메뉴 건너뛰기




Volumn 25, Issue 3, 2008, Pages 245-257

Membrane adsorption, folding, insertion and translocation of synthetic trans-membrane peptides

Author keywords

Generalized Born; Implicit membrane; KALP peptide; Membrane protein folding; Monte Carlo; WALP peptide

Indexed keywords

KALP16 PEPTIDE; SYNTHETIC PEPTIDE; UNCLASSIFIED DRUG; WALP16 PEPTIDE;

EID: 42449129998     PISSN: 09687688     EISSN: 14645203     Source Type: Journal    
DOI: 10.1080/09687680802020313     Document Type: Article
Times cited : (22)

References (51)
  • 1
    • 0035861454 scopus 로고    scopus 로고
    • Water permeation across biological membranes: Mechanism and dynamics of aquaporin-1 and GlpF
    • de Groot BL, Grubmuller H. 2001.Water permeation across biological membranes: Mechanism and dynamics of aquaporin-1 and GlpF. Science 294:2353-2357.
    • (2001) Science , vol.294 , pp. 2353-2357
    • de Groot, B.L.1    Grubmuller, H.2
  • 3
    • 0033066284 scopus 로고    scopus 로고
    • Interactions of alpha-helices with lipid bilayers: A review of simulation studies
    • Biggin PC, Sansom MS. 1999. Interactions of alpha-helices with lipid bilayers: a review of simulation studies. Biophys Chem 76:161-183.
    • (1999) Biophys Chem , vol.76 , pp. 161-183
    • Biggin, P.C.1    Sansom, M.S.2
  • 4
    • 0242696086 scopus 로고    scopus 로고
    • Membrane protein simulation: Ion channels and bacterial outer membrane proteins
    • Domene C, Bond P, Sansom MSP. 2003. Membrane protein simulation: Ion channels and bacterial outer membrane proteins. Adv Prot Chem 66:159-193.
    • (2003) Adv Prot Chem , vol.66 , pp. 159-193
    • Domene, C.1    Bond, P.2    Sansom, M.S.P.3
  • 5
    • 1942504108 scopus 로고    scopus 로고
    • Tools for channels: Moving towards molecular calculations of gating and permeation in ion channel biophysics
    • Woolf TB, Zuckerman DM, Lu ND, Jang HB. 2004. Tools for channels: Moving towards molecular calculations of gating and permeation in ion channel biophysics. J Molec Graphics Modelling 22:359-368.
    • (2004) J Molec Graphics Modelling , vol.22 , pp. 359-368
    • Woolf, T.B.1    Zuckerman, D.M.2    Lu, N.D.3    Jang, H.B.4
  • 7
    • 0344778061 scopus 로고
    • Semianalytical treatment of solvation for molecular mechanics and dynamics
    • Still WC, Tempczyk A, Hawley RC, Hendrickson T. 1990. Semianalytical treatment of solvation for molecular mechanics and dynamics. J Am Chem Soc 112:6127-6129.
    • (1990) J Am Chem Soc , vol.112 , pp. 6127-6129
    • Still, W.C.1    Tempczyk, A.2    Hawley, R.C.3    Hendrickson, T.4
  • 8
    • 17444426051 scopus 로고    scopus 로고
    • A generalized Born formalism for heterogeneous dielectric environments: Application to the implicit modeling of biological membranes
    • Tanizaki S, Feig M. 2005. A generalized Born formalism for heterogeneous dielectric environments: Application to the implicit modeling of biological membranes. J Chem Phys 122:124706.
    • (2005) J Chem Phys , vol.122 , pp. 124706
    • Tanizaki, S.1    Feig, M.2
  • 9
    • 0037194983 scopus 로고    scopus 로고
    • Introducing an implicit membrane in generalized Born/solvent accessibility continuum solvent models
    • Spassov VZ, Yan L, Szalma S. 2002. Introducing an implicit membrane in generalized Born/solvent accessibility continuum solvent models. J Phys Chem B 106:8726-8738.
