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Halim NFAA, Ali MSM, Leow ATC, Rahman RNZRA. Membrane-bound Δ12 fatty acid desaturase (FAD12); From Brassica napus to E. coli expression system. Int J Biol Macromol 2021; 180:242-251. [PMID: 33737181 DOI: 10.1016/j.ijbiomac.2021.03.072] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Revised: 03/12/2021] [Accepted: 03/13/2021] [Indexed: 11/17/2022]
Abstract
Fatty acid desaturase catalyzes the desaturation reactions by insertion of double bonds into the fatty acyl chain, producing unsaturated fatty acids. Though soluble fatty acid desaturases have been studied widely in advanced organisms, there are very limited studies of membrane fatty acid desaturases due to the difficulty of generating recombinant desaturase. Brassica napus is a rapeseed, which possesses a range of different membrane-bound desaturases capable of producing fatty acids including Δ3, Δ4, Δ8, Δ9, Δ12, and Δ15 fatty acids. The 1155 bp open reading frame of Δ12 fatty acid desaturase (FAD12) from Brassica napus codes for 383 amino acid residues with a molecular weight of 44 kDa. It was expressed in Escherichia coli at 37 °C in soluble and insoluble forms when induced with 0.5 mM IPTG. Soluble FAD12 has been purified using Ni2+-Sepharose affinity chromatography with a total protein yield of 0.728 mg/mL. Gas chromatography-mass spectrometry (GC-MS) analysis revealed that desaturase activity of FAD12 could produce linoleic acid from oleic acid at a retention time of 17.6 with a conversion rate of 47%. Characterization of purified FAD12 revealed the optimal temperature of FAD12 was 50 °C with 2 mM preferred substrate concentration of oleic acid. Analysis of circular dichroism (CD) showed FAD12 was made up of 47.3% and 0.9% of alpha-helix and β-sheet secondary structures. The predicted Tm value was 50.2 °C.
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Affiliation(s)
- Nur Farah Anis Abd Halim
- Enzyme and Microbial Technology Research Centre, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia; Department of Microbiology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia
| | - Mohd Shukuri Mohamad Ali
- Enzyme and Microbial Technology Research Centre, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia; Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia.
| | - Adam Thean Chor Leow
- Enzyme and Microbial Technology Research Centre, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia; Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia.
| | - Raja Noor Zaliha Raja Abd Rahman
- Enzyme and Microbial Technology Research Centre, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia; Department of Microbiology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia.
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2
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Bottorf L, Sahu ID, McCarrick RM, Lorigan GA. Utilization of 13C-labeled amino acids to probe the α-helical local secondary structure of a membrane peptide using electron spin echo envelope modulation (ESEEM) spectroscopy. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2018; 1860:1447-1451. [PMID: 29694834 PMCID: PMC5957090 DOI: 10.1016/j.bbamem.2018.04.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Revised: 03/27/2018] [Accepted: 04/09/2018] [Indexed: 11/22/2022]
Abstract
Electron spin echo envelope modulation (ESEEM) spectroscopy in combination with site-directed spin labeling (SDSL) has been established as a valuable biophysical technique to provide site-specific local secondary structure of membrane proteins. This pulsed electron paramagnetic resonance (EPR) method can successfully distinguish between α-helices, β-sheets, and 310-helices by strategically using 2H-labeled amino acids and SDSL. In this study, we have explored the use of 13C-labeled residues as the NMR active nuclei for this approach for the first time. 13C-labeled d5-valine (Val) or 13C-labeled d6-leucine (Leu) were substituted at a specific Val or Leu residue (i), and a nitroxide spin label was positioned 2 or 3 residues away (denoted i-2 and i-3) on the acetylcholine receptor M2δ (AChR M2δ) in a lipid bilayer. The 13C ESEEM peaks in the FT frequency domain data were observed for the i-3 samples, and no 13C peaks were observed in the i-2 samples. The resulting spectra were indicative of the α-helical local secondary structure of AChR M2δ in bicelles. This study provides more versatility and alternative options when using this ESEEM approach to study the more challenging recombinant membrane protein secondary structures.
