1
|
Structure and Functional Characterization of Membrane Integral Proteins in the Lipid Cubic Phase. J Mol Biol 2020; 432:5104-5123. [PMID: 32113953 DOI: 10.1016/j.jmb.2020.02.024] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2020] [Revised: 02/14/2020] [Accepted: 02/19/2020] [Indexed: 12/19/2022]
Abstract
The lipid cubic phase (LCP) has been used extensively as a medium for crystallizing membrane proteins. It is an attractive environment in which to perform such studies because it incorporates a lipid bilayer. It is therefore considered a useful and a faithful biomembrane mimetic. Here, we bring together evidence that supports this view. Biophysical characterizations are described demonstrating that the cubic phase is a porous medium into and out of which water-soluble molecules can diffuse for binding to and reaction with reconstituted proteins. The proteins themselves are shown to be functionally reconstituted into and to have full mobility in the bilayered membrane, a prerequisite for LCP crystallogenesis. Spectroscopic methods have been used to characterize the conformation and disposition of proteins in the mesophase. Procedures for performing activity assays on enzymes directly in the cubic phase have been reported. Specific examples described here include a kinase and two transferases, where quantitative kinetics and mechanism-defining measurements were performed directly or via a coupled assay system. Finally, ligand-binding assays are described, where binding to proteins in the mesophase membrane was monitored directly by eye and indirectly by fluorescence quenching, enabling binding constant determinations for targets with affinity values in the micromolar and nanomolar range. These results make a convincing case that the lipid bilayer of the cubic mesophase is an excellent membrane mimetic and a suitable medium in which to perform not only crystallogenesis but also biochemical and biophysical characterizations of membrane proteins.
Collapse
|
2
|
Boland C, Olatunji S, Bailey J, Howe N, Weichert D, Fetics SK, Yu X, Merino-Gracia J, Delsaut C, Caffrey M. Membrane (and Soluble) Protein Stability and Binding Measurements in the Lipid Cubic Phase Using Label-Free Differential Scanning Fluorimetry. Anal Chem 2018; 90:12152-12160. [DOI: 10.1021/acs.analchem.8b03176] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Coilín Boland
- School of Medicine and School of Biochemistry and Immunology, Trinity College Dublin DO2 R590, Ireland
| | - Samir Olatunji
- School of Medicine and School of Biochemistry and Immunology, Trinity College Dublin DO2 R590, Ireland
| | - Jonathan Bailey
- School of Medicine and School of Biochemistry and Immunology, Trinity College Dublin DO2 R590, Ireland
| | - Nicole Howe
- School of Medicine and School of Biochemistry and Immunology, Trinity College Dublin DO2 R590, Ireland
| | - Dietmar Weichert
- School of Medicine and School of Biochemistry and Immunology, Trinity College Dublin DO2 R590, Ireland
| | - Susan Kathleen Fetics
- School of Medicine and School of Biochemistry and Immunology, Trinity College Dublin DO2 R590, Ireland
| | - Xiaoxiao Yu
- School of Medicine and School of Biochemistry and Immunology, Trinity College Dublin DO2 R590, Ireland
| | - Javier Merino-Gracia
- School of Medicine and School of Biochemistry and Immunology, Trinity College Dublin DO2 R590, Ireland
| | - Clement Delsaut
- School of Medicine and School of Biochemistry and Immunology, Trinity College Dublin DO2 R590, Ireland
| | - Martin Caffrey
- School of Medicine and School of Biochemistry and Immunology, Trinity College Dublin DO2 R590, Ireland
| |
Collapse
|
3
|
Rayan G, Adrien V, Reffay M, Picard M, Ducruix A, Schmutz M, Urbach W, Taulier N. Surfactant bilayers maintain transmembrane protein activity. Biophys J 2015; 107:1129-1135. [PMID: 25185548 DOI: 10.1016/j.bpj.2014.07.016] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2013] [Revised: 06/21/2014] [Accepted: 07/07/2014] [Indexed: 11/26/2022] Open
Abstract
In vitro studies of membrane proteins are of interest only if their structure and function are significantly preserved. One approach is to insert them into the lipid bilayers of highly viscous cubic phases rendering the insertion and manipulation of proteins difficult. Less viscous lipid sponge phases are sometimes used, but their relatively narrow domain of existence can be easily disrupted by protein insertion. We present here a sponge phase consisting of nonionic surfactant bilayers. Its extended domain of existence and its low viscosity allow easy insertion and manipulation of membrane proteins. We show for the first time, to our knowledge, that transmembrane proteins, such as bacteriorhodopsin, sarcoplasmic reticulum Ca(2+)ATPase (SERCA1a), and its associated enzymes, are fully active in a surfactant phase.
