Literature DB >> 32270446

Theoretical identification of thermostabilizing amino acid mutations for G-protein-coupled receptors.

Takeshi Murata1,2, Satoshi Yasuda1,2,3, Tomohiko Hayashi3,4, Masahiro Kinoshita5.   

Abstract

Thermostabilization of a membrane proteins, especially G-protein-coupled receptors (GPCRs), is often necessary for biochemical applications and pharmaceutical studies involving structure-based drug design. Here we review our theoretical, physics-based method for identifying thermostabilizing amino acid mutations. Its novel aspects are the following: The entropic effect originating from the translational displacement of hydrocarbon groups within the lipid bilayer is treated as a pivotal factor; a reliable measure of thermostability is introduced and a mutation which enlarges the measure to a significant extent is chosen; and all the possible mutations can be examined with moderate computational effort. It was shown that mutating the residue at a position of NBW = 3.39 (NBW is the Ballesteros-Weinstein number) to Arg or Lys leads to the stabilization of significantly many different GPCRs of class A in the inactive state. Up to now, we have been successful in stabilizing several GPCRs and newly solving three-dimensional structures for the muscarinic acetylcholine receptor 2 (M2R), prostaglandin E receptor 4 (EP4), and serotonin 2A receptor (5-HT2AR) using X-ray crystallography. The subjects to be pursued in future studies are also discussed.

Entities:  

Keywords:  G-protein-coupled receptor; Integral equation theory; Lipid bilayer; Membrane protein; Morphometric approach; Protein folding; Solvation thermodynamics; Thermostabilizing mutation

Year:  2020        PMID: 32270446      PMCID: PMC7242571          DOI: 10.1007/s12551-020-00678-5

Source DB:  PubMed          Journal:  Biophys Rev        ISSN: 1867-2450


  44 in total

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Journal:  Nat Rev Mol Cell Biol       Date:  2002-09       Impact factor: 94.444

2.  Effects of side-chain packing on the formation of secondary structures in protein folding.

Authors:  Satoshi Yasuda; Takashi Yoshidome; Hiraku Oshima; Ryota Kodama; Yuichi Harano; Masahiro Kinoshita
Journal:  J Chem Phys       Date:  2010-02-14       Impact factor: 3.488

3.  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

4.  Structural stability of proteins in aqueous and nonpolar environments.

Authors:  Satoshi Yasuda; Hiraku Oshima; Masahiro Kinoshita
Journal:  J Chem Phys       Date:  2012-10-07       Impact factor: 3.488

5.  Naturally evolved G protein-coupled receptors adopt metastable conformations.

Authors:  Kuang-Yui Michael Chen; Fuguo Zhou; Bartlomiej G Fryszczyn; Patrick Barth
Journal:  Proc Natl Acad Sci U S A       Date:  2012-07-30       Impact factor: 11.205

Review 6.  Stabilizing membrane proteins through protein engineering.

Authors:  Daniel J Scott; Lutz Kummer; Dirk Tremmel; Andreas Plückthun
Journal:  Curr Opin Chem Biol       Date:  2013-04-29       Impact factor: 8.822

Review 7.  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

8.  Unraveling protein folding mechanism by analyzing the hierarchy of models with increasing level of detail.

Authors:  Tomohiko Hayashi; Satoshi Yasuda; Tatjana Škrbić; Achille Giacometti; Masahiro Kinoshita
Journal:  J Chem Phys       Date:  2017-09-28       Impact factor: 3.488

9.  Satisfying hydrogen bonding potential in proteins.

Authors:  I K McDonald; J M Thornton
Journal:  J Mol Biol       Date:  1994-05-20       Impact factor: 5.469

10.  Rapid Computational Prediction of Thermostabilizing Mutations for G Protein-Coupled Receptors.

Authors:  Supriyo Bhattacharya; Sangbae Lee; Reinhard Grisshammer; Christopher G Tate; Nagarajan Vaidehi
Journal:  J Chem Theory Comput       Date:  2014-10-14       Impact factor: 6.006

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  1 in total

1.  Biophysical Reviews' national biophysical society partnership program.

Authors:  Damien Hall
Journal:  Biophys Rev       Date:  2020-04-29
  1 in total

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