Literature DB >> 33340490

A 10-year meta-analysis of membrane protein structural biology: Detergents, membrane mimetics, and structure determination techniques.

Brendon C Choy1, Rosemary J Cater1, Filippo Mancia2, Edward E Pryor3.   

Abstract

Structure determination of membrane proteins is critical to the molecular understanding of many life processes, yet it has historically been a technically challenging endeavor. This past decade has given rise to a number of technological advancements, techniques, and reagents, which have facilitated membrane protein structural biology, resulting in an ever-growing number of membrane protein structures determined. To collate these advances, we have mined available literature to analyze the purification and structure determination specifics for all uniquely solved membrane protein structures from 2010 to 2019. Our analyses demonstrate the strong impact of single-particle cryo-electron microscopy on the field and illustrate how this technique has affected detergent and membrane mimetic usage. Furthermore, we detail how different structure determination methods, taxonomic domains and protein classes have unique detergent/membrane mimetic profiles, highlighting the importance of tailoring their selection. Our analyses provide a quantitative overview of where the field of membrane protein structural biology stands and how it has developed over time. We anticipate that these will serve as a useful tool to streamline future membrane protein structure determination by guiding the choice of detergent/membrane mimetic.
Copyright © 2020 Elsevier B.V. All rights reserved.

Entities:  

Keywords:  Amphipols; Detergent mimetics; Detergents; Membrane proteins; Nanodiscs; Single-particle cryo-electron microscopy; Structural biology; X-ray crystallography

Mesh:

Substances:

Year:  2020        PMID: 33340490      PMCID: PMC7856071          DOI: 10.1016/j.bbamem.2020.183533

Source DB:  PubMed          Journal:  Biochim Biophys Acta Biomembr        ISSN: 0005-2736            Impact factor:   3.747


  55 in total

1.  Lipid Nanodiscs as a Tool for High-Resolution Structure Determination of Membrane Proteins by Single-Particle Cryo-EM.

Authors:  Rouslan G Efremov; Christos Gatsogiannis; Stefan Raunser
Journal:  Methods Enzymol       Date:  2017-07-19       Impact factor: 1.600

2.  Fluorescence-detection size-exclusion chromatography for precrystallization screening of integral membrane proteins.

Authors:  Toshimitsu Kawate; Eric Gouaux
Journal:  Structure       Date:  2006-04       Impact factor: 5.006

3.  Amphipols: polymers that keep membrane proteins soluble in aqueous solutions.

Authors:  C Tribet; R Audebert; J L Popot
Journal:  Proc Natl Acad Sci U S A       Date:  1996-12-24       Impact factor: 11.205

Review 4.  How cryo-electron microscopy and X-ray crystallography complement each other.

Authors:  Hong-Wei Wang; Jia-Wei Wang
Journal:  Protein Sci       Date:  2016-09-07       Impact factor: 6.725

5.  Applications of phospholipid bilayer nanodiscs in the study of membranes and membrane proteins.

Authors:  Abhinav Nath; William M Atkins; Stephen G Sligar
Journal:  Biochemistry       Date:  2007-01-31       Impact factor: 3.162

Review 6.  Single-Particle Cryo-EM at Crystallographic Resolution.

Authors:  Yifan Cheng
Journal:  Cell       Date:  2015-04-23       Impact factor: 41.582

7.  Characteristics affecting expression and solubilization of yeast membrane proteins.

Authors:  Michael A White; Kathleen M Clark; Elizabeth J Grayhack; Mark E Dumont
Journal:  J Mol Biol       Date:  2006-10-06       Impact factor: 5.469

Review 8.  Perturbations of Native Membrane Protein Structure in Alkyl Phosphocholine Detergents: A Critical Assessment of NMR and Biophysical Studies.

Authors:  Christophe Chipot; François Dehez; Jason R Schnell; Nicole Zitzmann; Eva Pebay-Peyroula; Laurent J Catoire; Bruno Miroux; Edmund R S Kunji; Gianluigi Veglia; Timothy A Cross; Paul Schanda
Journal:  Chem Rev       Date:  2018-02-28       Impact factor: 60.622

9.  Cryo-EM sample preparation method for extremely low concentration liposomes.

Authors:  Lige Tonggu; Liguo Wang
Journal:  Ultramicroscopy       Date:  2019-09-30       Impact factor: 2.689

10.  Electron cryo-microscopy structure of the canonical TRPC4 ion channel.

Authors:  Deivanayagabarathy Vinayagam; Thomas Mager; Amir Apelbaum; Arne Bothe; Felipe Merino; Oliver Hofnagel; Christos Gatsogiannis; Stefan Raunser
Journal:  Elife       Date:  2018-05-02       Impact factor: 8.140

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  16 in total

1.  Sequence-Based Prediction of Transmembrane Protein Crystallization Propensity.

Authors:  Qizhi Zhu; Lihua Wang; Ruyu Dai; Wei Zhang; Wending Tang; Yannan Bin; Zeliang Wang; Junfeng Xia
Journal:  Interdiscip Sci       Date:  2021-06-18       Impact factor: 2.233

Review 2.  Membranes under the Magnetic Lens: A Dive into the Diverse World of Membrane Protein Structures Using Cryo-EM.

Authors:  Sarah J Piper; Rachel M Johnson; Denise Wootten; Patrick M Sexton
Journal:  Chem Rev       Date:  2022-07-18       Impact factor: 72.087

Review 3.  Structural Insights into Transporter-Mediated Drug Resistance in Infectious Diseases.

Authors:  Jonathan Kim; Rosemary J Cater; Brendon C Choy; Filippo Mancia
Journal:  J Mol Biol       Date:  2021-04-20       Impact factor: 6.151

4.  Cryo-EM grid optimization for membrane proteins.

Authors:  Domen Kampjut; Julia Steiner; Leonid A Sazanov
Journal:  iScience       Date:  2021-02-05

5.  The high-throughput production of membrane proteins.

Authors:  James Birch; Andrew Quigley
Journal:  Emerg Top Life Sci       Date:  2021-11-12

6.  Nanoparticles and photochemistry for native-like transmembrane protein footprinting.

Authors:  Jie Sun; Xiaoran Roger Liu; Shuang Li; Peng He; Weikai Li; Michael L Gross
Journal:  Nat Commun       Date:  2021-12-14       Impact factor: 14.919

Review 7.  Assessing the Role of Lipids in the Molecular Mechanism of Membrane Proteins.

Authors:  Léni Jodaitis; Thomas van Oene; Chloé Martens
Journal:  Int J Mol Sci       Date:  2021-07-06       Impact factor: 5.923

8.  Dependence of Protein Structure on Environment: FOD Model Applied to Membrane Proteins.

Authors:  Irena Roterman; Katarzyna Stapor; Krzysztof Gądek; Tomasz Gubała; Piotr Nowakowski; Piotr Fabian; Leszek Konieczny
Journal:  Membranes (Basel)       Date:  2021-12-30

Review 9.  Molecular mechanisms of metabotropic GABAB receptor function.

Authors:  Hamidreza Shaye; Benjamin Stauch; Cornelius Gati; Vadim Cherezov
Journal:  Sci Adv       Date:  2021-05-28       Impact factor: 14.136

Review 10.  Biological insights from SMA-extracted proteins.

Authors:  Lucas Unger; Alejandro Ronco-Campaña; Philip Kitchen; Roslyn M Bill; Alice J Rothnie
Journal:  Biochem Soc Trans       Date:  2021-06-30       Impact factor: 5.407

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