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Brasnett C, Squires AM, Smith AJ, Seddon AM. Lipid doping of the sponge (L 3) mesophase. SOFT MATTER 2023; 19:6569-6577. [PMID: 37603381 DOI: 10.1039/d3sm00578j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/22/2023]
Abstract
The polymorphism of lipid aggregates has long attracted detailed study due to the myriad factors that determine the final mesophase observed. This study is driven by the need to understand mesophase behaviour for a number of applications, such as drug delivery and membrane protein crystallography. In the case of the latter, the role of the so-called 'sponge' (L3) mesophase has been often noted, but not extensively studied by itself. The L3 mesophase can be formed in monoolein/water systems on the addition of butanediol to water, which partitions the headgroup region of the membrane, and decreases its elastic moduli. Like cubic mesophases, it is bicontinuous, but unlike them, has no long-range translational symmetry. In our present study, we show that the formation of the L3 phase can delicately depend on the addition of dopant lipids to the mesophase. While electrostatically neutral molecules similar in shape to monoolein (DOPE, cholesterol) have little effect on the general mesophase behaviour, others (DOPC, DDM) significantly reduce the composition at which it can form. Additionally, we show that by combining cholesterol with the anionic lipid DOPG, it is possible to form the largest stable L3 mesophases observed to date, with characteristic lengths over 220 Å.
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Affiliation(s)
| | - Adam M Squires
- Department of Chemistry, University of Bath, Bath, BA2 7AY, UK
| | - Andrew J Smith
- Diamond House, Diamond Light Source Ltd, Harwell Science and Innovation Campus, Fermi Ave., Didcot, OX11 0DE, UK
| | - Annela M Seddon
- School of Physics, University of Bristol, Tyndall Avenue, Bristol, BS8 1FD, UK.
- Bristol Centre for Functional Nanomaterials, School of Physics, University of Bristol, Tyndall Avenue, Bristol, BS8 1FD, UK
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2
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Båth P, Banacore A, Börjesson P, Bosman R, Wickstrand C, Safari C, Dods R, Ghosh S, Dahl P, Ortolani G, Björg Ulfarsdottir T, Hammarin G, García Bonete MJ, Vallejos A, Ostojić L, Edlund P, Linse JB, Andersson R, Nango E, Owada S, Tanaka R, Tono K, Joti Y, Nureki O, Luo F, James D, Nass K, Johnson PJM, Knopp G, Ozerov D, Cirelli C, Milne C, Iwata S, Brändén G, Neutze R. Lipidic cubic phase serial femtosecond crystallography structure of a photosynthetic reaction centre. Acta Crystallogr D Struct Biol 2022; 78:698-708. [PMID: 35647917 PMCID: PMC9159286 DOI: 10.1107/s2059798322004144] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Accepted: 04/19/2022] [Indexed: 03/28/2024] Open
Abstract
Serial crystallography is a rapidly growing method that can yield structural insights from microcrystals that were previously considered to be too small to be useful in conventional X-ray crystallography. Here, conditions for growing microcrystals of the photosynthetic reaction centre of Blastochloris viridis within a lipidic cubic phase (LCP) crystallization matrix that employ a seeding protocol utilizing detergent-grown crystals with a different crystal packing are described. LCP microcrystals diffracted to 2.25 Å resolution when exposed to XFEL radiation, which is an improvement of 0.15 Å over previous microcrystal forms. Ubiquinone was incorporated into the LCP crystallization media and the resulting electron density within the mobile QB pocket is comparable to that of other cofactors within the structure. As such, LCP microcrystallization conditions will facilitate time-resolved diffraction studies of electron-transfer reactions to the mobile quinone, potentially allowing the observation of structural changes associated with the two electron-transfer reactions leading to complete reduction of the ubiquinone ligand.
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Affiliation(s)
- Petra Båth
- Department of Chemistry and Molecular Biology, University of Gothenburg, Lundbergslaboratoriet Box 462, 405 30 Göteborg, Sweden
| | - Analia Banacore
- Department of Chemistry and Molecular Biology, University of Gothenburg, Lundbergslaboratoriet Box 462, 405 30 Göteborg, Sweden
| | - Per Börjesson
- Department of Chemistry and Molecular Biology, University of Gothenburg, Lundbergslaboratoriet Box 462, 405 30 Göteborg, Sweden
| | - Robert Bosman
- Department of Chemistry and Molecular Biology, University of Gothenburg, Lundbergslaboratoriet Box 462, 405 30 Göteborg, Sweden
| | - Cecilia Wickstrand
- Department of Chemistry and Molecular Biology, University of Gothenburg, Lundbergslaboratoriet Box 462, 405 30 Göteborg, Sweden
| | - Cecilia Safari
- Department of Chemistry and Molecular Biology, University of Gothenburg, Lundbergslaboratoriet Box 462, 405 30 Göteborg, Sweden
| | - Robert Dods
- Department of Chemistry and Molecular Biology, University of Gothenburg, Lundbergslaboratoriet Box 462, 405 30 Göteborg, Sweden
| | - Swagatha Ghosh
- Department of Chemistry and Molecular Biology, University of Gothenburg, Lundbergslaboratoriet Box 462, 405 30 Göteborg, Sweden
| | - Peter Dahl
- Department of Chemistry and Molecular Biology, University of Gothenburg, Lundbergslaboratoriet Box 462, 405 30 Göteborg, Sweden
| | - Giorgia Ortolani
- Department of Chemistry and Molecular Biology, University of Gothenburg, Lundbergslaboratoriet Box 462, 405 30 Göteborg, Sweden
| | - Tinna Björg Ulfarsdottir
- Department of Chemistry and Molecular Biology, University of Gothenburg, Lundbergslaboratoriet Box 462, 405 30 Göteborg, Sweden
| | - Greger Hammarin
- Department of Chemistry and Molecular Biology, University of Gothenburg, Lundbergslaboratoriet Box 462, 405 30 Göteborg, Sweden
| | - María-José García Bonete
- Department of Chemistry and Molecular Biology, University of Gothenburg, Lundbergslaboratoriet Box 462, 405 30 Göteborg, Sweden
| | - Adams Vallejos
- Department of Chemistry and Molecular Biology, University of Gothenburg, Lundbergslaboratoriet Box 462, 405 30 Göteborg, Sweden
| | - Lucija Ostojić
- Department of Chemistry and Molecular Biology, University of Gothenburg, Lundbergslaboratoriet Box 462, 405 30 Göteborg, Sweden
| | - Petra Edlund
- Department of Chemistry and Molecular Biology, University of Gothenburg, Lundbergslaboratoriet Box 462, 405 30 Göteborg, Sweden
| | - Johanna-Barbara Linse
- Department of Chemistry and Molecular Biology, University of Gothenburg, Lundbergslaboratoriet Box 462, 405 30 Göteborg, Sweden
| | - Rebecka Andersson
- Department of Chemistry and Molecular Biology, University of Gothenburg, Lundbergslaboratoriet Box 462, 405 30 Göteborg, Sweden
| | - Eriko Nango
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai 980-8577, Japan
| | - Shigeki Owada
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - Rie Tanaka
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - Kensuke Tono
- Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5198, Japan
| | - Yasumasa Joti
- Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5198, Japan
| | - Osamu Nureki
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Fangjia Luo
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Yoshida Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Daniel James
- SwissFEL, Paul Scherrer Institute, Forschungsstrasse 111, CH-5232 Villigen PSI, Switzerland
| | - Karol Nass
- SwissFEL, Paul Scherrer Institute, Forschungsstrasse 111, CH-5232 Villigen PSI, Switzerland
| | - Philip J. M. Johnson
- SwissFEL, Paul Scherrer Institute, Forschungsstrasse 111, CH-5232 Villigen PSI, Switzerland
| | - Gregor Knopp
- SwissFEL, Paul Scherrer Institute, Forschungsstrasse 111, CH-5232 Villigen PSI, Switzerland
| | - Dmitry Ozerov
- SwissFEL, Paul Scherrer Institute, Forschungsstrasse 111, CH-5232 Villigen PSI, Switzerland
| | - Claudio Cirelli
- SwissFEL, Paul Scherrer Institute, Forschungsstrasse 111, CH-5232 Villigen PSI, Switzerland
| | - Christopher Milne
- SwissFEL, Paul Scherrer Institute, Forschungsstrasse 111, CH-5232 Villigen PSI, Switzerland
| | - So Iwata
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Yoshida Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Gisela Brändén
- Department of Chemistry and Molecular Biology, University of Gothenburg, Lundbergslaboratoriet Box 462, 405 30 Göteborg, Sweden
| | - Richard Neutze
- Department of Chemistry and Molecular Biology, University of Gothenburg, Lundbergslaboratoriet Box 462, 405 30 Göteborg, Sweden
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Selikhanov G, Fufina T, Guenther S, Meents A, Gabdulkhakov A, Vasilieva L. X-ray structure of the Rhodobacter sphaeroides reaction center with an M197 Phe→His substitution clarifies the properties of the mutant complex. IUCRJ 2022; 9:261-271. [PMID: 35371503 PMCID: PMC8895020 DOI: 10.1107/s2052252521013178] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Accepted: 12/11/2021] [Indexed: 06/14/2023]
Abstract
The first steps of the global process of photosynthesis take place in specialized membrane pigment-protein complexes called photosynthetic reaction centers (RCs). The RC of the photosynthetic purple bacterium Rhodobacter sphaeroides, a relatively simple analog of the more complexly organized photosystem II in plants, algae and cyanobacteria, serves as a convenient model for studying pigment-protein interactions that affect photochemical processes. In bacterial RCs the bacteriochlorophyll (BChl) dimer P serves as the primary electron donor, and its redox potential is a critical factor in the efficient functioning of the RC. It has previously been shown that the replacement of Phe M197 by His strongly affects the oxidation potential of P (E m P/P+), increasing its value by 125 mV, as well as increasing the thermal stability of RC and its stability in response to external pressure. The crystal structures of F(M197)H RC at high resolution obtained using various techniques presented in this report clarify the optical and electrochemical properties of the primary electron donor and the increased resistance of the mutant complex to denaturation. The electron-density maps are consistent with the donation of a hydrogen bond from the imidazole group of His M197 to the C2-acetyl carbonyl group of BChl PB. The formation of this hydrogen bond leads to a considerable out-of-plane rotation of the acetyl carbonyl group and results in a 1.2 Å shift of the O atom of this group relative to the wild-type structure. Besides, the distance between BChl PA and PB in the area of pyrrole ring I was found to be increased by up to 0.17 Å. These structural changes are discussed in association with the spectral properties of BChl dimer P. The electron-density maps strongly suggest that the imidazole group of His M197 accepts another hydrogen bond from the nearest water molecule, which in turn appears to form two more hydrogen bonds to Asn M195 and Asp L155. As a result of the F(M197)H mutation, BChl PB finds itself connected to the extensive hydrogen-bonding network that pre-existed in wild-type RC. Dissimilarities in the two hydrogen-bonding networks near the M197 and L168 sites may account for the different changes of the E m P/P+ in F(M197)H and H(L168)F RCs. The involvement of His M197 in the hydrogen-bonding network also appears to be related to stabilization of the F(M197)H RC structure. Analysis of the experimental data presented here and of the data available in the literature points to the fact that the hydrogen-bonding networks in the vicinity of BChl dimer P may play an important role in fine-tuning the redox properties of the primary electron donor.
