A reinterpretation of neutron scattering experiments on a lipidated Ras peptide using replica exchange molecular dynamics

Biochimica et Biophysica Acta - Biomembranes

Volumn 1818, Issue 2, 2012, Pages 219-224

  Vogel, Alexander ^a   Roark, Matthew ^b   Feller, Scott E ^b  

^a UNIVERSITY OF LEIPZIG   (Germany)

^b WABASH COLLEGE   (United States)

Author keywords

Molecular dynamics; Neutron scattering; Ras protein; Replica exchange

Indexed keywords

RAS PROTEIN;

ARTICLE; CARBOXY TERMINAL SEQUENCE; COMPUTER SIMULATION; CONTROLLED STUDY; DENSITY; HUMAN; HYDROPHOBICITY; LIPID BILAYER; MOLECULAR DYNAMICS; NEUTRON SCATTERING; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN ASSEMBLY; PROTEIN FUNCTION; PROTEIN MODIFICATION; SIGNAL TRANSDUCTION; THICKNESS;

CELL MEMBRANE; HUMANS; LIPID BILAYERS; MOLECULAR DYNAMICS SIMULATION; PROTEIN BINDING; RAS PROTEINS;

EID: 84855464570     PISSN: 00052736     EISSN: 18792642     Source Type: Journal    
DOI: 10.1016/j.bbamem.2011.08.016     Document Type: Article

References (29)