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Affiliation(s)
- Lauren Bottorf
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH 45056, United States
| | - Indra D Sahu
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH 45056, United States
| | - Robert M McCarrick
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH 45056, United States
| | - Gary A Lorigan
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH 45056, United States.
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3
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Nazari M, Zarnani AH, Ghods R, Emamzadeh R, Najafzadeh S, Minai-Tehrani A, Mahmoudian J, Yousefi M, Vafaei S, Massahi S, Nejadmoghaddam MR. Optimized protocol for soluble prokaryotic expression, purification and structural analysis of human placenta specific-1(PLAC1). Protein Expr Purif 2017; 133:139-151. [PMID: 28315746 DOI: 10.1016/j.pep.2017.03.011] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2016] [Revised: 03/13/2017] [Accepted: 03/13/2017] [Indexed: 12/17/2022]
Abstract
Placenta specific -1 (PLAC1) has been recently introduced as a small membrane-associated protein mainly involved in placental development. Expression of PLAC1 transcript has been documented in almost one hundred cancer cell lines standing for fourteen distinct cancer types. The presence of two disulfide bridges makes difficult to produce functional recombinant PLAC1 in soluble form with high yield. This limitation also complicates the structural studies of PLAC1, which is important for prediction of its physiological roles. To address this issue, we employed an expression matrix consisting of two expression vectors, five different E. coli hosts and five solubilization conditions to optimize production of full and truncated forms of human PLAC1. The recombinant proteins were then characterized using an anti-PLAC1-specific antibody in Western blotting (WB) and enzyme linked immunosorbent assay (ELISA). Structure of full length protein was also investigated using circular dichroism (CD). We demonstrated the combination of Origami™ and pCold expression vector to yield substantial amount of soluble truncated PLAC1 without further need for solubilization step. Full length PLAC1, however, expressed mostly as inclusion bodies with higher yield in Origami™ and Rosetta2. Among solubilization buffers examined, buffer containing Urea 2 M, pH 12 was found to be more effective. Recombinant proteins exhibited excellent reactivity as detected by ELISA and WB. The secondary structure of full length PLAC1 was considered by CD spectroscopy. Taken together, we introduced here a simple, affordable and efficient expression system for soluble PLAC1 production.
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Affiliation(s)
- Mahboobeh Nazari
- Monoclonal Antibody Research Center, Avicenna Research Institute, ACECR, Tehran, Iran; Department of Tissue Engineering, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - Amir-Hassan Zarnani
- Department of Immunology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran; Immunology Research Center, Iran University of Medical Sciences, Tehran, Iran
| | - Roya Ghods
- Oncopathology Research Center, Iran University of Medical Sciences, Tehran, Iran; Department of Molecular Medicine, Faculty of Advanced Technologies in Medicine, Iran University of Medical Sciences, IUMS, Tehran, Iran
| | - Rahman Emamzadeh
- Department of Biology, Faculty of Sciences, University of Isfahan, Isfahan, Iran
| | - Somayeh Najafzadeh
- Nanobiotechnology Research Center, Avicenna Research Institute, ACECR, Tehran, Iran
| | - Arash Minai-Tehrani
- Nanobiotechnology Research Center, Avicenna Research Institute, ACECR, Tehran, Iran
| | - Jafar Mahmoudian
- Monoclonal Antibody Research Center, Avicenna Research Institute, ACECR, Tehran, Iran; Nanotechnology Research Centre, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran, Iran
| | - Maryam Yousefi
- Nanobiotechnology Research Center, Avicenna Research Institute, ACECR, Tehran, Iran