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Affiliation(s)
- Georgii Selikhanov
- Group of Structural Studies of Macromolecular Complexes, Institute of Protein Research, Russian Academy of Sciences, Institutskaya 4, Pushchino 142290, Moscow Region, Russian Federation
- Federal Research Center Pushchino Scientific Center for Biological Research PSCBR, Institute of Basic Biological Problems, Russian Academy of Sciences, Institutskaya 2, Pushchino 142290, Moscow Region, Russian Federation
| | - Tatiana Fufina
- Federal Research Center Pushchino Scientific Center for Biological Research PSCBR, Institute of Basic Biological Problems, Russian Academy of Sciences, Institutskaya 2, Pushchino 142290, Moscow Region, Russian Federation
| | - Sebastian Guenther
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Alke Meents
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
- Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Azat Gabdulkhakov
- Group of Structural Studies of Macromolecular Complexes, Institute of Protein Research, Russian Academy of Sciences, Institutskaya 4, Pushchino 142290, Moscow Region, Russian Federation
| | - Lyudmila Vasilieva
- Federal Research Center Pushchino Scientific Center for Biological Research PSCBR, Institute of Basic Biological Problems, Russian Academy of Sciences, Institutskaya 2, Pushchino 142290, Moscow Region, Russian Federation
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4
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Trampari S, Neumann C, Hjorth-Jensen SJ, Shahsavar A, Quistgaard EM, Nissen P. Insights into the mechanism of high lipid–detergent crystallization of membrane proteins. J Appl Crystallogr 2021. [DOI: 10.1107/s1600576721010669] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Obtaining well diffracting crystals of membrane proteins is often challenging, but chances can be improved by crystallizing them in lipidic conditions that mimic their natural membrane environments. One approach is the high lipid–detergent (HiLiDe) method, which works by mixing the target protein with high concentrations of lipid and detergent prior to crystallization. Although this approach is convenient and flexible, understanding the effects of systematically varying lipid/detergent ratios and a characterization of the lipid phases that form during crystallization would be useful. Here, a HiLiDe phase diagram is reported for the model membrane protein MhsT, which tracks the precipitation and crystallization zones as a function of lipid and detergent concentrations, and is augmented with data on crystal sizes and diffraction properties. Additionally, the crystallization of SERCA1a solubilized directly with native lipids is characterized as a function of detergent concentration. Finally, HiLiDe crystallization drops are analysed with transmission electron microscopy, which among other features reveals liposomes, stacked lamellae that may represent crystal precursors, and mature crystals with clearly discernible packing arrangements. The results emphasize the significance of optimizing lipid/detergent ratios over broad ranges and provide insights into the mechanism of HiLiDe crystallization.
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5
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Martynowycz MW, Shiriaeva A, Ge X, Hattne J, Nannenga BL, Cherezov V, Gonen T. MicroED structure of the human adenosine receptor determined from a single nanocrystal in LCP. Proc Natl Acad Sci U S A 2021; 118:e2106041118. [PMID: 34462357 PMCID: PMC8433539 DOI: 10.1073/pnas.2106041118] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
G protein-coupled receptors (GPCRs), or seven-transmembrane receptors, are a superfamily of membrane proteins that are critically important to physiological processes in the human body. Determining high-resolution structures of GPCRs without bound cognate signaling partners, such as a G protein, requires crystallization in lipidic cubic phase (LCP). GPCR crystals grown in LCP are often too small for traditional X-ray crystallography. These microcrystals are ideal for investigation by microcrystal electron diffraction (MicroED), but the gel-like nature of LCP makes traditional approaches to MicroED sample preparation insurmountable. Here, we show that the structure of a human A2A adenosine receptor can be determined by MicroED after converting the LCP into the sponge phase followed by focused ion-beam milling. We determined the structure of the A2A adenosine receptor to 2.8-Å resolution and resolved an antagonist in its orthosteric ligand-binding site, as well as four cholesterol molecules bound around the receptor. This study lays the groundwork for future structural studies of lipid-embedded membrane proteins by MicroED using single microcrystals that would be impossible with other crystallographic methods.
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Affiliation(s)
- Michael W Martynowycz
- HHMI, University of California, Los Angeles, CA 90095
- Department of Biological Chemistry, University of California, Los Angeles, CA 90095
| | - Anna Shiriaeva
- Bridge Institute, University of Southern California Michelson Center for Convergent Biosciences, University of Southern California, Los Angeles, CA 90007
- Department of Chemistry, University of Southern California, Los Angeles, CA 90007
| | - Xuanrui Ge
- Bridge Institute, University of Southern California Michelson Center for Convergent Biosciences, University of Southern California, Los Angeles, CA 90007
- Mork Family Department of Chemical Engineering and Materials Science, University of Southern California, Los Angeles, CA 90007
| | - Johan Hattne
- HHMI, University of California, Los Angeles, CA 90095
- Department of Biological Chemistry, University of California, Los Angeles, CA 90095
| | - Brent L Nannenga
- Chemical Engineering, School for Engineering of Matter, Transport, and Energy, Arizona State University, Tempe, AZ 85287
- Biodesign Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, AZ 85287
| | - Vadim Cherezov
- Bridge Institute, University of Southern California Michelson Center for Convergent Biosciences, University of Southern California, Los Angeles, CA 90007;
- Department of Chemistry, University of Southern California, Los Angeles, CA 90007
| | - Tamir Gonen
- HHMI, University of California, Los Angeles, CA 90095;
- Department of Biological Chemistry, University of California, Los Angeles, CA 90095
- Department of Physiology, University of California, Los Angeles, CA 90095
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Liu J, Cheng R, Heimann K, Wang Z, Wang J, Liu F. Temperature-sensitive lyotropic liquid crystals as systems for transdermal drug delivery. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2021.115310] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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Birch J, Cheruvara H, Gamage N, Harrison PJ, Lithgo R, Quigley A. Changes in Membrane Protein Structural Biology. BIOLOGY 2020; 9:E401. [PMID: 33207666 PMCID: PMC7696871 DOI: 10.3390/biology9110401] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Revised: 11/11/2020] [Accepted: 11/12/2020] [Indexed: 12/21/2022]
Abstract
Membrane proteins are essential components of many biochemical processes and are important pharmaceutical targets. Membrane protein structural biology provides the molecular rationale for these biochemical process as well as being a highly useful tool for drug discovery. Unfortunately, membrane protein structural biology is a difficult area of study due to low protein yields and high levels of instability especially when membrane proteins are removed from their native environments. Despite this instability, membrane protein structural biology has made great leaps over the last fifteen years. Today, the landscape is almost unrecognisable. The numbers of available atomic resolution structures have increased 10-fold though advances in crystallography and more recently by cryo-electron microscopy. These advances in structural biology were achieved through the efforts of many researchers around the world as well as initiatives such as the Membrane Protein Laboratory (MPL) at Diamond Light Source. The MPL has helped, provided access to and contributed to advances in protein production, sample preparation and data collection. Together, these advances have enabled higher resolution structures, from less material, at a greater rate, from a more diverse range of membrane protein targets. Despite this success, significant challenges remain. Here, we review the progress made and highlight current and future challenges that will be overcome.
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Affiliation(s)
- James Birch
- Membrane Protein Laboratory, Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot OX11 0DE, UK; (J.B.); (H.C.); (N.G.); (P.J.H.); (R.L.)
- Research Complex at Harwell (RCaH), Harwell Science and Innovation Campus, Didcot OX11 0FA, UK
| | - Harish Cheruvara
- Membrane Protein Laboratory, Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot OX11 0DE, UK; (J.B.); (H.C.); (N.G.); (P.J.H.); (R.L.)
- Research Complex at Harwell (RCaH), Harwell Science and Innovation Campus, Didcot OX11 0FA, UK
| | - Nadisha Gamage
- Membrane Protein Laboratory, Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot OX11 0DE, UK; (J.B.); (H.C.); (N.G.); (P.J.H.); (R.L.)
- Research Complex at Harwell (RCaH), Harwell Science and Innovation Campus, Didcot OX11 0FA, UK
| | - Peter J. Harrison
- Membrane Protein Laboratory, Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot OX11 0DE, UK; (J.B.); (H.C.); (N.G.); (P.J.H.); (R.L.)
- Research Complex at Harwell (RCaH), Harwell Science and Innovation Campus, Didcot OX11 0FA, UK
| | - Ryan Lithgo
- Membrane Protein Laboratory, Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot OX11 0DE, UK; (J.B.); (H.C.); (N.G.); (P.J.H.); (R.L.)
- Research Complex at Harwell (RCaH), Harwell Science and Innovation Campus, Didcot OX11 0FA, UK
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough LE12 5RD, Leicestershire, UK
| | - Andrew Quigley
- Membrane Protein Laboratory, Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot OX11 0DE, UK; (J.B.); (H.C.); (N.G.); (P.J.H.); (R.L.)
- Research Complex at Harwell (RCaH), Harwell Science and Innovation Campus, Didcot OX11 0FA, UK
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Membrane protein crystallography in the era of modern structural biology. Biochem Soc Trans 2020; 48:2505-2524. [DOI: 10.1042/bst20200066] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2020] [Revised: 10/15/2020] [Accepted: 10/16/2020] [Indexed: 02/07/2023]
Abstract
The aim of structural biology has been always the study of biological macromolecules structures and their mechanistic behaviour at molecular level. To achieve its goal, multiple biophysical methods and approaches have become part of the structural biology toolbox. Considered as one of the pillars of structural biology, X-ray crystallography has been the most successful method for solving three-dimensional protein structures at atomic level to date. It is however limited by the success in obtaining well-ordered protein crystals that diffract at high resolution. This is especially true for challenging targets such as membrane proteins (MPs). Understanding structure-function relationships of MPs at the biochemical level is vital for medicine and drug discovery as they play critical roles in many cellular processes. Though difficult, structure determination of MPs by X-ray crystallography has significantly improved in the last two decades, mainly due to many relevant technological and methodological developments. Today, numerous MP crystal structures have been solved, revealing many of their mechanisms of action. Yet the field of structural biology has also been through significant technological breakthroughs in recent years, particularly in the fields of single particle electron microscopy (cryo-EM) and X-ray free electron lasers (XFELs). Here we summarise the most important advancements in the field of MP crystallography and the significance of these developments in the present era of modern structural biology.
