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Müh F, Bothe A, Zouni A. Towards understanding the crystallization of photosystem II: influence of poly(ethylene glycol) of various molecular sizes on the micelle formation of alkyl maltosides. PHOTOSYNTHESIS RESEARCH 2024:10.1007/s11120-024-01079-5. [PMID: 38488943 DOI: 10.1007/s11120-024-01079-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Accepted: 01/24/2024] [Indexed: 03/17/2024]
Abstract
The influence of poly(ethylene glycol) (PEG) polymers H-(O-CH2-CH2)p-OH with different average molecular sizes p on the micelle formation of n-alkyl-β-D-maltoside detergents with the number of carbon atoms in the alkyl chain ranging from 10 to 12 is investigated with the aim to learn more about the detergent behavior under conditions suitable for the crystallization of the photosynthetic pigment-protein complex photosystem II. PEG is shown to increase the critical micelle concentration (CMC) of all three detergents in the crystallization buffer in a way that the free energy of micelle formation increases linearly with the concentration of oxyethylene units (O-CH2-CH2) irrespective of the actual molecular weight of the polymer. The CMC shift is modeled by assuming for simplicity that it is dominated by the interaction between PEG and detergent monomers and is interpreted in terms of an increase of the transfer free energy of a methylene group of the alkyl chain by 0.2 kJ mol-1 per 1 mol L-1 increase of the concentration of oxyethylene units at 298 K. Implications of this effect for the solubilization and crystallization of protein-detergent complexes as well as detergent extraction from crystals are discussed.
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Affiliation(s)
- Frank Müh
- Institut für Theoretische Physik, Johannes Kepler Universität Linz, Altenberger Strasse 69, 4040, Linz, Austria.
| | - Adrian Bothe
- Institut für Molekularbiologie und Biophysik, ETH Zürich, HPK, Otto-Stern-Weg 5, CH-8093, Zurich, Switzerland
| | - Athina Zouni
- Institut für Biologie, Humboldt Universität zu Berlin, Leonor-Michaelis-Haus, Philippstrasse 13, 10095, Berlin, Germany
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2
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Rivera-Rivera LY, Moore TC, Glotzer SC. Inverse design of triblock Janus spheres for self-assembly of complex structures in the crystallization slot via digital alchemy. SOFT MATTER 2023; 19:2726-2736. [PMID: 36974942 DOI: 10.1039/d2sm01593e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
The digital alchemy framework is an extended ensemble simulation technique that incorporates particle attributes as thermodynamic variables, enabling the inverse design of colloidal particles for desired behavior. Here, we extend the digital alchemy framework for the inverse design of patchy spheres that self-assemble into target crystal structures. To constrain the potentials to non-trivial solutions, we conduct digital alchemy simulations with constant second virial coefficient. We optimize the size, range, and strength of patchy interactions in model triblock Janus spheres to self-assemble the 2D kagome and snub square lattices and the 3D pyrochlore lattice, and demonstrate self-assembly of all three target structures with the designed models. The particles designed for the kagome and snub square lattices assemble into high quality clusters of their target structures, while competition from similar polymorphs lower the yield of the pyrochlore assemblies. We find that the alchemically designed potentials do not always match physical intuition, illustrating the ability of the method to find nontrivial solutions to the optimization problem. We identify a window of second virial coefficients that result in self-assembly of the target structures, analogous to the crystallization slot in protein crystallization.
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Affiliation(s)
| | - Timothy C Moore
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI, USA.
| | - Sharon C Glotzer
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI, USA.
- Biointerfaces Institute, University of Michigan, Ann Arbor, MI, USA
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3
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Krueger S, Curtis JE, Scott DR, Grishaev A, Glenn G, Smith G, Ellingsworth L, Borisov O, Maynard EL. Structural Characterization and Modeling of a Respiratory Syncytial Virus Fusion Glycoprotein Nanoparticle Vaccine in Solution. Mol Pharm 2021; 18:359-376. [PMID: 33322901 PMCID: PMC10467610 DOI: 10.1021/acs.molpharmaceut.0c00986] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
The respiratory syncytial virus (RSV) fusion (F) protein/polysorbate 80 (PS80) nanoparticle vaccine is the most clinically advanced vaccine for maternal immunization and protection of newborns against RSV infection. It is composed of a near-full-length RSV F glycoprotein, with an intact membrane domain, formulated into a stable nanoparticle with PS80 detergent. To understand the structural basis for the efficacy of the vaccine, a comprehensive study of its structure and hydrodynamic properties in solution was performed. Small-angle neutron scattering experiments indicate that the nanoparticle contains an average of 350 PS80 molecules, which form a cylindrical micellar core structure and five RSV F trimers that are arranged around the long axis of the PS80 core. All-atom models of full-length RSV F trimers were built from crystal structures of the soluble ectodomain and arranged around the long axis of the PS80 core, allowing for the generation of an ensemble of conformations that agree with small-angle neutron and X-ray scattering data as well as transmission electron microscopy (TEM) images. Furthermore, the hydrodynamic size of the RSV F nanoparticle was found to be modulated by the molar ratio of PS80 to protein, suggesting a mechanism for nanoparticle assembly involving addition of RSV F trimers to and growth along the long axis of the PS80 core. This study provides structural details of antigen presentation and conformation in the RSV F nanoparticle vaccine, helping to explain the induction of broad immunity and observed clinical efficacy. Small-angle scattering methods provide a general strategy to visualize surface glycoproteins from other pathogens and to structurally characterize nanoparticle vaccines.