Collapse
Affiliation(s)
- Gamal Rayan
- Laboratoire de Physique Statistique de l'École Normale Supérieure, UPMC, Université Paris Diderot, CNRS, UMR 8550, Paris, France
| | - Vladimir Adrien
- Laboratoire de Physique Statistique de l'École Normale Supérieure, UPMC, Université Paris Diderot, CNRS, UMR 8550, Paris, France; Laboratoire de Cristallographie et RMN Biologiques, Université Paris Descartes, CNRS, UMR 8015, Paris, France
| | - Myriam Reffay
- Laboratoire de Physique Statistique de l'École Normale Supérieure, UPMC, Université Paris Diderot, CNRS, UMR 8550, Paris, France
| | - Martin Picard
- Laboratoire de Cristallographie et RMN Biologiques, Université Paris Descartes, CNRS, UMR 8015, Paris, France
| | - Arnaud Ducruix
- Laboratoire de Cristallographie et RMN Biologiques, Université Paris Descartes, CNRS, UMR 8015, Paris, France
| | - Marc Schmutz
- Institut Charles Sadron - UPR 022 - CNRS - Unistra, Strasbourg, France
| | - Wladimir Urbach
- Laboratoire de Physique Statistique de l'École Normale Supérieure, UPMC, Université Paris Diderot, CNRS, UMR 8550, Paris, France; Sorbonnes Université Univ Paris 6, UMR 7371, UMR_S 1146, Laboratoire d'Imagerie Biomédicale, Paris, France; CNRS, UMR 7371, Laboratoire d'Imagerie Biomédicale, Paris, France; INSERM, UMR_S 1146, Laboratoire d'Imagerie Biomédicale, Paris, France
| | - Nicolas Taulier
- Sorbonnes Université Univ Paris 6, UMR 7371, UMR_S 1146, Laboratoire d'Imagerie Biomédicale, Paris, France; CNRS, UMR 7371, Laboratoire d'Imagerie Biomédicale, Paris, France; INSERM, UMR_S 1146, Laboratoire d'Imagerie Biomédicale, Paris, France.
| |
Collapse
|
4
|
Caffrey M, Li D, Dukkipati A. Membrane protein structure determination using crystallography and lipidic mesophases: recent advances and successes. Biochemistry 2012; 51:6266-88. [PMID: 22783824 DOI: 10.1021/bi300010w] [Citation(s) in RCA: 81] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
The crystal structure of the β(2)-adrenergic receptor in complex with an agonist and its cognate G protein has just recently been determined. It is now possible to explore in molecular detail the means by which this paradigmatic transmembrane receptor binds agonist, communicates the impulse or signaling event across the membrane, and sets in motion a series of G protein-directed intracellular responses. The structure was determined using crystals of the ternary complex grown in a rationally designed lipidic mesophase by the so-called in meso method. The method is proving to be particularly useful in the G protein-coupled receptor field where the structures of 13 distinct receptor types have been determined in the past 5 years. In addition to receptors, the method has proven to be useful with a wide variety of integral membrane protein classes that include bacterial and eukaryotic rhodopsins, light-harvesting complex II (LHII), photosynthetic reaction centers, cytochrome oxidases, β-barrels, an exchanger, and an integral membrane peptide. This attests to the versatility and range of the method and supports the view that the in meso method should be included in the arsenal of the serious membrane structural biologist. For this to happen, however, the reluctance to adopt it attributable, in part, to the anticipated difficulties associated with handling the sticky, viscous cubic mesophase in which crystals grow must be overcome. Harvesting and collecting diffraction data with the mesophase-grown crystals are also viewed with some trepidation. It is acknowledged that there are challenges associated with the method. Over the years, we have endeavored to establish how the method works at a molecular level and to make it user-friendly. To these ends, tools for handling the mesophase in the pico- to nanoliter volume range have been developed for highly efficient crystallization screening in manual and robotic modes. Methods have been implemented for evaluating the functional activity of membrane proteins reconstituted into the bilayer of the cubic phase as a prelude to crystallogenesis. Glass crystallization plates that provide unparalleled optical quality and sensitivity to nascent crystals have been built. Lipid and precipitant screens have been designed for a more rational approach to crystallogenesis such that the method can now be applied to an even wider variety of membrane protein types. In this work, these assorted advances are outlined along with a summary of the membrane proteins that have yielded to the method. The prospects for and the challenges that must be overcome to further develop the method are described.