    • (2002) J Phys Chem B , vol.106 , pp. 8726-8738
    • Spassov, V.Z.1    Yan, L.2    Szalma, S.3
  • 10
    • 0242322528 scopus 로고    scopus 로고
    • An implicit membrane generalized born theory for the study of structure, stability, and interactions of membrane proteins
    • Im W, Feig M, Brooks III CL. 2003. An implicit membrane generalized born theory for the study of structure, stability, and interactions of membrane proteins. Biophys J 85:2900-2918.
    • (2003) Biophys J , vol.85 , pp. 2900-2918
    • Im, W.1    Feig, M.2    Brooks III, C.L.3
  • 11
    • 34047240165 scopus 로고    scopus 로고
    • A generalized Born implicit membrane representation compared to experimental insertion free energies
    • Ulmschneider MB, Ulmschneider JP, Sansom MSP, Di Nola A. 2007. A generalized Born implicit membrane representation compared to experimental insertion free energies. Biophys J 92:2338-2349.
    • (2007) Biophys J , vol.92 , pp. 2338-2349
    • Ulmschneider, M.B.1    Ulmschneider, J.P.2    Sansom, M.S.P.3    Di Nola, A.4
  • 12
    • 0037234367 scopus 로고    scopus 로고
    • Breaking non-native hydrophobic clusters is the rate-limiting step in the folding of an alanine-based peptide
    • Chowdhury S, Zhang W, Wu C, Xiong GM, Duan Y. 2003. Breaking non-native hydrophobic clusters is the rate-limiting step in the folding of an alanine-based peptide. Biopolymers 68:63-75.
    • (2003) Biopolymers , vol.68 , pp. 63-75
    • Chowdhury, S.1    Zhang, W.2    Wu, C.3    Xiong, G.M.4    Duan, Y.5
  • 13
    • 0037042264 scopus 로고    scopus 로고
    • Molecular dynamics study of peptides in implicit water: Ab initio folding of beta-hairpin, beta-sheet, and beta beta alpha- motif
    • Jang S, Shin S, Pak Y. 2002. Molecular dynamics study of peptides in implicit water: Ab initio folding of beta-hairpin, beta-sheet, and beta beta alpha- motif. J Am Chem Soc 124:4976-4977.
    • (2002) J Am Chem Soc , vol.124 , pp. 4976-4977
    • Jang, S.1    Shin, S.2    Pak, Y.3
  • 14
    • 0037174385 scopus 로고    scopus 로고
    • All-atom structure prediction and folding simulations of a stable protein
    • Simmerling C, Strockbine B, Roitberg AE. 2002. All-atom structure prediction and folding simulations of a stable protein. J Am Chem Soc 124:11258-11259.
    • (2002) J Am Chem Soc , vol.124 , pp. 11258-11259
    • Simmerling, C.1    Strockbine, B.2    Roitberg, A.E.3
  • 15
    • 0037038372 scopus 로고    scopus 로고
    • Absolute comparison of simulated and experimental protein-folding dynamics
    • Snow CD, Nguyen N, Pande VS, Gruebele M. 2002. Absolute comparison of simulated and experimental protein-folding dynamics. Nature 420:102-106.
    • (2002) Nature , vol.420 , pp. 102-106
    • Snow, C.D.1    Nguyen, N.2    Pande, V.S.3    Gruebele, M.4
  • 16
    • 36649008718 scopus 로고    scopus 로고
    • Folding simulations of the trans-membrane helix of virus protein U in an implicit membrane model
    • Ulmschneider JP, Ulmschneider MB. 2007. Folding simulations of the trans-membrane helix of virus protein U in an implicit membrane model. J Chem Theory Computation 3:2335-2346.