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Selikhanov G, Fufina T, Vasilieva L, Betzel C, Gabdulkhakov A. Novel approaches for the lipid sponge phase crystallization of the Rhodobacter sphaeroides photosynthetic reaction center. IUCRJ 2020; 7:1084-1091. [PMID: 33209319 PMCID: PMC7642779 DOI: 10.1107/s2052252520012142] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Accepted: 09/02/2020] [Indexed: 06/11/2023]
Abstract
With the recent developments in the field of free-electron-laser-based serial femtosecond crystallography, the necessity to obtain a large number of high-quality crystals has emerged. In this work crystallization techniques were selected, tested and optimized for the lipid mesophase crystallization of the Rhodobacter sphaeroides membrane pigment-protein complex, known as the photosynthetic reaction center (RC). Novel approaches for lipid sponge phase crystallization in comparatively large volumes using Hamilton gas-tight glass syringes and plastic pipetting tips are described. An analysis of RC crystal structures obtained by lipid mesophase crystallization revealed non-native ligands that displaced the native electron-transfer cofactors (carotenoid sphero-idene and a ubi-quinone molecule) from their binding pockets. These ligands were identified and were found to be lipids that are major mesophase components. The selection of distinct co-crystallization conditions with the missing cofactors facilitated the restoration of sphero-idene in its binding site.
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Affiliation(s)
- Georgii Selikhanov
- Institute of Protein Research, Russian Academy of Sciences, Institutskaya 4, Puschino, Moscow region 142290, Russian Federation
- Institute of Basic Biological Problems, Russian Academy of Sciences, Institutskaya 2, Puschino, Moscow region 142290, Russian Federation
| | - Tatiana Fufina
- Institute of Basic Biological Problems, Russian Academy of Sciences, Institutskaya 2, Puschino, Moscow region 142290, Russian Federation
| | - Lyudmila Vasilieva
- Institute of Basic Biological Problems, Russian Academy of Sciences, Institutskaya 2, Puschino, Moscow region 142290, Russian Federation
| | - Christian Betzel
- Institute of Biochemistry and Molecular Biology, University of Hamburg, at Deutsches Elektronen-Synchrotron (DESY), Notkestrasse 85, Hamburg, 22607, Germany
- The Hamburg Centre for Ultrafast Imaging (CUI), Luruper Chaussee 149, Hamburg, 22761, Germany
| | - Azat Gabdulkhakov
- Institute of Protein Research, Russian Academy of Sciences, Institutskaya 4, Puschino, Moscow region 142290, Russian Federation
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Zhu L, Bu G, Jing L, Shi D, Lee MY, Gonen T, Liu W, Nannenga BL. Structure Determination from Lipidic Cubic Phase Embedded Microcrystals by MicroED. Structure 2020; 28:1149-1159.e4. [PMID: 32735770 PMCID: PMC7544639 DOI: 10.1016/j.str.2020.07.006] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 06/02/2020] [Accepted: 07/13/2020] [Indexed: 01/22/2023]
Abstract
The lipidic cubic phase (LCP) technique has proved to facilitate the growth of high-quality crystals that are otherwise difficult to grow by other methods. However, the crystal size optimization process could be time and resource consuming, if it ever happens. Therefore, improved techniques for structure determination using these small crystals is an important strategy in diffraction technology development. Microcrystal electron diffraction (MicroED) is a technique that uses a cryo-transmission electron microscopy to collect electron diffraction data and determine high-resolution structures from very thin micro- and nanocrystals. In this work, we have used modified LCP and MicroED protocols to analyze crystals embedded in LCP converted by 2-methyl-2,4-pentanediol or lipase, including Proteinase K crystals grown in solution, cholesterol crystals, and human adenosine A2A receptor crystals grown in LCP. These results set the stage for the use of MicroED to analyze microcrystalline samples grown in LCP, especially for those highly challenging membrane protein targets.
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Affiliation(s)
- Lan Zhu
- Biodesign Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, 727 East Tyler Street, Tempe, AZ 85287, USA; School of Molecular Sciences, Arizona State University, 551 East University Drive, Tempe, AZ 85287, USA
| | - Guanhong Bu
- Biodesign Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, 727 East Tyler Street, Tempe, AZ 85287, USA; School for Engineering of Matter, Transport and Energy, Arizona State University, Tempe, AZ, USA
| | - Liang Jing
- Biodesign Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, 727 East Tyler Street, Tempe, AZ 85287, USA; School of Molecular Sciences, Arizona State University, 551 East University Drive, Tempe, AZ 85287, USA
| | - Dan Shi
- Structural Biophysics Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD, USA
| | - Ming-Yue Lee
- Biodesign Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, 727 East Tyler Street, Tempe, AZ 85287, USA; School of Molecular Sciences, Arizona State University, 551 East University Drive, Tempe, AZ 85287, USA
| | - Tamir Gonen
- Howard Hughes Medical Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA; Departments of Biological Chemistry and Physiology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Wei Liu
- Biodesign Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, 727 East Tyler Street, Tempe, AZ 85287, USA; School of Molecular Sciences, Arizona State University, 551 East University Drive, Tempe, AZ 85287, USA.
| | - Brent L Nannenga
- Biodesign Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, 727 East Tyler Street, Tempe, AZ 85287, USA; School for Engineering of Matter, Transport and Energy, Arizona State University, Tempe, AZ, USA.
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11
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Zabelin AA, Khristin AM, Shkuropatova VA, Khatypov RA, Shkuropatov AY. Primary electron transfer in Rhodobacter sphaeroides R-26 reaction centers under dehydration conditions. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2020; 1861:148238. [PMID: 32533935 DOI: 10.1016/j.bbabio.2020.148238] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Revised: 05/28/2020] [Accepted: 06/03/2020] [Indexed: 11/26/2022]
Abstract
The photoinduced charge separation in QB-depleted reaction centers (RCs) from Rhodobacter sphaeroides R-26 in solid air-dried and vacuum-dried (~10-2 Torr) films, obtained in the presence of detergent n-dodecyl-β-D-maltoside (DM), is characterized using ultrafast transient absorption spectroscopy. It is shown that drying of RC-DM complexes is accompanied by reversible blue shifts of the ground-state absorption bands of the pigment ensemble, which suggest that no dehydration-induced structural destruction of RCs occurs in both types of films. In air-dried films, electron transfer from the excited primary electron donor P⁎ to the photoactive bacteriopheophytin HA proceeds in 4.7 ps to form the P+HA- state with essentially 100% yield. P+HA- decays in 260 ps both by electron transfer to the primary quinone QA to give the state P+QA- (87% yield) and by charge recombination to the ground state (13% yield). In vacuum-dried films, P⁎ decay is characterized by two kinetic components with time constants of 4.1 and 46 ps in a proportion of ~55%/45%, and P+HA- decays about 2-fold slower (462 ps) than in air-dried films. Deactivation of both P⁎ and P+HA- to the ground state effectively competes with the corresponding forward electron-transfer reactions in vacuum-dried RCs, reducing the yield of P+QA- to 68%. The results are compared with the data obtained for fully hydrated RCs in solution and are discussed in terms of the presence in the RC complexes of different water molecules, the removal/displacement of which affects spectral properties of pigment cofactors and rates and yields of the electron-transfer reactions.
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Affiliation(s)
- Alexey A Zabelin
- Institute of Basic Biological Problems of the Russian Academy of Sciences, Federal Research Center "Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences", 142290 Pushchino, Moscow Region, Russian Federation
| | - Anton M Khristin
- Institute of Basic Biological Problems of the Russian Academy of Sciences, Federal Research Center "Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences", 142290 Pushchino, Moscow Region, Russian Federation
| | - Valentina A Shkuropatova
- Institute of Basic Biological Problems of the Russian Academy of Sciences, Federal Research Center "Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences", 142290 Pushchino, Moscow Region, Russian Federation
| | - Ravil A Khatypov
- Institute of Basic Biological Problems of the Russian Academy of Sciences, Federal Research Center "Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences", 142290 Pushchino, Moscow Region, Russian Federation
| | - Anatoly Ya Shkuropatov
- Institute of Basic Biological Problems of the Russian Academy of Sciences, Federal Research Center "Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences", 142290 Pushchino, Moscow Region, Russian Federation.
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12
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Studying hydrogen bonding and dynamics of the acetylate groups of the Special Pair of Rhodobacter sphaeroides WT. Sci Rep 2019; 9:10528. [PMID: 31324886 PMCID: PMC6642110 DOI: 10.1038/s41598-019-46903-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Accepted: 07/08/2019] [Indexed: 11/17/2022] Open
Abstract
Although the cofactors in the bacterial reaction centre of Rhodobacter sphaeroides wild type (WT) are arranged almost symmetrically in two branches, the light-induced electron transfer occurs selectively in one branch. As origin of this functional symmetry break, a hydrogen bond between the acetyl group of PL in the primary donor and His-L168 has been discussed. In this study, we investigate the existence and rigidity of this hydrogen bond with solid-state photo-CIDNP MAS NMR methods offering information on the local electronic structure due to highly sensitive and selective NMR experiments. On the time scale of the experiment, the hydrogen bond between PL and His-L168 appears to be stable and not to be affected by illumination confirming a structural asymmetry within the Special Pair.
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13
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A vesicle-to-sponge transition via the proliferation of membrane-linking pores in ω-3 polyunsaturated fatty acid-containing lipid assemblies. J Mol Liq 2019. [DOI: 10.1016/j.molliq.2019.01.124] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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14
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Birch J, Axford D, Foadi J, Meyer A, Eckhardt A, Thielmann Y, Moraes I. The fine art of integral membrane protein crystallisation. Methods 2018; 147:150-162. [PMID: 29778646 DOI: 10.1016/j.ymeth.2018.05.014] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Revised: 05/13/2018] [Accepted: 05/15/2018] [Indexed: 11/29/2022] Open
Abstract
Integral membrane proteins are among the most fascinating and important biomolecules as they play a vital role in many biological functions. Knowledge of their atomic structures is fundamental to the understanding of their biochemical function and key in many drug discovery programs. However, over the years, structure determination of integral membrane proteins has proven to be far from trivial, hence they are underrepresented in the protein data bank. Low expression levels, insolubility and instability are just a few of the many hurdles one faces when studying these proteins. X-ray crystallography has been the most used method to determine atomic structures of membrane proteins. However, the production of high quality membrane protein crystals is always very challenging, often seen more as art than a rational experiment. Here we review valuable approaches, methods and techniques to successful membrane protein crystallisation.
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Affiliation(s)
- James Birch
- Membrane Protein Laboratory, Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, UK; Research Complex at Harwell, Rutherford Appleton Laboratory, Harwell Science and Innovation Campus, Didcot OX11 0FA, UK
| | - Danny Axford
- Diamond Light Source, Harwell Science and Innovation Campus, Oxfordshire OX11 0DE, UK
| | - James Foadi
- Department of Mathematical Sciences, University of Bath, Claverton Down, Bath BA2 7AY, UK
| | - Arne Meyer
- XtalConcepts GmbH, Schnackenburgallee 13, 22525 Hamburg, Germany
| | - Annette Eckhardt
- XtalConcepts GmbH, Schnackenburgallee 13, 22525 Hamburg, Germany
| | - Yvonne Thielmann
- Max Planck Institute of Biophysics, Molecular Membrane Biology, Max-von-Laue-Strasse 3, 60438 Frankfurt, Germany
| | - Isabel Moraes
- Research Complex at Harwell, Rutherford Appleton Laboratory, Harwell Science and Innovation Campus, Didcot OX11 0FA, UK; Diamond Light Source, Harwell Science and Innovation Campus, Oxfordshire OX11 0DE, UK; National Physical Laboratory, Hampton Road, Teddington TW11 0LW, UK.
