Backbone conformational flexibility of the lipid modified membrane anchor of the human N-Ras protein investigated by solid-state NMR and molecular dynamics simulation
Tài liệu tham khảo
Bartlett, 2009, An expanding arsenal of experimental methods yields an explosion of insights into protein folding mechanisms, Nat. Struct. Mol. Biol., 16, 582, 10.1038/nsmb.1592
Korzhnev, 2004, Low-populated folding intermediates of Fyn SH3 characterized by relaxation dispersion NMR, Nature, 430, 586, 10.1038/nature02655
Huster, 2001, Solid-state NMR investigation of the dynamics of the soluble and membrane-bound colicin Ia channel-forming domain, Biochemistry, 40, 7662, 10.1021/bi0027231
Fanucci, 2003, Membrane mimetic environments alter the conformation of the outer membrane protein BtuB, J. Am. Chem. Soc., 125, 13932, 10.1021/ja0376442
Hwang, 2004, The integral membrane enzyme PagP alternates between two dynamically distinct states, Proc. Nat. Acad. Sci. U. S. A., 101, 9618, 10.1073/pnas.0402324101
Saito, 2004, Dynamic pictures of membrane proteins in two-dimensional crystal, lipid bilayer and detergent as revealed by site-directed solid-state C-13 NMR, Chem. Phys. Lipids, 132, 101, 10.1016/j.chemphyslip.2004.09.009
Durr, 2007, The cytochromes P450 and b(5) and their reductases—promising targets for structural studies by advanced solid-state NMR spectroscopy, Biochim. Biophys. Acta-Biomembr., 1768, 3235, 10.1016/j.bbamem.2007.08.007
White, 2001, How membranes shape protein structure, J. Biol. Chem., 276, 32395, 10.1074/jbc.R100008200
Huster, 1999, Investigation of lipid organization in biological membranes by two-dimensional nuclear Overhauser enhancement spectroscopy, J. Phys. Chem. B, 103, 243, 10.1021/jp983428h
Wittinghofer, 2000, Ras—a molecular switch involved in tumor formation, Angew. Chem. Int. Ed., 39, 4192, 10.1002/1521-3773(20001201)39:23<4192::AID-ANIE4192>3.0.CO;2-Y
Hall, 1994, A biochemical function for ras—at last, Science, 264, 1413, 10.1126/science.8197454
Hart, 1997, Derivatives of activated H-ras lacking C-terminal lipid modifications retain transforming ability if targeted to the correct subcellular location, Oncogene, 14, 945, 10.1038/sj.onc.1200908
Gelb, 2006, Therapeutic intervention based on protein prenylation and associated modifications, Nat. Chem. Biol., 2, 518, 10.1038/nchembio818
Sousa, 2008, Farnesyltransferase inhibitors: a detailed chemical view on an elusive biological problem, Curr. Med. Chem., 15, 1478, 10.2174/092986708784638825
Reuther, 2000, The Ras branch of small GTPases: Ras family members don't fall far from the tree, Curr. Opin. Cell Biol., 12, 157, 10.1016/S0955-0674(99)00071-X
Prior, 2001, Compartmentalization of Ras proteins, J. Cell Sci., 114, 1603, 10.1242/jcs.114.9.1603
Brunsveld, 2009, Membrane binding of lipidated Ras peptides and proteins—the structural point of view, Biochim. Biophys. Acta, 1788, 273, 10.1016/j.bbamem.2008.08.006
Parton, 2004, Lipid rafts and plasma membrane microorganization: insights from Ras, Trends Cell Biol., 14, 141, 10.1016/j.tcb.2004.02.001
Rocks, 2006, Spatio-temporal segregation of Ras signals: one ship, three anchors, many harbors, Curr. Opin. Cell Biol., 18, 351, 10.1016/j.ceb.2006.06.007
Schroeder, 1997, S-Acylation and plasma membrane targeting of the farnesylated carboxyl-terminal peptide of N-ras in mammalian fibroblasts, Biochemistry, 36, 13102, 10.1021/bi9709497
Bader, 2000, Bioorganic synthesis of lipid-modified proteins for the study of signal transduction, Nature, 403, 223, 10.1038/35003249
Baldus, 2002, Correlation experiments for assignment and structure elucidation of immobilized polypeptides under magic angle spinning, Prog. Nucl. Magn. Reson. Spectrosc., 41, 1, 10.1016/S0079-6565(02)00007-9
Huster, 2005, Investigations of the structure and dynamics of membrane-associated peptides by magic angle spinning NMR, Prog. Nucl. Magn. Reson. Spectrosc., 46, 79, 10.1016/j.pnmrs.2005.01.001
Reuther, 2006, Structural model of the membrane-bound C terminus of lipid-modified human N-ras protein, Angew. Chem. Int. Ed., 45, 5387, 10.1002/anie.200504266
