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Zhang CYC, Zhao SQ, Zhang SL, Luo LH, Liu DC, Ding WH, Fu DJ, Deng XD, Yin DC. Database Study on the Expression and Purification of Membrane Proteins. Protein Pept Lett 2021; 28:972-982. [PMID: 33858308 DOI: 10.2174/0929866528666210415120234] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Revised: 02/04/2021] [Accepted: 03/10/2021] [Indexed: 11/22/2022]
Abstract
Membrane proteins are crucial for biological processes, and many of them are important to drug targets. Understanding the three-dimensional structures of membrane proteins are essential to evaluate their bio function and drug design. High-purity membrane proteins are important for structural determination. Membrane proteins have low yields and are difficult to purify because they tend to aggregate. We summarized membrane protein expression systems, vectors, tags, and detergents, which have deposited in the Protein Data Bank (PDB) in recent four-and-a-half years. Escherichia coli is the most expression system for membrane proteins, and HEK293 cells are the most commonly cell lines for human membrane protein expression. The most frequently vectors are pFastBac1 for alpha-helical membrane proteins, pET28a for beta-barrel membrane proteins, and pTRC99a for monotopic membrane proteins. The most used tag for membrane proteins is the 6×His-tag. FLAG commonly used for alpha-helical membrane proteins, Strep and GST for beta-barrel and monotopic membrane proteins, respectively. The detergents and their concentrations used for alpha-helical, beta-barrel, and monotopic membrane proteins are different, and DDM is commonly used for membrane protein purification. It can guide the expression and purification of membrane proteins, thus contributing to their structure and bio function studying.
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Affiliation(s)
- Chen-Yan China Zhang
- Institute for Special Environmental Biophysics, Key Laboratory for Space Bioscience and Biotechnology, School of Life Sciences, Northwestern Polytechnical University, Xi'an 710072, Shaanxi. China
| | - Shi-Qi Zhao
- Institute for Special Environmental Biophysics, Key Laboratory for Space Bioscience and Biotechnology, School of Life Sciences, Northwestern Polytechnical University, Xi'an 710072, Shaanxi. China
| | - Shi-Long Zhang
- Institute for Special Environmental Biophysics, Key Laboratory for Space Bioscience and Biotechnology, School of Life Sciences, Northwestern Polytechnical University, Xi'an 710072, Shaanxi. China
| | - Li-Heng Luo
- Institute for Special Environmental Biophysics, Key Laboratory for Space Bioscience and Biotechnology, School of Life Sciences, Northwestern Polytechnical University, Xi'an 710072, Shaanxi. China
| | - Ding-Chang Liu
- Institute for Special Environmental Biophysics, Key Laboratory for Space Bioscience and Biotechnology, School of Life Sciences, Northwestern Polytechnical University, Xi'an 710072, Shaanxi. China
| | - Wei-Hang Ding
- Institute for Special Environmental Biophysics, Key Laboratory for Space Bioscience and Biotechnology, School of Life Sciences, Northwestern Polytechnical University, Xi'an 710072, Shaanxi. China
| | - Dong-Jie Fu
- Institute for Special Environmental Biophysics, Key Laboratory for Space Bioscience and Biotechnology, School of Life Sciences, Northwestern Polytechnical University, Xi'an 710072, Shaanxi. China
| | - Xu-Dong Deng
- Institute for Special Environmental Biophysics, Key Laboratory for Space Bioscience and Biotechnology, School of Life Sciences, Northwestern Polytechnical University, Xi'an 710072, Shaanxi. China
| | - Da-Chuan Yin
- Institute for Special Environmental Biophysics, Key Laboratory for Space Bioscience and Biotechnology, School of Life Sciences, Northwestern Polytechnical University, Xi'an 710072, Shaanxi. China
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2
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Unveiling the Uniqueness of Crystal Structure and Crystalline Phase Behavior of Anhydrous Octyl β-D-Glucoside Using Aligned Assembly on a Surface. Polymers (Basel) 2020; 12:polym12030671. [PMID: 32192160 PMCID: PMC7183315 DOI: 10.3390/polym12030671] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 03/13/2020] [Accepted: 03/13/2020] [Indexed: 11/17/2022] Open
Abstract
Although the anomalous low crystallinity of octyl β-D-glucoside (β-OGlu) was first proposed more than 30 years ago, many fundamental aspects of its crystal structure and of the crystalline phase behavior of the pure substance have remained uncertain. In this paper, we employ grazing-incidence wide-angle X-ray-diffraction measurements using a two-dimensional detector (2D-GI-WAXD) and perpendicularly aligned crystalline films to demonstrate that β-OGlu forms crystal structures consisting of an intermediate phase-like a ripple phase with two large crystal-lattice constants, a and c, comparable to the lengths of its bilayer structures. Furthermore, solid-to-solid phase transitions accompanied by latent heat confirm the existence of a solid-solution-like phase consisting of a crystalline and a liquid-crystal (LC) phase, which persists over a 20 °C temperature range, in a single-component system. In addition, the system forms a superlattice, accompanied by a change in packing of the component sugars in the partial-melting state; this shift is different from the gel-crystal transition observed for a typical lipid system. These facts indicate that even in the crystalline phase formed from a single component, each individual β-OGlu molecule in a single-component phase plays a versatile role in the crystallisation and melting processes. These findings must somewhat explain the specific co-assembling features with proteins of β-OGlu, which has long been used empirically in biochemistry.