| | - Sedigheh Vafaei
- Nanobiotechnology Research Center, Avicenna Research Institute, ACECR, Tehran, Iran
| | - Sam Massahi
- Nanobiotechnology Research Center, Avicenna Research Institute, ACECR, Tehran, Iran
| | - Mohammad-Reza Nejadmoghaddam
- Nanobiotechnology Research Center, Avicenna Research Institute, ACECR, Tehran, Iran; Nanotechnology Research Centre, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran, Iran
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4
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Liu L, Sahu ID, McCarrick RM, Lorigan GA. Probing the Secondary Structure of Membrane Peptides Using (2)H-Labeled d(10)-Leucine via Site-Directed Spin-Labeling and Electron Spin Echo Envelope Modulation Spectroscopy. J Phys Chem B 2016; 120:633-40. [PMID: 26735335 DOI: 10.1021/acs.jpcb.5b09040] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Previously, we reported an electron spin echo envelope modulation (ESEEM) spectroscopic approach for probing the local secondary structure of membrane proteins and peptides utilizing (2)H isotopic labeling and site-directed spin-labeling (SDSL). In order to probe the secondary structure of a peptide sequence, an amino acid residue (i) side chain was (2)H-labeled, such as (2)H-labeled d10-Leucine, and a cysteine residue was strategically placed at a subsequent nearby position (denoted as i + 1 to i + 4) to which a nitroxide spin label was attached. In order to fully access and demonstrate the feasibility of this new ESEEM approach with (2)H-labeled d10-Leu, four Leu residues within the AChR M2δ peptide were fully mapped out using this ESEEM method. Unique (2)H-ESEEM patterns were observed with the (2)H-labeled d10-Leu for the AChR M2δ α-helical model peptide. For proteins and peptides with an α-helical secondary structure, deuterium modulation can be clearly observed for i ± 3 and i ± 4 samples, but not for i ± 2 samples. Also, a deuterium peak centered at the (2)H Larmor frequency of each i ± 4 sample always had a significantly higher intensity than the corresponding i + 3 sample. This unique feature can be potentially used to distinguish an α-helix from a π-helix or 310-helix. Moreover, (2)H modulation depth for ESEEM samples on Leu10 were significantly enhanced which was consistent with a kinked or curved structural model of the AChR M2δ peptide as suggested by previous MD simulations and NMR experiments.
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Affiliation(s)
- Lishan Liu
- Department of Chemistry and Biochemistry, Miami University , Oxford, Ohio 45056, United States
| | - Indra D Sahu
- 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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5
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Abstract
Symmetry is a common feature among natural systems, including protein structures. A strong propensity toward symmetric architectures has long been recognized for water-soluble proteins, and this propensity has been rationalized from an evolutionary standpoint. Proteins residing in cellular membranes, however, have traditionally been less amenable to structural studies, and thus the prevalence and significance of symmetry in this important class of molecules is not as well understood. In the past two decades, researchers have made great strides in this area, and these advances have provided exciting insights into the range of architectures adopted by membrane proteins. These structural studies have revealed a similarly strong bias toward symmetric arrangements, which were often unexpected and which occurred despite the restrictions imposed by the membrane environment on the possible symmetry groups. Moreover, membrane proteins disproportionately contain internal structural repeats resulting from duplication and fusion of smaller segments. This article discusses the types and origins of symmetry in membrane proteins and the implications of symmetry for protein function.