    • (2007) J Chem Theory Computation , vol.3 , pp. 2335-2346
    • Ulmschneider, J.P.1    Ulmschneider, M.B.2
  • 18
    • 1542358793 scopus 로고    scopus 로고
    • De novo folding of membrane proteins: An exploration of the structure and NMR properties of the fd coat protein
    • Im W, Brooks III CL. 2004. De novo folding of membrane proteins: An exploration of the structure and NMR properties of the fd coat protein. J Molec Biol 337:513-519.
    • (2004) J Molec Biol , vol.337 , pp. 513-519
    • Im, W.1    Brooks III, C.L.2
  • 19
    • 0037337891 scopus 로고    scopus 로고
    • Monte Carlo backbone sampling for polypeptides with variable bond angles and dihedral angles using concerted rotations and a Gaussian bias
    • Ulmschneider JP, Jorgensen WL. 2003. Monte Carlo backbone sampling for polypeptides with variable bond angles and dihedral angles using concerted rotations and a Gaussian bias. J Chem Phys 118:4261-4271.
    • (2003) J Chem Phys , vol.118 , pp. 4261-4271
    • Ulmschneider, J.P.1    Jorgensen, W.L.2
  • 20
    • 1242314248 scopus 로고    scopus 로고
    • Polypeptide folding using Monte Carlo sampling, concerted rotation, and continuum solvation
    • Ulmschneider JP, Jorgensen WL. 2004. Polypeptide folding using Monte Carlo sampling, concerted rotation, and continuum solvation. J Am Chem Soc 126:1849-1857.
    • (2004) J Am Chem Soc , vol.126 , pp. 1849-1857
    • Ulmschneider, J.P.1    Jorgensen, W.L.2
  • 21
    • 33748574268 scopus 로고    scopus 로고
    • Monte Carlo vs. Molecular Dynamics for all-atom polypeptide folding simulations
    • Ulmschneider JP, Ulmschneider MB, Di Nola A. 2006. Monte Carlo vs. Molecular Dynamics for all-atom polypeptide folding simulations. J Phys Chem B 110:16733-16742.
    • (2006) J Phys Chem B , vol.110 , pp. 16733-16742
    • Ulmschneider, J.P.1    Ulmschneider, M.B.2    Di Nola, A.3
  • 22
    • 0242405501 scopus 로고    scopus 로고
    • Synthetic peptides as models for intrinsic membrane proteins
    • Killian JA. 2003. Synthetic peptides as models for intrinsic membrane proteins. FEBS Lett 555:134-138.
    • (2003) FEBS Lett , vol.555 , pp. 134-138
    • Killian, J.A.1
  • 23
    • 0242659352 scopus 로고    scopus 로고
    • Protein-lipid interactions studied with designed transmembrane peptides: Role of hydrophobic matching and interfacial anchoring (Review)
    • de Planque MRR, Killian JA. 2003. Protein-lipid interactions studied with designed transmembrane peptides: Role of hydrophobic matching and interfacial anchoring (Review). Molec Membrane Biol 20:271-284.
    • (2003) Molec Membrane Biol , vol.20 , pp. 271-284
    • de Planque, M.R.R.1    Killian, J.A.2
  • 24
    • 18844362955 scopus 로고    scopus 로고
    • Folding is not required for bilayer insertion: Replica exchange simulations of an alpha-helical peptide with an explicit lipid bilayer
    • Nymeyer H, Woolf TB, Garcia AE. 2005. Folding is not required for bilayer insertion: Replica exchange simulations of an alpha-helical peptide with an explicit lipid bilayer. Proteins-Structure Function and Bioinformatics 59:783-790.
    • (2005) Proteins-Structure Function and Bioinformatics , vol.59 , pp. 783-790
    • Nymeyer, H.1    Woolf, T.B.2    Garcia, A.E.3
  • 25
    • 18744403982 scopus 로고    scopus 로고
    • Interfacial folding and membrane insertion of designed peptides studied by molecular dynamics simulations
    • Im W, Brooks CL. 2005. Interfacial folding and membrane insertion of designed peptides studied by molecular dynamics simulations. Proc Nat Acad Sci USA 102:6771-6776.