Collapse
Affiliation(s)
- Martin Caffrey
- Membrane Structural and Functional Biology Group, School of Medicine and School of Biochemistry and Immunology, Trinity College Dublin, Dublin, Ireland.
| | | | | |
Collapse
|
5
|
Lipid cubic phase as a membrane mimetic for integral membrane protein enzymes. Proc Natl Acad Sci U S A 2011; 108:8639-44. [PMID: 21555546 DOI: 10.1073/pnas.1101815108] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The lipidic cubic mesophase has been used to crystallize important membrane proteins for high-resolution structure determination. To date, however, no integral membrane enzymes have yielded to this method, the in meso. For a crystal structure to be meaningful the target protein must be functional. Using the in meso method with a membrane enzyme requires that the protein is active in the mesophase that grows crystals. Because the cubic phase is sticky and viscous and is bicontinuous topologically, quantitatively assessing enzyme activity in meso is a challenge. Here, we describe a procedure for characterizing the catalytic properties of the integral membrane enzyme, diacylglycerol kinase, reconstituted into the bilayer of the lipidic cubic phase. The kinase activity of this elusive crystallographic target was monitored spectrophotometrically using a coupled assay in a high-throughput, 96-well plate format. In meso, the enzyme exhibits classic Michaelis-Menten kinetics and works with a range of lipid substrates. The fact that the enzyme and its lipid substrate and product remain confined to the porous mesophase while its water-soluble substrate and product are free to partition into the aqueous bathing solution suggests a general and convenient approach for characterizing membrane enzymes that function with lipids in a membrane-like environment. The distinctive rheology of the cubic phase means that a procedural step to physically separate substrate from product is not needed. Because of its open, bicontinuous nature, the cubic phase offers the added benefit that the protein is accessible for assay from both sides of the membrane.
Collapse
|
6
|
Cashion MP, Long TE. Biomimetic design and performance of polymerizable lipids. Acc Chem Res 2009; 42:1016-25. [PMID: 19453103 DOI: 10.1021/ar800191s] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Bilayer lipid membranes (BLMs) have received significant attention over the past several decades because of their applications in biological and material sciences. BLMs consist of two amphiphilic lipid layers arranged with their hydrophilic head region exposed to the surrounding aqueous environment and hydrophobic domains in the core. In biology, lipid membranes confine and support the cell structure while selectively controlling the diffusion of ions and proteins between the intra- and extracellular matrix (ECM). Naturally derived lipid monomers spontaneously self-assemble to develop smart gateways that recognize and incorporate desired protein transporters or ion channels. BLMs are useful research models of lamellar lipid assemblies and associated protein receptors in cell membranes. The transport properties of lipid membranes can be tuned through careful consideration of the solution medium, transporter functionality, and pH, as well as other environmental conditions. BLMs are of particular interest in the design of biofunctional coatings, controlled release technologies, and biosensors; however, high-performance applications require lipid membranes to remain stable under harsh denaturing conditions. Accordingly, synthetic strategies are often proposed to increase the chemical and mechanical stability of lipid assemblies. The polymerization of self-assembled lipid structures is a strategy that results in robust biocompatible architectures, and diverse reactive functional groups are available for the synthesis of monomeric lipids. The selection of the polymerizable functionality and its precise location within the lipid assembly influences the ultimate supramolecular microstructure and polymerization efficiency. The biomimetic potential of polymerized lipids depends on the stability and robustness of the self-assembled membranes, and it is essential that the polymerizable functionality not disturb the amphiphilic nature of the lipid to maintain biocompatibility. Innovative applications are the motivational force for the development of durable polylipid compositions. Surface modification with biocompatible polylipids provides the opportunity for specific binding of biological molecules for applications as sensors or controlled release delivery vehicles. The ability to create stable lipid assemblies requires a comprehensive understanding of the mechanism of lipid polymerization in confined supramolecular geometries. The future is exciting as researchers begin to fully understand the morphology of polylipids in an effort to successfully produce naturally derived sustainable materials. In this Account, we highlight recent efforts to covalently stabilize lipid membranes and discuss emerging applications of mechanically robust self-assembled lipid architectures.
