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Successful amphiphiles as the key to crystallization of membrane proteins: Bridging theory and practice. Biochim Biophys Acta Gen Subj 2018; 1863:437-455. [PMID: 30419284 DOI: 10.1016/j.bbagen.2018.11.004] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Revised: 10/31/2018] [Accepted: 11/07/2018] [Indexed: 12/17/2022]
Abstract
BACKGROUND Membrane proteins constitute a major group of proteins and are of great significance as pharmaceutical targets, but underrepresented in the Protein Data Bank. Particular reasons are their low expression yields and the constant need for cautious and diligent handling in a sufficiently stable hydrophobic environment substituting for the native membrane. When it comes to protein crystallization, such an environment is often established by detergents. SCOPE OF REVIEW In this review, 475 unique membrane protein X-ray structures from the online data bank "Membrane proteins of known 3D structure" are presented with a focus on the detergents essential for protein crystallization. By systematic analysis of the most successful compounds, including current trends in amphiphile development, we provide general insights for selection and design of detergents for membrane protein crystallization. MAJOR CONCLUSIONS The most successful detergents share common features, giving rise to favorable protein interactions. The hydrophile-lipophile balance concept of well-balanced hydrophilic and hydrophobic detergent portions is still the key to successful protein crystallization. Although a single detergent compound is sufficient in most cases, sometimes a suitable mixture of detergents has to be found to alter the resulting protein-detergent complex. Protein crystals with a high diffraction limit involve a tight crystal packing generally favored by detergents with shorter alkyl chains. GENERAL SIGNIFICANCE The formation of well-diffracting membrane protein crystals strongly depends on suitable surfactants, usually screened in numerous crystallization trials. The here-presented findings provide basic criteria for the assessment of surfactants within the vast space of potential crystallization conditions for membrane proteins.
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Recent advances in biophysical studies of rhodopsins - Oligomerization, folding, and structure. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2017; 1865:1512-1521. [PMID: 28844743 DOI: 10.1016/j.bbapap.2017.08.007] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2017] [Revised: 08/06/2017] [Accepted: 08/11/2017] [Indexed: 12/19/2022]
Abstract
Retinal-binding proteins, mainly known as rhodopsins, function as photosensors and ion transporters in a wide range of organisms. From halobacterial light-driven proton pump, bacteriorhodopsin, to bovine photoreceptor, visual rhodopsin, they have served as prototypical α-helical membrane proteins in a large number of biophysical studies and aided in the development of many cutting-edge techniques of structural biology and biospectroscopy. In the last decade, microbial and animal rhodopsin families have expanded significantly, bringing into play a number of new interesting structures and functions. In this review, we will discuss recent advances in biophysical approaches to retinal-binding proteins, primarily microbial rhodopsins, including those in optical spectroscopy, X-ray crystallography, nuclear magnetic resonance, and electron paramagnetic resonance, as applied to such fundamental biological aspects as protein oligomerization, folding, and structure.
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Orwick‐Rydmark M, Arnold T, Linke D. The Use of Detergents to Purify Membrane Proteins. ACTA ACUST UNITED AC 2016; 84:4.8.1-4.8.35. [DOI: 10.1002/0471140864.ps0408s84] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
| | - Thomas Arnold
- Boehringer‐Ingelheim Veterinary Research Center Hannover Germany
| | - Dirk Linke
- University of Oslo, Department of Biosciences Oslo Norway
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Chae PS, Cho KH, Wander MJ, Bae HE, Gellman SH, Laible PD. Hydrophobic variants of ganglio-tripod amphiphiles for membrane protein manipulation. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2013; 1838:278-86. [PMID: 24064323 DOI: 10.1016/j.bbamem.2013.09.011] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2013] [Revised: 08/25/2013] [Accepted: 09/16/2013] [Indexed: 12/13/2022]
Abstract
Membrane proteins operate in unique cellular environments. Once removed from their native context for the purification that is required for most types of structural or functional analyses, they are prone to denature if not properly stabilized by membrane mimetics. Detergent micelles have prominently been used to stabilize membrane proteins in aqueous environments as their amphipathic nature allows for shielding of the hydrophobic surfaces of these bio-macromolecules while supporting solubility and monodispersity in water. This study expands the utility of branched diglucoside-bearing tripod agents, designated ganglio-tripod amphiphiles, with introduction of key variations in their hydrophobic sections and shows how these latter elements can be fine-tuned to maximize membrane protein solubilization while preserving characteristics of these molecules that afford stabilization of rather fragile assemblies. Their efficacy rivals benchmark detergents heavily used today, such as n-dodecyl-β-d-maltoside.
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Affiliation(s)
- Pil Seok Chae
- Department of Bionano Engineering, Hanyang University, Ansan 426-791, Republic of Korea.
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Steroid-based facial amphiphiles for stabilization and crystallization of membrane proteins. Proc Natl Acad Sci U S A 2013; 110:E1203-11. [PMID: 23479627 DOI: 10.1073/pnas.1221442110] [Citation(s) in RCA: 117] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Amphiphile selection is a critical step for structural studies of membrane proteins (MPs). We have developed a family of steroid-based facial amphiphiles (FAs) that are structurally distinct from conventional detergents and previously developed FAs. The unique FAs stabilize MPs and form relatively small protein-detergent complexes (PDCs), a property considered favorable for MP crystallization. We attempted to crystallize several MPs belonging to different protein families, including the human gap junction channel protein connexin 26, the ATP binding cassette transporter MsbA, the seven-transmembrane G protein-coupled receptor-like bacteriorhodopsin, and cytochrome P450s (peripheral MPs). Using FAs alone or mixed with other detergents or lipids, we obtained 3D crystals of the above proteins suitable for X-ray crystallographic analysis. The fact that FAs enhance MP crystallizability compared with traditional detergents can be attributed to several properties, including increased protein stability, formation of small PDCs, decreased PDC surface flexibility, and potential to mediate crystal lattice contacts.