    • (2005) Proc Nat Acad Sci USA , vol.102 , pp. 6771-6776
    • Im, W.1    Brooks, C.L.2
  • 27
    • 4043171970 scopus 로고    scopus 로고
    • The GB/ SA continuum model for solvation. A fast analytical method for the calculation of approximate Born radii
    • Qiu D, Shenkin PS, Hollinger FP, Still WC. 1997. The GB/ SA continuum model for solvation. A fast analytical method for the calculation of approximate Born radii. J Phys Chem A 101:3005-3014.
    • (1997) J Phys Chem A , vol.101 , pp. 3005-3014
    • Qiu, D.1    Shenkin, P.S.2    Hollinger, F.P.3    Still, W.C.4
  • 28
    • 7044260905 scopus 로고    scopus 로고
    • Free energies of hydration from a generalized Born model and an ALL-atom force field
    • Jorgensen WL, Ulmschneider JP, Tirado-Rives J. 2004. Free energies of hydration from a generalized Born model and an ALL-atom force field. J Phys Chem B 108:16264-16270.
    • (2004) J Phys Chem B , vol.108 , pp. 16264-16270
    • Jorgensen, W.L.1    Ulmschneider, J.P.2    Tirado-Rives, J.3
  • 29
    • 0014481138 scopus 로고
    • Energy of an ion crossing a low dielectric membrane: Solutions to four relevant electrostatic problems
    • Parsegian A. 1969. Energy of an ion crossing a low dielectric membrane: Solutions to four relevant electrostatic problems. Nature 221:844-846.
    • (1969) Nature , vol.221 , pp. 844-846
    • Parsegian, A.1
  • 30
    • 33845280446 scopus 로고
    • Comparing the polarities of the amino-acids - side-chain distribution coefficients between the vapor-phase, cyclohexane, 1-octanol, and neutral aqueous-solution
    • Radzicka A, Wolfenden R. 1988. Comparing the polarities of the amino-acids - side-chain distribution coefficients between the vapor-phase, cyclohexane, 1-octanol, and neutral aqueous-solution. Biochemistry 27:1664-1670.
    • (1988) Biochemistry , vol.27 , pp. 1664-1670
    • Radzicka, A.1    Wolfenden, R.2
  • 31
    • 0029912748 scopus 로고    scopus 로고
    • Development and testing of the OPLS all-atom force field on conformational energetics and properties of organic liquids
    • Jorgensen WL, Maxwell DS, Tirado-Rives J. 1996. Development and testing of the OPLS all-atom force field on conformational energetics and properties of organic liquids. J Am Chem Soc 118:11225-11236.
    • (1996) J Am Chem Soc , vol.118 , pp. 11225-11236
    • Jorgensen, W.L.1    Maxwell, D.S.2    Tirado-Rives, J.3
  • 32
    • 8344258212 scopus 로고    scopus 로고
    • Monte Carlo backbone sampling for nucleic acids using concerted rotations including variable bond angles
    • Ulmschneider JP, Jorgensen WL. 2004. Monte Carlo backbone sampling for nucleic acids using concerted rotations including variable bond angles. J Phys Chem B 108:16883-16892.
    • (2004) J Phys Chem B , vol.108 , pp. 16883-16892
    • Ulmschneider, J.P.1    Jorgensen, W.L.2
  • 33
    • 28844454252 scopus 로고    scopus 로고
    • Parallel tempering: Theory, applications, and new perspectives
    • Earl DJ, Deem MW. 2005. Parallel tempering: Theory, applications, and new perspectives. Phys Chem Chem Phys 7:3910-3916.