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Affiliation(s)
- Susan Krueger
- NIST Center for Neutron Research, National Institute of Standards and Technology, 100 Bureau Drive, Gaithersburg, Maryland 20899, United States
| | - Joseph E Curtis
- NIST Center for Neutron Research, National Institute of Standards and Technology, 100 Bureau Drive, Gaithersburg, Maryland 20899, United States
| | - Daniel R Scott
- Novavax, Inc., 21 Firstfield Road, Gaithersburg, Maryland 20878, United States
| | - Alexander Grishaev
- Institute for Bioscience and Biotechnology Research, National Institute of Standards and Technology, 9600 Gudelsky Drive, Rockville, Maryland 20850, United States
| | - Greg Glenn
- Novavax, Inc., 21 Firstfield Road, Gaithersburg, Maryland 20878, United States
| | - Gale Smith
- Novavax, Inc., 21 Firstfield Road, Gaithersburg, Maryland 20878, United States
| | - Larry Ellingsworth
- Novavax, Inc., 21 Firstfield Road, Gaithersburg, Maryland 20878, United States
| | - Oleg Borisov
- Novavax, Inc., 21 Firstfield Road, Gaithersburg, Maryland 20878, United States
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Bonneté F, Loll PJ. Characterization of New Detergents and Detergent Mimetics by Scattering Techniques for Membrane Protein Crystallization. Methods Mol Biol 2017; 1635:169-193. [PMID: 28755369 DOI: 10.1007/978-1-4939-7151-0_9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/08/2022]
Abstract
Membrane proteins are difficult to manipulate and stabilize once they have been removed from their native membranes. However, despite these difficulties, successes in membrane-protein structure determination have continued to accumulate for over two decades, thanks to advances in chemistry and technology. Many of these advances have resulted from efforts focused on protein engineering, high-throughput expression, and development of detergent screens, all with the aim of enhancing protein stability for biochemistry and biophysical studies. In contrast, considerably less work has been done to decipher the basic mechanisms that underlie the structure of protein-detergent complexes and to describe the influence of detergent structure on stabilization and crystallization. These questions can be addressed using scattering techniques (employing light, X-rays, and/or neutrons), which are suitable to describe the structure and conformation of macromolecules in solution, as well as to assess weak interactions between particles, both of which are clearly germane to crystallization. These techniques can be used either in batch modes or coupled to size-exclusion chromatography, and offer the potential to describe the conformation of a detergent-solubilized membrane protein and to quantify and model detergent bound to the protein in order to optimize crystal packing. We will describe relevant techniques and present examples of scattering experiments, which allow one to explore interactions between micelles and between membrane protein complexes, and relate these interactions to membrane protein crystallization.
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Affiliation(s)
- Françoise Bonneté
- Institut des Biomolécules Max Mousseron (IBMM) UMR 5247 CNRS-UM-ENSCM, Chimie BioOrganique et Systèmes Amphiphiles, Université d'Avignon, 301, rue Baruch de Spinoza, F84000, Avignon, France.
| | - Patrick J Loll
- Department of Biochemistry and Molecular Biology, Drexel University College of Medicine, 245 North 15th Street, Philadelphia, PA, 19102, USA
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Wilson WW, DeLucas LJ. Applications of the second virial coefficient: protein crystallization and solubility. Corrigendum. Acta Crystallogr F Struct Biol Commun 2016; 72:255-6. [PMID: 26919532 PMCID: PMC4774888 DOI: 10.1107/s2053230x16000340] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
A number of citations in the article by Wilson & DeLucas [(2014). Acta Cryst. F70, 543-554] are corrected.
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Affiliation(s)
| | - Lawrence J. DeLucas
- Center for Structural Biology, University of Alabama at Birmingham, 1720 Second Avenue South, Birmingham, AL 35294, USA
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6
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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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7
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Quantification of detergent using colorimetric methods in membrane protein crystallography. Methods Enzymol 2015; 557:95-116. [PMID: 25950961 DOI: 10.1016/bs.mie.2014.12.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/02/2023]
Abstract
Membrane protein crystallography has the potential to greatly aid our understanding of membrane protein biology. Yet, membrane protein crystals remain challenging to produce. Although robust methods for the expression and purification of membrane proteins continue to be developed, the detergent component of membrane protein samples is equally important to crystallization efforts. This chapter describes the development of three colorimetric assays for the quantitation of detergent in membrane protein samples and provides detailed protocols. All of these techniques use small sample volumes and have potential applications in crystallography. The application of these techniques in crystallization prescreening, detergent concentration modification, and detergent exchange experiments is demonstrated. It has been observed that the concentration of detergent in a membrane protein sample can be just as important as the protein concentration when attempting to reproduce crystallization lead conditions.
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8
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Lewus RA, Levy NE, Lenhoff AM, Sandler SI. A comparative study of monoclonal antibodies. 1. Phase behavior and protein-protein interactions. Biotechnol Prog 2015; 31:268-76. [PMID: 25378269 PMCID: PMC5891218 DOI: 10.1002/btpr.2011] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2014] [Revised: 11/01/2014] [Indexed: 01/18/2023]
Abstract
Protein phase behavior is involved in numerous aspects of downstream processing, either by design as in crystallization or precipitation processes, or as an undesired effect, such as aggregation. This work explores the phase behavior of eight monoclonal antibodies (mAbs) that exhibit liquid-liquid separation, aggregation, gelation, and crystallization. The phase behavior has been studied systematically as a function of a number of factors, including solution composition and pH, in order to explore the degree of variability among different antibodies. Comparisons of the locations of phase boundaries show consistent trends as a function of solution composition; however, changing the solution pH has different effects on each of the antibodies studied. Furthermore, the types of dense phases formed varied among the antibodies. Protein-protein interactions, as reflected by values of the osmotic second virial coefficient, are used to correlate the phase behavior. The primary findings are that values of the osmotic second virial coefficient are useful for correlating phase boundary locations, though there is appreciable variability among the antibodies in the apparent strengths of the intrinsic protein-protein attraction manifested. However, the osmotic second virial coefficient does not provide a clear basis to predict the type of dense phase likely to result under a given set of solution conditions.
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Affiliation(s)
| | | | - Abraham M. Lenhoff
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE 19716, USA
| | - Stanley I. Sandler
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE 19716, USA
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9
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Müh F, DiFiore D, Zouni A. The influence of poly(ethylene glycol) on the micelle formation of alkyl maltosides used in membrane protein crystallization. Phys Chem Chem Phys 2015; 17:11678-91. [DOI: 10.1039/c5cp00431d] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The influence of poly(ethylene glycol) on the micelle formation of alkyl maltosides under conditions of membrane protein crystallization is investigated.
