A generalized born implicit-membrane representation compared to experimental insertion free energies.

An implicit-membrane representation based on the generalized Born theory of solvation has been developed. The method was parameterized against the water-to-cyclohexane insertion free energies of hydrophobic side-chain analogs. Subsequently, the membrane was compared with experimental data from translocon inserted polypeptides and validated by comparison with an independent dataset of six membrane-associated peptides and eight integral membrane proteins of known structure and orientation. Comparison of the insertion energy of alpha-helical model peptides with the experimental values from the biological hydrophobicity scale of Hessa et al. gave a correlation of 93% with a mean unsigned error of 0.64 kcal/mol, when charged residues were ignored. The membrane insertion energy was found to be dependent on residue position. This effect is particularly pronounced for charged and polar residues, which strongly prefer interfacial locations. All integral membrane proteins investigated orient and insert correctly into the implicit-membrane model. Remarkably, the membrane model correctly predicts a partially inserted configuration for the monotopic membrane protein cyclooxygenase, matching experimental and theoretical predictions. To test the applicability and usefulness of the implicit-membrane method, molecular simulations of influenza A M2 as well as the glycophorin A dimer were performed. Both systems remain structurally stable and integrated into the membrane.

[1]  T. Lazaridis.  Effective energy function for proteins in lipid membranes , 2003, Proteins.

[2]  A. Parsegian,et al.  Energy of an Ion crossing a Low Dielectric Membrane: Solutions to Four Relevant Electrostatic Problems , 1969, Nature.

[3]  K. Hahm,et al.  Role of the hinge region and the tryptophan residue in the synthetic antimicrobial peptides, cecropin A(1-8)-magainin 2(1-12) and its analogues, on their antibiotic activities and structures. , 2000, Biochemistry.

[4]  R G Efremov,et al.  A solvent model for simulations of peptides in bilayers. I. Membrane-promoting alpha-helix formation. , 1999, Biophysical journal.

[5]  G. Terstappen,et al.  In silico research in drug discovery. , 2001, Trends in pharmacological sciences.

[6]  T. Creamer,et al.  Solvation energies of amino acid side chains and backbone in a family of host-guest pentapeptides. , 1996, Biochemistry.

[7]  H. Nymeyer,et al.  Folding is not required for bilayer insertion: Replica exchange simulations of an α‐helical peptide with an explicit lipid bilayer , 2004, Proteins.

[8]  Soonmin Jang,et al.  Molecular Dynamics Study of Peptides in Implicit Water: Ab Initio Folding of β-Hairpin, β-Sheet, and ββα-motif , 2002 .

[9]  S H White,et al.  Structure of a fluid dioleoylphosphatidylcholine bilayer determined by joint refinement of x-ray and neutron diffraction data. III. Complete structure. , 1992, Biophysical journal.

[10]  M. B. Pinto,et al.  Optimized δ expansion for relativistic nuclear models , 1997, nucl-th/9709049.

[11]  C. Brooks,et al.  An implicit membrane generalized born theory for the study of structure, stability, and interactions of membrane proteins. , 2003, Biophysical journal.

[12]  D. Peter Tieleman,et al.  Implicit solvent model estimates of the stability of model structures of the alamethicin channel , 2004, European Biophysics Journal.

[13]  William L. Jorgensen,et al.  Monte Carlo Backbone Sampling for Nucleic Acids Using Concerted Rotations Including Variable Bond Angles , 2004 .

[14]  William L. Jorgensen,et al.  Monte Carlo backbone sampling for polypeptides with variable bond angles and dihedral angles using concerted rotations and a Gaussian bias , 2003 .

[15]  G. Heijne,et al.  Genome‐wide analysis of integral membrane proteins from eubacterial, archaean, and eukaryotic organisms , 1998, Protein science : a publication of the Protein Society.

[16]  W. C. Still,et al.  The GB/SA Continuum Model for Solvation. A Fast Analytical Method for the Calculation of Approximate Born Radii , 1997 .

[17]  A. Waring,et al.  Impact of single-residue mutations on the structure and function of ovispirin/novispirin antimicrobial peptides. , 2002, Protein engineering.

[18]  Bong-Gyoon Han,et al.  Structural basis of water-specific transport through the AQP1 water channel , 2001, Nature.

[19]  Soonmin Jang,et al.  Molecular dynamics study of peptides in implicit water: ab initio folding of beta-hairpin, beta-sheet, and beta beta alpha-motif. , 2002, Journal of the American Chemical Society.

[20]  J. Gesell,et al.  Structures of the M2 channel-lining segments from nicotinic acetylcholine and NMDA receptors by NMR spectroscopy , 1999, Nature Structural Biology.

[21]  G von Heijne,et al.  Membrane protein structure prediction. Hydrophobicity analysis and the positive-inside rule. , 1992, Journal of molecular biology.

[22]  S. Opella,et al.  Structure and orientation of the antibiotic peptide magainin in membranes by solid‐state nuclear magnetic resonance spectroscopy , 1993, Protein science : a publication of the Protein Society.

[23]  A Monte Carlo model of fd and Pf1 coat proteins in lipid membranes. , 1995, Biophysical journal.

