PIP2 Influences the Conformational Dynamics of Membrane bound KRAS4b

KRAS4b is a small GTPase involved in cellular signaling through receptor tyrosine kinases. Activation of KRAS4b is achieved through the interaction with nucleotide exchange factors while inactivation is regulated by through interaction with GTPase activating proteins. The activation of KRAS4b only occurs after recruitment of the regulatory proteins to the plasma membrane thus making the role of the phospholipid bilayer an integral part of the activation mechanism. The phospholipids, primarily with anionic head groups, interact with both the membrane anchoring hypervariable region and the G-domain, thus influencing the orientation of KRAS at the membrane surface. The orientation of the G-domain at the membrane surface is believed to play a role in the regulation of KRAS activation. Much of the research has focused on the role of phosphatidyl serine but little has been done regarding the important signaling lipid phosphatidylinositol-4,5-bisphosphate (PIP2). We report here the use of fluorescence anisotropy decay, atomic force microscopy, and molecular dynamic simulations to show that the presence of PIP2 in the bilayer promotes the interaction of the G-domain with the bilayer surface. The stability of these interactions significantly alters the dynamics of KRAS4b bound to the membrane indicating a potential role for PIP2 in the regulation of KRAS4b activity.

[1]  Douglas B. Litwin,et al.  Dynamics of Membrane-Bound G12V-KRAS from Simulations and Single-Molecule FRET in Native Nanodiscs. , 2020, Biophysical journal.

[2]  M. Buck,et al.  K-Ras G-domain binding with signaling lipid phosphatidylinositol (4,5)-phosphate (PIP2): membrane association, protein orientation, and function , 2019, The Journal of Biological Chemistry.

[3]  Jumin Lee,et al.  CHARMM‐GUI Nanodisc Builder for modeling and simulation of various nanodisc systems , 2019, J. Comput. Chem..

[4]  Priyanka Prakash,et al.  Ras and the Plasma Membrane: A Complicated Relationship. , 2018, Cold Spring Harbor perspectives in medicine.

[5]  Frank McCormick,et al.  RAS Proteins and Their Regulators in Human Disease , 2017, Cell.

[6]  Michael C. Gregory,et al.  Interaction of KRas4b with anionic membranes: A special role for PIP2. , 2017, Biochemical and biophysical research communications.

[7]  Matthias Buck,et al.  Computational Modeling Reveals that Signaling Lipids Modulate the Orientation of K-Ras4A at the Membrane Reflecting Protein Topology. , 2017, Structure.

[8]  Ingmar Schoen,et al.  Structural Insights How PIP2 Imposes Preferred Binding Orientations of FAK at Lipid Membranes. , 2017, The journal of physical chemistry. B.

[9]  S. Sligar,et al.  Nanodiscs in Membrane Biochemistry and Biophysics. , 2017, Chemical reviews.

[10]  Priyanka Prakash,et al.  Lipid-Sorting Specificity Encoded in K-Ras Membrane Anchor Regulates Signal Output , 2017, Cell.

[11]  R. Ghirlando,et al.  Structural basis of recognition of farnesylated and methylated KRAS4b by PDEδ , 2016, Proceedings of the National Academy of Sciences.

[12]  Priyanka Prakash,et al.  Oncogenic K-Ras Binds to an Anionic Membrane in Two Distinct Orientations: A Molecular Dynamics Analysis. , 2016, Biophysical journal.

[13]  Wonpil Im,et al.  CHARMM-GUI HMMM Builder for Membrane Simulations with the Highly Mobile Membrane-Mimetic Model. , 2015, Biophysical journal.

[14]  P. Alexander,et al.  Farnesylated and methylated KRAS4b: high yield production of protein suitable for biophysical studies of prenylated protein-lipid interactions , 2015, Scientific Reports.

[15]  Mitsuhiko Ikura,et al.  Oncogenic and RASopathy-associated K-RAS mutations relieve membrane-dependent occlusion of the effector-binding site , 2015, Proceedings of the National Academy of Sciences.