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3
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Kieber M, Ono T, Oliver RC, Nyenhuis SB, Tieleman DP, Columbus L. The Fluidity of Phosphocholine and Maltoside Micelles and the Effect of CHAPS. Biophys J 2019; 116:1682-1691. [PMID: 31023535 DOI: 10.1016/j.bpj.2019.03.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Revised: 03/13/2019] [Accepted: 03/20/2019] [Indexed: 11/17/2022] Open
Abstract
The dynamics of phosphocholine and maltoside micelles, detergents frequently used for membrane protein structure determination, were investigated using electron paramagnetic resonance of spin probes doped into the micelles. Specifically, phosphocholines are frequently used detergents in NMR studies, and maltosides are frequently used in x-ray crystallography structure determination. Beyond the structural and electrostatic differences, this study aimed to determine whether there are differences in the local chain dynamics (i.e., fluidity). The nitroxide probe rotational dynamics in longer chain detergents is more restricted than in shorter chain detergents, and maltoside micelles are more restricted than phosphocholine micelles. Furthermore, the micelle microviscosity can be modulated with mixtures, as demonstrated with mixtures of 3-[(3-cholamidopropyl)dimethylammonio]-1-propanesulfonate with n-dodecylphosphocholine, n-tetradecylphosphocholine, n-decyl-β-D-maltoside, or n-dodecyl-β-D-maltoside. These results indicate that observed differences in membrane protein stability in these detergents could be due to fluidity in addition to the already determined structural differences.
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Affiliation(s)
- Marissa Kieber
- Department of Chemistry, University of Virginia, Charlottesville, Virginia
| | - Tomihiro Ono
- Department of Chemistry, University of Virginia, Charlottesville, Virginia
| | - Ryan C Oliver
- Department of Chemistry, University of Virginia, Charlottesville, Virginia
| | - Sarah B Nyenhuis
- Department of Chemistry, University of Virginia, Charlottesville, Virginia
| | - D Peter Tieleman
- Department of Biological Sciences and Centre for Molecular Simulation, University of Calgary, Calgary, Alberta, Canada
| | - Linda Columbus
- Department of Chemistry, University of Virginia, Charlottesville, Virginia.