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Affiliation(s)
- Frank Müh
- Institut für Theoretische Physik
- Johannes Kepler Universität Linz
- A-4040 Linz
- Austria
| | - Dörte DiFiore
- Max-Volmer-Laboratorium für Biophysikalische Chemie
- Technische Universität Berlin
- D-10623 Berlin
- Germany
| | - Athina Zouni
- Institut für Biologie
- Humboldt Universität zu Berlin
- D-10095 Berlin
- Germany
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10
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Loll PJ. Membrane proteins, detergents and crystals: what is the state of the art? ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY COMMUNICATIONS 2014; 70:1576-83. [PMID: 25484203 DOI: 10.1107/s2053230x14025035] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2014] [Accepted: 11/14/2014] [Indexed: 12/19/2022]
Abstract
At the time when the first membrane-protein crystal structure was determined, crystallization of these molecules was widely perceived as extremely arduous. Today, that perception has changed drastically, and the process is regarded as routine (or nearly so). On the occasion of the International Year of Crystallography 2014, this review presents a snapshot of the current state of the art, with an emphasis on the role of detergents in this process. A survey of membrane-protein crystal structures published since 2012 reveals that the direct crystallization of protein-detergent complexes remains the dominant methodology; in addition, lipidic mesophases have proven immensely useful, particularly in specific niches, and bicelles, while perhaps undervalued, have provided important contributions as well. Evolving trends include the addition of lipids to protein-detergent complexes and the gradual incorporation of new detergents into the standard repertoire. Stability has emerged as a critical parameter controlling how a membrane protein behaves in the presence of detergent, and efforts to enhance stability are discussed. Finally, although discovery-based screening approaches continue to dwarf mechanistic efforts to unravel crystallization, recent technical advances offer hope that future experiments might incorporate the rational manipulation of crystallization behaviors.
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Affiliation(s)
- Patrick J Loll
- Department of Biochemistry and Molecular Biology, Drexel University College of Medicine, 245 North 15th Street, Philadelphia, PA 19102, USA
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11
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Detergent quantification in membrane protein samples and its application to crystallization experiments. Amino Acids 2013; 45:1293-302. [PMID: 24105076 DOI: 10.1007/s00726-013-1600-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2013] [Accepted: 09/19/2013] [Indexed: 10/26/2022]
Abstract
The structural characterization of membrane proteins remains a challenging field, largely because the use of stabilizing detergents is required. Researchers must first select a suitable detergent for the solubility and stability of their protein during in vitro studies. In addition, an appropriate concentration of detergent in membrane protein samples can be essential for protein solubility, stability, and experimental success. For example, in membrane protein crystallography, detergent concentration in the crystallization drop can be a critical parameter influencing crystal growth. Over the past decade, multiple techniques have been developed for the measurement of detergent concentration using a wide variety of strategies. These methods include colorimetric reactions, which target specific detergent classes, and analytical techniques applicable to a wide variety of detergents. This review will summarize and discuss the available options. It will be a useful resource to those selecting a strategy that best fits their experimental requirements and available instruments.
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12
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Barret LA, Barrot-Ivolot C, Raynal S, Jungas C, Polidori A, Bonneté F. Influence of Hydrophobic Micelle Structure on Crystallization of the Photosynthetic RC-LH1-PufX Complex from Rhodobacter blasticus. J Phys Chem B 2013; 117:8770-81. [DOI: 10.1021/jp403483q] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Laurie-Anne Barret
- Institut des Biomolécules
Max Mousseron (IBMM) UMR 5247 CNRS-Universités Montpellier
1 et 2, Chimie Bioorganique et Systèmes Amphiphiles, Université d’Avignon et des Pays de Vaucluse, 33 rue Louis Pasteur, F-84000 Avignon, France
- CEA DSV IBEB Lab Bioenerget Cellulaire, CNRS UMR Biol Veget & Microbiol Environ, Aix-Marseille Université, Saint-Paul-lez-Durance, F-13108, France
| | - Cherone Barrot-Ivolot
- Institut des Biomolécules
Max Mousseron (IBMM) UMR 5247 CNRS-Universités Montpellier
1 et 2, Chimie Bioorganique et Systèmes Amphiphiles, Université d’Avignon et des Pays de Vaucluse, 33 rue Louis Pasteur, F-84000 Avignon, France
| | - Simon Raynal
- Institut des Biomolécules
Max Mousseron (IBMM) UMR 5247 CNRS-Universités Montpellier
1 et 2, Chimie Bioorganique et Systèmes Amphiphiles, Université d’Avignon et des Pays de Vaucluse, 33 rue Louis Pasteur, F-84000 Avignon, France
| | - Colette Jungas
- CEA DSV IBEB Lab Bioenerget Cellulaire, CNRS UMR Biol Veget & Microbiol Environ, Aix-Marseille Université, Saint-Paul-lez-Durance, F-13108, France
| | - Ange Polidori
- Institut des Biomolécules
Max Mousseron (IBMM) UMR 5247 CNRS-Universités Montpellier
1 et 2, Chimie Bioorganique et Systèmes Amphiphiles, Université d’Avignon et des Pays de Vaucluse, 33 rue Louis Pasteur, F-84000 Avignon, France
| | - Françoise Bonneté
- Institut des Biomolécules
Max Mousseron (IBMM) UMR 5247 CNRS-Universités Montpellier
1 et 2, Chimie Bioorganique et Systèmes Amphiphiles, Université d’Avignon et des Pays de Vaucluse, 33 rue Louis Pasteur, F-84000 Avignon, France
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Prince C, Jia Z. Measurement of detergent concentration using 2,6-dimethylphenol in membrane-protein crystallization. ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2012; 68:1694-6. [DOI: 10.1107/s0907444912040176] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2012] [Accepted: 09/21/2012] [Indexed: 11/10/2022]
Abstract
Methods have previously been developed to measure detergent concentration in membrane-protein samples, but most have significant limitations, such as requiring specialized equipment or consuming a significant amount of precious sample. This work explores the use of 2,6-dimethylphenol in a phenol–sulfuric acid assay to accurately measure the concentration of common glycosidic-based detergents used in crystallization. This method is amenable to routine laboratory use, provides excellent sensitivity and significantly reduces the sample volume required. Using anEscherichia colityrosine kinase (Etk) construct as an example, it is shown that the crystallization potential of Etk is directly influenced by measurable changes in detergent concentration.
