45056, United States
| | - Robert M McCarrick
- Department of Chemistry and Biochemistry, Miami University , Oxford, Ohio 45056, United States
| | - Brett M Kroncke
- Department of Biochemistry and Center for Structural Biology, Vanderbilt University , Nashville, Tennessee 37232, United States
| | - Charles R Sanders
- Department of Biochemistry and Center for Structural Biology, Vanderbilt University , Nashville, Tennessee 37232, United States
| | - Gary A Lorigan
- Department of Chemistry and Biochemistry, Miami University , Oxford, Ohio 45056, United States
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Zhang R, Sahu ID, Gibson KR, Muhammad NB, Bali AP, Comer RG, Liu L, Craig AF, Mccarrick RM, Dabney-Smith C, Sanders CR, Lorigan GA. Development of electron spin echo envelope modulation spectroscopy to probe the secondary structure of recombinant membrane proteins in a lipid bilayer. Protein Sci 2015; 24:1707-13. [PMID: 26355804 DOI: 10.1002/pro.2795] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2015] [Revised: 08/24/2015] [Accepted: 08/25/2015] [Indexed: 12/19/2022]
Abstract
Membrane proteins conduct many important biological functions essential to the survival of organisms. However, due to their inherent hydrophobic nature, it is very difficult to obtain structural information on membrane-bound proteins using traditional biophysical techniques. We are developing a new approach to probe the secondary structure of membrane proteins using the pulsed EPR technique of Electron Spin Echo Envelope Modulation (ESEEM) Spectroscopy. This method has been successfully applied to model peptides made synthetically. However, in order for this ESEEM technique to be widely applicable to larger membrane protein systems with no size limitations, protein samples with deuterated residues need to be prepared via protein expression methods. For the first time, this study shows that the ESEEM approach can be used to probe the local secondary structure of a (2) H-labeled d8 -Val overexpressed membrane protein in a membrane mimetic environment. The membrane-bound human KCNE1 protein was used with a known solution NMR structure to demonstrate the applicability of this methodology. Three different α-helical regions of KCNE1 were probed: the extracellular domain (Val21), transmembrane domain (Val50), and cytoplasmic domain (Val95). These results indicated α-helical structures in all three segments, consistent with the micelle structure of KCNE1. Furthermore, KCNE1 was incorporated into a lipid bilayer and the secondary structure of the transmembrane domain (Val50) was shown to be α-helical in a more native-like environment. This study extends the application of this ESEEM approach to much larger membrane protein systems that are difficult to study with X-ray crystallography and/or NMR spectroscopy.
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Affiliation(s)
- Rongfu Zhang
- Cell, Molecular, and Structural Biology Graduate Program, Miami University, Oxford, Ohio, 45056.,Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio, 45056
| | - Indra D Sahu
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio, 45056
| | - Kaylee R Gibson
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio, 45056
| | - Nefertiti B Muhammad
- Cell, Molecular, and Structural Biology Graduate Program, Miami University, Oxford, Ohio, 45056.,Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio, 45056
| | - Avnika P Bali
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio, 45056
| | - Raven G Comer
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio, 45056
| | - Lishan Liu
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio, 45056
| | - Andrew F Craig
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio, 45056
| | - Robert M Mccarrick
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio, 45056
| | - Carole Dabney-Smith
- Cell, Molecular, and Structural Biology Graduate Program, Miami University, Oxford, Ohio, 45056.,Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio, 45056
| | - Charles R Sanders
- Department of Biochemistry and Center for Structural Biology, Vanderbilt University, Nashville, Tennessee, 37232
| | - Gary A Lorigan
- Cell, Molecular, and Structural Biology Graduate Program, Miami University, Oxford, Ohio, 45056.,Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio, 45056
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Craig AF, Sahu ID, Zhang R, Dunagan MM, Wang K, McCarrick RM, Lorigan GA. Probing the Protein-Protein Interactions between KCNQ1 and KCNE1 using Electron Paramagnetic Resonance (EPR) Spectroscopy. Biophys J 2015. [DOI: 10.1016/j.bpj.2014.11.3349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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