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4
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Larkin TJ, Garvey CJ, Shishmarev D, Kuchel PW, Momot KI. Na + and solute diffusion in aqueous channels of Myverol bicontinuous cubic phase: PGSE NMR and computer modelling. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2017; 55:464-471. [PMID: 27002682 DOI: 10.1002/mrc.4432] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Revised: 02/19/2016] [Accepted: 02/23/2016] [Indexed: 06/05/2023]
Abstract
The apparent diffusion coefficients of 23 Na+ ions and the solute 2-fluoroethylamine present in the aqueous domain of a Myverol/water bulk bicontinuous cubic phase (BCP) were measured using pulsed field-gradient spin echo (PGSE) NMR spectroscopy. The measured values were dependent on the diffusion time interval, which is a characteristic of restricted diffusion. The translational motion of 23 Na+ and water in the aqueous channels of a cubic phase were simulated using a Monte-Carlo random walk algorithm, and the simulation results were compared with those from real PGSE NMR experiments. The simulations indicated that diffusion of 23 Na+ ions and water would appear to be restricted even on the shortest timescales available to PGSE NMR experiments. The micro-viscosity of the aqueous domain of the BCPs was estimated from the longitudinal relaxation times of 23 Na+ and 2-fluoroethylamine; this was three times higher than in free solution and suggests one of (but not the only) likely impediments to the release of hydrophilic drugs from stabilised aqueous dispersions of BCPs (cubosomes) when they are used therapeutically in vivo. Monte Carlo simulations of diffusive efflux from cubosomes suggest that the principal impediment to drug release is presented by a surfactant or lipid barrier at the cubosome surface, which separates the BCP aqueous channels from the bulk solution. The dynamics inferred from these studies informs quantitative predictions of drug delivery from cubosomes. Copyright © 2016 John Wiley & Sons, Ltd.
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Affiliation(s)
- Timothy J Larkin
- Neurosurgery Unit, Department of Clinical Neurosciences, University of Cambridge, United Kingdom
| | - Christopher J Garvey
- Australian Nuclear Science and Technology Organization, Lucas Heights, New South Wales, Australia
| | - Dmitry Shishmarev
- School of Molecular Bioscience, University of Sydney, Sydney, New South Wales, Australia
| | - Philip W Kuchel
- School of Molecular Bioscience, University of Sydney, Sydney, New South Wales, Australia
| | - Konstantin I Momot
- School of Chemistry, Physics and Mechanical Engineering, Queensland University of Technology (QUT), Brisbane, Queensland, Australia
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5
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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.
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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
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6
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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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7
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Chae PS, Guzei IA, Gellman SH. Crystallographic characterization of N-oxide tripod amphiphiles. J Am Chem Soc 2010; 132:1953-9. [PMID: 20095541 PMCID: PMC3090072 DOI: 10.1021/ja9085148] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Tripod amphiphiles are designed to promote the solubilization and stabilization of intrinsic membrane proteins in aqueous solution; facilitation of crystallization is a long-range goal. Membrane proteins are subjects of extensive interest because of their critical biological roles, but proteins of this type can be difficult to study because of their low solubility in water. The nonionic detergents that are typically used to achieve solubility can have the unintended effect of causing protein denaturation. Tripod amphiphiles differ from conventional detergents in that the lipophilic segment contains a branchpoint, and previous work has shown that this unusual amphiphilic architecture can be advantageous relative to traditional detergent structures. Here, we report the crystal structures of several tripod amphiphiles that contain an N-oxide hydrophilic group. The data suggest that tripods can adapt themselves to a nonpolar surface by altering the hydrophobic appendage that projects toward that surface and their overall orientation relative to that surface. Although it is not possible to draw firm conclusions regarding amphiphile association in solution from crystallographic data, trends observed among the packing patterns reported here suggest design strategies to be implemented in future studies.
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Affiliation(s)
- Pil Seok Chae
- Department of Chemistry, University of Wisconsin, Madison, WI 53706
| | - Ilia A. Guzei
- Department of Chemistry, University of Wisconsin, Madison, WI 53706
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Chae PS, Laible PD, Gellman SH. Tripod Amphiphiles for Membrane Protein Manipulation. MOLECULAR BIOSYSTEMS 2010; 6:89-94. [PMID: 23814603 PMCID: PMC3693755 DOI: 10.1039/b915162c] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
Integral membrane proteins (IMPs) are crucial biological components, mediating the transfer of material and information between cells and their environment. Many IMPs have proven to be difficult to isolate and study. High-resolution structural information on this class of proteins is limited, largely because of difficulties in generating soluble forms of such proteins that retain native folding and activity, and difficulties in generating high-quality crystals from such preparations. Isolated IMPs typically do not dissolve in aqueous solution, a property that arises from the large patches of hydrophobic surface necessary for favorable interactions with the core of a lipid bilayer. Detergents are generally required for IMP solubilization: hydrophobic segments of detergent molecules cluster around and shield from water the hydrophobic protein surfaces. The critical role played by detergents in membrane protein manipulation, and the fact that many IMPs are recalcitrant to solubilization and/or crystallization with currently available detergents, suggest that it should be valuable to explore new types of amphiphiles for these purposes. This review constitutes a progress report on our long-term effort to develop a new class of organic molecules, collectively designated "tripod amphiphiles," that are intended as alternatives to conventional detergents for membrane protein manipulation. One long-range goal of this research is to identify new types of amphiphiles that facilitate IMP crystallization. This review should help introduce an important biochemical need to organic chemists, and perhaps inspire new approaches to the problem.