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Salon JA, Lodowski DT, Palczewski K. The significance of G protein-coupled receptor crystallography for drug discovery. Pharmacol Rev 2012; 63:901-37. [PMID: 21969326 DOI: 10.1124/pr.110.003350] [Citation(s) in RCA: 160] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Crucial as molecular sensors for many vital physiological processes, seven-transmembrane domain G protein-coupled receptors (GPCRs) comprise the largest family of proteins targeted by drug discovery. Together with structures of the prototypical GPCR rhodopsin, solved structures of other liganded GPCRs promise to provide insights into the structural basis of the superfamily's biochemical functions and assist in the development of new therapeutic modalities and drugs. One of the greatest technical and theoretical challenges to elucidating and exploiting structure-function relationships in these systems is the emerging concept of GPCR conformational flexibility and its cause-effect relationship for receptor-receptor and receptor-effector interactions. Such conformational changes can be subtle and triggered by relatively small binding energy effects, leading to full or partial efficacy in the activation or inactivation of the receptor system at large. Pharmacological dogma generally dictates that these changes manifest themselves through kinetic modulation of the receptor's G protein partners. Atomic resolution information derived from increasingly available receptor structures provides an entrée to the understanding of these events and practically applying it to drug design. Supported by structure-activity relationship information arising from empirical screening, a unified structural model of GPCR activation/inactivation promises to both accelerate drug discovery in this field and improve our fundamental understanding of structure-based drug design in general. This review discusses fundamental problems that persist in drug design and GPCR structural determination.
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Affiliation(s)
- John A Salon
- Department of Molecular Structure, Amgen Incorporated, Thousand Oaks, California, USA
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15
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Gan SW, Vararattanavech A, Nordin N, Eshaghi S, Torres J. A cost-effective method for simultaneous homo-oligomeric size determination and monodispersity conditions for membrane proteins. Anal Biochem 2011; 416:100-6. [PMID: 21624344 DOI: 10.1016/j.ab.2011.05.007] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2011] [Revised: 04/29/2011] [Accepted: 05/04/2011] [Indexed: 10/18/2022]
Abstract
The use of blue native polyacrylamide gel electrophoresis (BN-PAGE) has been reported in the literature to retain both water-soluble and membrane protein complexes in their native hetero-oligomeric state and to determine the molecular weight of membrane proteins. However, membrane proteins show abnormal mobility when compared with water-soluble markers. Although one could use membrane proteins as markers or apply a conversion factor to the observed molecular weight to account for the bound Coomassie blue dye, when one just wants to assess homo-oligomeric size, these methods appear to be too time-consuming or might not be generally applicable. Here, during detergent screening studies to identify the best detergent for achieving a monodisperse sample, we observed that under certain conditions membrane proteins tend to form ladders of increasing oligomeric size. Although the ladders themselves contain no indication of which band represents the correct oligomeric size, they provide a scale that can be compared with a single band, representing the native homo-oligomeric size, obtained in other conditions of the screen. We show that this approach works for three membrane proteins: CorA (42 kDa), aquaporin Z (25 kDa), and small hydrophobic (SH) protein from respiratory syncytial virus (8 kDa). In addition, polydispersity results and identification of the most suitable detergent correlate optimally not only with size exclusion chromatography (SEC) but also with results from sedimentation velocity and equilibrium experiments. Because it involves minute quantities of sample and detergent, this method can be used in high-throughput approaches as a low-cost technique.
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Affiliation(s)
- Siok Wan Gan
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
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16
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Vergis JM, Purdy MD, Wiener MC. A high-throughput differential filtration assay to screen and select detergents for membrane proteins. Anal Biochem 2010; 407:1-11. [PMID: 20667442 DOI: 10.1016/j.ab.2010.07.019] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2010] [Revised: 07/19/2010] [Accepted: 07/20/2010] [Indexed: 10/19/2022]
Abstract
Structural studies on integral membrane proteins are routinely performed on protein-detergent complexes (PDCs) consisting of purified protein solubilized in a particular detergent. Of all the membrane protein crystal structures solved to date, a subset of only four detergents has been used in more than half of these structures. Unfortunately, many membrane proteins are not well behaved in these four detergents and/or fail to yield well-diffracting crystals. Identification of detergents that maintain the solubility and stability of a membrane protein is a critical step and can be a lengthy and "protein-expensive" process. We have developed an assay that characterizes the stability and size of membrane proteins exchanged into a panel of 94 commercially available and chemically diverse detergents. This differential filtration assay (DFA), using a set of filtered microplates, requires sub-milligram quantities of purified protein and small quantities of detergents and other reagents and is performed in its entirety in several hours.
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Affiliation(s)
- James M Vergis
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22908, USA
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17
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Crisman RL, Randolph TW. Crystallization of recombinant human growth hormone at elevated pressures: Pressure effects on PEG-induced volume exclusion interactions. Biotechnol Bioeng 2010; 107:663-72. [DOI: 10.1002/bit.22832] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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18
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Gabrielsen M, Nagy LA, DeLucas LJ, Cogdell RJ. Self-interaction chromatography as a tool for optimizing conditions for membrane protein crystallization. ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2009; 66:44-50. [PMID: 20057048 DOI: 10.1107/s0907444909043972] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2009] [Accepted: 10/23/2009] [Indexed: 11/11/2022]
Abstract
The second virial coefficient, or B value, is a measurement of how well a protein interacts with itself in solution. These interactions can lead to protein crystallization or precipitation, depending on their strength, with a narrow range of B values (the 'crystallization slot') being known to promote crystallization. A convenient method of determining the B value is by self-interaction chromatography. This paper describes how the light-harvesting complex 1-reaction centre core complex from Allochromatium vinosum yielded single straight-edged crystals after iterative cycles of self-interaction chromatography and crystallization. This process allowed the rapid screening of small molecules and detergents as crystallization additives. Here, a description is given of how self-interaction chromatography has been utilized to improve the crystallization conditions of a membrane protein.
