Literature DB >> 34384763

Membrane-bound KRAS approximates an entropic ensemble of configurations.

Frank Heinrich1, Que N Van2, Frantz Jean-Francois2, Andrew G Stephen2, Mathias Lösche3.   

Abstract

KRAS4B is a membrane-anchored signaling protein and a primary target in cancer research. Predictions from molecular dynamics simulations that have previously shaped our mechanistic understanding of KRAS signaling disagree with recent experimental results from neutron reflectometry, NMR, and thermodynamic binding studies. To gain insight into these discrepancies, we compare this body of biophysical data to back-calculated experimental results from a series of molecular simulations that implement different subsets of molecular interactions. Our results show that KRAS4B approximates an entropic ensemble of configurations at model membranes containing 30% phosphatidylserine lipids, which is not significantly shaped by interactions between the globular G-domain of KRAS4B and the lipid membrane. These findings revise our understanding of KRAS signaling and promote a model in which the protein samples the accessible conformational space in a near-uniform manner while being available to bind to effector proteins.
Copyright © 2021 Biophysical Society. All rights reserved.

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Year:  2021        PMID: 34384763      PMCID: PMC8510975          DOI: 10.1016/j.bpj.2021.08.008

Source DB:  PubMed          Journal:  Biophys J        ISSN: 0006-3495            Impact factor:   3.699


  63 in total

1.  The Ras G Domain Lacks the Intrinsic Propensity to Form Dimers.

Authors:  Elizaveta A Kovrigina; Azamat R Galiakhmetov; Evgenii L Kovrigin
Journal:  Biophys J       Date:  2015-09-01       Impact factor: 4.033

Review 2.  CHARMM: the biomolecular simulation program.

Authors:  B R Brooks; C L Brooks; A D Mackerell; L Nilsson; R J Petrella; B Roux; Y Won; G Archontis; C Bartels; S Boresch; A Caflisch; L Caves; Q Cui; A R Dinner; M Feig; S Fischer; J Gao; M Hodoscek; W Im; K Kuczera; T Lazaridis; J Ma; V Ovchinnikov; E Paci; R W Pastor; C B Post; J Z Pu; M Schaefer; B Tidor; R M Venable; H L Woodcock; X Wu; W Yang; D M York; M Karplus
Journal:  J Comput Chem       Date:  2009-07-30       Impact factor: 3.376

3.  Lipid-Sorting Specificity Encoded in K-Ras Membrane Anchor Regulates Signal Output.

Authors:  Yong Zhou; Priyanka Prakash; Hong Liang; Kwang-Jin Cho; Alemayehu A Gorfe; John F Hancock
Journal:  Cell       Date:  2016-12-29       Impact factor: 41.582

4.  Membrane Anchoring of Hck Kinase via the Intrinsically Disordered SH4-U and Length Scale Associated with Subcellular Localization.

Authors:  Matthew P Pond; Rebecca Eells; Bradley W Treece; Frank Heinrich; Mathias Lösche; Benoît Roux
Journal:  J Mol Biol       Date:  2019-12-23       Impact factor: 5.469

5.  Dynamics of Membrane-Bound G12V-KRAS from Simulations and Single-Molecule FRET in Native Nanodiscs.

Authors:  Priyanka Prakash; Douglas Litwin; Hong Liang; Suparna Sarkar-Banerjee; Drew Dolino; Yong Zhou; John F Hancock; Vasanthi Jayaraman; Alemayehu A Gorfe
Journal:  Biophys J       Date:  2018-12-20       Impact factor: 4.033

6.  Quantitative biophysical analysis defines key components modulating recruitment of the GTPase KRAS to the plasma membrane.

Authors:  Bindu Lakshman; Simon Messing; Eva M Schmid; Jeffrey D Clogston; William K Gillette; Dominic Esposito; Bailey Kessing; Daniel A Fletcher; Dwight V Nissley; Frank McCormick; Andrew G Stephen; Frantz L Jean-Francois
Journal:  J Biol Chem       Date:  2018-12-17       Impact factor: 5.157

7.  GTP-Dependent K-Ras Dimerization.

Authors:  Serena Muratcioglu; Tanmay S Chavan; Benjamin C Freed; Hyunbum Jang; Lyuba Khavrutskii; R Natasha Freed; Marzena A Dyba; Karen Stefanisko; Sergey G Tarasov; Attila Gursoy; Ozlem Keskin; Nadya I Tarasova; Vadim Gaponenko; Ruth Nussinov
Journal:  Structure       Date:  2015-06-04       Impact factor: 5.006

8.  Membrane-mediated induction and sorting of K-Ras microdomain signaling platforms.

Authors:  Katrin Weise; Shobhna Kapoor; Christian Denter; Jörg Nikolaus; Norbert Opitz; Sebastian Koch; Gemma Triola; Andreas Herrmann; Herbert Waldmann; Roland Winter
Journal:  J Am Chem Soc       Date:  2010-12-09       Impact factor: 15.419

9.  Oncogenic K-Ras Binds to an Anionic Membrane in Two Distinct Orientations: A Molecular Dynamics Analysis.

Authors:  Priyanka Prakash; Yong Zhou; Hong Liang; John F Hancock; Alemayehu A Gorfe
Journal:  Biophys J       Date:  2016-03-08       Impact factor: 4.033

10.  CHARMM-GUI Membrane Builder for mixed bilayers and its application to yeast membranes.

Authors:  Sunhwan Jo; Joseph B Lim; Jeffery B Klauda; Wonpil Im
Journal:  Biophys J       Date:  2009-07-08       Impact factor: 4.033

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