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Affiliation(s)
- Pil Seok Chae
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, WI 53706 (USA). Fax: (+1) 608-265-4534; Tel: (+1) 608-262-3303
| | - Philip D. Laible
- Biosciences Division Argonne National Laborotory, 9700 South Cass Avenue, Argonne, IL 60439 (USA). Fax: (+1) 630-252-3387
| | - Samuel H. Gellman
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, WI 53706 (USA). Fax: (+1) 608-265-4534; Tel: (+1) 608-262-3303
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9
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In Cubo Crystallization of Membrane Proteins. ACTA ACUST UNITED AC 2010. [DOI: 10.1016/b978-0-12-381266-7.00009-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/08/2023]
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10
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Kors CA, Wallace E, Davies DR, Li L, Laible PD, Nollert P. Effects of impurities on membrane-protein crystallization in different systems. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2009; 65:1062-73. [PMID: 19770503 PMCID: PMC2748966 DOI: 10.1107/s0907444909029163] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/11/2009] [Accepted: 07/22/2009] [Indexed: 11/18/2022]
Abstract
When starting a protein-crystallization project, scientists are faced with several unknowns. Amongst them are these questions: (i) is the purity of the starting material sufficient? and (ii) which type of crystallization experiment is the most promising to conduct? The difficulty in purifying active membrane-protein samples for crystallization trials and the high costs associated with producing such samples require an extremely pragmatic approach. Additionally, practical guidelines are needed to increase the efficiency of membrane-protein crystallization. In order to address these conundrums, the effects of commonly encountered impurities on various membrane-protein crystallization regimes have been investigated and it was found that the lipidic cubic phase (LCP) based crystallization methodology is more robust than crystallization in detergent environments using vapor diffusion or microbatch approaches in its ability to tolerate contamination in the forms of protein, lipid or other general membrane components. LCP-based crystallizations produced crystals of the photosynthetic reaction center (RC) of Rhodobacter sphaeroides from samples with substantial levels of residual impurities. Crystals were obtained with protein contamination levels of up to 50% and the addition of lipid material and membrane fragments to pure samples of RC had little effect on the number or on the quality of crystals obtained in LCP-based crystallization screens. If generally applicable, this tolerance for impurities may avoid the need for samples of ultrahigh purity when undertaking initial crystallization screening trials to determine preliminary crystallization conditions that can be optimized for a given target protein.
