Abstract
The results of full-atom molecular dynamics simulations of the transmembrane domains (TMDs) of both native, and Glu664-mutant (either protonated or unprotonated) Neu in an explicit fully hydrated dimyristoylphosphatidylcholine (DMPC) lipid bilayer are presented. For the native TMD peptide, a 10.05 ns trajectory was collected, while for the mutant TMD peptides 5.05 ns trajectories were collected for each. The peptides in all three simulations display stable predominantly α-helical hydrogen bonding throughout the trajectories. The only significant exception occurs near the C-terminal end of the native and unprotonated mutant TMDs just outside the level of the lipid headgroups, where π-helical hydrogen bonding develops, introducing a kink in the backbone structure. However, there is no indication of the formation of a π bulge within the hydrophobic region of either native or mutant peptides. Over the course of the simulation of the mutant peptide, it is found that a significant number of water molecules penetrate the hydrophobic region of the surrounding lipid molecules, effectively hydrating Glu664. If the energy cost of such water penetration is significant enough, this may be a factor in the enhanced dimerization affinity of Glu664-mutant Neu.
Similar content being viewed by others
References
Anézo C, de Vries AH, Höltje H-D, Tieleman DP, Marrink S-J (2003) Methodological issues in lipid bilayer simulations. J Phys Chem 107:9424–9433
Bargmann CI, Weinberg RA (1988) Oncogenic activation of the neu-encoded receptor protein by point mutation and deletion. EMBO J 7:2043–2052
Bargmann CI, Hung MC, Weinberg RA (1986a) Multiple independent activations of the neu oncogene by a point mutation altering the transmembrane domain of p185. Cell 45:649–657
Bargmann CI, Hung MC, Weinberg RA (1986b) The neu oncogene encodes an epidermal growth factor receptor-related protein. Nature 319:226–230
Belohorcová K, Davis JH, Woolf TB, Roux B (1997) Structure and dynamics of an amphiphilic peptide in a lipid bilayer: a molecular dynamics study. Biophys J 73:3039–3055
Bernèche S, Roux B (2000) Molecular dynamics of the KcsA K+ channel in a bilayer membrane. Biophys J 78:2900–2917
Bernèche S, Nina M, Roux B (1998) Molecular dynamics simulation of melittin in a dimyristoylphosphatidylcholine bilayer membrane. Biophys J 75:1603–1618
Brandt-Rauf PW, Pincus MR, Monaco R (1995) Conformation of the transmembrane domain of the c-erbB-2 oncogene-encoded protein in its monomeric and dimeric states. J Protein Chem 14:33–40
Brennan PJ, Kumogai T, Berezov A, Murali R, Greene MI (2000) HER2/Neu: mechanisms of dimerization/oligomerization. Oncogene 19:6093–6101
Brooks BR, Bruccoleri RE, Olafson BD, States DJ, Swaminathan S, Karplus M (1983) CHARMM: a program for macromolecular energy, minimization, and dynamics calculations. J Comp Chem 4:187–217
Burke C, Stern DF (1998) Activation of Neu (ErbB-2) mediated by disulfide bond-induced dimerization reveals a receptor tyrosine kinase dimer interface. Mol Cell Biol 18:5371–5379
Cao H, Bangalore L, Bormann BJ, Stern DF (1992a) A subdomain in the transmembrane domain is necessary for p185neu* activation. EMBO J 11:923–932
Cao H, Bangalore L, Dompe C, Bormann BJ, Stern DF (1992b) An extra cysteine proximal to the transmembrane domain induces crosslinking of p185neu and p185neu*. J Biol Chem 267:20489–20492
Cho H-S, Mason K, Ramyar KX, Stanley AM, Gabelli SB, Denney Jr. DW, and Leahy DJ. (2003) Structure of the extracellular region of Her2 alone and in complex with the herceptin Fab. Nature 421:756–760
Creighton TE (1984) Proteins: structures and molecular properties. WH Freeman, New York
Darden T, York D, Pederson L (1993) Particle mesh Ewald: an n·log(n) method for Ewald sums in large systems. J Chem Phys 98:10089–10092.