    • (2005) Phys Chem Chem Phys , vol.7 , pp. 3910-3916
    • Earl, D.J.1    Deem, M.W.2
  • 35
    • 0025249842 scopus 로고
    • Membrane-protein folding and oligomerization - the 2-stage model
    • Popot JL, Engelman DM. 1990. Membrane-protein folding and oligomerization - the 2-stage model. Biochemistry 29:4031-4037.
    • (1990) Biochemistry , vol.29 , pp. 4031-4037
    • Popot, J.L.1    Engelman, D.M.2
  • 36
    • 0024558250 scopus 로고
    • The nature of the hydrophobic binding of small peptides at the bilayer interface: Implications for the insertion of transbilayer helices
    • 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.
    • (1989) Biochemistry , vol.28 , pp. 3421-3437
    • Jacobs, R.E.1    White, S.H.2
  • 38
    • 0030736114 scopus 로고    scopus 로고
    • Free energy of amide hydrogen bond formation in vacuum, in water, and in liquid alkane solution
    • BenTal N, Sitkoff D, Topol IA, Yang AS, Burt SK, Honig B. 1997. Free energy of amide hydrogen bond formation in vacuum, in water, and in liquid alkane solution. J Phys Chem B 101:450-457.
    • (1997) J Phys Chem B , vol.101 , pp. 450-457
    • BenTal, N.1    Sitkoff, D.2    Topol, I.A.3    Yang, A.S.4    Burt, S.K.5    Honig, B.6
  • 39
    • 0024278757 scopus 로고
    • Hydrophobicity of the peptide C= O . . . H-N hydrogen-bonded group
    • Roseman MA. 1988. Hydrophobicity of the peptide C= O . . . H-N hydrogen-bonded group. J Mol Biol 201:621-623.
    • (1988) J Mol Biol , vol.201 , pp. 621-623
    • Roseman, M.A.1
  • 40
    • 0030005250 scopus 로고    scopus 로고
    • Solvation energies of amino acid side chains and backbone in a family of host-guest pentapeptides
    • Wimley WC, Creamer TP, White SH. 1996. Solvation energies of amino acid side chains and backbone in a family of host-guest pentapeptides. Biochemistry 35:5109-5124.
    • (1996) Biochemistry , vol.35 , pp. 5109-5124
    • Wimley, W.C.1    Creamer, T.P.2    White, S.H.3
  • 42
    • 84986512474 scopus 로고    scopus 로고
    • Brooks BR, Bruccoleri RE, Olafson BD, States DJ, Swaminathan S, Karplus M. 1983. Charmm - a program for macromolecular energy, minimization, and dynamics calculations. J Computational Chem 4:187-217.
    • Brooks BR, Bruccoleri RE, Olafson BD, States DJ, Swaminathan S, Karplus M. 1983. Charmm - a program for macromolecular energy, minimization, and dynamics calculations. J Computational Chem 4:187-217.
  • 43
    • 33847242278 scopus 로고    scopus 로고
    • Coarse-grained molecular dynamics simulations of membrane proteins and peptides
    • Bond PJ, Holyoake J, Ivetac A, Khalid S, Sansom MSP. 2007. Coarse-grained molecular dynamics simulations of membrane proteins and peptides. J Structural Biol 157:593-605.
    • (2007) J Structural Biol , vol.157 , pp. 593-605
    • Bond, P.J.1    Holyoake, J.2    Ivetac, A.3    Khalid, S.4    Sansom, M.S.P.5
  • 44
    • 0035942298 scopus 로고    scopus 로고
    • Sensitivity of single membrane-spanning alpha-helical peptides to hydrophobic mismatch with a lipid bilayer: Effects on backbone structure, orientation, and extent of membrane incorporation
    • de Planque MRR, Goormaghtigh E, Greathouse DV, Koeppe RE, Kruijtzer JAW, Liskamp RMJ, de Kruijff B, Killian JA. 2001. Sensitivity of single membrane-spanning alpha-helical peptides to hydrophobic mismatch with a lipid bilayer: Effects on backbone structure, orientation, and extent of membrane incorporation. Biochemistry 40:5000-5010.