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Affiliation(s)
- Christopher A. Kors
- Biosciences Division, Argonne National Laboratory, 9700 South Cass Avenue, Argonne, IL 60439, USA
| | - Ellen Wallace
- deCODE biostructures, 7869 NE Day Road West, Bainbridge Island, WA 98110, USA
| | - Douglas R. Davies
- deCODE biostructures, 7869 NE Day Road West, Bainbridge Island, WA 98110, USA
| | - Liang Li
- Department of Chemistry and Institute for Biophysical Dynamics, University of Chicago, 929 East 57th Street, Chicago, IL 60637, USA
| | - Philip D. Laible
- Biosciences Division, Argonne National Laboratory, 9700 South Cass Avenue, Argonne, IL 60439, USA
| | - Peter Nollert
- deCODE biostructures, 7869 NE Day Road West, Bainbridge Island, WA 98110, USA
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11
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Fromme P, Grotjohann I. Chapter 9 Crystallization of Photosynthetic Membrane Proteins. CURRENT TOPICS IN MEMBRANES 2009. [DOI: 10.1016/s1063-5823(09)63009-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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12
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Chapter 3 Harnessing Photosynthetic Bacteria for Membrane Protein Production. CURRENT TOPICS IN MEMBRANES 2009. [DOI: 10.1016/s1063-5823(09)63003-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register]
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13
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Chae PS, Wander MJ, Bowling AP, Laible PD, Gellman SH. Glycotripod amphiphiles for solubilization and stabilization of a membrane-protein superassembly: importance of branching in the hydrophilic portion. Chembiochem 2008; 9:1706-9. [PMID: 18576450 DOI: 10.1002/cbic.200800169] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Pil S Chae
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, WI 53706, USA
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14
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Momot KI, Takegoshi K, Kuchel PW, Larkin TJ. Inhomogeneous NMR line shape as a probe of microscopic organization of bicontinuous cubic phases. J Phys Chem B 2008; 112:6636-45. [PMID: 18457445 DOI: 10.1021/jp8006415] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
NMR line shapes of the lipid and aqueous species in bicontinuous cubic phase (BCP) samples prepared by centrifugation are inhomogeneously broadened. The broadening of the lipid peaks is removed by magic-angle spinning (MAS). In this work, we studied the mechanism of this broadening using (1)H and (13)C NMR spectroscopy of a myverol/water BCP. It is demonstrated that the inhomogeneity possesses an intrinsic contribution that is independent of instrumental or setup factors and can be attributed to the microscopic organization of the BCP bilayer. A mechanism of the inhomogeneous broadening is proposed, which involves a spatially nonuniform diamagnetically induced magnetic field determined by the mesoscopic structure and the diamagnetic susceptibilities of the two BCP domains. The proposed mechanism does not require that molecular reorientation of the lipid be slow for the inhomogeneous broadening to survive. We discuss how this inhomogeneous broadening can be employed as a probe of compositional uniformity and microscopic organization of BCP samples.
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Affiliation(s)
- Konstantin I Momot
- School of Physical and Chemical Sciences, Queensland University of Technology, GPO Box 2434, Brisbane, Qld 4001, Australia.
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15
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van der Wel PCA, Reed ND, Greathouse DV, Koeppe RE. Orientation and motion of tryptophan interfacial anchors in membrane-spanning peptides. Biochemistry 2007; 46:7514-24. [PMID: 17530863 PMCID: PMC2532949 DOI: 10.1021/bi700082v] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The tryptophans of integral membrane proteins have been suggested to play specific roles as "interfacial anchors", based on their preference for a location near the lipid head groups. Still, the underlying mechanism behind this behavior remains unclear. NMR experiments can provide an important tool to study this interaction in an actual bilayer environment. Here solid-state deuterium nuclear magnetic resonance was used to study the tryptophans in membrane-spanning model peptides from the WALP family (acetyl-GWW(LA)nWWA-ethanolamide with n = 5 and 6.5) in samples of mechanically aligned dimyristoylphosphatidylcholine (DMPC) bilayers. The data indicate that the tryptophans near the C-terminal end of the peptide display a significantly different behavior from those near the N-terminus. This is reflected prominently in a large difference in the motion experienced by the indoles at either end of the peptide, highlighting the directionality of the helix. Nevertheless, our observations indicate high levels of motional freedom for all tryptophans in these membrane spanning domains that exceed the dynamics for the helix itself. These observations signify that steric and dynamic features of the polypeptide context modulate the tryptophan anchoring in the membrane interface. Measurements of WALP19 in the ether-linked DMPC analogue ditetradecylphosphatidylcholine (missing the lipid carbonyls) show very similar Trp dynamics and suggest similar orientations for some or all of the tryptophans. This suggests that the lipid acyl chain carbonyls play at most a minor role in the anchoring interaction between these Trp residues and the DMPC interfacial region.
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Affiliation(s)
- Patrick C A van der Wel
- Department of Chemistry & Biochemistry, University of Arkansas, Fayetteville, Arkansas 72701, USA.