Reuther, 2006, 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, 13840, 10.1021/ja063635s
Cornilescu, 1999, Protein backbone angle restraints from searching a database for chemical shift and sequence homology, J. Biomol. NMR, 13, 289, 10.1023/A:1008392405740
Shen, 2007, Protein backbone chemical shifts predicted from searching a database for torsion angle and sequence homology, J. Biomol. NMR, 38, 289, 10.1007/s10858-007-9166-6
Neal, 2003, Rapid and accurate calculation of protein H-1, C-13 and N-15 chemical shifts, J. Biomol. NMR, 26, 215, 10.1023/A:1023812930288
Huster, 2001, 1H high-resolution magic angle spinning NMR spectroscopy for the investigation of a Ras lipopeptide in a lipid membrane, Angew. Chem. Int. Ed., 40, 1056, 10.1002/1521-3773(20010316)40:6<1056::AID-ANIE10560>3.0.CO;2-7
Huster, 2003, Membrane insertion of a lipidated Ras peptide studied by FTIR, solid-state NMR, and neutron diffraction spectroscopy, J. Am. Chem. Soc., 125, 4070, 10.1021/ja0289245
Gorfe, 2004, Membrane localization and flexibility of a lipidated ras peptide studied by molecular dynamics simulations, J. Am. Chem. Soc., 126, 15277, 10.1021/ja046607n
Huber, 2002, Structure of docosahexaenoic acid-containing phospholipid bilayers as studied by H-2 NMR and molecular dynamics simulations, J. Am. Chem. Soc., 124, 298, 10.1021/ja011383j
Salgado, 2009, Structural studies of HIV-1 Gag p6ct and its interaction with Vpr determined by solution nuclear magnetic resonance, Biochemistry, 48, 2355, 10.1021/bi801794v
Shi, 2009, Tilt and azimuthal angles of a transmembrane peptide: a comparison between molecular dynamics calculations and solid-state NMR data of sarcolipin in lipid membranes, Biophys. J., 96, 3648, 10.1016/j.bpj.2009.02.025
Lange, 2009, A combined solid-state NMR and MD characterization of the stability and dynamics of the HET-s(218-289) prion in its amyloid conformation, ChemBioChem, 10, 1657, 10.1002/cbic.200900019
Dvinskikh, 2006, Heteronuclear isotropic mixing separated local field NMR spectroscopy, J. Chem. Phys., 125
Dvinskikh, 2007, High-resolution 2D NMR spectroscopy of bicelles to measure the membrane interaction of ligands, J. Am. Chem. Soc., 129, 794, 10.1021/ja065536k
Hinterding, 1998, Organic synthesis and biological signal transduction, Angew. Chem. Int. Ed., 37, 688, 10.1002/(SICI)1521-3773(19980403)37:6<688::AID-ANIE688>3.0.CO;2-B
Nagele, 1998, Chemoenzymatic synthesis of N-Ras lipopeptides, J. Am. Chem. Soc., 120, 6889, 10.1021/ja9805627
Schelhaas, 1996, Enzymatic synthesis of peptides and Ras lipopeptides employing choline ester as a solubilizing, protecting, and activating group, Angew. Chem. Int. Ed., 35, 106, 10.1002/anie.199601061
Hong, 1997, Site-resolved determination of peptide torsion angle phi from the relative orientations of backbone N–H and C–H bonds by solid-state NMR, J. Phys. Chem. B, 101, 5869, 10.1021/jp970887u
Bielecki, 1989, Frequency-switched pulse sequences—homonuclear decoupling and dilute spin NMR in solids, Chem. Phys. Lett., 155, 341, 10.1016/0009-2614(89)87166-0
Barre, 2003, Structural and dynamical changes of the bindin B18 peptide upon binding to lipid membranes. A solid-state NMR study, Biochemistry, 42, 8377, 10.1021/bi034239e
Clore, 1990, Deviations from the simple two-parameter model-free approach to the interpretation of nitrogen-15 nuclear magnetic relaxation of proteins, J. Am. Chem. Soc., 112, 4989, 10.1021/ja00168a070
Palmer, 1996, Nuclear magnetic resonance studies of biopolymer dynamics, J. Phys. Chem. B, 100, 13293, 10.1021/jp9606117
Jo, 2007, Automated builder and database of protein/membrane complexes for molecular dynamics simulations, Plos One, 2
Petrache, 2000, Area per lipid and acyl length distributions in fluid phosphatidylcholines determined by H-2 NMR spectroscopy, Biophys. J., 79, 3172, 10.1016/S0006-3495(00)76551-9
Brooks, 1983, CHARMM—a program for macromolecular energy, minimization, and dynamics calculations, J. Comput. Chem., 4, 187, 10.1002/jcc.540040211