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15
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Selikhanov GK, Fando MS, Dontsova MV, Gabdulkhakov AG. Investigations of Photosensitive Proteins by Serial Crystallography. BIOCHEMISTRY (MOSCOW) 2018; 83:S163-S175. [DOI: 10.1134/s0006297918140134] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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16
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Schieferstein JM, Pawate AS, Sun C, Wan F, Sheraden PN, Broecker J, Ernst OP, Gennis RB, Kenis PJA. X-ray transparent microfluidic chips for high-throughput screening and optimization of in meso membrane protein crystallization. BIOMICROFLUIDICS 2017; 11:024118. [PMID: 28469762 PMCID: PMC5403737 DOI: 10.1063/1.4981818] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2017] [Accepted: 04/10/2017] [Indexed: 05/10/2023]
Abstract
Elucidating and clarifying the function of membrane proteins ultimately requires atomic resolution structures as determined most commonly by X-ray crystallography. Many high impact membrane protein structures have resulted from advanced techniques such as in meso crystallization that present technical difficulties for the set-up and scale-out of high-throughput crystallization experiments. In prior work, we designed a novel, low-throughput X-ray transparent microfluidic device that automated the mixing of protein and lipid by diffusion for in meso crystallization trials. Here, we report X-ray transparent microfluidic devices for high-throughput crystallization screening and optimization that overcome the limitations of scale and demonstrate their application to the crystallization of several membrane proteins. Two complementary chips are presented: (1) a high-throughput screening chip to test 192 crystallization conditions in parallel using as little as 8 nl of membrane protein per well and (2) a crystallization optimization chip to rapidly optimize preliminary crystallization hits through fine-gradient re-screening. We screened three membrane proteins for new in meso crystallization conditions, identifying several preliminary hits that we tested for X-ray diffraction quality. Further, we identified and optimized the crystallization condition for a photosynthetic reaction center mutant and solved its structure to a resolution of 3.5 Å.
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Affiliation(s)
- Jeremy M Schieferstein
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Ashtamurthy S Pawate
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Chang Sun
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Frank Wan
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Paige N Sheraden
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Jana Broecker
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5S IA8, Canada
| | | | - Robert B Gennis
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Paul J A Kenis
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
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Zabara A, Meikle TG, Newman J, Peat TS, Conn CE, Drummond CJ. The nanoscience behind the art of in-meso crystallization of membrane proteins. NANOSCALE 2017; 9:754-763. [PMID: 27976759 DOI: 10.1039/c6nr07634c] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
The structural changes occurring at the nanoscale level within the lipid bilayer and driving the in-meso formation of large well-diffracting membrane protein crystals have been uniquely characterized for a model membrane protein, intimin. Importantly, the order to order transitions taking place within the bilayer and the lipidic nanostructures required for crystal growth have been shown to be general, occurring for both the cubic and the sponge mesophase crystallization pathways. For the first time, a transient fluid lamellar phase has been observed and unambiguously assigned for both crystallization pathways, present at the earliest stages of protein crystallogenesis but no longer observed once the crystals surpass the size of the average lyotropic liquid crystalline domain. The reported time-resolved structural investigation provides a significantly improved and general understanding of the nanostructural changes taking place within the mesophase during in-meso crystallization which is a fundamental advance in the enabling area of membrane protein structural biology.
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Affiliation(s)
- Alexandru Zabara
- RMIT University, School of Science, College of Science Engineering and Health 124 La Trobe Street, Melbourne, Victoria 3000, Australia. and Biomedical Manufacturing Program, Commonwealth Scientific and Industrial Research Organisation (CSIRO), 343 Royal Parade, Parkville, Victoria 3052, Australia
| | - Thomas G Meikle
- School of Chemistry, Bio21 Institute, The University of Melbourne, Melbourne, Victoria 3010, Australia
| | - Janet Newman
- Biomedical Manufacturing Program, Commonwealth Scientific and Industrial Research Organisation (CSIRO), 343 Royal Parade, Parkville, Victoria 3052, Australia
| | - Thomas S Peat
- Biomedical Manufacturing Program, Commonwealth Scientific and Industrial Research Organisation (CSIRO), 343 Royal Parade, Parkville, Victoria 3052, Australia
| | - Charlotte E Conn
- RMIT University, School of Science, College of Science Engineering and Health 124 La Trobe Street, Melbourne, Victoria 3000, Australia.
| | - Calum J Drummond
- RMIT University, School of Science, College of Science Engineering and Health 124 La Trobe Street, Melbourne, Victoria 3000, Australia.
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18
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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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19
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Abstract
Membrane proteins are crucial components of cellular membranes and are responsible for a variety of physiological functions. The advent of new tools and technologies for structural biology of membrane proteins has led to a significant increase in the number of structures deposited to the Protein Data Bank during the past decade. This new knowledge has expanded our fundamental understanding of their mechanism of function and contributed to the drug-design efforts. In this chapter we discuss current approaches for membrane protein expression, solubilization, crystallization, and data collection. Additionally, we describe the protein quality-control assays that are often instrumental as a guideline for a shorter path toward the structure.
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Affiliation(s)
- Andrii Ishchenko
- Department of Chemistry, Bridge Institute, University of Southern California, Los Angeles, CA, 90089, USA
| | - Enrique E Abola
- Department of Chemistry, Bridge Institute, University of Southern California, Los Angeles, CA, 90089, USA
| | - Vadim Cherezov
- Department of Chemistry, Bridge Institute, University of Southern California, Los Angeles, CA, 90089, USA.
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20
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21
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Adrien V, Rayan G, Reffay M, Porcar L, Maldonado A, Ducruix A, Urbach W, Taulier N. Characterization of a Biomimetic Mesophase Composed of Nonionic Surfactants and an Aqueous Solvent. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2016; 32:10268-10275. [PMID: 27618561 DOI: 10.1021/acs.langmuir.6b02744] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
We have investigated the physical and biomimetic properties of a sponge (L3) phase composed of pentaethylene glycol monododecyl ether (C12E5), a nonionic surfactant, an aqueous solvent, and a cosurfactant. The following cosurfactants, commonly used for solubilizing membrane proteins, were incorporated: n-octyl-β-d-glucopyranoside (β-OG), n-dodecyl-β-d-maltopyranoside (DDM), 4-cyclohexyl-1-butyl-β-d-maltoside (CYMAL-4), and 5-cyclohexyl-1-pentyl-β-d-maltoside (CYMAL-5). Partial phase diagrams of these systems were created. The L3 phase was characterized using crossed polarizers, diffusion of a fluorescent probe by fluorescence recovery after pattern photobleaching (FRAPP), and freeze fracture electron microscopy (FFEM). By varying the hydration of the phase, we were able to tune the distance between adjacent bilayers. The characteristic distance (db) of the phase was obtained from small angle scattering (SAXS/SANS) as well as from FFEM, which yielded complementary db values. These db values were neither affected by the nature of the cosurfactant nor by the addition of membrane proteins. These findings illustrate that a biomimetic surfactant sponge phase can be created in the presence of several common membrane protein-solubilizing detergents, thus making it a versatile medium for membrane protein studies.
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Affiliation(s)
- V Adrien
- Laboratoire de Physique Statistique, Ecole Normale Supérieure, PSL Research University; Université Paris Diderot Sorbonne Paris Cité; Sorbonne Universités UPMC Univ Paris 06, CNRS, 24 rue Lhomond, 75005 Paris, France
- Univ Paris Descartes, Sorbonne Paris Cité. Laboratoire de Cristallographie et RMN Biologiques, CNRS UMR 8015, Paris, France
| | - G Rayan
- Laboratoire de Physique Statistique, Ecole Normale Supérieure, PSL Research University; Université Paris Diderot Sorbonne Paris Cité; Sorbonne Universités UPMC Univ Paris 06, CNRS, 24 rue Lhomond, 75005 Paris, France
| | - M Reffay
- Laboratoire de Physique Statistique, Ecole Normale Supérieure, PSL Research University; Université Paris Diderot Sorbonne Paris Cité; Sorbonne Universités UPMC Univ Paris 06, CNRS, 24 rue Lhomond, 75005 Paris, France
| | - L Porcar
- Institut Laue-Langevin, 71 avenue des Martyrs, CS 20156, 38042 Grenoble Cedex 9, France
| | - A Maldonado
- Departamento de Física, Universidad de Sonora , Apdo Postal 1626, 83000 Hermosillo, Sonora Mexico
| | - A Ducruix
- Univ Paris Descartes, Sorbonne Paris Cité. Laboratoire de Cristallographie et RMN Biologiques, CNRS UMR 8015, Paris, France
| | - W Urbach
- Laboratoire de Physique Statistique, Ecole Normale Supérieure, PSL Research University; Université Paris Diderot Sorbonne Paris Cité; Sorbonne Universités UPMC Univ Paris 06, CNRS, 24 rue Lhomond, 75005 Paris, France
- Sorbonne Universités, UPMC Univ Paris 06, CNRS, INSERM, Laboratoire d'Imagerie Biomédicale, F-75006, Paris, France
| | - N Taulier
- Sorbonne Universités, UPMC Univ Paris 06, CNRS, INSERM, Laboratoire d'Imagerie Biomédicale, F-75006, Paris, France
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22
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van 't Hag L, Knoblich K, Seabrook SA, Kirby NM, Mudie ST, Lau D, Li X, Gras SL, Mulet X, Call ME, Call MJ, Drummond CJ, Conn CE. Exploring the in meso crystallization mechanism by characterizing the lipid mesophase microenvironment during the growth of single transmembrane α-helical peptide crystals. PHILOSOPHICAL TRANSACTIONS. SERIES A, MATHEMATICAL, PHYSICAL, AND ENGINEERING SCIENCES 2016; 374:rsta.2015.0125. [PMID: 27298442 PMCID: PMC4920275 DOI: 10.1098/rsta.2015.0125] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 02/12/2016] [Indexed: 05/19/2023]
Abstract
The proposed mechanism for in meso crystallization of transmembrane proteins suggests that a protein or peptide is initially uniformly dispersed in the lipid self-assembly cubic phase but that crystals grow from a local lamellar phase, which acts as a conduit between the crystal and the bulk cubic phase. However, there is very limited experimental evidence for this theory. We have developed protocols to investigate the lipid mesophase microenvironment during crystal growth using standard procedures readily available in crystallography laboratories. This technique was used to characterize the microenvironment during crystal growth of the DAP12-TM peptide using synchrotron small angle X-ray scattering (SAXS) with a micro-sized X-ray beam. Crystal growth was found to occur from the gyroid cubic mesophase. For one in four crystals, a highly oriented local lamellar phase was observed, providing supporting evidence for the proposed mechanism for in meso crystallization. A new observation of this study was that we can differentiate diffraction peaks from crystals grown in meso, from peaks originating from the surrounding lipid matrix, potentially opening up the possibility of high-throughput SAXS analysis of in meso grown crystals.This article is part of the themed issue 'Soft interfacial materials: from fundamentals to formulation'.