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Affiliation(s)
- Lucy R Forrest
- Computational Structural Biology Group, Porter Neuroscience Center, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland 20852;
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6
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Liu L, Mayo DJ, Sahu ID, Zhou A, Zhang R, McCarrick RM, Lorigan GA. Determining the Secondary Structure of Membrane Proteins and Peptides Via Electron Spin Echo Envelope Modulation (ESEEM) Spectroscopy. Methods Enzymol 2015; 564:289-313. [PMID: 26477255 DOI: 10.1016/bs.mie.2015.06.037] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Revealing detailed structural and dynamic information of membrane embedded or associated proteins is challenging due to their hydrophobic nature which makes NMR and X-ray crystallographic studies challenging or impossible. Electron paramagnetic resonance (EPR) has emerged as a powerful technique to provide essential structural and dynamic information for membrane proteins with no size limitations in membrane systems which mimic their natural lipid bilayer environment. Therefore, tremendous efforts have been devoted toward the development and application of EPR spectroscopic techniques to study the structure of biological systems such as membrane proteins and peptides. This chapter introduces a novel approach established and developed in the Lorigan lab to investigate membrane protein and peptide local secondary structures utilizing the pulsed EPR technique electron spin echo envelope modulation (ESEEM) spectroscopy. Detailed sample preparation strategies in model membrane protein systems and the experimental setup are described. Also, the ability of this approach to identify local secondary structure of membrane proteins and peptides with unprecedented efficiency is demonstrated in model systems. Finally, applications and further developments of this ESEEM approach for probing larger size membrane proteins produced by overexpression systems are discussed.
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Affiliation(s)
- Lishan Liu
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio, USA.
| | - Daniel J Mayo
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio, USA
| | - Indra D Sahu
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio, USA
| | - Andy Zhou
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio, USA
| | - Rongfu Zhang
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio, USA
| | - Robert M McCarrick
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio, USA
| | - Gary A Lorigan
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio, USA
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7
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Pogozheva ID, Mosberg HI, Lomize AL. Life at the border: adaptation of proteins to anisotropic membrane environment. Protein Sci 2014; 23:1165-96. [PMID: 24947665 DOI: 10.1002/pro.2508] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2014] [Revised: 06/17/2014] [Accepted: 06/18/2014] [Indexed: 12/25/2022]
Abstract
This review discusses main features of transmembrane (TM) proteins which distinguish them from water-soluble proteins and allow their adaptation to the anisotropic membrane environment. We overview the structural limitations on membrane protein architecture, spatial arrangement of proteins in membranes and their intrinsic hydrophobic thickness, co-translational and post-translational folding and insertion into lipid bilayers, topogenesis, high propensity to form oligomers, and large-scale conformational transitions during membrane insertion and transport function. Special attention is paid to the polarity of TM protein surfaces described by profiles of dipolarity/polarizability and hydrogen-bonding capacity parameters that match polarity of the lipid environment. Analysis of distributions of Trp resides on surfaces of TM proteins from different biological membranes indicates that interfacial membrane regions with preferential accumulation of Trp indole rings correspond to the outer part of the lipid acyl chain region-between double bonds and carbonyl groups of lipids. These "midpolar" regions are not always symmetric in proteins from natural membranes. We also examined the hydrophobic effect that drives insertion of proteins into lipid bilayer and different free energy contributions to TM protein stability, including attractive van der Waals forces and hydrogen bonds, side-chain conformational entropy, the hydrophobic mismatch, membrane deformations, and specific protein-lipid binding.
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Affiliation(s)
- Irina D Pogozheva
- Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, Ann Arbor, Michigan, 48109-1065
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8
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Rösner HI, Kragelund BB. Structure and dynamic properties of membrane proteins using NMR. Compr Physiol 2013; 2:1491-539. [PMID: 23798308 DOI: 10.1002/cphy.c110036] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Integral membrane proteins are one of the most challenging groups of macromolecules despite their apparent conformational simplicity. They manage and drive transport, circulate information, and participate in cellular movements via interactions with other proteins and through intricate conformational changes. Their structural and functional decoding is challenging and has imposed demanding experimental development. Solution nuclear magnetic resonance (NMR) spectroscopy is one of the techniques providing the capacity to make a significant difference in the deciphering of the membrane protein structure-function paradigm. The method has evolved dramatically during the last decade resulting in a plethora of new experiments leading to a significant increase in the scientific repertoire for studying membrane proteins. Besides solving the three-dimensional structures using state-of-the-art approaches, a large variety of developments of well-established techniques are available providing insight into membrane protein flexibility, dynamics, and interactions. Inspired by the speed of development in the application of new strategies, by invention of methods to measure solvent accessibility and describe low-populated states, this review seeks to introduce the vast possibilities solution NMR can offer to the study of membrane protein structure-function analyses with special focus on applicability.