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Affiliation(s)
- Mads Gabrielsen
- Division of Molecular and Cellular Biology, Faculty of Biological Life Sciences, University of Glasgow, Scotland
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19
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Park Y, Choi G. Effects of pH, salt type, and ionic strength on the second virial coefficients of aqueous bovine serum albumin solutions. KOREAN J CHEM ENG 2009. [DOI: 10.1007/s11814-009-0032-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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20
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Wilson WW, Whited G, Payne RW, Henry C, Johnson DH, DeLucas L. Chapter 7 Tools to Enhance Membrane Protein Crystallization. CURRENT TOPICS IN MEMBRANES 2009. [DOI: 10.1016/s1063-5823(09)63007-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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21
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Oates J, Hicks M, Dafforn TR, DiMaio D, Dixon AM. In vitro dimerization of the bovine papillomavirus E5 protein transmembrane domain. Biochemistry 2008; 47:8985-92. [PMID: 18672907 DOI: 10.1021/bi8006252] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The E5 protein from bovine papillomavirus is a type II membrane protein and the product of the smallest known oncogene. E5 causes cell transformation by binding and activating the platelet-derived growth factor beta receptor (PDGFbetaR). In order to productively interact with the receptor, it is thought that E5 binds as a dimer. However, wild-type E5 and various mutants have also been shown to form trimers, tetramers, and even higher order oligomers. The residues in E5 that drive and stabilize a dimeric state are also still in question. At present, two different models for the E5 dimer exist in the literature, one symmetric and one asymmetric. There is universal agreement, however, that the transmembrane (TM) domain plays a vital role in stabilizing the functional oligomer; indeed, mutation of various TM domain residues can abolish E5 function. In order to better resolve the role of the E5 TM domain in function, we have undertaken the first quantitative in vitro characterization of the E5 TM domain in detergent micelles and liposomes. Circular and linear dichroism analyses verify that the TM domain adopts a stable alpha-helical structure and is able to partition efficiently across lipid bilayers. SDS-PAGE and analytical ultracentrifugation demonstrate for the first time that the TM domain of E5 forms a strong dimer with a standard state free energy of dissociation of 5.0 kcal mol (-1). We have used our new results to interpret existing models of E5 dimer formation and provide a direct link between TM helix interactions and E5 function.
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Affiliation(s)
- Joanne Oates
- Department of Chemistry, University of Warwick, Coventry CV4 7AL, United Kingdom
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22
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Tessier PM, Jinkoji J, Cheng YC, Prentice JL, Lenhoff AM. Self-Interaction Nanoparticle Spectroscopy: A Nanoparticle-Based Protein Interaction Assay. J Am Chem Soc 2008; 130:3106-12. [DOI: 10.1021/ja077624q] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Peter M. Tessier
- Center for Molecular and Engineering Thermodynamics, Department of Chemical Engineering, University of Delaware, Newark, Delaware 19716
| | - Jun Jinkoji
- Center for Molecular and Engineering Thermodynamics, Department of Chemical Engineering, University of Delaware, Newark, Delaware 19716
| | - Yu-Chia Cheng
- Center for Molecular and Engineering Thermodynamics, Department of Chemical Engineering, University of Delaware, Newark, Delaware 19716
| | - Jessica L. Prentice
- Center for Molecular and Engineering Thermodynamics, Department of Chemical Engineering, University of Delaware, Newark, Delaware 19716
| | - Abraham M. Lenhoff
- Center for Molecular and Engineering Thermodynamics, Department of Chemical Engineering, University of Delaware, Newark, Delaware 19716
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23
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BioFeedback. Biotechniques 2007. [DOI: 10.2144/000112679] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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24
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Arnold T, Linke D. Phase separation in the isolation and purification of membrane proteins. Biotechniques 2007; 43:427-30, 432, 434 passim. [DOI: 10.2144/000112566] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Phase separation is a simple, efficient, and cheap method to purify and concentrate detergent-solubilized membrane proteins. In spite of this, phase separation is not widely used or even known among membrane protein scientists, and ready-to-use protocols are available for only relatively few detergent/membrane protein combinations. Here, we summarize the physical and chemical parameters that influence the phase separation behavior of detergents commonly used for membrane protein studies. Examples for the successful purification of membrane proteins using this method with different classes of detergents are provided. As the choice of the detergent is critical in many downstream applications (e.g., membrane protein crystallization or functional assays), we discuss how new phase separation protocols can be developed for a given detergent buffer system.
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Affiliation(s)
- Thomas Arnold
- Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Dirk Linke
- Max Planck Institute for Developmental Biology, Tübingen, Germany
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25
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Winzor DJ, Deszczynski M, Harding SE, Wills PR. Nonequivalence of second virial coefficients from sedimentation equilibrium and static light scattering studies of protein solutions. Biophys Chem 2007; 128:46-55. [PMID: 17382457 DOI: 10.1016/j.bpc.2007.03.001] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2007] [Revised: 03/02/2007] [Accepted: 03/02/2007] [Indexed: 10/23/2022]
Abstract
Experimental data for ovalbumin and lysozyme are presented to highlight the nonequivalence of second virial coefficients obtained for proteins by sedimentation equilibrium and light scattering. Theoretical considerations confirm that the quantity deduced from sedimentation equilibrium distributions is B(22), the osmotic second virial coefficient describing thermodynamic nonideality arising solely from protein self-interaction. On the other hand, the virial coefficient determined by light scattering is shown to reflect the combined contributions of protein-protein and protein-buffer interactions to thermodynamic nonideality of the protein solution. Misidentification of the light scattering parameter as B(22) accounts for published reports of negative osmotic second virial coefficients as indicators of conditions conducive to protein crystal growth. Finally, textbook assertions about the equivalence of second virial coefficients obtained by sedimentation equilibrium and light scattering reflect the restriction of consideration to single-solute systems. Although sedimentation equilibrium distributions for buffered protein solutions are, indeed, amenable to interpretation in such terms, the same situation does not apply to light scattering measurements because buffer constituents cannot be regarded as part of the solvent: instead they must be treated as non-scattering cosolutes.