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Affiliation(s)
- Leonie van 't Hag
- Department of Chemical and Biomolecular Engineering, The University of Melbourne, Parkville, Victoria 3052, Australia Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, 30 Flemington Road, Parkville, Victoria 3052, Australia CSIRO Manufacturing Flagship, Private Bag 10, Clayton, Victoria 3169, Australia
| | - Konstantin Knoblich
- Department of Medical Biology, The University of Melbourne, Parkville, Victoria 3052, Australia Structural Biology Division, The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Victoria 3052, Australia
| | - Shane A Seabrook
- CSIRO Manufacturing Flagship, 343 Royal Parade, Parkville, Victoria 3052, Australia
| | - Nigel M Kirby
- Australian Synchrotron, 800 Blackburn Road, Clayton, Victoria 3168, Australia
| | - Stephen T Mudie
- Australian Synchrotron, 800 Blackburn Road, Clayton, Victoria 3168, Australia
| | - Deborah Lau
- CSIRO Manufacturing Flagship, Private Bag 10, Clayton, Victoria 3169, Australia
| | - Xu Li
- Department of Chemical and Biomolecular Engineering, The University of Melbourne, Parkville, Victoria 3052, Australia Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, 30 Flemington Road, Parkville, Victoria 3052, Australia
| | - Sally L Gras
- Department of Chemical and Biomolecular Engineering, The University of Melbourne, Parkville, Victoria 3052, Australia Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, 30 Flemington Road, Parkville, Victoria 3052, Australia The ARC Dairy Innovation Hub, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Xavier Mulet
- CSIRO Manufacturing Flagship, Private Bag 10, Clayton, Victoria 3169, Australia
| | - Matthew E Call
- Department of Medical Biology, The University of Melbourne, Parkville, Victoria 3052, Australia Structural Biology Division, The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Victoria 3052, Australia
| | - Melissa J Call
- Department of Medical Biology, The University of Melbourne, Parkville, Victoria 3052, Australia Structural Biology Division, The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Victoria 3052, Australia
| | - Calum J Drummond
- CSIRO Manufacturing Flagship, Private Bag 10, Clayton, Victoria 3169, Australia School of Applied Sciences, College of Science, Engineering and Health, RMIT University, GPO Box 2476, Melbourne, Victoria 3001, Australia
| | - Charlotte E Conn
- School of Applied Sciences, College of Science, Engineering and Health, RMIT University, GPO Box 2476, Melbourne, Victoria 3001, Australia
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23
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Sun W, Vallooran JJ, Fong WK, Mezzenga R. Lyotropic Liquid Crystalline Cubic Phases as Versatile Host Matrices for Membrane-Bound Enzymes. J Phys Chem Lett 2016; 7:1507-1512. [PMID: 27050734 DOI: 10.1021/acs.jpclett.6b00416] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Lyotropic liquid crystalline cubic mesophases can function as host matrices for enzymes because of their biomimetic structural characteristics, optical transparency, and capability to coexist with water. This study demonstrates that the in meso immobilized membrane-bound enzyme d-fructose dehydrogenase (FDH) preserves its full activity, follows ideal Michaelis-Menten kinetics, and shows improved stability compared to its behavior in solution. Even after 5 days, the immobilized FDH retained its full activity in meso, whereas a model hydrophilic enzyme, horseradish peroxidase, maintained only 21% of its original activity. We reason that the lipidic bilayers in the three-dimensional structures of cubic mesophases provide an ideal environment for the reconstitution of a membrane-bound enzyme. The preserved activity, long-term stability, and reusability demonstrate that these hybrid nanomaterials are ideal matrices for biosensing and biocatalytic fuel cell applications.
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Affiliation(s)
- Wenjie Sun
- Food and Soft Materials Science, Department of Health Science and Technology, ETH Zurich , Schmelzbergstrasse 9, CH-8092 Zurich, Switzerland
| | - Jijo J Vallooran
- Food and Soft Materials Science, Department of Health Science and Technology, ETH Zurich , Schmelzbergstrasse 9, CH-8092 Zurich, Switzerland
| | - Wye-Khay Fong
- Food and Soft Materials Science, Department of Health Science and Technology, ETH Zurich , Schmelzbergstrasse 9, CH-8092 Zurich, Switzerland
- Drug Delivery, Disposition and Dynamics, Monash Institute of Pharmaceutical Sciences, Monash University , 381 Royal Parade, Parkville, Victoria 3052, Australia
| | - Raffaele Mezzenga
- Food and Soft Materials Science, Department of Health Science and Technology, ETH Zurich , Schmelzbergstrasse 9, CH-8092 Zurich, Switzerland
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Electrostatics of the photosynthetic bacterial reaction center. Protonation of Glu L 212 and Asp L 213 — A new method of calculation. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2015. [DOI: 10.1016/j.bbabio.2015.07.010] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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25
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Tu Y, Peng F, Adawy A, Men Y, Abdelmohsen LKEA, Wilson DA. Mimicking the Cell: Bio-Inspired Functions of Supramolecular Assemblies. Chem Rev 2015; 116:2023-78. [DOI: 10.1021/acs.chemrev.5b00344] [Citation(s) in RCA: 211] [Impact Index Per Article: 23.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Yingfeng Tu
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - Fei Peng
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - Alaa Adawy
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - Yongjun Men
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - Loai K. E. A. Abdelmohsen
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - Daniela A. Wilson
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
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Milanovsky GE, Shuvalov VA, Semenov AY, Cherepanov DA. Elastic Vibrations in the Photosynthetic Bacterial Reaction Center Coupled to the Primary Charge Separation: Implications from Molecular Dynamics Simulations and Stochastic Langevin Approach. J Phys Chem B 2015; 119:13656-67. [PMID: 26148224 DOI: 10.1021/acs.jpcb.5b03036] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Primary electron transfer reactions in the bacterial reaction center are difficult for theoretical explication: the reaction kinetics, almost unalterable over a wide range of temperature and free energy changes, revealed oscillatory features observed initially by Shuvalov and coauthors (1997, 2002). Here the reaction mechanism was studied by molecular dynamics and analyzed within a phenomenological Langevin approach. The spectral function of polarization around the bacteriochlorophyll special pair PLPM and the dielectric response upon the formation of PL(+)PM(-) dipole within the special pair were calculated. The system response was approximated by Langevin oscillators; the respective frequencies, friction, and energy coupling coefficients were determined. The protein dynamics around PL and PM were distinctly asymmetric. The polarization around PL included slow modes with the frequency 30-80 cm(-1) and the total amplitude of 130 mV. Two main low-frequency modes of protein response around PM had frequencies of 95 and 155 cm(-1) and the total amplitude of 30 mV. In addition, a slowly damping mode with the frequency of 118 cm(-1) and the damping time >1.1 ps was coupled to the formation of PL(+)PM(-) dipole. It was attributed to elastic vibrations of α-helices in the vicinity of PLPM. The proposed trapping of P excitation energy in the form of the elastic vibrations can rationalize the observed properties of the primary electron transfer reactions, namely, the unusual temperature and ΔG dependences, the oscillating phenomena in kinetics, and the asymmetry of the charge separation reactions.
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Affiliation(s)
- Georgy E Milanovsky
- A. N. Belozersky Institute of Physical-Chemical Biology, Moscow State University , Leninskiye Gory, 119992 Moscow, Russia
| | - Vladimir A Shuvalov
- A. N. Belozersky Institute of Physical-Chemical Biology, Moscow State University , Leninskiye Gory, 119992 Moscow, Russia.,N. N. Semenov Institute of Chemical Physics, Russian Academy of Sciences , Kosygina st., 4, 117977 Moscow, Russia
| | - Alexey Yu Semenov
- A. N. Belozersky Institute of Physical-Chemical Biology, Moscow State University , Leninskiye Gory, 119992 Moscow, Russia.,N. N. Semenov Institute of Chemical Physics, Russian Academy of Sciences , Kosygina st., 4, 117977 Moscow, Russia
| | - Dmitry A Cherepanov
- A. N. Belozersky Institute of Physical-Chemical Biology, Moscow State University , Leninskiye Gory, 119992 Moscow, Russia.,A. N. Frumkin Institute of Physical Chemistry and Electrochemistry, Russian Academy of Sciences , 31, Leninsky Prospect, 119071 Moscow, Russia
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27
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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.
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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.
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28
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Wu P, Noland C, Ultsch M, Edwards B, Harris D, Mayer R, Harris SF. Developments in the Implementation of Acoustic Droplet Ejection for Protein Crystallography. ACTA ACUST UNITED AC 2015; 21:97-106. [PMID: 26275619 DOI: 10.1177/2211068215598938] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2015] [Indexed: 11/16/2022]
Abstract
Acoustic droplet ejection (ADE) enables crystallization experiments at the low-nanoliter scale, resulting in rapid vapor diffusion equilibration dynamics and efficient reagent usage in the empirical discovery of structure-enabling protein crystallization conditions. We extend our validation of this technology applied to the diverse physicochemical property space of aqueous crystallization reagents where dynamic fluid analysis coupled to ADE aids in accurate and precise dispensations. Addition of crystallization seed stocks, chemical additives, or small-molecule ligands effectively modulates crystallization, and we here provide examples in optimization of crystal morphology and diffraction quality by the acoustic delivery of ultra-small volumes of these cofactors. Additional applications are discussed, including set up of in situ proteolysis and alternate geometries of crystallization that leverage the small scale afforded by acoustic delivery. Finally, we describe parameters of a system of automation in which the acoustic liquid handler is integrated with a robotic arm, plate centrifuge, peeler, sealer, and stacks, which allows unattended high-throughput crystallization experimentation.