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Affiliation(s)
- Heike I Rösner
- Structural Biology and NMR Laboratory, Department of Biology, University of Copenhagen, Copenhagen, Denmark
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9
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Cross TA, Murray DT, Watts A. Helical membrane protein conformations and their environment. EUROPEAN BIOPHYSICS JOURNAL : EBJ 2013; 42:731-55. [PMID: 23996195 PMCID: PMC3818118 DOI: 10.1007/s00249-013-0925-x] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2013] [Revised: 07/25/2013] [Accepted: 08/12/2013] [Indexed: 02/02/2023]
Abstract
Evidence that membrane proteins respond conformationally and functionally to their environment is growing. Structural models, by necessity, have been characterized in preparations where the protein has been removed from its native environment. Different structural methods have used various membrane mimetics that have recently included lipid bilayers as a more native-like environment. Structural tools applied to lipid bilayer-embedded integral proteins are informing us about important generic characteristics of how membrane proteins respond to the lipid environment as compared with their response to other nonlipid environments. Here, we review the current status of the field, with specific reference to observations of some well-studied α-helical membrane proteins, as a starting point to aid the development of possible generic principles for model refinement.
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Affiliation(s)
- Timothy A. Cross
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL 32306, USA
- Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306, USA
- National High Magnetic Field Laboratory, Florida State University, Tallahassee, FL 32310, USA
| | - Dylan T. Murray
- Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306, USA
- National High Magnetic Field Laboratory, Florida State University, Tallahassee, FL 32310, USA
| | - Anthony Watts
- Biomembrane structure Unit, Biochemistry Department, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
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10
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Xia Y, Peng L. Photoactivatable Lipid Probes for Studying Biomembranes by Photoaffinity Labeling. Chem Rev 2013; 113:7880-929. [DOI: 10.1021/cr300419p] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Yi Xia
- Aix-Marseille Université, Centre Interdisciplinaire de Nanoscience de Marseille, CNRS UMR 7325, Campus de Luminy, 13288 Marseille, France
| | - Ling Peng
- Aix-Marseille Université, Centre Interdisciplinaire de Nanoscience de Marseille, CNRS UMR 7325, Campus de Luminy, 13288 Marseille, France
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Zhou A, Abu-Baker S, Sahu ID, Liu L, McCarrick RM, Dabney-Smith C, Lorigan GA. Determining α-helical and β-sheet secondary structures via pulsed electron spin resonance spectroscopy. Biochemistry 2012; 51:7417-9. [PMID: 22966895 DOI: 10.1021/bi3010736] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A new method has been developed to determine α-helical and β-sheet secondary structural components of aqueous and membrane-bound proteins using pulsed electron paramagnetic resonance (EPR) spectroscopy. The three-pulse electron spin echo envelope modulation (ESEEM) technique was used to detect weakly coupled (2)H-labeled nuclei on side chains in the proximity of a strategically placed nitroxide spin-label up to 8 Å away. Changes in the ESEEM spectra for different samples correlate directly to periodic structural differences between α-helical and β-sheet motifs. These distinct trends were demonstrated with α-helical (M2δ subunit of the acetylcholine receptor) and β-sheet (ubiquitin) peptides in biologically relevant sample environments.
