Literature DB >> 22783824

Membrane protein structure determination using crystallography and lipidic mesophases: recent advances and successes.

Martin Caffrey1, Dianfan Li, Abhiram Dukkipati.   

Abstract

The crystal structure of the β(2)-adrenergic receptor in complex with an agonist and its cognate G protein has just recently been determined. It is now possible to explore in molecular detail the means by which this paradigmatic transmembrane receptor binds agonist, communicates the impulse or signaling event across the membrane, and sets in motion a series of G protein-directed intracellular responses. The structure was determined using crystals of the ternary complex grown in a rationally designed lipidic mesophase by the so-called in meso method. The method is proving to be particularly useful in the G protein-coupled receptor field where the structures of 13 distinct receptor types have been determined in the past 5 years. In addition to receptors, the method has proven to be useful with a wide variety of integral membrane protein classes that include bacterial and eukaryotic rhodopsins, light-harvesting complex II (LHII), photosynthetic reaction centers, cytochrome oxidases, β-barrels, an exchanger, and an integral membrane peptide. This attests to the versatility and range of the method and supports the view that the in meso method should be included in the arsenal of the serious membrane structural biologist. For this to happen, however, the reluctance to adopt it attributable, in part, to the anticipated difficulties associated with handling the sticky, viscous cubic mesophase in which crystals grow must be overcome. Harvesting and collecting diffraction data with the mesophase-grown crystals are also viewed with some trepidation. It is acknowledged that there are challenges associated with the method. Over the years, we have endeavored to establish how the method works at a molecular level and to make it user-friendly. To these ends, tools for handling the mesophase in the pico- to nanoliter volume range have been developed for highly efficient crystallization screening in manual and robotic modes. Methods have been implemented for evaluating the functional activity of membrane proteins reconstituted into the bilayer of the cubic phase as a prelude to crystallogenesis. Glass crystallization plates that provide unparalleled optical quality and sensitivity to nascent crystals have been built. Lipid and precipitant screens have been designed for a more rational approach to crystallogenesis such that the method can now be applied to an even wider variety of membrane protein types. In this work, these assorted advances are outlined along with a summary of the membrane proteins that have yielded to the method. The prospects for and the challenges that must be overcome to further develop the method are described.

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Year:  2012        PMID: 22783824      PMCID: PMC3461499          DOI: 10.1021/bi300010w

Source DB:  PubMed          Journal:  Biochemistry        ISSN: 0006-2960            Impact factor:   3.162


  133 in total

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Journal:  Chem Phys Lipids       Date:  1999-07       Impact factor: 3.329

3.  Rational design of lipid for membrane protein crystallization.

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Journal:  J Struct Biol       Date:  2004-11       Impact factor: 2.867

4.  X-ray structures of LeuT in substrate-free outward-open and apo inward-open states.

Authors:  Harini Krishnamurthy; Eric Gouaux
Journal:  Nature       Date:  2012-01-09       Impact factor: 49.962

5.  Crystallizing membrane proteins for structure-function studies using lipidic mesophases.

Authors:  Martin Caffrey
Journal:  Biochem Soc Trans       Date:  2011-06       Impact factor: 5.407

Review 6.  Nanobody stabilization of G protein-coupled receptor conformational states.

Authors:  Jan Steyaert; Brian K Kobilka
Journal:  Curr Opin Struct Biol       Date:  2011-07-21       Impact factor: 6.809

7.  In meso crystal structure and docking simulations suggest an alternative proteoglycan binding site in the OpcA outer membrane adhesin.

Authors:  Vadim Cherezov; Wei Liu; Jeremy P Derrick; Binquan Luan; Aleksei Aksimentiev; Vsevolod Katritch; Martin Caffrey
Journal:  Proteins       Date:  2008-04

8.  A lipidic-sponge phase screen for membrane protein crystallization.

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Journal:  Structure       Date:  2008-07       Impact factor: 5.006

9.  Agonist-bound adenosine A2A receptor structures reveal common features of GPCR activation.

Authors:  Guillaume Lebon; Tony Warne; Patricia C Edwards; Kirstie Bennett; Christopher J Langmead; Andrew G W Leslie; Christopher G Tate
Journal:  Nature       Date:  2011-05-18       Impact factor: 49.962

10.  Mass spectrometry of membrane transporters reveals subunit stoichiometry and interactions.

Authors:  Nelson P Barrera; Shoshanna C Isaacson; Min Zhou; Vassiliy N Bavro; Alex Welch; Theresia A Schaedler; Markus A Seeger; Ricardo Núñez Miguel; Vladimir M Korkhov; Hendrik W van Veen; Henrietta Venter; Adrian R Walmsley; Christopher G Tate; Carol V Robinson
Journal:  Nat Methods       Date:  2009-07-05       Impact factor: 28.547