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Affiliation(s)
- Ping Wu
- Department of Structural Biology, Genentech, Inc, South San Francisco, CA, USA
| | - Cameron Noland
- Department of Structural Biology, Genentech, Inc, South San Francisco, CA, USA
| | - Mark Ultsch
- Department of Structural Biology, Genentech, Inc, South San Francisco, CA, USA
| | | | | | - Robert Mayer
- Department of Structural Biology, Genentech, Inc, South San Francisco, CA, USA
| | - Seth F Harris
- Department of Structural Biology, Genentech, Inc, South San Francisco, CA, USA
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Abstract
G protein-coupled receptors (GPCRs) are of particular importance for drug discovery, being the targets of many existing drugs, and being linked to many diseases where new therapies are required. However, as integral membrane proteins, they are generally unstable when removed from their membrane environment, precluding them from the wide range of structural and biophysical techniques which can be applied to soluble proteins such as kinases. Through the use of protein engineering methods, mutations can be identified which both increase the thermostability of GPCRs when purified in detergent, as well as biasing the receptor toward a specific physiologically relevant conformational state. The resultant stabilized receptor (known as a StaR) can be purified in multiple-milligram quantities, whilst retaining correct folding, thus enabling the generation of reagents suitable for a broad range of structural and biophysical studies. Example protocols for the purification of StaR proteins for analysis, ligand screening with the thiol-specific fluorochrome N-[4-(7-diethylamino-4-methyl-3-coumarinyl)phenyl]maleimide (CPM), surface plasmon resonance (SPR), and crystallization for structural studies are presented.
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Khvostichenko D, Schieferstein JM, Pawate AS, Laible PD, Kenis PJA. X-ray Transparent Microfluidic Chip for Mesophase-Based Crystallization of Membrane Proteins and On-Chip Structure Determination. CRYSTAL GROWTH & DESIGN 2014; 14:4886-4890. [PMID: 25285049 PMCID: PMC4181584 DOI: 10.1021/cg5011488] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2014] [Indexed: 05/23/2023]
Abstract
Crystallization from lipidic mesophase matrices is a promising route to diffraction-quality crystals and structures of membrane proteins. The microfluidic approach reported here eliminates two bottlenecks of the standard mesophase-based crystallization protocols: (i) manual preparation of viscous mesophases and (ii) manual harvesting of often small and fragile protein crystals. In the approach reported here, protein-loaded mesophases are formulated in an X-ray transparent microfluidic chip using only 60 nL of the protein solution per crystallization trial. The X-ray transparency of the chip enables diffraction data collection from multiple crystals residing in microfluidic wells, eliminating the normally required manual harvesting and mounting of individual crystals. We validated our approach by on-chip crystallization of photosynthetic reaction center, a membrane protein from Rhodobacter sphaeroides, followed by solving its structure to a resolution of 2.5 Å using X-ray diffraction data collected on-chip under ambient conditions. A moderate conformational change in hydrophilic chains of the protein was observed when comparing the on-chip, room temperature structure with known structures for which data were acquired under cryogenic conditions.
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Affiliation(s)
- Daria
S. Khvostichenko
- Department
of Chemical & Biomolecular Engineering, University of Illinois at Urbana−Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, United States
| | - Jeremy M. Schieferstein
- Department
of Chemical & Biomolecular Engineering, University of Illinois at Urbana−Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, United States
| | - Ashtamurthy S. Pawate
- Department
of Chemical & Biomolecular Engineering, University of Illinois at Urbana−Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, United States
| | - Philip D. Laible
- Biosciences
Division, Argonne National Laboratory, Argonne, Illinois 60439, United States
| | - Paul J. A. Kenis
- Department
of Chemical & Biomolecular Engineering, University of Illinois at Urbana−Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, United States
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31
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Liu W, Ishchenko A, Cherezov V. Preparation of microcrystals in lipidic cubic phase for serial femtosecond crystallography. Nat Protoc 2014; 9:2123-34. [PMID: 25122522 DOI: 10.1038/nprot.2014.141] [Citation(s) in RCA: 94] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
We have recently established a procedure for serial femtosecond crystallography (SFX) in lipidic cubic phase (LCP) for protein structure determination at X-ray free-electron lasers (XFELs). LCP-SFX uses the gel-like LCP as a matrix for growth and delivery of membrane protein microcrystals for crystallographic data collection. LCP is a liquid-crystalline mesophase composed of lipids and water. It provides a membrane-mimicking environment that stabilizes membrane proteins and supports their crystallization. Here we describe detailed procedures for the preparation and characterization of microcrystals for LCP-SFX applications. The advantages of LCP-SFX over traditional crystallographic methods include the capability of collecting room-temperature high-resolution data with minimal effects of radiation damage from sub-10-μm crystals of membrane and soluble proteins that are difficult to crystallize, while eliminating the need for crystal harvesting and cryo-cooling. Compared with SFX methods for microcrystals in solution using liquid injectors, LCP-SFX reduces protein consumption by 2-3 orders of magnitude for data collection at currently available XFELs. The whole procedure typically takes 3-5 d, including the time required for the crystals to grow.
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Affiliation(s)
- Wei Liu
- 1] Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, USA. [2] Jiangsu Key Laboratory of Marine Pharmaceutical Compound Screening and Marine Drug Research Institute, Huaihai Institute of Technology, Lianyungang, China
| | - Andrii Ishchenko
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, USA
| | - Vadim Cherezov
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, USA
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32
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Oka T, Hojo H. Single crystallization of an inverse bicontinuous cubic phase of a lipid. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2014; 30:8253-8257. [PMID: 25007349 DOI: 10.1021/la502002r] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
We report a simple method to produce a single crystal region of an inverse bicontinuous cubic (QII) phase of a lipid, 1-monoolein. By starting with the lipid of the sponge (L3) phase in the presence of 1,4-butanediol, we can obtain a single crystal region of the double-diamond QII phase in 1 week by controlled dilution of 1,4-butanediol. The length of the single crystal region in a 0.5 mm diameter capillary was on the order of millimeters. X-ray diffraction images of the region showed diffraction "spots", but not "rings" as in powder diffraction. The diffraction images also changed rotation angle dependently. We could assign Miller indices to all of the distinguishable diffraction spots from the region. This method would bring benefits to the basic and applied research areas of the Q phases.
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Affiliation(s)
- Toshihiko Oka
- Department of Physics, Graduate School of Science, §Nanomaterials Research Division, Research Institute of Electronics, and ‡Department of Physics, Faculty of Science, Shizuoka University , Shizuoka 422-8529, Japan
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33
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Johansson LC, Arnlund D, Katona G, White TA, Barty A, DePonte DP, Shoeman RL, Wickstrand C, Sharma A, Williams GJ, Aquila A, Bogan MJ, Caleman C, Davidsson J, Doak RB, Frank M, Fromme R, Galli L, Grotjohann I, Hunter MS, Kassemeyer S, Kirian RA, Kupitz C, Liang M, Lomb L, Malmerberg E, Martin AV, Messerschmidt M, Nass K, Redecke L, Seibert MM, Sjöhamn J, Steinbrener J, Stellato F, Wang D, Wahlgren WY, Weierstall U, Westenhoff S, Zatsepin NA, Boutet S, Spence JCH, Schlichting I, Chapman HN, Fromme P, Neutze R. Structure of a photosynthetic reaction centre determined by serial femtosecond crystallography. Nat Commun 2014; 4:2911. [PMID: 24352554 PMCID: PMC3905732 DOI: 10.1038/ncomms3911] [Citation(s) in RCA: 73] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2013] [Accepted: 11/08/2013] [Indexed: 11/22/2022] Open
Abstract
Serial femtosecond crystallography is an X-ray free-electron-laser-based method with considerable potential to have an impact on challenging problems in structural biology. Here we present X-ray diffraction data recorded from microcrystals of the Blastochloris viridis photosynthetic reaction centre to 2.8 Å resolution and determine its serial femtosecond crystallography structure to 3.5 Å resolution. Although every microcrystal is exposed to a dose of 33 MGy, no signs of X-ray-induced radiation damage are visible in this integral membrane protein structure. Serial femtosecond crystallography is an X-ray free-electron-laser-based method that uses X-ray bursts to determine protein structures. Here the authors present the structure of a photosynthetic reaction centre, an integral membrane protein, achieved with no sign of X-ray-induced radiation damage.
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Affiliation(s)
- Linda C Johansson
- Department of Chemistry and Molecular Biology, University of Gothenburg, 405 30 Gothenburg, Sweden
| | - David Arnlund
- Department of Chemistry and Molecular Biology, University of Gothenburg, 405 30 Gothenburg, Sweden
| | - Gergely Katona
- Department of Chemistry and Molecular Biology, University of Gothenburg, 405 30 Gothenburg, Sweden
| | - Thomas A White
- Center for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Anton Barty
- Center for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Daniel P DePonte
- Center for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Robert L Shoeman
- 1] Max-Planck-Institut für Medizinische Forschung, Jahnstrasse 29, 69120 Heidelberg, Germany [2] Max Planck Advanced Study Group, Center for Free-Electron Laser Science, Notkestrasse 85, 22607 Hamburg, Germany
| | - Cecilia Wickstrand
- Department of Chemistry and Molecular Biology, University of Gothenburg, 405 30 Gothenburg, Sweden
| | - Amit Sharma
- Department of Chemistry and Molecular Biology, University of Gothenburg, 405 30 Gothenburg, Sweden
| | - Garth J Williams
- Linac Coherent Light Source, LCLS, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, 94025 California, USA
| | - Andrew Aquila
- Center for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Michael J Bogan
- PULSE Institute, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, 94025 California, USA
| | - Carl Caleman
- Center for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Jan Davidsson
- Department of Chemistry-Ångström Laboratory, Uppsala University, Box 523, 75120 Uppsala, Sweden
| | - R Bruce Doak
- Department of Physics, Arizona State University, Tempe, 85287 Arizona, USA
| | - Matthias Frank
- Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, 94550 California, USA
| | - Raimund Fromme
- Department of Chemistry and Biochemistry, Arizona State University, Tempe, 85287-1604 Arizona, USA
| | - Lorenzo Galli
- 1] Center for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany [2] Department of Physics, University of Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Ingo Grotjohann
- Department of Chemistry and Biochemistry, Arizona State University, Tempe, 85287-1604 Arizona, USA
| | - Mark S Hunter
- Department of Chemistry and Biochemistry, Arizona State University, Tempe, 85287-1604 Arizona, USA
| | - Stephan Kassemeyer
- 1] Max-Planck-Institut für Medizinische Forschung, Jahnstrasse 29, 69120 Heidelberg, Germany [2] Max Planck Advanced Study Group, Center for Free-Electron Laser Science, Notkestrasse 85, 22607 Hamburg, Germany
| | - Richard A Kirian
- Department of Physics, Arizona State University, Tempe, 85287 Arizona, USA
| | - Christopher Kupitz
- Department of Chemistry and Biochemistry, Arizona State University, Tempe, 85287-1604 Arizona, USA
| | - Mengning Liang
- Center for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Lukas Lomb
- 1] Max-Planck-Institut für Medizinische Forschung, Jahnstrasse 29, 69120 Heidelberg, Germany [2] Max Planck Advanced Study Group, Center for Free-Electron Laser Science, Notkestrasse 85, 22607 Hamburg, Germany
| | - Erik Malmerberg
- Department of Chemistry and Molecular Biology, University of Gothenburg, 405 30 Gothenburg, Sweden
| | - Andrew V Martin
- Center for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Marc Messerschmidt
- Linac Coherent Light Source, LCLS, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, 94025 California, USA
| | - Karol Nass
- 1] Center for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany [2] Department of Physics, University of Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Lars Redecke
- Joint Laboratory for Structural Biology of Infection and Inflammation, Institute of Biochemistry and Molecular Biology, University of Hamburg and Institute of Biochemistry, University of Lübeck at DESY, 22607 Hamburg, Germany
| | - M Marvin Seibert
- Linac Coherent Light Source, LCLS, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, 94025 California, USA
| | - Jennie Sjöhamn
- Department of Chemistry and Molecular Biology, University of Gothenburg, 405 30 Gothenburg, Sweden
| | - Jan Steinbrener
- 1] Max-Planck-Institut für Medizinische Forschung, Jahnstrasse 29, 69120 Heidelberg, Germany [2] Max Planck Advanced Study Group, Center for Free-Electron Laser Science, Notkestrasse 85, 22607 Hamburg, Germany
| | - Francesco Stellato
- Center for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Dingjie Wang
- Department of Physics, Arizona State University, Tempe, 85287 Arizona, USA
| | - Weixaio Y Wahlgren
- Department of Chemistry and Molecular Biology, University of Gothenburg, 405 30 Gothenburg, Sweden
| | - Uwe Weierstall
- Department of Physics, Arizona State University, Tempe, 85287 Arizona, USA
| | - Sebastian Westenhoff
- Department of Chemistry and Molecular Biology, University of Gothenburg, 405 30 Gothenburg, Sweden
| | - Nadia A Zatsepin
- Department of Physics, Arizona State University, Tempe, 85287 Arizona, USA
| | - Sébastien Boutet
- Linac Coherent Light Source, LCLS, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, 94025 California, USA
| | - John C H Spence
- Department of Physics, Arizona State University, Tempe, 85287 Arizona, USA
| | - Ilme Schlichting
- 1] Max-Planck-Institut für Medizinische Forschung, Jahnstrasse 29, 69120 Heidelberg, Germany [2] Max Planck Advanced Study Group, Center for Free-Electron Laser Science, Notkestrasse 85, 22607 Hamburg, Germany
| | - Henry N Chapman
- 1] Center for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany [2] Department of Physics, University of Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Petra Fromme
- Department of Chemistry and Biochemistry, Arizona State University, Tempe, 85287-1604 Arizona, USA
| | - Richard Neutze
- Department of Chemistry and Molecular Biology, University of Gothenburg, 405 30 Gothenburg, Sweden
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Feld GK, Frank M. Enabling membrane protein structure and dynamics with X-ray free electron lasers. Curr Opin Struct Biol 2014; 27:69-78. [PMID: 24930119 DOI: 10.1016/j.sbi.2014.05.002] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2014] [Revised: 05/09/2014] [Accepted: 05/12/2014] [Indexed: 10/25/2022]
Abstract
Determining the three-dimensional structures and dynamics of membrane proteins remains one of the great challenges of modern biology. The recent availability of X-ray free electron laser (XFEL) light sources has opened the door to a new and revolutionary approach to performing X-ray analysis of these important biomolecules. Recent advances in sample delivery, data reduction, and phasing have enabled the high-resolution structural probing of membrane proteins at room temperature. While considerable challenges remain, the recent developments described in this review may ultimately provide structural biologists with powerful tools for obtaining unprecedented atomic-scale and dynamic visualization of membrane proteins at near-physiological conditions.