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Corin K, Baaske P, Ravel DB, Song J, Brown E, Wang X, Wienken CJ, Jerabek-Willemsen M, Duhr S, Luo Y, Braun D, Zhang S. Designer lipid-like peptides: a class of detergents for studying functional olfactory receptors using commercial cell-free systems. PLoS One 2011; 6:e25067. [PMID: 22132066 PMCID: PMC3223156 DOI: 10.1371/journal.pone.0025067] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2011] [Accepted: 08/26/2011] [Indexed: 01/18/2023] Open
Abstract
A crucial bottleneck in membrane protein studies, particularly G-protein coupled receptors, is the notorious difficulty of finding an optimal detergent that can solubilize them and maintain their stability and function. Here we report rapid production of 12 unique mammalian olfactory receptors using short designer lipid-like peptides as detergents. The peptides were able to solubilize and stabilize each receptor. Circular dichroism showed that the purified olfactory receptors had alpha-helical secondary structures. Microscale thermophoresis suggested that the receptors were functional and bound their odorants. Blot intensity measurements indicated that milligram quantities of each olfactory receptor could be produced with at least one peptide detergent. The peptide detergents' capability was comparable to that of the detergent Brij-35. The ability of 10 peptide detergents to functionally solubilize 12 olfactory receptors demonstrates their usefulness as a new class of detergents for olfactory receptors, and possibly other G-protein coupled receptors and membrane proteins.
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Affiliation(s)
- Karolina Corin
- Center for Biomedical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | | | - Deepali B. Ravel
- Center for Biomedical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Junyao Song
- Center for Biomedical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Emily Brown
- Center for Biomedical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Xiaoqiang Wang
- Center for Biomedical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- Center for Bioengineering and Biotechnology, China University of Petroleum (East China), Qingdao, Shandong, China
| | - Christoph J. Wienken
- Systems Biophysics, Functional Nanosystems, Ludwig-Maximilians University Munich, München, Germany
| | - Moran Jerabek-Willemsen
- Systems Biophysics, Functional Nanosystems, Ludwig-Maximilians University Munich, München, Germany
| | - Stefan Duhr
- NanoTemper Technologies GmbH, München, Germany
| | - Yuan Luo
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, Maryland, United States of America
| | - Dieter Braun
- Systems Biophysics, Functional Nanosystems, Ludwig-Maximilians University Munich, München, Germany
| | - Shuguang Zhang
- Center for Biomedical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
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Popot JL. Amphipols, Nanodiscs, and Fluorinated Surfactants: Three Nonconventional Approaches to Studying Membrane Proteins in Aqueous Solutions. Annu Rev Biochem 2010; 79:737-75. [DOI: 10.1146/annurev.biochem.052208.114057] [Citation(s) in RCA: 241] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Jean-Luc Popot
- Laboratoire de Physico-Chimie Moléculaire des Protéines Membranaires, Unité Mixte de Recherche 7099, Centre National de la Recherche Scientifique and Université Paris-7 Denis Diderot, Institut de Biologie Physico-Chimique, F-75005 Paris, France; e-mail:
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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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Amphipols and fluorinated surfactants: Two alternatives to detergents for studying membrane proteins in vitro. Methods Mol Biol 2010; 601:219-45. [PMID: 20099149 DOI: 10.1007/978-1-60761-344-2_14] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/08/2022]
Abstract
Handling integral membrane proteins in aqueous solutions traditionally relies on the use of detergents, which are surfactants capable of dispersing the components of biological membranes into mixed micelles. The dissociating character of detergents, however, most often causes solubilized membrane proteins to be unstable. This has prompted the development of alternative, less-aggressive surfactants designed to keep membrane proteins soluble, after they have been solubilized, under milder conditions. A short overview is presented of the structure, properties, and uses of two families of such surfactants: amphiphilic polymers ("amphipols") and fluorinated surfactants.
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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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13
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Kim HJ, Howell SC, Van Horn WD, Jeon YH, Sanders CR. Recent Advances in the Application of Solution NMR Spectroscopy to Multi-Span Integral Membrane Proteins. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2009; 55:335-360. [PMID: 20161395 PMCID: PMC2782866 DOI: 10.1016/j.pnmrs.2009.07.002] [Citation(s) in RCA: 119] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Affiliation(s)
- Hak Jun Kim
- Korea Polar Research Institute, Korea Ocean Research and Development Institute, Incheon, 406-840, Korea
| | - Stanley C. Howell
- Department of Biochemistry, Center for Structural Biology, Vanderbilt University School of Medicine, Nashville, TN, 37232-8725, USA
| | - Wade D. Van Horn
- Department of Biochemistry, Center for Structural Biology, Vanderbilt University School of Medicine, Nashville, TN, 37232-8725, USA
| | - Young Ho Jeon
- Center for Magnetic Resonance, Korea Basic Research Institute, Daejon, 305-333, Korea
| | - Charles R. Sanders
- Department of Biochemistry, Center for Structural Biology, Vanderbilt University School of Medicine, Nashville, TN, 37232-8725, USA
- Corresponding Author: ; phone: 615-936-3756; fax: 615-936-2211
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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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