MacKerell, 1998, All-atom empirical potential for molecular modeling and dynamics studies of proteins, J. Phys. Chem. B, 102, 3586, 10.1021/jp973084f
MacKerell, 2004, Improved treatment of the protein backbone in empirical force fields, J. Am. Chem. Soc., 126, 698, 10.1021/ja036959e
Klauda, 2005, 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, 5300, 10.1021/jp0468096
Essmann, 1995, A smooth particle mesh Ewald method, J. Chem. Phys., 103, 8577, 10.1063/1.470117
Vangunsteren, 1977, Algorithms for macromolecular dynamics and constraint dynamics, Mol. Phys., 34, 1311, 10.1080/00268977700102571
Maragakis, 2007, Optimal estimates of free energies from multistate nonequilibrium work data (vol 96, art no 100602, 2006), Phys. Rev. Lett., 98, 259901, 10.1103/PhysRevLett.98.259901
Hukushima, 1996, Exchange Monte Carlo method and application to spin glass simulations, J. Phys. Soc. Jpn., 65, 1604, 10.1143/JPSJ.65.1604
Rhee, 2003, Multiplexed-replica exchange molecular dynamics method for protein folding simulation, Biophys. J., 84, 775, 10.1016/S0006-3495(03)74897-8
Maragakis, 2006, Optimal estimates of free energies from multistate nonequilibrium work data, Phys. Rev. Lett., 96, 100602, 10.1103/PhysRevLett.96.100602
Ye, 1993, Carbon-13 chemical shift anisotropies of solid amino acids, Magn. Reson. Chem., 31, 699, 10.1002/mrc.1260310802
Feller, 1999, Interpretation of NOESY cross-relaxation rates from molecular dynamics simulation of a lipid bilayer, J. Am. Chem. Soc., 121, 8963, 10.1021/ja991456n
Schmidt-Rohr, 1994
Vogel, 2007, Flexibility of ras lipid modifications studied by H-2 solid-state NMR and molecular dynamics simulations, Biophys. J., 93, 2697, 10.1529/biophysj.107.104562
Vogel, 2005, 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, 12263, 10.1021/ja051856c
Thapar, 2004, NMR characterization of full-length farnesylated and non-farnesylated H-ras and its implications for raf activation, J. Mol. Biol., 343, 1391, 10.1016/j.jmb.2004.08.106
Peitzsch, 1993, Binding of acylated peptides and fatty acids to phospholipid vesicles: pertinence to myristoylated proteins, Biochemistry, 32, 10436, 10.1021/bi00090a020
Pool, 1998, Chain length and temperature dependence of the reversible association of model acylated proteins with lipid bilayers, Biochemistry, 37, 10246, 10.1021/bi980385m
Tanford, 1980
Saito, 2002, Residue-specific millisecond to microsecond fluctuations in bacteriorhodopsin induced by disrupted or disorganized two-dimensional crystalline lattice, through modified lipid-helix and helix-helix interactions, as revealed by C-13 NMR, Biochim. Biophys. Acta, 1565, 97, 10.1016/S0005-2736(02)00513-8
Colnago, 1987, Dynamics of Fd-coat protein in the bacteriophage, Biochemistry, 26, 847, 10.1021/bi00377a028
Silvius, 1994, Fluorimetric evaluation of the affinities of isoprenylated peptides for lipid bilayers, Biochemistry, 33, 3014, 10.1021/bi00176a034
Zahn, 2000, Evaluation of isoprenoid conformation in solution and in the active site of protein-farnesyl transferase using carbon-13 labeling in conjunction with solution- and solid-state NMR, J. Am. Chem. Soc., 122, 7153, 10.1021/ja000860f
Rowat, 2004, Farnesol-DMPC phase behaviour: a H-2-NMR study, Biochim. Biophys. Acta, 1661, 178, 10.1016/j.bbamem.2004.01.002
Leevers, 1994, Requirement for Ras in Raf activation is overcome by targeting Raf to the plasma membrane, Nature, 369, 411, 10.1038/369411a0
Weise, 2009, Influence of the lipidation motif on the partitioning and association of N-Ras in model membrane subdomains, J. Am. Chem. Soc., 131, 1557, 10.1021/ja808691r
Kuzmin, 2005, Line tension and interaction energies of membrane rafts calculated from lipid splay and tilt, Biophys. J., 88, 1120, 10.1529/biophysj.104.048223
Keller, 2005, A quantitative model describing the selective solubilization of membrane domains, J. Am. Chem. Soc., 127, 11469, 10.1021/ja052764q
Vogel, 2009, The lipid modifications of ras sense the membrane environment and induce local enrichment, Angew. Chem. Int. Ed., 48, 8784, 10.1002/anie.200903396