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  45 in total

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Authors:  Hyoung Eun Bae; Cristina Cecchetti; Yang Du; Satoshi Katsube; Jonas S Mortensen; Weijiao Huang; Shahid Rehan; Ho Jin Lee; Claus J Loland; Lan Guan; Brian K Kobilka; Bernadette Byrne; Pil Seok Chae
Journal:  Acta Biomater       Date:  2020-06-06       Impact factor: 8.947

2.  Host Lipid and Temperature as Important Screening Variables for Crystallizing Integral Membrane Proteins in Lipidic Mesophases. Trials with Diacylglycerol Kinase.

Authors:  Dianfan Li; Syed T A Shah; Martin Caffrey
Journal:  Cryst Growth Des       Date:  2013-07-03       Impact factor: 4.076

3.  Novel tripod amphiphiles for membrane protein analysis.

Authors:  Pil Seok Chae; Andrew C Kruse; Kamil Gotfryd; Rohini R Rana; Kyung Ho Cho; Søren G F Rasmussen; Hyoung Eun Bae; Richa Chandra; Ulrik Gether; Lan Guan; Brian K Kobilka; Claus J Loland; Bernadette Byrne; Samuel H Gellman
Journal:  Chemistry       Date:  2013-10-02       Impact factor: 5.236

4.  Maltose neopentyl glycol-3 (MNG-3) analogues for membrane protein study.

Authors:  Kyung Ho Cho; Mohd Husri; Anowarul Amin; Kamil Gotfryd; Ho Jin Lee; Juyeon Go; Jin Woong Kim; Claus J Loland; Lan Guan; Bernadette Byrne; Pil Seok Chae
Journal:  Analyst       Date:  2015-03-27       Impact factor: 4.616

5.  Surfactant bilayers maintain transmembrane protein activity.

Authors:  Gamal Rayan; Vladimir Adrien; Myriam Reffay; Martin Picard; Arnaud Ducruix; Marc Schmutz; Wladimir Urbach; Nicolas Taulier
Journal:  Biophys J       Date:  2014-09-02       Impact factor: 4.033

6.  Cloning, expression, purification, crystallization and preliminary X-ray diffraction of a lysine-specific permease from Pseudomonas aeruginosa.

Authors:  Emmanuel Nji; Dianfan Li; Declan A Doyle; Martin Caffrey
Journal:  Acta Crystallogr F Struct Biol Commun       Date:  2014-09-25       Impact factor: 1.056

7.  The lipid cubic phase or in meso method for crystallizing proteins. Bushings for better manual dispensing.

Authors:  Martin Caffrey; Robert Eifert; Dianfan Li; Nicole Howe
Journal:  J Appl Crystallogr       Date:  2014-08-16       Impact factor: 3.304

8.  Exploring the in meso crystallization mechanism by characterizing the lipid mesophase microenvironment during the growth of single transmembrane α-helical peptide crystals.

Authors:  Leonie van 't Hag; Konstantin Knoblich; Shane A Seabrook; Nigel M Kirby; Stephen T Mudie; Deborah Lau; Xu Li; Sally L Gras; Xavier Mulet; Matthew E Call; Melissa J Call; Calum J Drummond; Charlotte E Conn
Journal:  Philos Trans A Math Phys Eng Sci       Date:  2016-07-28       Impact factor: 4.226

9.  Serial femtosecond crystallography of G protein-coupled receptors.

Authors:  Wei Liu; Daniel Wacker; Cornelius Gati; Gye Won Han; Daniel James; Dingjie Wang; Garrett Nelson; Uwe Weierstall; Vsevolod Katritch; Anton Barty; Nadia A Zatsepin; Dianfan Li; Marc Messerschmidt; Sébastien Boutet; Garth J Williams; Jason E Koglin; M Marvin Seibert; Chong Wang; Syed T A Shah; Shibom Basu; Raimund Fromme; Christopher Kupitz; Kimberley N Rendek; Ingo Grotjohann; Petra Fromme; Richard A Kirian; Kenneth R Beyerlein; Thomas A White; Henry N Chapman; Martin Caffrey; John C H Spence; Raymond C Stevens; Vadim Cherezov
Journal:  Science       Date:  2013-12-20       Impact factor: 47.728

10.  Structure Determination from Lipidic Cubic Phase Embedded Microcrystals by MicroED.

Authors:  Lan Zhu; Guanhong Bu; Liang Jing; Dan Shi; Ming-Yue Lee; Tamir Gonen; Wei Liu; Brent L Nannenga
Journal:  Structure       Date:  2020-07-30       Impact factor: 5.006

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