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Affiliation(s)
- Andy Zhou
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH 45056, USA
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12
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Liu L, Sahu ID, Mayo DJ, McCarrick RM, Troxel K, Zhou A, Shockley E, Lorigan GA. Enhancement of electron spin echo envelope modulation spectroscopic methods to investigate the secondary structure of membrane proteins. J Phys Chem B 2012; 116:11041-5. [PMID: 22908896 DOI: 10.1021/jp304669b] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
This paper reports on a significant improvement of a new structural biology approach designed to probe the secondary structure of membrane proteins using the pulsed EPR technique of electron spin echo envelope modulation (ESEEM) spectroscopy. Previously, we showed that we could characterize an α-helical secondary structure with ESEEM spectroscopy using a (2)H-labeled Val side chain coupled with site-directed spin-labeling (SDSL). In order to further develop this new approach, molecular dynamic (MD) simulations were conducted on several different hydrophobic residues that are commonly found in membrane proteins. (2)H-SL distance distributions from the MD results indicated that (2)H-labeled Leu was a very strong candidate to significantly improve this ESEEM approach. In order to test this hypothesis, the secondary structure of the α-helical M2δ peptide of the acetylcholine receptor (AChR) incorporated into a bicelle was investigated with (2)H-labeled Leu d(10) at position 10 (i) and nitroxide spin labels positioned 1, 2, 3, and 4 residues away (denoted i+1 to i+4) with ESEEM spectroscopy. The ESEEM data reveal a unique pattern that is characteristic of an α-helix (3.6 residues per turn). Strong (2)H modulation was detected for the i+3 and i+4 samples, but not for the i+2 sample. The (2)H modulation depth observed for (2)H-labeled d(10) Leu was significantly enhanced (×4) when compared to previous ESEEM measurements that used (2)H-labeled d(8) Val. Computational studies indicate that deuterium nuclei on the Leu side chain are closer to the spin label when compared to Val. The enhancement of (2)H modulation and the corresponding Fourier Transform (FT) peak intensity for (2)H-labeled Leu significantly reduces the ESEEM data acquisition time for Leu when compared to Val. This research demonstrates that a different (2)H-labeled amino acid residue can be used as an efficient ESEEM probe further substantiating this important biophysical technique. Finally, this new method can provide pertinent qualitative structural information on membrane proteins in a short time (few minutes) at low sample concentrations (~50 μM).
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Affiliation(s)
- Lishan Liu
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio, USA
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14
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Bernaudat F, Frelet-Barrand A, Pochon N, Dementin S, Hivin P, Boutigny S, Rioux JB, Salvi D, Seigneurin-Berny D, Richaud P, Joyard J, Pignol D, Sabaty M, Desnos T, Pebay-Peyroula E, Darrouzet E, Vernet T, Rolland N. Heterologous expression of membrane proteins: choosing the appropriate host. PLoS One 2011; 6:e29191. [PMID: 22216205 PMCID: PMC3244453 DOI: 10.1371/journal.pone.0029191] [Citation(s) in RCA: 96] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2011] [Accepted: 11/22/2011] [Indexed: 11/19/2022] Open
Abstract
Background Membrane proteins are the targets of 50% of drugs, although they only represent 1% of total cellular proteins. The first major bottleneck on the route to their functional and structural characterisation is their overexpression; and simply choosing the right system can involve many months of trial and error. This work is intended as a guide to where to start when faced with heterologous expression of a membrane protein. Methodology/Principal Findings The expression of 20 membrane proteins, both peripheral and integral, in three prokaryotic (E. coli, L. lactis, R. sphaeroides) and three eukaryotic (A. thaliana, N. benthamiana, Sf9 insect cells) hosts was tested. The proteins tested were of various origins (bacteria, plants and mammals), functions (transporters, receptors, enzymes) and topologies (between 0 and 13 transmembrane segments). The Gateway system was used to clone all 20 genes into appropriate vectors for the hosts to be tested. Culture conditions were optimised for each host, and specific strategies were tested, such as the use of Mistic fusions in E. coli. 17 of the 20 proteins were produced at adequate yields for functional and, in some cases, structural studies. We have formulated general recommendations to assist with choosing an appropriate system based on our observations of protein behaviour in the different hosts. Conclusions/Significance Most of the methods presented here can be quite easily implemented in other laboratories. The results highlight certain factors that should be considered when selecting an expression host. The decision aide provided should help both newcomers and old-hands to select the best system for their favourite membrane protein.