Davis J H, Auger M (1999) Static and magic angle spinning NMR of membrane peptides and proteins. Prog NMR Spectrosc 35:1–84
De Loof H, Harvey SC, Segrest JP, Pastor RW (1991) Mean field stochastic boundary molecular dynamics simulation of a phospholipid in a membrane. Biochemistry 30:2099–2113
Dunbrack RL, Karplus M (1993) Backbone-dependent rotamer library for proteins. J Mol Biol 230:543–574
Duneau J-P, Genest D, Genest M (1996) Detailed description of an α-helix→π-bulge transition detected by molecular dynamics simulations of the p185c-erbB2 V659G transmembrane domain. J Biomol Struct Dyn 13:753–769
Duneau J-P, Garnier N, Genest M (1997) Insight into signal transduction: structural alterations in transmembrane helices probed by multi- 1 ns molecular dynamics simulations. J Biomol Struct Dyn 15:555–572
Duneau J-P, Crouzy S, Garnier N, Chapron Y, Genest M (1999) Molecular dynamics simulations of the erbB-2 transmembrane domain within an explicit membrane environment: comparison with vacuum simulations. Biophys Chem 76:35–53
Egberts E, Marrink SJ, Berendsen HJC (1994) Molecular dynamics simulation of a phospholipid membrane. Eur Biophys J 22:423–436
Engh RA, Huber R (1991) Accurate bond and angle parameters for x-ray protein structure refinement. Acta Cryst A47:392–400
Feig M, MacKerell AD Jr, Brooks CL III (2003) Force field influence on the observation of π-helical protein structures in molecular dynamics simulations. J Phys Chem B 107:2831–2836
Feller SE, Zhang Y, Pastor RW, Brooks BR (1995) Constant pressure molecular dynamics simulation: the Langevin piston method. J Chem Phys 103:4613–4621
Finean JB, Coleman R, Michell RH (1984) Membranes and their cellular functions, 3rd edn. Blackwell, Boston
Fleishman FJ, Schlessinger J, Ben-Tal N (2003) A putative molecular-activation switch in the transmembrane domain of erbB2. Proc Natl Acad Sci USA 99:15937–15940
Forrest LR, Kukol A, Arkin IT, Tieleman DP, Sansom MSP (2000) Exploring models of the influenza A M2 channel: MD simulations in a phospholipid bilayer. Biophys J 78:55–69
Franks NP (1976) Structural analysis of hydrated egg lecithin and cholesterol bilayers I. X-ray diffraction. J Mol Biol 100:345–358
Garnier N, Genest D, Duneau J-P, Genest M (1994) Influence of a mutation in the transmembrane domain of the p185c-erbB2 oncogene-encoded protein studied by molecular dynamics simulations. J Biomol Struct Dyn 11:983–1002
Garnier N, Genest D, Duneau J-P, Genest M (1997) Molecular modeling of c-erbB2 receptor dimerization: coiled-coil structure of wild and oncogenic transmembrane domains—stabilization by interhelical hydrogen bonds in the oncogenic form. Biopolymers 42:157–168
Garnier N, Crouzy S, Genest M (2003) Molecular dynamics simulations of the transmembrane domain of the oncogenic ErbB2 receptor dimer in a DMPC bilayer. J Biomol Struct Dyn 21:179–199
Gennis R B (1989) Biomembranes: molecular structure and function. Springer, Berlin Heidelberg New York
Goetz M, Carlotti C, Bontemps F, Dufourc EJ (2001) Evidence for an α-helix→π-bulge helicity modulation for the Neu/ErbB-2 membrane-spanning segment. A 1H NMR and circular dichroism study. Biochemistry 40:6534–6540
Goldstein DJ, Andresson T, Sparkowski JJ, Schlegel R (1992) The BPV-1 E5 protein, the 16 kDa membrane pore-forming protein and the PDGF receptor exist in a complex that is dependent on hydrophobic transmembrane interactions. EMBO J 11:4851–4859
Gullick WJ, Bottomley AC, Lofts FJ, Doak DG, Mulvey D, Newman R, Crumpton JJ, Sternberg MJ, Campbell ID (1992) Three dimensional structure of the transmembrane region of the proto-oncogenic and oncogenic forms of the Neu protein. EMBO J 11:43–48
Haile JM (1992) Molecular dynamics simulations: elementary methods. John Wiley, Toronto
Hardy BJ, Pastor RW (1994) Conformational sampling of hydrocarbon lipid chains in an orienting potential. J Comp Chem 15:208–226
Ho C, Stubbs CD (1992) Hydration at the membrane protein–lipid interface. Biophys J 63:897–902
Houliston RS, Hodges RS, Sharom FJ, Davis JH (2003) Comparison of proto-oncogenic and mutant forms of the transmembrane region of the Neu receptor in TFE. FEBS Lett 535:39–43
Houliston RS, Hodges RS, Sharom FJ, Davis JH (2004) Characterization of the proto-oncogenic and mutant forms of the transmembrane region of Neu in micelles. J Biol Chem (in press.)
Hynes NE, Stern DF (1994) The biology of erbB-2/neu/HER-2 and its role in cancer. Biochim Biophys Acta 1198:165–184.