Collapse
Affiliation(s)
- Matthew P. Cashion
- Department of Chemistry, Macromolecules and Interfaces Institute, Virginia Tech (0212), Blacksburg, Virginia 24061
| | - Timothy E. Long
- Department of Chemistry, Macromolecules and Interfaces Institute, Virginia Tech (0212), Blacksburg, Virginia 24061
| |
Collapse
|
7
|
Abstract
The principal route to determine the structure and the function and interactions of membrane proteins is via macromolecular crystallography. For macromolecular crystallography to be successful, structure-quality crystals of the target protein must be forthcoming, and crystallogenesis represents a major challenge. Several techniques are employed to crystallize membrane proteins, and the bulk of these techniques make direct use of solubilized protein-surfactant complexes by the more traditional, so-called in surfo methods. An alternative in meso approach, which employs a bicontinuous lipidic mesophase, has emerged as a method with considerable promise in part because it involves reconstitution of the solubilized protein back into a stabilizing and organizing lipid bilayer reservoir as a prelude to crystallogenesis. A hypothesis for how the method works at the molecular level and experimental evidence in support of the proposal are reviewed here. The latest advances, successes, and challenges associated with the method are described.
Collapse
|
8
|
Abstract
The need for high-resolution structure information on membrane proteins is immediate and growing. Currently, the only reliable way to get it is crystallographically. The rate-limiting step from protein to structure is crystal production. An overview of the current ideas and experimental approaches prevailing in the area of membrane protein crystallization is presented. The long-established surfactant-based method has been reviewed extensively and is not examined in detail here. The focus instead is on the latest methods, all of which exploit the spontaneous self-assembling properties of lipids and detergent as vesicles (vesicle-fusion method), discoidal micelles (bicelle method), and liquid crystals or mesophases (in meso or cubic-phase method). In the belief that a knowledge of the underlying phase science is integral to understanding the molecular basis of these assorted crystallization strategies, the article begins with a brief primer on lipids, mesophases, and phase science, and the related issue of form and function as applied to lipids is addressed. The experimental challenges associated with and the solutions for procuring adequate amounts of homogeneous membrane proteins, or parts thereof, are examined. The cubic-phase method is described from the following perspectives: how it is done in practice, its general applicability and successes to date, and the nature of the mesophases integral to the process. Practical aspects of the method are examined with regard to salt, detergent, and screen solution effects; crystallization at low temperatures; tailoring the cubic phase to suit the target protein; different cubic-phase types; dealing with low-protein samples, colorless proteins, microcrystals, and radiation damage; transport within the cubic phase for drug design, cofactor retention, and phasing; using spectroscopy for quality control; harvesting crystals; and miniaturization and robotization for high-throughput screening. The section ends with a hypothesis for nucleation and growth of membrane protein crystals in meso. Thus far, the bicelle and vesicle-fusion methods have produced crystals of one membrane protein, bacteriorhodopsin. The experimental details of both methods are reviewed and their general applicability in the future is commented on. The three new methods are rationalized by analogy to crystallization in microgravity and with respect to epitaxy. A list of Web resources in the area of membrane protein crystallogenesis is included.