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Affiliation(s)
- Florent Bernaudat
- Institut de Biologie Structurale Jean-Pierre Ebel, CEA, Grenoble, France.
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15
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Gabrielsen M, Kroner F, Black I, Isaacs NW, Roe AJ, McLuskey K. High-throughput identification of purification conditions leads to preliminary crystallization conditions for three inner membrane proteins. Mol Membr Biol 2011; 28:445-53. [DOI: 10.3109/09687688.2011.628954] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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16
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Orłowski A, St-Pierre JF, Magarkar A, Bunker A, Pasenkiewicz-Gierula M, Vattulainen I, Róg T. Properties of the Membrane Binding Component of Catechol-O-methyltransferase Revealed by Atomistic Molecular Dynamics Simulations. J Phys Chem B 2011; 115:13541-50. [DOI: 10.1021/jp207177p] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Adam Orłowski
- Department of Computational Biophysics and Bioinformatics, Faculty of Biotechnology, Biochemistry and Biophysics, Jagiellonian University, Gronostajowa 7, Poland
- Department of Physics, Tampere University of Technology, P.O. Box 692, FI-33101 Tampere, Finland
| | - Jean-François St-Pierre
- Departement de Physique and Regroupement Quebecois sur les Materiaux de Pointe, Universite de Montreal, C.P. 6128, Succursale Centre-ville, Montreal (Quebec), Canada
| | - Aniket Magarkar
- Centre for Drug Research, Faculty of Pharmacy, University of Helsinki, P.O. Box 56, FI-00014, University of Helsinki, Finland
| | - Alex Bunker
- Centre for Drug Research, Faculty of Pharmacy, University of Helsinki, P.O. Box 56, FI-00014, University of Helsinki, Finland
- Department of Chemistry, Aalto University School of Science, P.O. Box 6100, FI-02015, AALTO, Espoo, Finland
| | - Marta Pasenkiewicz-Gierula
- Department of Computational Biophysics and Bioinformatics, Faculty of Biotechnology, Biochemistry and Biophysics, Jagiellonian University, Gronostajowa 7, Poland
| | - Ilpo Vattulainen
- Department of Physics, Tampere University of Technology, P.O. Box 692, FI-33101 Tampere, Finland
- Department of Applied Physics, Aalto University School of Science, Finland
- MEMPHYS−Center for Biomembrane Physics, University of Southern Denmark, Odense, Denmark
| | - Tomasz Róg
- Department of Physics, Tampere University of Technology, P.O. Box 692, FI-33101 Tampere, Finland
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17
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Mayo D, Zhou A, Sahu I, McCarrick R, Walton P, Ring A, Troxel K, Coey A, Hawn J, Emwas AH, Lorigan GA. Probing the structure of membrane proteins with electron spin echo envelope modulation spectroscopy. Protein Sci 2011; 20:1100-4. [PMID: 21563228 DOI: 10.1002/pro.656] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2010] [Revised: 04/26/2011] [Accepted: 05/03/2011] [Indexed: 11/09/2022]
Abstract
A new approach has been developed to probe the structural properties of membrane peptides and proteins using the pulsed electron paramagnetic resonance technique of electron spin echo envelope modulation (ESEEM) spectroscopy and the α-helical M2δ subunit of the acetylcholine receptor incorporated into phospholipid bicelles. To demonstrate the practicality of this method, a cysteine-mutated nitroxide spin label (SL) is positioned 1, 2, 3, and 4 residues away from a fully deuterated Val side chain (denoted i + 1 to i + 4). The characteristic periodicity of the α-helical structure gives rise to a unique pattern in the ESEEM spectra. In the i + 1 and i + 2 samples, the ²H nuclei are too far away to be detected. However, with the 3.6 residue per turn pattern of an α-helix, the i + 3 and i + 4 samples reveal a strong signal from the ²H nuclei of the Val side chain. Modeling studies verify these data suggesting that the closest ²H-labeled Val to SL distance would in fact be expected in the i + 3 and i + 4 samples. This technique is very advantageous, because it provides pertinent qualitative structural information on an inherently difficult system like membrane proteins in a short period of time (minutes) with small amounts of protein (μg).