[24]  N. Ben-Tal,et al.  Interactions of hydrophobic peptides with lipid bilayers: Monte Carlo simulations with M2delta. , 2003, Biophysical journal.

[25]  W. C. Still,et al.  Semianalytical treatment of solvation for molecular mechanics and dynamics , 1990 .

[26]  B Honig,et al.  Free-energy determinants of alpha-helix insertion into lipid bilayers. , 1996, Biophysical journal.

[27]  T. Woolf,et al.  Tools for channels: moving towards molecular calculations of gating and permeation in ion channel biophysics. , 2004, Journal of molecular graphics & modelling.

[28]  D. Nolde,et al.  Peptides and proteins in membranes: what can we learn via computer simulations? , 2004, Current medicinal chemistry.

[29]  G. von Heijne,et al.  Stop-transfer function of pseudo-random amino acid segments during translocation across prokaryotic and eukaryotic membranes. , 1998, European journal of biochemistry.

[30]  M. Feig,et al.  A generalized Born formalism for heterogeneous dielectric environments: application to the implicit modeling of biological membranes. , 2005, The Journal of chemical physics.

[31]  G. Heijne.  Membrane protein structure prediction. Hydrophobicity analysis and the positive-inside rule. , 1992, Journal of molecular biology.

[32]  Robert M Stroud,et al.  Architecture and Selectivity in Aquaporins: 2.5 Å X-Ray Structure of Aquaporin Z , 2003, PLoS biology.

[33]  S. White,et al.  Location of hexane in lipid bilayers determined by neutron diffraction , 1981, Nature.

[34]  Richard Wolfenden,et al.  Comparing the polarities of the amino acids: side-chain distribution coefficients between the vapor phase, cyclohexane, 1-octanol, and neutral aqueous solution , 1988 .

[35]  M. Karplus,et al.  Solution conformations and thermodynamics of structured peptides: molecular dynamics simulation with an implicit solvation model. , 1998, Journal of molecular biology.

[36]  M. Born.  Volumen und Hydratationswärme der Ionen , 1920 .

[37]  Stephen H. White,et al.  Experimentally determined hydrophobicity scale for proteins at membrane interfaces , 1996, Nature Structural Biology.

[38]  Berk Hess,et al.  LINCS: A linear constraint solver for molecular simulations , 1997, J. Comput. Chem..

[39]  Marialuisa Pellegrini-Calace,et al.  Towards genome-scale structure prediction for transmembrane proteins , 2006, Philosophical Transactions of the Royal Society B: Biological Sciences.

[40]  J Wang,et al.  Structure of the transmembrane region of the M2 protein H+ channel , 2001, Protein science : a publication of the Protein Society.

[41]  S. Opella,et al.  Structure determination of membrane proteins by NMR spectroscopy. , 2004, Chemical reviews.

[42]  S. Opella,et al.  Simultaneous assignment and structure determination of a membrane protein from NMR orientational restraints , 2003, Protein science : a publication of the Protein Society.

[43]  M. Longo,et al.  A Monte Carlo study of peptide insertion into lipid bilayers: equilibrium conformations and insertion mechanisms. , 2002, Biophysical journal.

[44]  Martin B Ulmschneider,et al.  Evaluating tilt angles of membrane-associated helices: comparison of computational and NMR techniques. , 2006, Biophysical journal.

[45]  S. White,et al.  Fluid bilayer structure determination by the combined use of x-ray and neutron diffraction. II. "Composition-space" refinement method. , 1991, Biophysical journal.

[46]  T. Woolf,et al.  Dipole lattice membrane model for protein calculations , 2000, Proteins.

[47]  Gunnar von Heijne,et al.  Membrane Insertion of a Potassium-Channel Voltage Sensor , 2005, Science.

[48]  M. Sansom,et al.  Interactions of alpha-helices with lipid bilayers: a review of simulation studies. , 1999, Biophysical chemistry.

[49]  Roman G. Efremov,et al.  A Solvent Model for Simulations of Peptides in Bilayers. II. Membrane-Spanning α-Helices , 1999 .

[50]  A. Waring,et al.  Orientation and dynamics of an antimicrobial peptide in the lipid bilayer by solid-state NMR spectroscopy. , 2001, Biophysical journal.

[51]  D. Case,et al.  Generalized Born Models of Macromolecular Solvation Effects , 2001 .

[52]  S. White,et al.  Fluid bilayer structure determination by the combined use of x-ray and neutron diffraction. I. Fluid bilayer models and the limits of resolution. , 1991, Biophysical journal.

[53]  W. L. Jorgensen,et al.  Polypeptide folding using Monte Carlo sampling, concerted rotation, and continuum solvation. , 2004, Journal of the American Chemical Society.

[54]  Velin Z. Spassov,et al.  Introducing an Implicit Membrane in Generalized Born/Solvent Accessibility Continuum Solvent Models , 2002 .

[55]  Roman G. Efremov,et al.  A Solvent Model for Simulations of Peptides in Bilayers. I. Membrane-Promoting α-Helix Formation , 1999 .