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Affiliation(s)
- Geoffrey K Feld
- Biosciences and Biotechnology Division, Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Matthias Frank
- Physics Division, Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA.
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35
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Zheng X, Dong S, Zheng J, Li D, Li F, Luo Z. Expression, stabilization and purification of membrane proteins via diverse protein synthesis systems and detergents involving cell-free associated with self-assembly peptide surfactants. Biotechnol Adv 2014; 32:564-74. [PMID: 24566241 DOI: 10.1016/j.biotechadv.2014.02.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2013] [Revised: 06/13/2013] [Accepted: 02/17/2014] [Indexed: 12/21/2022]
Abstract
G-protein coupled receptors (GPCRs) are involved in regulating most of physiological actions and metabolism in the bodies, which have become most frequently addressed therapeutic targets for various disorders and diseases. Purified GPCR-based drug discoveries have become routine that approaches to structural study, novel biophysical and biochemical function analyses. However, several bottlenecks that GPCR-directed drugs need to conquer the problems including overexpression, solubilization, and purification as well as stabilization. The breakthroughs are to obtain efficient protein yield and stabilize their functional conformation which are both urgently requiring of effective protein synthesis system methods and optimal surfactants. Cell-free protein synthesis system is superior to the high yields and post-translation modifications, and early signs of self-assembly peptide detergents also emerged to superiority in purification of membrane proteins. We herein focus several predominant protein synthesis systems and surfactants involving the novel peptide detergents, and uncover the advantages of cell-free protein synthesis system with self-assembling peptide detergents in purification of functional GPCRs. This review is useful to further study in membrane proteins as well as the new drug exploration.
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Affiliation(s)
- Xuan Zheng
- College of Basic Medical Sciences, Molecular Medicine and Cancer Research Center, Chongqing Medical University, Chongqing, China
| | - Shuangshuang Dong
- College of Basic Medical Sciences, Molecular Medicine and Cancer Research Center, Chongqing Medical University, Chongqing, China
| | - Jie Zheng
- College of laboratory Medicine, Chongqing Medical University, Chongqing, China
| | - Duanhua Li
- Sichuan Industrial Institute of Antibiotics, Chengdu University, Chengdu, China
| | - Feng Li
- China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute, Zhengzhou, China
| | - Zhongli Luo
- College of Basic Medical Sciences, Molecular Medicine and Cancer Research Center, Chongqing Medical University, Chongqing, China.
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36
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Buschmann S, Richers S, Ermler U, Michel H. A decade of crystallization drops: crystallization of the cbb3 cytochrome c oxidase from Pseudomonas stutzeri. Protein Sci 2014; 23:411-22. [PMID: 24488923 DOI: 10.1002/pro.2423] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2013] [Revised: 01/08/2014] [Accepted: 01/09/2014] [Indexed: 11/11/2022]
Abstract
The cbb3 cytochrome c oxidases are distant members of the superfamily of heme copper oxidases. These terminal oxidases couple O2 reduction with proton transport across the plasma membrane and, as a part of the respiratory chain, contribute to the generation of an electrochemical proton gradient. Compared with other structurally characterized members of the heme copper oxidases, the recently determined cbb3 oxidase structure at 3.2 Å resolution revealed significant differences in the electron supply system, the proton conducting pathways and the coupling of O2 reduction to proton translocation. In this paper, we present a detailed report on the key steps for structure determination. Improvement of the protein quality was achieved by optimization of the number of lipids attached to the protein as well as the separation of two cbb3 oxidase isoenzymes. The exchange of n-dodecyl-β-D-maltoside for a precisely defined mixture of two α-maltosides and decanoylsucrose as well as the choice of the crystallization method had a most profound impact on crystal quality. This report highlights problems frequently encountered in membrane protein crystallization and offers meaningful approaches to improve crystal quality.
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Affiliation(s)
- Sabine Buschmann
- Molecular Membrane Biology, Max Planck Institute of Biophysics, Frankfurt am Main, Max-von-Laue-Str.3, D-60438, Germany
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Lundholm I, Wahlgren WY, Piccirilli F, Di Pietro P, Duelli A, Berntsson O, Lupi S, Perucchi A, Katona G. Terahertz absorption of illuminated photosynthetic reaction center solution: a signature of photoactivation? RSC Adv 2014. [DOI: 10.1039/c4ra03787a] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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Moraes I, Evans G, Sanchez-Weatherby J, Newstead S, Stewart PDS. Membrane protein structure determination - the next generation. BIOCHIMICA ET BIOPHYSICA ACTA 2014; 1838:78-87. [PMID: 23860256 PMCID: PMC3898769 DOI: 10.1016/j.bbamem.2013.07.010] [Citation(s) in RCA: 160] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/29/2013] [Revised: 06/28/2013] [Accepted: 07/07/2013] [Indexed: 11/19/2022]
Abstract
The field of Membrane Protein Structural Biology has grown significantly since its first landmark in 1985 with the first three-dimensional atomic resolution structure of a membrane protein. Nearly twenty-six years later, the crystal structure of the beta2 adrenergic receptor in complex with G protein has contributed to another landmark in the field leading to the 2012 Nobel Prize in Chemistry. At present, more than 350 unique membrane protein structures solved by X-ray crystallography (http://blanco.biomol.uci.edu/mpstruc/exp/list, Stephen White Lab at UC Irvine) are available in the Protein Data Bank. The advent of genomics and proteomics initiatives combined with high-throughput technologies, such as automation, miniaturization, integration and third-generation synchrotrons, has enhanced membrane protein structure determination rate. X-ray crystallography is still the only method capable of providing detailed information on how ligands, cofactors, and ions interact with proteins, and is therefore a powerful tool in biochemistry and drug discovery. Yet the growth of membrane protein crystals suitable for X-ray diffraction studies amazingly remains a fine art and a major bottleneck in the field. It is often necessary to apply as many innovative approaches as possible. In this review we draw attention to the latest methods and strategies for the production of suitable crystals for membrane protein structure determination. In addition we also highlight the impact that third-generation synchrotron radiation has made in the field, summarizing the latest strategies used at synchrotron beamlines for screening and data collection from such demanding crystals. This article is part of a Special Issue entitled: Structural and biophysical characterisation of membrane protein-ligand binding.
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Affiliation(s)
- Isabel Moraes
- Department of Life Sciences, Imperial College London, London SW7 2AZ, UK; Membrane Protein Laboratory, Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, UK; Research Complex at Harwell Rutherford Appleton Laboratory, Harwell Science and Innovation Campus, Didcot OX11 0FA, UK.
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Evenbratt H, Nordstierna L, Ericson MB, Engström S. Cubic and sponge phases in ether lipid-solvent-water ternary systems: phase behavior and NMR characterization. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2013; 29:13058-13065. [PMID: 24060205 DOI: 10.1021/la402732a] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
The phase behavior of 1-glyceryl monoleyl ether (GME) in mixtures of water and the solvents 1,5-pentanediol (POL) or N-methyl-2-pyrrolidone (NMP) was investigated by ocular inspection, polarization microscopy, and small-angle X-ray diffraction (SAXD). Phase diagrams were constructed based on analyses of more than 200 samples prepared using the two different solvents at 20 °C. The inverse hexagonal phase formed by GME in excess of water was transformed into the cubic and sponge phase with the increasing amount of each solvent. Particularly POL allowed for the formation of an extended sponge phase area in the phase diagram, comprising up to 70% POL-water mixture. The phase behavior using NMP was found to be similar to the earlier investigated solvent propylene glycol. The extended sponge phase for the POL system was attributed to POLs strong surface/interfacial activity with the potential to stabilize the polar/apolar interface of the sponge phase. The cubic and sponge phases formed using POL were further studied by NMR in order to measure the partitioning of POL between the lipid and aqueous domains of the phases. The domain partition coefficient K (lipid domain/aqueous domain) for POL in cubic and sponge phases was found to be 0.78 ± 0.14 and constant for the two phases.