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Affiliation(s)
- Daniel Mayo
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio, USA
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18
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Miyano M, Ago H, Saino H, Hori T, Ida K. Internally bridging water molecule in transmembrane α-helical kink. Curr Opin Struct Biol 2010; 20:456-63. [DOI: 10.1016/j.sbi.2010.05.008] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2010] [Revised: 05/19/2010] [Accepted: 05/24/2010] [Indexed: 11/29/2022]
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19
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Smolarek D, Bertrand O, Czerwinski M, Colin Y, Etchebest C, de Brevern AG. Multiple interests in structural models of DARC transmembrane protein. Transfus Clin Biol 2010; 17:184-96. [PMID: 20655787 DOI: 10.1016/j.tracli.2010.05.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2010] [Accepted: 05/21/2010] [Indexed: 12/23/2022]
Abstract
Duffy Antigen Receptor for Chemokines (DARC) is an unusual transmembrane chemokine receptor which (i) binds the two main chemokine families and (ii) does not transduct any signal as it lacks the DRY consensus sequence. It is considered as silent chemokine receptor, a tank useful for chemiotactism. DARC had been particularly studied as a major actor of malaria infection by Plasmodium vivax. It is also implicated in multiple chemokine inflammation, inflammatory diseases, in cancer and might play a role in HIV infection and AIDS. In this review, we focus on the interest to build structural model of DARC to understand more precisely its abilities to bind its physiological ligand CXCL8 and its malaria ligand. We also present innovative development on VHHs able to bind DARC protein. We underline difficulties and limitations of such bioinformatics approaches and highlight the crucial importance of biological data to conduct these kinds of researches.
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Affiliation(s)
- D Smolarek
- Inserm UMR-S 665, dynamique des structures et interactions des macromolecules biologiques (DSIMB), 6, rue Alexandre-Cabanel, 75739 Paris cedex 15, France
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20
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Membrane domain structures of three classes of histidine kinase receptors by cell-free expression and rapid NMR analysis. Proc Natl Acad Sci U S A 2010; 107:10902-7. [PMID: 20498088 DOI: 10.1073/pnas.1001656107] [Citation(s) in RCA: 93] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
NMR structural studies of membrane proteins (MP) are hampered by complications in MP expression, technical difficulties associated with the slow process of NMR spectral peak assignment, and limited distance information obtainable for transmembrane (TM) helices. To overcome the inherent challenges in the determination of MP structures, we have developed a rapid and cost-efficient strategy that combines cell-free (CF) protein synthesis, optimized combinatorial dual-isotope labeling for nearly instant resonance assignment, and fast acquisition of long-distance information using paramagnetic probes. Here we report three backbone structures for the TM domains of the three classes of Escherichia coli histidine kinase receptors (HKRs). The ArcB and QseC TM domains are both two-helical motifs, whereas the KdpD TM domain comprises a four-helical bundle with shorter second and third helices. The interhelical distances (up to 12 A) reveal weak interactions within the TM domains of all three receptors. Determined consecutively within 8 months, these structures offer insight into the abundant and underrepresented in the Protein Data Bank class of 2-4 TM crossers and demonstrate the efficiency of our CF combinatorial dual-labeling strategy, which can be applied to solve MP structures in high numbers and at a high speed. Our results greatly expand the current knowledge of HKR structure, opening the doors to studies on their widespread and pharmaceutically important bacterial signaling mechanism.
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