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16
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Chen DL, Li L, Reyes S, Adamson DN, Ismagilov RF. Using three-phase flow of immiscible liquids to prevent coalescence of droplets in microfluidic channels: criteria to identify the third liquid and validation with protein crystallization. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2007; 23:2255-60. [PMID: 17279722 PMCID: PMC1986632 DOI: 10.1021/la062152z] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
This manuscript describes the effect of interfacial tensions on three-phase liquid-liquid-liquid flow in microfluidic channels and the use of this flow to prevent microfluidic plugs from coalescing. One problem in using microfluidic plugs as microreactors is the coalescence of adjacent plugs caused by the relative motion of plugs during flow. Here, coalescence of reagent plugs was eliminated by using plugs of a third immiscible liquid as spacers to separate adjacent reagent plugs. This work tested the requirements of interfacial tensions for plugs of a third liquid to be effective spacers. Two candidates satisfying the requirements were identified, and one of these liquids was used in the crystallization of protein human Tdp1 to demonstrate its compatibility with protein crystallization in plugs. This method for identifying immiscible liquids for use as a spacer will also be useful for applications involving manipulation of large arrays of droplets in microfluidic channels.
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Affiliation(s)
- Delai L Chen
- Department of Chemistry and Institute for Biophysical Dynamics, The University of Chicago, 929 East 57th Street, Chicago, Illinois 60637, USA
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17
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Abstract
Studying how protein transmembrane domains transmit signals across membranes is beset by unique challenges. Here, we discuss the circumstances that have led to success and reflect on what has been learned from these examples. Such efforts suggest that some of the most interesting properties of transmembrane helix interactions may be the least amenable to study by current techniques.
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Affiliation(s)
- Erin E Matthews
- Department of Chemistry, Yale University, 266 Whitney Avenue, New Haven, CT 06520, USA
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18
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Li L, Mustafi D, Fu Q, Tereshko V, Chen DL, Tice JD, Ismagilov RF. Nanoliter microfluidic hybrid method for simultaneous screening and optimization validated with crystallization of membrane proteins. Proc Natl Acad Sci U S A 2006; 103:19243-8. [PMID: 17159147 PMCID: PMC1748211 DOI: 10.1073/pnas.0607502103] [Citation(s) in RCA: 210] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
High-throughput screening and optimization experiments are critical to a number of fields, including chemistry and structural and molecular biology. The separation of these two steps may introduce false negatives and a time delay between initial screening and subsequent optimization. Although a hybrid method combining both steps may address these problems, miniaturization is required to minimize sample consumption. This article reports a "hybrid" droplet-based microfluidic approach that combines the steps of screening and optimization into one simple experiment and uses nanoliter-sized plugs to minimize sample consumption. Many distinct reagents were sequentially introduced as approximately 140-nl plugs into a microfluidic device and combined with a substrate and a diluting buffer. Tests were conducted in approximately 10-nl plugs containing different concentrations of a reagent. Methods were developed to form plugs of controlled concentrations, index concentrations, and incubate thousands of plugs inexpensively and without evaporation. To validate the hybrid method and demonstrate its applicability to challenging problems, crystallization of model membrane proteins and handling of solutions of detergents and viscous precipitants were demonstrated. By using 10 microl of protein solution, approximately 1,300 crystallization trials were set up within 20 min by one researcher. This method was compatible with growth, manipulation, and extraction of high-quality crystals of membrane proteins, demonstrated by obtaining high-resolution diffraction images and solving a crystal structure. This robust method requires inexpensive equipment and supplies, should be especially suitable for use in individual laboratories, and could find applications in a number of areas that require chemical, biochemical, and biological screening and optimization.