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Affiliation(s)
- Donald J Winzor
- Department of Biochemistry, School of Molecular and Microbial Sciences, University of Queensland, Brisbane, Queensland 4072, Australia.
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26
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Santonicola MG, Yocum MA, Lenhoff AM, Kaler EW. Self-assembly of medium-chain alkyl monoglucosides in ammonium sulfate solutions with poly(ethylene glycol). LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2007; 23:5358-66. [PMID: 17429988 DOI: 10.1021/la063427d] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
We study the phase behavior and microstructure of alkyl-beta-monoglucosides with intermediate chain lengths (octyl- and nonyl-beta-glucoside) in aqueous solutions containing ammonium sulfate and poly(ethylene glycol) (PEG). When the glucoside surfactants are mixed with PEG of molecular weight 3350 or larger, two different phase transitions are observed in the temperature range 0-100 degrees C, with lower and upper miscibility gaps separated by a one-phase isotropic region. Isothermal titration calorimetry is used to quantify the effect of PEG on the micellization properties of the alkyl monoglucosides, whereas small-angle neutron scattering gives insight into the microstructure of the surfactant/polymer mixtures near the liquid-liquid phase boundary. Results show that the range and the strength of the interactions in these solutions are highly affected by the presence of PEG. Solutions with nonyl-beta-glucoside contain larger micelles than those with octyl-beta-glucoside, and the intermicellar interactions are much stronger and longer ranged. The relevance of these findings for membrane protein crystallization is discussed.
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Affiliation(s)
- M Gabriella Santonicola
- Center for Molecular and Engineering Thermodynamics, Department of Chemical Engineering, University of Delaware, Newark, Delaware 19716, USA
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27
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Affiliation(s)
- Michael C Wiener
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia 22908-0736, USA.
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28
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Abstract
Although the examination of the protein data bank reveals an important backlog in the number of three-dimensional structures of membrane proteins, several recent successes are serving as preludes to what will become a very prosperous decade in this field. Systematic investigations of various factors affecting the stability of membrane proteins, as well as their potential to crystallize three dimensionally, have paved the way for such achievements. The importance of the role of detergents both at the level of purification and crystallization is now well established. In addition, the recognition of the protein-detergent complex as the entity to crystallize, as well as the understanding of its physical-chemical properties and discovery of factors affecting these, have permitted the design of better crystallization strategies. As a consequence of the various efforts in the field, new crystallization methods for membrane proteins are being implemented. These have already been successful and are expected to contribute significantly to the future successes. This chapter will review some basic principles in membrane protein crystallization and give an overview of the current state of the art in the field. Some practical guidelines to help the novice approach the problem of membrane protein crystallization from the initial step of protein purification to crystallogenesis will also be given.
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Affiliation(s)
- James Féthière
- European Molecular Biology Laboratory, Heidelberg, Germany
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29
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Berger BW, Gendron CM, Lenhoff AM, Kaler EW. Effects of additives on surfactant phase behavior relevant to bacteriorhodopsin crystallization. Protein Sci 2006; 15:2682-96. [PMID: 17088325 PMCID: PMC2242436 DOI: 10.1110/ps.062370506] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
The interactions leading to crystallization of the integral membrane protein bacteriorhodopsin solubilized in n-octyl-beta-D-glucoside were investigated. Osmotic second virial coefficients (B(22)) were measured by self-interaction chromatography using a wide range of additives and precipitants, including polyethylene glycol (PEG) and heptane-1,2,3-triol (HT). In all cases, attractive protein-detergent complex (PDC) interactions were observed near the surfactant cloud point temperature, and there is a correlation between the surfactant cloud point temperatures and PDC B(22) values. Light scattering, isothermal titration calorimetry, and tensiometry reveal that although the underlying reasons for the patterns of interaction may be different for various combinations of precipitants and additives, surfactant phase behavior plays an important role in promoting crystallization. In most cases, solution conditions that led to crystallization fell within a similar range of slightly negative B(22) values, suggesting that weakly attractive interactions are important as they are for soluble proteins. However, the sensitivity of the cloud point temperatures and resultant coexistence curves varied significantly as a function of precipitant type, which suggests that different types of forces are involved in driving phase separation depending on the precipitant used.
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Affiliation(s)
- Bryan W Berger
- Center for Molecular and Engineering Thermodynamics, Department of Chemical Engineering, University of Delaware, Newark, Delaware 19716, USA.
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30
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Ahamed T, Ottens M, van Dedem GWK, van der Wielen LAM. Design of self-interaction chromatography as an analytical tool for predicting protein phase behavior. J Chromatogr A 2005; 1089:111-24. [PMID: 16130779 DOI: 10.1016/j.chroma.2005.06.065] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Solution conditions under which proteins have a tendency to crystallize correspond to a slightly negative osmotic second virial coefficient (B22). A positive B22 value guarantees no crystallization to occur. On the other hand, a B22 value within the so called "crystallization slot" thermodynamically supports the crystallization processes but does not guarantee successful crystal growth. It is, however, a prerequisite for protein crystallization that the B22 value must be in the slightly negative regime. Self-interaction chromatography (SIC) is designed in this work as an analytical tool for determining B22 in a precise and reproducible way. The methodology was demonstrated in detail in terms of its theoretical basis, experimental methodology, troubleshooting and data analysis for different protein samples and solution conditions. The inherent error limit of SIC is found to be comparatively less than other B22 measurement techniques. The designed experimental approach was applied for mapping crystallization conditions of a model protein, i.e. lysozyme. Good agreement between the obtained lysozyme B22 values and literature values confirms the accuracy of the approach.