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Affiliation(s)
- Hanne Evenbratt
- Department of Chemical and Biological Engineering, Pharmaceutical Technology, Chalmers University of Technology , SE-41296 Gothenburg, Sweden
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Krauss IR, Merlino A, Vergara A, Sica F. An overview of biological macromolecule crystallization. Int J Mol Sci 2013; 14:11643-91. [PMID: 23727935 PMCID: PMC3709751 DOI: 10.3390/ijms140611643] [Citation(s) in RCA: 87] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2013] [Revised: 05/08/2013] [Accepted: 05/20/2013] [Indexed: 12/11/2022] Open
Abstract
The elucidation of the three dimensional structure of biological macromolecules has provided an important contribution to our current understanding of many basic mechanisms involved in life processes. This enormous impact largely results from the ability of X-ray crystallography to provide accurate structural details at atomic resolution that are a prerequisite for a deeper insight on the way in which bio-macromolecules interact with each other to build up supramolecular nano-machines capable of performing specialized biological functions. With the advent of high-energy synchrotron sources and the development of sophisticated software to solve X-ray and neutron crystal structures of large molecules, the crystallization step has become even more the bottleneck of a successful structure determination. This review introduces the general aspects of protein crystallization, summarizes conventional and innovative crystallization methods and focuses on the new strategies utilized to improve the success rate of experiments and increase crystal diffraction quality.
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Affiliation(s)
- Irene Russo Krauss
- Department of Chemical Sciences, University of Naples Federico II, Complesso Universitario di Monte Sant’Angelo, Via Cintia, Napoli I-80126, Italy; E-Mails: (I.R.K.); (A.M.); (A.V.)
| | - Antonello Merlino
- Department of Chemical Sciences, University of Naples Federico II, Complesso Universitario di Monte Sant’Angelo, Via Cintia, Napoli I-80126, Italy; E-Mails: (I.R.K.); (A.M.); (A.V.)
- Institute of Biostructures and Bioimages, C.N.R, Via Mezzocannone 16, Napoli I-80134, Italy
| | - Alessandro Vergara
- Department of Chemical Sciences, University of Naples Federico II, Complesso Universitario di Monte Sant’Angelo, Via Cintia, Napoli I-80126, Italy; E-Mails: (I.R.K.); (A.M.); (A.V.)
- Institute of Biostructures and Bioimages, C.N.R, Via Mezzocannone 16, Napoli I-80134, Italy
| | - Filomena Sica
- Department of Chemical Sciences, University of Naples Federico II, Complesso Universitario di Monte Sant’Angelo, Via Cintia, Napoli I-80126, Italy; E-Mails: (I.R.K.); (A.M.); (A.V.)
- Institute of Biostructures and Bioimages, C.N.R, Via Mezzocannone 16, Napoli I-80134, Italy
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +39-81-674-479; Fax: +39-81-674-090
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Kang HJ, Lee C, Drew D. Breaking the barriers in membrane protein crystallography. Int J Biochem Cell Biol 2013; 45:636-44. [DOI: 10.1016/j.biocel.2012.12.018] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2012] [Revised: 12/03/2012] [Accepted: 12/21/2012] [Indexed: 10/27/2022]
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42
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Kulichikhin VG, Yampolskaya GP. Colloid-chemical aspects of protein crystallization. Russ Chem Bull 2013. [DOI: 10.1007/s11172-013-0045-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/03/2023]
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43
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Recent Developments in the Production, Analysis, and Applications of Cubic Phases Formed by Lipids. ACTA ACUST UNITED AC 2013. [DOI: 10.1016/b978-0-12-411515-6.00006-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
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44
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Effects of dehydration on light-induced conformational changes in bacterial photosynthetic reaction centers probed by optical and differential FTIR spectroscopy. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2012; 1827:328-39. [PMID: 23103449 DOI: 10.1016/j.bbabio.2012.10.009] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2012] [Revised: 10/16/2012] [Accepted: 10/19/2012] [Indexed: 11/22/2022]
Abstract
Following light-induced electron transfer between the primary donor (P) and quinone acceptor (Q(A)) the bacterial photosynthetic reaction center (RC) undergoes conformational relaxations which stabilize the primary charge separated state P(+)Q(A)(-). Dehydration of RCs from Rhodobacter sphaeroides hinders these conformational dynamics, leading to acceleration of P(+)Q(A)(-) recombination kinetics [Malferrari et al., J. Phys. Chem. B 115 (2011) 14732-14750]. To clarify the structural basis of the conformational relaxations and the involvement of bound water molecules, we analyzed light-induced P(+)Q(A)(-)/PQ(A) difference FTIR spectra of RC films at two hydration levels (relative humidity r=76% and r=11%). Dehydration reduced the amplitude of bands in the 3700-3550cm(-1) region, attributed to water molecules hydrogen bonded to the RC, previously proposed to stabilize the charge separation by dielectric screening [Iwata et al., Biochemistry 48 (2009) 1220-1229]. Other features of the FTIR difference spectrum were affected by partial depletion of the hydration shell (r=11%), including contributions from modes of P (9-keto groups), and from NH or OH stretching modes of amino acidic residues, absorbing in the 3550-3150cm(-1) range, a region so far not examined in detail for bacterial RCs. To probe in parallel the effects of dehydration on the RC conformational relaxations, we analyzed by optical absorption spectroscopy the kinetics of P(+)Q(A)(-) recombination following the same photoexcitation used in FTIR measurements (20s continuous illumination). The results suggest a correlation between the observed FTIR spectral changes and the conformational rearrangements which, in the hydrated system, strongly stabilize the P(+)Q(A)(-) charge separated state over the second time scale.
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Kulkarni CV. Lipid crystallization: from self-assembly to hierarchical and biological ordering. NANOSCALE 2012; 4:5779-91. [PMID: 22899223 DOI: 10.1039/c2nr31465g] [Citation(s) in RCA: 97] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Lipid crystallization is ubiquitous in nature, observed in biological structures as well as in commercial products and applications. In a dehydrated state most of the lipids form well ordered crystals, whereas in an aqueous environment they self-assemble into various crystalline, liquid crystalline or sometimes macroscopically disordered phases. Lipid self-organization extends further to hierarchical levels including structured emulsions and nanostructured particles. Many consumer products including cosmetics, foods and medicines account for such lipid architectures. Cell membranes primarily consist of planar lipid bilayers; however sub-cellular biomembranes are more of a convoluted type. Some of the biological entities have lipids in truly crystalline form; yet liquid crystalline lipid phases are prevalent, in general. Crystallization of fats - triglyceride lipids - has been relatively well documented and reviewed more often, but this review features other areas where lipid organization is crucial and diverse. Some recent advances along with a few explicit examples of model lipid phases and biological evidences are also reported.
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Affiliation(s)
- Chandrashekhar V Kulkarni
- Biological and Soft Systems, Cavendish Laboratory, University of Cambridge, J. J. Thomson Avenue, Cambridge CB3 0HE, UK.
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Parker JL, Newstead S. Current trends in α-helical membrane protein crystallization: an update. Protein Sci 2012; 21:1358-65. [PMID: 22811290 DOI: 10.1002/pro.2122] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2012] [Revised: 06/22/2012] [Accepted: 07/05/2012] [Indexed: 11/10/2022]
Abstract
α-Helical membrane proteins (MPs) are the targets for many pharmaceutical drugs and play important roles in human physiology. In recent years, significant progress has been made in determining their atomic structure using X-ray crystallography. However, a major bottleneck in MP crystallography still remains, namely, the identification of conditions that give crystals that are suitable for structural determination. In 2008, we undertook an analysis of the crystallization conditions for 121 α-helical MPs to design a rationalized sparse matrix crystallization screen, MemGold. We now report an updated analysis that includes a further 133 conditions. The results reveal the current trends in α-helical MP crystallization with notable differences since 2008. The updated information has been used to design new crystallization and additive screens that should prove useful for both initial crystallization scouting and subsequent crystal optimization.
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Affiliation(s)
- Joanne L Parker
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, United Kingdom
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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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Kubicek J, Schlesinger R, Baeken C, Büldt G, Schäfer F, Labahn J. Controlled in meso phase crystallization--a method for the structural investigation of membrane proteins. PLoS One 2012; 7:e35458. [PMID: 22536388 PMCID: PMC3334905 DOI: 10.1371/journal.pone.0035458] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2011] [Accepted: 03/18/2012] [Indexed: 11/19/2022] Open
Abstract
We investigated in meso crystallization of membrane proteins to develop a fast screening technology which combines features of the well established classical vapor diffusion experiment with the batch meso phase crystallization, but without premixing of protein and monoolein. It inherits the advantages of both methods, namely (i) the stabilization of membrane proteins in the meso phase, (ii) the control of hydration level and additive concentration by vapor diffusion. The new technology (iii) significantly simplifies in meso crystallization experiments and allows the use of standard liquid handling robots suitable for 96 well formats. CIMP crystallization furthermore allows (iv) direct monitoring of phase transformation and crystallization events. Bacteriorhodopsin (BR) crystals of high quality and diffraction up to 1.3 Å resolution have been obtained in this approach. CIMP and the developed consumables and protocols have been successfully applied to obtain crystals of sensory rhodopsin II (SRII) from Halobacterium salinarum for the first time.
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Affiliation(s)
| | - Ramona Schlesinger
- Molecular Biophysics, Institute of Structural Biology and Biophysics (ISB-2), Research Center Jülich, Jülich, Germany
| | - Christian Baeken
- Molecular Biophysics, Institute of Structural Biology and Biophysics (ISB-2), Research Center Jülich, Jülich, Germany
| | - Georg Büldt
- Molecular Biophysics, Institute of Structural Biology and Biophysics (ISB-2), Research Center Jülich, Jülich, Germany
| | | | - Jörg Labahn
- Molecular Biophysics, Institute of Structural Biology and Biophysics (ISB-2), Research Center Jülich, Jülich, Germany
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HU YT, ZHANG CY, MA XL, YIN DC. Progresses on Crystallization Methodology of Membrane Proteins*. PROG BIOCHEM BIOPHYS 2012. [DOI: 10.3724/sp.j.1206.2011.00235] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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50
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Lipidic phase membrane protein serial femtosecond crystallography. Nat Methods 2012; 9:263-5. [PMID: 22286383 DOI: 10.1038/nmeth.1867] [Citation(s) in RCA: 119] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2011] [Accepted: 12/16/2011] [Indexed: 11/08/2022]
Abstract
X-ray free electron laser (X-FEL)-based serial femtosecond crystallography is an emerging method with potential to rapidly advance the challenging field of membrane protein structural biology. Here we recorded interpretable diffraction data from micrometer-sized lipidic sponge phase crystals of the Blastochloris viridis photosynthetic reaction center delivered into an X-FEL beam using a sponge phase micro-jet.
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