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Affiliation(s)
- Liang Li
- *Department of Chemistry and Institute for Biophysical Dynamics and
| | - Debarshi Mustafi
- *Department of Chemistry and Institute for Biophysical Dynamics and
| | - Qiang Fu
- *Department of Chemistry and Institute for Biophysical Dynamics and
| | - Valentina Tereshko
- Department of Biochemistry and Molecular Biology, University of Chicago, 929 East 57th Street, Chicago, IL 60637
| | - Delai L. Chen
- *Department of Chemistry and Institute for Biophysical Dynamics and
| | - Joshua D. Tice
- *Department of Chemistry and Institute for Biophysical Dynamics and
| | - Rustem F. Ismagilov
- *Department of Chemistry and Institute for Biophysical Dynamics and
- To whom correspondence should be addressed. E-mail:
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Angelov B, Angelova A, Papahadjopoulos-Sternberg B, Lesieur S, Sadoc JF, Ollivon M, Couvreur P. Detailed Structure of Diamond-Type Lipid Cubic Nanoparticles. J Am Chem Soc 2006; 128:5813-7. [PMID: 16637650 DOI: 10.1021/ja060082c] [Citation(s) in RCA: 68] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Supramolecular three-dimensional self-assembly of nonlamellar lipids with fragments of the protein immunoglobulin results in a bicontinuous cubic phase fragmented into nanoparticles with open water channels (cubosomes). The structure of the diamond-type cubic nanoparticles is characterized experimentally by freeze-fracture electron microscopy, and it is mathematically modeled with nodal surfaces emphasizing the fluid-like undulations of the cubosomic interfaces. Based on scaling-up and scaling-down approaches, we present stable and intermediate-kind nanoparticles resulting from the cubosomic growth. Our results reveal the smallest stable diamond-type cubosomic entity that can serve as a building block of more complex nanostructured fluid drug delivery vehicles of therapeutic proteins. The evidence presented for lipid-bilayer undulations in the surface region of the protein/lipid cubosomes could have important consequences for possible applications of these hierarchically organized porous nanoparticles.
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Affiliation(s)
- Borislav Angelov
- Institute of Biophysics, Bulgarian Academy of Sciences, Acad. G. Bonchev Str. Bl.21, BG-1113 Sofia, Bulgaria
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Schwartz R, King J. Frequencies of hydrophobic and hydrophilic runs and alternations in proteins of known structure. Protein Sci 2006; 15:102-12. [PMID: 16373477 PMCID: PMC2242367 DOI: 10.1110/ps.051741806] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Patterns of alternation of hydrophobic and polar residues are a profound aspect of amino acid sequences, but a feature not easily interpreted for soluble proteins. Here we report statistics of hydrophobicity patterns in proteins of known structure in a current protein database as compared with results from earlier, more limited structure sets. Previous studies indicated that long hydrophobic runs, common in membrane proteins, are underrepresented in soluble proteins. Long runs of hydrophobic residues remain significantly underrepresented in soluble proteins, with none longer than 16 residues observed. These long runs most commonly occur as buried alpha helices, with extended hydrophobic strands less common. Avoiding aggregation of partially folded intermediates during intracellular folding remains a viable explanation for the rarity of long hydrophobic runs in soluble proteins. Comparison between database editions reveals robustness of statistics on aqueous proteins despite an approximately twofold increase in nonredundant sequences. The expanded database does now allow us to explain several deviations of hydrophobicity statistics from models of random sequence in terms of requirements of specific secondary structure elements. Comparison to prior membrane-bound protein sequences, however, shows significant qualitative changes, with the average hydrophobicity and frequency of long runs of hydrophobic residues noticeably increasing between the database editions. These results suggest that the aqueous proteins of solved structure may represent an essentially complete sample of the universe of aqueous sequences, while the membrane proteins of known structure are not yet representative of the universe of membrane-associated proteins, even by relatively simple measures of hydrophobic patterns.
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Affiliation(s)
- Russell Schwartz
- Department of Biological Sciences, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, PA 15213, USA.
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Kelly E, Privé GG, Tieleman DP. Molecular Models of Lipopeptide Detergents: Large Coiled-Coils with Hydrocarbon Interiors. J Am Chem Soc 2005; 127:13446-7. [PMID: 16190678 DOI: 10.1021/ja051275n] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We have constructed molecular models of octameric micelles formed by a recently developed lipopeptide detergent consisting of a single amphipathic alpha-helix coupled to two acyl chains at either end of the helix. The models explain the experimentally observed aggregation behavior of peptides with different acyl chain lengths. The octameric micelles form a unique coiled-coil structure, with the acyl chains in a nearly frozen conformation inside the cylindrical assemblies. Two extreme models with helices either all parallel or in an alternating orientation suggest that the alternating orientation is energetically more favorable. The models suggest several new directions for further diversifying this new class of detergents for the structural studies of membrane proteins.
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Affiliation(s)
- Evan Kelly
- Department of Biological Sciences, Structural Biology Research Group, University of Calgary, Calgary, Alberta, Canada T2N 1N4
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