Jacobs RE, White SH (1989) The nature of the hydrophobic binding of small peptides at the bilayer interface. Implications for the insertion of transbilayer helices. Biochemistry 28:3421–3437
Jorgensen WL, Chandrasekhar J, Madura JD, Impey RW, Klein ML (1983) Comparison of simple potential functions for simulating liquid water. J Chem Phys 79:926–935
Koenig BW, Strey HH, Gawrisch, K (1997) Membrane lateral compressibility determined by NMR and X-ray diffraction: effect of acyl chain polyunsaturation. Biophys J 73:1954–1966
Kovacs H, Mark AE, Johansson J, van Gunsteren WF (1995) The effect of environment on the stability of an integral membrane helix: molecular dynamics simulations of surfactant protein C in chloroform, methanol, and water. J Mol Biol 247:808–822
Mackerell AD, Bashford D, Bellot M, Dunbrack RL, Field MJ, Fischer S, Gao J, Guo H, Joseph D, Ha S, Kuchnir L, Kuczera K, Lau FTK, Matos C, Michnick S, Nguyen DT, Ngo T, Prodhom B, Roux B, Schlenkrich B, Smith J, Stote R, Staub J, Wiorkiewicz-Kuczera J, Karplus M (1992) Self-consistent parametrization of biomolecules for molecular modelling and condensed phase simulations. Biophys J 61:A143
Nelander JC, Blaurock AE (1978) Disorder in nerve myelin: phasing the higher order reflections by means of the diffuse scatter. J Mol Biol 118:497–532
Nosé S (1984a) Constant temperature molecular dynamics. J Chem Phys 81:511–519
Nosé S (1984b) A molecular dynamics method for simulations in the canonical ensemble. Mol Phys 52:255–268
O’Neil KT, DeGrado WF (1990) A thermodynamic scale for the helix-forming tendencies of the commonly occurring amino acids. Science 250:646–651
Pastor RW, Venable RM, Karplus M (1991) Model for the structure of the lipid bilayer. Proc Natl Acad Sci USA 88:892–896
Patra M, Karttunen M, Hyvönen MT, Falck E, Lindqvist P, Vattulainen I (2003) Molecular dynamics simulations of lipid bilayers: major artifacts due to truncating electrostatic interactions. Biophys J 84:3636–3645
Petrache HI, Tristam-Nagle S, Nagle JF (1998) Fluid phase structure of EPC and DMPC bilayers. Chem Phys Lipids 95:83–94
Petrache HI, Dodd SW, Brown MF (2000) Area per lipid and acyl length distributions in fluid phosphatidylcholines determined by 2H NMR spectroscopy. Biophys J 79:3172–3192
Press MF, Bernstein L, Thomas PA, Meisner F, Zhou JY, Ma Y, Hung G, Robinson RA, Harris C, El-Naggar A, Slamon D J, Phillips RN, Ross JS, Wolman SR, Flom KJ (1997) HER-2 neu gene amplification characterized by fluorescence in situ hybridization: poor prognosis in node-negative breast carcinomas. J Clin Oncol 15:2894–2904
Roux B, Woolf TB (1996) Molecular dynamics of Pf1 coat protein in a phospholipid bilayer. In: Merz Jr KM, Roux B (eds) Biological membranes: a molecular perspective from computation and experiment. Birkhauser, Boston, pp 555–587
Ryckaert JP, Ciccotti G, Berendsen HJC (1977) Numerical integration of the Cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes. J Comp Phys 23:327–341
Sajot N, Genest M (2000) Structure prediction of the dimeric Neu/ErbB-2 transmembrane domain from multi-nanosecond molecular dynamics simulations. Eur Biophys J 28:648–662
Smith SO, Smith CS, Bormann BJ (1996) Strong hydrogen bonding interactions involving a buried glutamic acid in the transmembrane sequence of the Neu/ErbB-2 receptor. Nat Struct Biol 3:252–258
Smith SO, Smith C, Shekar S, Peersen O, Ziliox M, Aimoto S (2002) Transmembrane interactions in the activation of the Neu receptor tyrosine kinase. Biochemistry 41:9321–9332
Tieleman DP, Berendsen HJC, Sansom MSP (1999) An Alamethicin channel in a lipid bilayer: molecular dynamics simulations. Biophys J 76:1757–1769
Sternberg MJE, Gullick WJ (1990) A sequence motif in the transmembrane region of growth factor receptors with tyrosine kinase activity mediates dimerization. Prot Eng 3:245–248
Venable RM, Zhang Y, Hardy BJ, Pastor RW (1993) Molecular dynamics simulations of a lipid bilayer and of hexadecane: an investigation of membrane fluidity. Science 262:223–226
Verlet L (1967) Computer ‘experiments’ on classical fluids. I. Thermodynamical properties of Lennard-Jones molecules. Phys Rev 159:98–103
Weiner DB, Liu J, Cohen JA, Williams WV, Greene MI (1989) A point mutation in the Neu oncogene mimics ligand induction of receptor aggregation. Nature 339:230–231
Zhou FX, Merianos HJ, Brunger AT, Engelman DM (2001) Polar residues drive association of polyleucine transmembrane helices. Proc Natl Acad Sci USA 98:2250–2255
Acknowledgements
We would like to thank Professor Bernie Nickel of the Department of Physics at the University of Guelph and Simon Bernèche and Professor Benoit Roux of the Departments of Chemistry and Physics at the Université de Montréal. This work was supported by grants from the Natural Sciences and Engineering Research Council of Canada (NSERC). B.M.V. was supported by a NSERC PGS A scholarship in the course of this work.
Author information
Authors and Affiliations
Corresponding author
Rights and permissions
About this article
Cite this article
van der Ende, B.M., Sharom, F.J. & Davis, J.H. The transmembrane domain of Neu in a lipid bilayer: molecular dynamics simulations. Eur Biophys J 33, 596–610 (2004). https://doi.org/10.1007/s00249-004-0407-2
Received:
Revised:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s00249-004-0407-2