Collapse
|
9
|
Dastmalchi S, Morris MB, Church WB. Modeling of the structural features of integral-membrane proteins reverse-environment prediction of integral membrane protein structure (REPIMPS). Protein Sci 2001; 10:1529-38. [PMID: 11468350 PMCID: PMC2374085 DOI: 10.1110/ps.6301] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
The Profiles-3D application, an inverse-folding methodology appropriate for water-soluble proteins, has been modified to allow the determination of structural properties of integral-membrane proteins (IMPs) and for testing the validity of solved and model structures of IMPs. The modification, known as reverse-environment prediction of integral membrane protein structure (REPIMPS), takes into account the fact that exposed areas of side chains for many residues in IMPs are in contact with lipid and not the aqueous phase. This (1) allows lipid-exposed residues to be classified into the correct physicochemical environment class, (2) significantly improves compatibility scores for IMPs whose structures have been solved, and (3) reduces the possibility of rejecting a three-dimensional structure for an IMP because the presence of lipid was not included. Validation tests of REPIMPS showed that it (1) can locate the transmembrane domain of IMPs with single transmembrane helices more frequently than a range of other methodologies, (2) can rotationally orient transmembrane helices with respect to the lipid environment and surrounding helices in IMPs with multiple transmembrane helices, and (3) has the potential to accurately locate transmembrane domains in IMPs with multiple transmembrane helices. We conclude that correcting for the presence of the lipid environment surrounding the transmembrane segments of IMPs is an essential step for reasonable modeling and verification of the three-dimensional structures of these proteins.
Collapse
Affiliation(s)
- S Dastmalchi
- Faculty of Pharmacy, The University of Sydney, Sydney, N.S.W. 2006, Australia
| | | | | |
Collapse
|
10
|
Abstract
Lipidic mesophases have been used to produce diffraction-quality crystals of several membrane proteins. The mechanism by which the method works is a mystery. The thrust is to continue to use it whilst deciphering the underlying mechanism and solving the second 'phase problem' in membrane protein crystallography. The method, which probably shares similarities with crystal growth in microgravity, is examined here from a lipid and a phase science perspective.
Collapse
Affiliation(s)
- M Caffrey
- Department of Chemistry, The Ohio State University, Columbus 43210, USA.
| |
Collapse
|
11
|
Charge recombination kinetics of photosynthetic reaction centres in phospholipid organized systems. J CHEM SCI 1998. [DOI: 10.1007/bf02870005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
|
12
|
Beckmann D, Müller A, Gruber R. Immobilization of bacteriorhodopsin in liquid crystals. Biosens Bioelectron 1997. [DOI: 10.1016/s0956-5663(97)00019-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
|
13
|
Landau EM, Rosenbusch JP. Lipidic cubic phases: a novel concept for the crystallization of membrane proteins. Proc Natl Acad Sci U S A 1996; 93:14532-5. [PMID: 8962086 PMCID: PMC26167 DOI: 10.1073/pnas.93.25.14532] [Citation(s) in RCA: 721] [Impact Index Per Article: 25.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/1996] [Accepted: 09/30/1996] [Indexed: 02/03/2023] Open
Abstract
Understanding the mechanisms of action of membrane proteins requires the elucidation of their structures to high resolution. The critical step in accomplishing this by x-ray crystallography is the routine availability of well-ordered three-dimensional crystals. We have devised a novel, rational approach to meet this goal using quasisolid lipidic cubic phases. This membrane system, consisting of lipid, water, and protein in appropriate proportions, forms a structured, transparent, and complex three-dimensional lipidic array, which is pervaded by an intercommunicating aqueous channel system. Such matrices provide nucleation sites ("seeding") and support growth by lateral diffusion of protein molecules in the membrane ("feeding"). Bacteriorhodopsin crystals were obtained from bicontinuous cubic phases, but not from micellar systems, implying a critical role of the continuity of the diffusion space (the bilayer) on crystal growth. Hexagonal bacteriorhodopsin crystals diffracted to 3.7 A resolution, with a space group P6(3), and unit cell dimensions of a = b = 62 A, c = 108 A; alpha = beta = 90 degrees and gamma = 120 degrees.
Collapse
Affiliation(s)
- E M Landau
- Biozentrum, University of Basel, Switzerland
| | | |
Collapse
|