Literature DB >> 36173170

A methodology for creating mutants of G-protein coupled receptors stabilized in active state by combining statistical thermodynamics and evolutionary molecular engineering.

Taisei Yamamoto1, Satoshi Yasuda1,2,3, Rinshi S Kasai4,5, Ryosuke Nakano1, Simon Hikiri6, Kanna Sugaya1, Tomohiko Hayashi7,8, Satoshi Ogasawara1,2,3,9, Mitsunori Shiroishi10, Takahiro K Fujiwara11, Masahiro Kinoshita1,2,8,12, Takeshi Murata1,2,3.   

Abstract

We challenged the stabilization of a G-protein coupled receptor (GPCR) in the active state solely by multiple amino-acid mutations without the agonist binding. For many GPCRs, the free energy of the active state is higher than that of the inactive state. When the inactive state is stabilized through the lowering of its free energy, the apparent midpoint temperature of thermal denaturation Tm exhibits a significant increase. However, this is not always the case for the stabilization of the active state. We constructed a modified version of our methodology combining statistical thermodynamics and evolutionary molecular engineering, which was recently developed for the inactive state. First, several residues to be mutated are determined using our statistical-thermodynamics theory. Second, a gene (mutant) library is constructed using Escherichia coli cells to efficiently explore most of the mutational space. Third, for the mutant screening, the mutants prepared in accordance with the library are expressed in engineered Saccharomyces cerevisiae YB14 cells which can grow only when a GPCR mutant stabilized in the active state has signaling function. For the adenosine A2A receptor tested, the methodology enabled us to sort out two triple mutants and a double mutant. It was experimentally corroborated that all the mutants exhibit much higher binding affinity for G protein than the wild type. Analyses indicated that the mutations make the structural characteristics shift toward those of the active state. However, only slight increases in Tm resulted from the mutations, suggesting the unsuitability of Tm to the stability measure for the active state.
© 2022 The Protein Society.

Entities:  

Keywords:  G protein; G-protein coupled receptor; active state; agonist; amino-acid mutation; configurational entropy; hydrocarbon group; hydrogen bond; lipid molecule; site-directed saturation mutagenesis

Mesh:

Substances:

Year:  2022        PMID: 36173170      PMCID: PMC9490800          DOI: 10.1002/pro.4425

Source DB:  PubMed          Journal:  Protein Sci        ISSN: 0961-8368            Impact factor:   6.993


  48 in total

1.  Analyses based on statistical thermodynamics for large difference between thermophilic rhodopsin and xanthorhodopsin in terms of thermostability.

Authors:  Satoshi Yasuda; Tomohiko Hayashi; Yuta Kajiwara; Takeshi Murata; Masahiro Kinoshita
Journal:  J Chem Phys       Date:  2019-02-07       Impact factor: 3.488

2.  Controlling the Dissociation of Ligands from the Adenosine A2A Receptor through Modulation of Salt Bridge Strength.

Authors:  Elena Segala; Dong Guo; Robert K Y Cheng; Andrea Bortolato; Francesca Deflorian; Andrew S Doré; James C Errey; Laura H Heitman; Adriaan P IJzerman; Fiona H Marshall; Robert M Cooke
Journal:  J Med Chem       Date:  2016-07-01       Impact factor: 7.446

Review 3.  GPCR Dynamics: Structures in Motion.

Authors:  Naomi R Latorraca; A J Venkatakrishnan; Ron O Dror
Journal:  Chem Rev       Date:  2016-09-13       Impact factor: 60.622

4.  Fluorescence-based optimization of human bitter taste receptor expression in Saccharomyces cerevisiae.

Authors:  Taishi Sugawara; Keisuke Ito; Mitsunori Shiroishi; Natsuko Tokuda; Hidetsugu Asada; Takami Yurugi-Kobayashi; Tatsuro Shimamura; Takumi Misaka; Norimichi Nomura; Takeshi Murata; Keiko Abe; So Iwata; Takuya Kobayashi
Journal:  Biochem Biophys Res Commun       Date:  2009-03-21       Impact factor: 3.575

5.  Platform for the rapid construction and evaluation of GPCRs for crystallography in Saccharomyces cerevisiae.

Authors:  Mitsunori Shiroishi; Hirokazu Tsujimoto; Hisayoshi Makyio; Hidetsugu Asada; Takami Yurugi-Kobayashi; Tatsuro Shimamura; Takeshi Murata; Norimichi Nomura; Tatsuya Haga; So Iwata; Takuya Kobayashi
Journal:  Microb Cell Fact       Date:  2012-06-13       Impact factor: 5.328

6.  Full characterization of GPCR monomer-dimer dynamic equilibrium by single molecule imaging.

Authors:  Rinshi S Kasai; Kenichi G N Suzuki; Eric R Prossnitz; Ikuko Koyama-Honda; Chieko Nakada; Takahiro K Fujiwara; Akihiro Kusumi
Journal:  J Cell Biol       Date:  2011-02-07       Impact factor: 10.539

7.  Confined diffusion of transmembrane proteins and lipids induced by the same actin meshwork lining the plasma membrane.

Authors:  Takahiro K Fujiwara; Kokoro Iwasawa; Ziya Kalay; Taka A Tsunoyama; Yusuke Watanabe; Yasuhiro M Umemura; Hideji Murakoshi; Kenichi G N Suzuki; Yuri L Nemoto; Nobuhiro Morone; Akihiro Kusumi
Journal:  Mol Biol Cell       Date:  2016-02-10       Impact factor: 4.138

8.  Mini-G proteins: Novel tools for studying GPCRs in their active conformation.

Authors:  Rony Nehmé; Byron Carpenter; Ankita Singhal; Annette Strege; Patricia C Edwards; Courtney F White; Haijuan Du; Reinhard Grisshammer; Christopher G Tate
Journal:  PLoS One       Date:  2017-04-20       Impact factor: 3.240

9.  Structure of the adenosine A(2A) receptor bound to an engineered G protein.

Authors:  Byron Carpenter; Rony Nehmé; Tony Warne; Andrew G W Leslie; Christopher G Tate
Journal:  Nature       Date:  2016-07-27       Impact factor: 49.962

10.  Highly accurate protein structure prediction with AlphaFold.

Authors:  John Jumper; Richard Evans; Alexander Pritzel; Tim Green; Michael Figurnov; Olaf Ronneberger; Kathryn Tunyasuvunakool; Russ Bates; Augustin Žídek; Anna Potapenko; Alex Bridgland; Clemens Meyer; Simon A A Kohl; Andrew J Ballard; Andrew Cowie; Bernardino Romera-Paredes; Stanislav Nikolov; Rishub Jain; Demis Hassabis; Jonas Adler; Trevor Back; Stig Petersen; David Reiman; Ellen Clancy; Michal Zielinski; Martin Steinegger; Michalina Pacholska; Tamas Berghammer; Sebastian Bodenstein; David Silver; Oriol Vinyals; Andrew W Senior; Koray Kavukcuoglu; Pushmeet Kohli
Journal:  Nature       Date:  2021-07-15       Impact factor: 49.962

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