    • (2001) Biochemistry , vol.40 , pp. 5000-5010
    • de Planque, M.R.R.1    Goormaghtigh, E.2    Greathouse, D.V.3    Koeppe, R.E.4    Kruijtzer, J.A.W.5    Liskamp, R.M.J.6    de Kruijff, B.7    Killian, J.A.8
  • 45
    • 0036708458 scopus 로고    scopus 로고
    • Geometry and intrinsic tilt of a tryptophan-anchored transmembrane alpha-helix determined by H-2 NMR
    • van der Wel PCA, Strandberg E, Killian JA, Koeppe RE. 2002. Geometry and intrinsic tilt of a tryptophan-anchored transmembrane alpha-helix determined by H-2 NMR. Biophysical J 83:1479-1488.
    • (2002) Biophysical J , vol.83 , pp. 1479-1488
    • van der Wel, P.C.A.1    Strandberg, E.2    Killian, J.A.3    Koeppe, R.E.4
  • 47
    • 0032581038 scopus 로고    scopus 로고
    • Influence of lipid/peptide hydrophobic mismatch on the thickness of diacylphosphatidylcholine bilayers. A H-2 NMR and ESR study using designed transmembrane alpha-helical peptides and gramicidin A
    • de Planque MRR, Greathouse DV, Koeppe RE, Schafer H, Marsh D, Killian JA. 1998. Influence of lipid/peptide hydrophobic mismatch on the thickness of diacylphosphatidylcholine bilayers. A H-2 NMR and ESR study using designed transmembrane alpha-helical peptides and gramicidin A. Biochemistry 37:9333-9345.
    • (1998) Biochemistry , vol.37 , pp. 9333-9345
    • de Planque, M.R.R.1    Greathouse, D.V.2    Koeppe, R.E.3    Schafer, H.4    Marsh, D.5    Killian, J.A.6
  • 48
    • 13944255096 scopus 로고    scopus 로고
    • Understanding the energetics of helical peptide orientation in membranes. Proteins-Structure Funct
    • Sengupta D, Meinhold L, Langosch D, Ullmann GM, Smith JC. 2005. Understanding the energetics of helical peptide orientation in membranes. Proteins-Structure Funct Genetics 58:913-922.
    • (2005) Genetics , vol.58 , pp. 913-922
    • Sengupta, D.1    Meinhold, L.2    Langosch, D.3    Ullmann, G.M.4    Smith, J.C.5
  • 49
    • 0037881905 scopus 로고    scopus 로고
    • Interfacial anchor properties of tryptophan residues in transmembrane peptides can dominate over hydrophobic matching effects in peptide-lipid interactions
    • de Planque MR, Bonev BB, Demmers JA, Greathouse DV, Koeppe RE, 2nd, Separovic F, Watts A, Killian JA. 2003. Interfacial anchor properties of tryptophan residues in transmembrane peptides can dominate over hydrophobic matching effects in peptide-lipid interactions. Biochemistry 42:5341-5348.
    • (2003) Biochemistry , vol.42 , pp. 5341-5348
    • de Planque, M.R.1    Bonev, B.B.2    Demmers, J.A.3    Greathouse, D.V.4    Koeppe 2nd, R.E.5    Separovic, F.6    Watts, A.7    Killian, J.A.8
  • 50
    • 33645641242 scopus 로고    scopus 로고
    • Im W, Chen J, Brooks CL 3rd. 2005. Peptide and protein folding and conformational equilibria: theoretical treatment of electrostatics and hydrogen bonding with implicit solvent models. Adv Protein Chem 72:173-198.
    • Im W, Chen J, Brooks CL 3rd. 2005. Peptide and protein folding and conformational equilibria: theoretical treatment of electrostatics and hydrogen bonding with implicit solvent models. Adv Protein Chem 72:173-198.


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.