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Affiliation(s)
- Tangir Ahamed
- Department of Biotechnology, Delft University of Technology, Julianalaan 67, 2628 BC Delft, The Netherlands
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31
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Zakharov SD, Eroukova VY, Rokitskaya TI, Zhalnina MV, Sharma O, Loll PJ, Zgurskaya HI, Antonenko YN, Cramer WA. Colicin occlusion of OmpF and TolC channels: outer membrane translocons for colicin import. Biophys J 2004; 87:3901-11. [PMID: 15465872 PMCID: PMC1304901 DOI: 10.1529/biophysj.104.046151] [Citation(s) in RCA: 66] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The interaction of colicins with target cells is a paradigm for protein import. To enter cells, bactericidal colicins parasitize Escherichia coli outer membrane receptors whose physiological purpose is the import of essential metabolites. Colicins E1 and E3 initially bind to the BtuB receptor, whose beta-barrel pore is occluded by an N-terminal globular "plug". The x-ray structure of a complex of BtuB with the coiled-coil BtuB-binding domain of colicin E3 did not reveal displacement of the BtuB plug that would allow passage of the colicin (Kurisu, G., S. D. Zakharov, M. V. Zhalnina, S. Bano, V. Y. Eroukova, T. I. Rokitskaya, Y. N. Antonenko, M. C. Wiener, and W. A. Cramer. 2003. Nat. Struct. Biol. 10:948-954). This correlates with the inability of BtuB to form ion channels in planar bilayers, shown in this work, suggesting that an additional outer membrane protein(s) is required for colicin import across the outer membrane. The identity and interaction properties of this OMP were analyzed in planar bilayer experiments.OmpF and TolC channels in planar bilayers were occluded by colicins E3 and E1, respectively, from the trans-side of the membrane. Occlusion was dependent upon a cis-negative transmembrane potential. A positive potential reversibly opened OmpF and TolC channels. Colicin N, which uses only OmpF for entry, occludes OmpF in planar bilayers with the same orientation constraints as colicins E1 and E3. The OmpF recognition sites of colicins E3 and N, and the TolC recognition site of colicin E1, were found to reside in the N-terminal translocation domains. These data are considered in the context of a two-receptor translocon model for colicin entry into cells.
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Affiliation(s)
- Stanislav D Zakharov
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana, USA.
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32
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Vivarès D, Bonneté F. Liquid−Liquid Phase Separations in Urate Oxidase/PEG Mixtures: Characterization and Implications for Protein Crystallization. J Phys Chem B 2004; 108:6498-507. [DOI: 10.1021/jp037502u] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- D. Vivarès
- CRMCN-CNRS, Campus de Luminy, Case 913, F-13288 Marseille Cedex 09, France, and LMCP-UMR7590, Case 115, 4 place Jussieu, F-75252 Paris Cedex 05, France
| | - F. Bonneté
- CRMCN-CNRS, Campus de Luminy, Case 913, F-13288 Marseille Cedex 09, France, and LMCP-UMR7590, Case 115, 4 place Jussieu, F-75252 Paris Cedex 05, France
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33
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34
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Tessier PM, Lenhoff AM. Measurements of protein self-association as a guide to crystallization. Curr Opin Biotechnol 2003; 14:512-6. [PMID: 14580581 DOI: 10.1016/s0958-1669(03)00114-9] [Citation(s) in RCA: 58] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
The challenge of crystallizing proteins has led to a significant amount of research in understanding protein self-association and assembly. Arguably the most influential finding in this field in the past decade has been that weakly attractive protein interactions, characterized in terms of the osmotic second virial coefficient, correlate with solution conditions that are conducive to crystallization. Recent work in this area has focused on the development of more efficient techniques for measuring the second virial coefficient, as traditional characterization methods suffer from poor efficiency in terms of time and protein consumption. The resulting measurements have provided new insights into patterns of protein interactions and their relation to protein phase behavior.
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Affiliation(s)
- Peter M Tessier
- Center for Molecular and Engineering Thermodynamics, Department of Chemical Engineering, University of Delaware, Newark, DE 19716, USA
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35
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Tanaka S, Ataka M, Onuma K, Kubota T. Rationalization of membrane protein crystallization with polyethylene glycol using a simple depletion model. Biophys J 2003; 84:3299-306. [PMID: 12719259 PMCID: PMC1302890 DOI: 10.1016/s0006-3495(03)70054-x] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Based on the importance of crystallizing membrane proteins in a rational way, cytochrome bc(1) complex (BC1) was crystallized using polyethylene glycol (PEG) as a sole crystallization agent. Interaction between protein-detergent complexes of BC1 was estimated by dynamic light scattering, and was compared with the numerical calculation using the Derjaguin-Landau-Verwey-Overbeek potential plus a depletion potential, without considering specific surface properties of the protein-detergent complexes. The experiments and calculation were found to be consistent and we obtained a relation between PEG molecular weight M and the range of depletion zone delta as delta approximately M(0.48+/-0.02). The stability of liquid phase of BC1 solutions was controlled by a ratio of (the range of depletion zone)/(the radius of a BC1 particle), which was consistent with recent theoretical predictions. The crystallization was most successful under a condition where the stability of the liquid phase changed from stable to unstable. The PEG molecular weight that fulfilled this condition coincided with the one used empirically to crystallize BC1 in the past by a number of groups. These results are compared to the fact that membrane proteins were often successfully crystallized close to the detergent cloud point.
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Affiliation(s)
- Shinpei Tanaka
- Special Division for Human Life Technology, National Institute of Advanced Industrial Science and Technology, Ikeda 563-8577, Japan
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36
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Abstract
Static and dynamic light scattering are discussed as particularly useful tools for studying various aspects of protein crystal growth. Specific applications for prenucleation assays as well as for monitoring postnucleation growth processes are presented. Protein-protein interactions determined by light scattering, which serve as a predictor for favorable crystallization conditions as well as for protein solubility behavior, are detailed. Several precautions regarding the practical aspects of light scattering and interpretation of data are also discussed.