1. A. Wittinghofer, and H. Waldmann Ras - a molecular switch involved in tumor formation Angew. Chem. Int. Ed. 39 2000 4193 4214
2. E.F. Pai, W. Kabsch, U. Krengel, K.C. Holmes, J. John, and A. Wittinghofer Structure of the guanine-nucleotide-binding domain of the Ha-Ras oncogene product P21 in the triphosphate conformation Nature 341 1989 209 214 (Pubitemid 19231720)
3. G. Reuther, K.T. Tan, A. Vogel, C. Nowak, K. Arnold, J. Kuhlmann, H. Waldmann, and D. Huster The lipidated membrane anchor of full length N-Ras protein shows an extensive dynamics as revealed by solid-state NMR spectroscopy J. Am. Chem. Soc. 128 2006 13840 13846 (Pubitemid 44632863)
4. A. Vogel, G. Reuther, M.B. Roark, K.T. Tan, H. Waldmann, S.E. Feller, and D. Huster Backbone conformational flexibility of the lipid modified membrane anchor of the human N-Ras protein investigated by solid-state NMR and molecular dynamics simulation Biochim. Biophys. Acta Biomembranes 1798 2010 275 285
5. A. Vogel, G. Reuther, K. Weise, G. Triola, J. Nikolaus, K.T. Tan, C. Nowak, A. Herrmann, H. Waldmann, R. Winter, and D. Huster The lipid modifications of Ras that sense membrane environments and induce local enrichment Angew. Chem. Int. Ed. 48 2009 8784 8787
6. A. Vogel, T. Schroder, C. Lange, and D. Huster Characterization of the myristoyl lipid modification of membrane-bound GCAP-2 by H-2 solid-state NMR spectroscopy Biochim. Biophys. Acta Biomembranes 1768 2007 3171 3181 (Pubitemid 350236086)
7. D. Abankwa, A.A. Gorfe, K. Inder, and J.F. Hancock Ras membrane orientation and nanodomain localization generate isoform diversity Proc. Natl Acad. Sci. USA 107 2008 1130 1135
8. D. Abankwa, A.A. Gorfe, and J.F. Hancock Mechanisms of Ras membrane organization and signaling: Ras on a rocker Cell Cycle 7 2008 2667 2673
9. A.A. Gorfe, M. Hanzal-Bayer, D. Abankwa, J.F. Hancock, and J.A. McCammon Structure and dynamics of the full-length lipid-modified H-ras protein in a 1,2-dimyristoylglycero-3-phosphocholine bilayer J. Med. Chem. 50 2007 674 684 (Pubitemid 46332980)
10. L. Janosi, and A.A. Gorfe Segregation of negatively charged phospholipids by the polycationic and farnesylated membrane anchor of Kras Biophys. J. 99 2010 3666 3674
11. S. Lukman, B.J. Grant, A.A. Gorfe, G.H. Grant, and J.A. McCammon The distinct conformational dynamics of K-Ras and H-Ras A59G Plos Comput. Biol. 6 9 2010 e1000922
12. G. Reuther, K.T. Tan, J. Kohler, C. Nowak, A. Pampel, K. Arnold, J. Kuhlmann, H. Waldmann, and D. Huster Structural model of the membrane-bound C terminus of lipid-modified human N-ras protein Angew. Chem. Int. Ed. 45 2006 5387 5390 (Pubitemid 44289385)
13. Y. Sugita, and Y. Okamoto Replica-exchange molecular dynamics method for protein folding Chem. Phys. Lett. 314 1999 141 151 (Pubitemid 129556751)
14. F. Bringezu, M. Majerowicz, S.Y. Wen, G. Reuther, K.T. Tan, J. Kuhlmann, H. Waldmann, and D. Huster Membrane binding of a lipidated N-Ras protein studied in lipid monolayers Eur. Biophys. J. Biophys. Lett. 36 2007 491 498 (Pubitemid 46626201)
15. D. Huster Investigations of the structure and dynamics of membrane-associated peptides by magic angle spinning NMR Prog. Nucl. Magn. Reson. Spectrosc. 46 2005 79 107 (Pubitemid 40749325)
16. D. Huster, K. Kuhn, D. Kadereit, H. Waldmann, and K. Arnold H-1 high-resolution magic angle spinning NMR spectroscopy for the investigation of a Ras lipopeptide in a lipid membrane Angew. Chem. Int. Ed. 40 2001 1056-+
17. D. Huster, A. Vogel, C. Katzka, H.A. Scheidt, H. Binder, S. Dante, T. Gutberlet, O. Zschornig, H. Waldmann, and K. Arnold Membrane insertion of a lipidated Ras peptide studied by FTIR, solid-state NMR, and neutron diffraction spectroscopy J. Am. Chem. Soc. 125 2003 4070 4079 (Pubitemid 36512300)
18. A. Vogel, C.P. Katzka, H. Waldmann, K. Arnold, M.F. Brown, and D. Huster Lipid modifications of a Ras peptide exhibit altered packing and mobility versus host membrane as detected by 2H solid-state NMR J. Am. Chem. Soc. 127 2005 12263 12272 (Pubitemid 41279250)
19. A. Vogel, K.-T. Tan, H. Waldmann, S.E. Feller, M.F. Brown, and D. Huster Flexibility of Ras lipid modifications studied by 2H solid-state NMR and molecular dynamics simulations Biophys. J. 93 2007 2697 2712 (Pubitemid 47607807)
20. B.R. Brooks, R.E. Bruccoler, B.D. Olafson, D.J. States, S. Swaminathan, and M. Karplus CHARMM: a program for macromolecular energy, minimization, and dynamics calculations J. Comput. Chem. 4 1983 187 217
21. A.D. MacKerell, M. Feig, and C.L. Brooks Improved treatment of the protein backbone in empirical force fields J. Am. Chem. Soc. 126 2004 698 699 (Pubitemid 38114337)
22. J.B. Klauda, B.R. Brooks, A.D. MacKerell Jr., R.M. Venable, and R.W. Pastor An ab initio study on the torsional surface of alkanes and its effect on molecular simulations of alkanes and a DPPC bilayer J. Phys. Chem. B 109 2005 5300 5311 (Pubitemid 40407752)
23. U. Essmann, L. Perera, M.L. Berkowitz, T. Darden, H. Lee, and L.G. Pedersen A smooth particle mesh Ewald method J. Chem. Phys. 103 1995 8577
24. J.P. Ryckaert, G. Ciccotti, and H.J.C. Berendsen Numerical integration of the cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes J. Comput. Phys. 23 1977 327 341
25. M.C. Wiener, and S.H. White Structure of a fluid dioleoylphosphatidylcholine bilayer determined by joint refinement of X-ray and neutron diffraction data. III. Complete structure Biophys. J. 61 1992 434
26. N. Kucerka, Y. Liu, N. Chu, H.I. Petrache, S. Tristram-Nagle, and J.F. Nagle Structure of fully hydrated fluid phase DMPC and DLPC lipid bilayers using X-ray scattering from oriented multilamellar arrays and from unilamellar vesicles Biophys. J. 88 2005 2626 2637 (Pubitemid 40976131)
27. A. Arbuzova, L.B. Wang, J.Y. Wang, G. Hangyas-Mihalyne, D. Murray, B. Honig, and S. McLaughlin Membrane binding of peptides containing both basic and aromatic residues. Experimental studies with peptides corresponding to the scaffolding region of caveolin and the effector region of MARCKS Biochemistry 39 2000 10330 10339 (Pubitemid 30665202)
28. D. Murray, L.H. Matsumoto, C.A. Buser, J. Tsang, C.T. Sigal, N. Ben-Tal, B. Honig, M.D. Resh, and S. McLaughlin Electrostatics and the membrane association of Src: theory and experiment Biochemistry 37 1998 2145 2159 (Pubitemid 28119288)
29. H.A. Scheidt, and D. Huster Structure and dynamics of the myristoyl lipid modification of Src peptides determined by H-2 solid-state NMR spectroscopy Biophys. J. 96 2009 3663 3672