[56]  V. Pande,et al.  Absolute comparison of simulated and experimental protein-folding dynamics , 2002, Nature.

[57]  Jeremy C. Smith,et al.  Understanding the energetics of helical peptide orientation in membranes , 2005, Proteins.

[58]  D. van der Spoel,et al.  GROMACS: A message-passing parallel molecular dynamics implementation , 1995 .

[59]  J Skolnick,et al.  Insertion of peptide chains into lipid membranes: An off‐lattice Monte Carlo dynamics model , 1993, Proteins.

[60]  J. Killian,et al.  Synthetic peptides as models for intrinsic membrane proteins , 2003, FEBS letters.

[61]  R. B. Merrifield,et al.  Orientation of cecropin A helices in phospholipid bilayers determined by solid-state NMR spectroscopy. , 1999, Biophysical journal.

[62]  B Honig,et al.  Association entropy in adsorption processes. , 2000, Biophysical journal.

[63]  C. Brooks,et al.  De novo folding of membrane proteins: an exploration of the structure and NMR properties of the fd coat protein. , 2004, Journal of molecular biology.

[64]  J. Killian,et al.  Protein–lipid interactions studied with designed transmembrane peptides: role of hydrophobic matching and interfacial anchoring (Review) , 2003, Molecular membrane biology.

[65]  C. Tate,et al.  Overexpression of integral membrane proteins for structural studies , 1995, Quarterly Reviews of Biophysics.

[66]  M S Sansom,et al.  Membrane simulations: bigger and better? , 2000, Current opinion in structural biology.

[67]  Carmen Domene,et al.  Membrane protein simulations: ion channels and bacterial outer membrane proteins. , 2003, Advances in protein chemistry.

[68]  Y. Shai,et al.  Structure and orientation of the mammalian antibacterial peptide cecropin P1 within phospholipid membranes. , 1996, Journal of molecular biology.

[69]  William L. Jorgensen,et al.  Free Energies of Hydration from a Generalized Born Model and an All-Atom Force Field , 2004 .

[70]  W. L. Jorgensen,et al.  Development and Testing of the OPLS All-Atom Force Field on Conformational Energetics and Properties of Organic Liquids , 1996 .

[71]  R. B. Merrifield,et al.  Binding and action of cecropin and cecropin analogues: antibacterial peptides from insects. , 1988, Biochimica et biophysica acta.

[72]  R. Dutzler,et al.  X-ray structure of a ClC chloride channel at 3.0 Å reveals the molecular basis of anion selectivity , 2002, Nature.

[73]  D. Engelman,et al.  Membrane protein folding and oligomerization: the two-stage model. , 1990, Biochemistry.

[74]  S. Opella,et al.  Three-dimensional solid-state NMR spectroscopy of a peptide oriented in membrane bilayers , 1995, Journal of biomolecular NMR.

[75]  S. White,et al.  The preference of tryptophan for membrane interfaces. , 1998, Biochemistry.

[76]  R. Kurumbail,et al.  Structural basis for selective inhibition of cyclooxygenase-2 by anti-inflammatory agents , 1997, Nature.

[77]  David T. Jones.  Do transmembrane protein superfolds exist? , 1998, FEBS letters.

[78]  A. Roitberg,et al.  All-atom structure prediction and folding simulations of a stable protein. , 2002, Journal of the American Chemical Society.

[79]  Chun Wu,et al.  Breaking non-native hydrophobic clusters is the rate-limiting step in the folding of an alanine-based peptide. , 2003, Biopolymers.

[80]  Nir Ben-Tal,et al.  Interactions of the M2delta segment of the acetylcholine receptor with lipid bilayers: a continuum-solvent model study. , 2003, Biophysical journal.

[81]  Karl Edman,et al.  X-ray structure of sensory rhodopsin II at 2.1-Å resolution , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[82]  Martin B Ulmschneider,et al.  Properties of integral membrane protein structures: Derivation of an implicit membrane potential , 2005, Proteins.

[83]  D. T. Jones,et al.  Folding in lipid membranes (FILM): A novel method for the prediction of small membrane protein 3D structures , 2003, Proteins.

[84]  Jakob P Ulmschneider,et al.  Monte Carlo vs molecular dynamics for all-atom polypeptide folding simulations. , 2006, The journal of physical chemistry. B.

[85]  Alessandro Senes,et al.  Membrane protein folding: beyond the two stage model , 2003, FEBS letters.

[86]  A. Krogh,et al.  Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. , 2001, Journal of molecular biology.

[87]  G. Heijne,et al.  Recognition of transmembrane helices by the endoplasmic reticulum translocon , 2005, Nature.

[88]  Maxim Totrov,et al.  Accurate and efficient generalized born model based on solvent accessibility: Derivation and application for LogP octanol/water prediction and flexible peptide docking , 2004, J. Comput. Chem..

[89]  P. Ormos,et al.  Structural alterations for proton translocation in the M state of wild-type bacteriorhodopsin , 2000, Nature.

[90]  James H. Prestegard,et al.  A Transmembrane Helix Dimer: Structure and Implications , 1997, Science.