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Affiliation(s)
- W William Wilson
- Department of Chemistry, Mississippi State University, Box 9573, 39762, Mississippi State, MS, USA
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37
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38
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Tessier PM, Johnson HR, Pazhianur R, Berger BW, Prentice JL, Bahnson BJ, Sandler SI, Lenhoff AM. Predictive crystallization of ribonuclease A via rapid screening of osmotic second virial coefficients. Proteins 2003; 50:303-11. [PMID: 12486724 DOI: 10.1002/prot.10249] [Citation(s) in RCA: 59] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Important progress has been made in recent years toward developing a molecular-level understanding of protein phase behavior in terms of the osmotic second virial coefficient, a thermodynamic parameter that characterizes pairwise protein interactions. Yet there has been little practical application of this knowledge to the field of protein crystallization, largely because of the difficult and time-consuming nature of traditional techniques for characterizing protein interactions. Self-interaction chromatography has recently been proposed as a highly efficient method for measuring the osmotic second virial coefficient. The utility of the technique is examined in this work by characterizing virial coefficients for ribonuclease A under 59 solution conditions using several crystallization additives, including PEG, sodium chloride, ammonium sulfate, and propanol. The virial coefficient measurements show some counterintuitive trends and shed light on the previous difficulties in crystallizing ribonuclease A. Crystallization experiments at the corresponding solution conditions were conducted by using ultracentrifugal crystallization. Using this methodology, ribonuclease A crystals were obtained under conditions for which the virial coefficients fell within the "crystallization slot." Crystallographic characterization showed that the crystals diffract to high resolution. Metastable crystals were also obtained for conditions outside, but near, the "crystallization slot," and they could also be frozen and used to collect structural information.
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Affiliation(s)
- Peter M Tessier
- Center for Molecular and Engineering Thermodynamics, Department of Chemical Engineering, University of Delaware, Newark, Delaware, USA
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39
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Finet S, Vivarès D, Bonneté F, Tardieu A. Controlling Biomolecular Crystallization by Understanding the Distinct Effects of PEGs and Salts on Solubility. Methods Enzymol 2003; 368:105-29. [PMID: 14674271 DOI: 10.1016/s0076-6879(03)68007-9] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- Stéphanie Finet
- European Synchrotron Radiation Facility, 6 Rue Jules Horowitz, BP200 F38043 Grenoble, France
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40
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Tanaka S, Ataka M. Protein crystallization induced by polyethylene glycol: A model study using apoferritin. J Chem Phys 2002. [DOI: 10.1063/1.1477456] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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41
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Tessier PM, Lenhoff AM, Sandler SI. Rapid measurement of protein osmotic second virial coefficients by self-interaction chromatography. Biophys J 2002; 82:1620-31. [PMID: 11867474 PMCID: PMC1301960 DOI: 10.1016/s0006-3495(02)75513-6] [Citation(s) in RCA: 147] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Weak protein interactions are often characterized in terms of the osmotic second virial coefficient (B(22)), which has been shown to correlate with protein phase behavior, such as crystallization. Traditional methods for measuring B(22), such as static light scattering, are too expensive in terms of both time and protein to allow extensive exploration of the effects of solution conditions on B(22). In this work we have measured protein interactions using self-interaction chromatography, in which protein is immobilized on chromatographic particles and the retention of the same protein is measured in isocratic elution. The relative retention of the protein reflects the average protein interactions, which we have related to the second virial coefficient via statistical mechanics. We obtain quantitative agreement between virial coefficients measured by self-interaction chromatography and traditional characterization methods for both lysozyme and chymotrypsinogen over a wide range of pH and ionic strengths, yet self-interaction chromatography requires at least an order of magnitude less time and protein than other methods. The method thus holds significant promise for the characterization of protein interactions requiring only commonly available laboratory equipment, little specialized expertise, and relatively small investments of both time and protein.
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Affiliation(s)
- Peter M Tessier
- Center for Molecular and Engineering Thermodynamics, Department of Chemical Engineering, University of Delaware, Newark, Delaware 19716, USA
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42
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Abstract
Detergents are invaluable tools for studying membrane proteins. However, these deceptively simple, amphipathic molecules exhibit complex behavior when they self-associate and interact with other molecules. The phase behavior and assembled structures of detergents are markedly influenced not only by their unique chemical and physical properties but also by concentration, ionic conditions, and the presence of other lipids and proteins. In this minireview, we discuss the various aggregate forms detergents assume and some misconceptions about their structure. The distinction between detergents and the membrane lipids that they may (or may not) replace is emphasized in the most recent high resolution structures of membrane proteins. Detergents are clearly friends and foes, but with the knowledge of how they work, we can use the increasing variety of detergents to our advantage.
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Affiliation(s)
- R M Garavito
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824-1319, USA.
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43
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Wiener MC. Existing and emergent roles for surfactants in the three-dimensional crystallization of integral membrane proteins. Curr Opin Colloid Interface Sci 2001. [DOI: 10.1016/s1359-0294(01)00107-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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44
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45
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Abstract
Fueled by initial space shuttle results, the National Aeronautics and Space Administration (NASA) has been supporting fundamental studies of macromolecular crystal growth since 1985. The majority of this research is directed at understanding the relationship between experimental variables and important crystal characteristics. The program has resulted in new methods and technology that will benefit the crystallography community's effort to meet the ever-increasing demand for protein structural information. Microgravity crystallization results indicate a potential impact on structural biology's more challenging problems, as soon as long-duration experiments can be performed on the International Space Station.
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Affiliation(s)
- L J. DeLucas
- University of Alabama at Birmingham, Center for Biophysical Sciences and Engineering, 35294, Tel: +1 205 934 5329; fax: +1 205 934 2659, Birmingham, AL, USA
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