[16]  John C Hunter,et al.  In situ selectivity profiling and crystal structure of SML-8-73-1, an active site inhibitor of oncogenic K-Ras G12C , 2014, Proceedings of the National Academy of Sciences.

[17]  D. Esposito,et al.  Dragging ras back in the ring. , 2014, Cancer cell.

[18]  E. Olejniczak,et al.  Approach for targeting Ras with small molecules that activate SOS-mediated nucleotide exchange , 2014, Proceedings of the National Academy of Sciences.

[19]  Carla Mattos,et al.  A comprehensive survey of Ras mutations in cancer. , 2012, Cancer research.

[20]  Emad Tajkhorshid,et al.  Accelerating membrane insertion of peripheral proteins with a novel membrane mimetic model. , 2012, Biophysical journal.

[21]  E. Tajkhorshid,et al.  Capturing Spontaneous Partitioning of Peripheral Proteins Using a Biphasic Membrane-Mimetic Model , 2011, The journal of physical chemistry. B.

[22]  P. Bastiaens,et al.  The Palmitoylation Machinery Is a Spatially Organizing System for Peripheral Membrane Proteins , 2010, Cell.

[23]  Jodi Gureasko,et al.  Role of the histone domain in the autoinhibition and activation of the Ras activator Son of Sevenless , 2010, Proceedings of the National Academy of Sciences.

[24]  A. Gorfe,et al.  Ras membrane orientation and nanodomain localization generate isoform diversity , 2010, Proceedings of the National Academy of Sciences.

[25]  J. Hancock,et al.  Activation of the MAPK module from different spatial locations generates distinct system outputs. , 2008, Molecular biology of the cell.

[26]  Jodi Gureasko,et al.  Membrane-dependent signal integration by the Ras activator Son of sevenless , 2008, Nature Structural &Molecular Biology.

[27]  A. Gorfe,et al.  A novel switch region regulates H‐ras membrane orientation and signal output , 2008, The EMBO journal.

[28]  Gerrit Groenhof,et al.  GROMACS: Fast, flexible, and free , 2005, J. Comput. Chem..

[29]  D. Murray,et al.  Plasma membrane phosphoinositide organization by protein electrostatics , 2005, Nature.

[30]  Herbert Waldmann,et al.  An Acylation Cycle Regulates Localization and Activity of Palmitoylated Ras Isoforms , 2005, Science.

[31]  Stephen G. Sligar,et al.  Self-Assembly of Discoidal Phospholipid Bilayer Nanoparticles with Membrane Scaffold Proteins , 2002 .

[32]  S. Sligar,et al.  Single-molecule height measurements on microsomal cytochrome P450 in nanometer-scale phospholipid bilayer disks , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[33]  J. Lakowicz,et al.  Long-lifetime Ru(II) complexes as labeling reagents for sulfhydryl groups. , 1998, Analytical biochemistry.

[34]  T. Pawson,et al.  High Affinity Binding of the Pleckstrin Homology Domain of mSos1 to Phosphatidylinositol (4,5)-Bisphosphate* , 1997, The Journal of Biological Chemistry.

[35]  K Schulten,et al.  VMD: visual molecular dynamics. , 1996, Journal of molecular graphics.

[36]  T. Darden,et al.  Particle mesh Ewald: An N⋅log(N) method for Ewald sums in large systems , 1993 .

[37]  J. Kuśba,et al.  Review of fluorescence anisotropy decay analysis by frequency-domain fluorescence spectroscopy , 1993, Journal of Fluorescence.

[38]  S. Nosé A unified formulation of the constant temperature molecular dynamics methods , 1984 .

[39]  W. L. Jorgensen,et al.  Comparison of simple potential functions for simulating liquid water , 1983 .

[40]  M. Parrinello,et al.  Polymorphic transitions in single crystals: A new molecular dynamics method , 1981 .

[41]  J. Vance Molecular and cell biology of phosphatidylserine and phosphatidylethanolamine metabolism. , 2003, Progress in nucleic acid research and molecular biology.

[42]  P. Markiewicz,et al.  Atomic force microscopy probe tip visualization and improvement of images using a simple deconvolution procedure , 1994 .