메뉴 건너뛰기




Volumn 68, Issue 3, 2007, Pages 662-669

Parallel tempering molecular dynamics folding simulation of a signal peptide in explicit water

Author keywords

Aldehyde dehydrogenase; Enhanced sampling; Solvation; Structure determination; Structure prediction

Indexed keywords

SIGNAL PEPTIDASE; WATER;

EID: 34447511613     PISSN: 08873585     EISSN: 10970134     Source Type: Journal    
DOI: 10.1002/prot.21268     Document Type: Article
Times cited : (10)

References (44)
  • 4
    • 1542358892 scopus 로고    scopus 로고
    • Nascent membrane and secretory proteins differ in FRET-detected folding far inside the ribosome and in their exposure to ribosomal proteins
    • Woolhead CA, McCormick PJ, Johnson AE. Nascent membrane and secretory proteins differ in FRET-detected folding far inside the ribosome and in their exposure to ribosomal proteins. Cell 2004;116:725-736.
    • (2004) Cell , vol.116 , pp. 725-736
    • Woolhead, C.A.1    McCormick, P.J.2    Johnson, A.E.3
  • 6
    • 0032511879 scopus 로고    scopus 로고
    • Protein transport: Life and death of a signal peptide
    • von Heijne G. Protein transport: life and death of a signal peptide. Nature 1998;396:111-113.
    • (1998) Nature , vol.396 , pp. 111-113
    • von Heijne, G.1
  • 8
    • 42749102158 scopus 로고    scopus 로고
    • Dielectric modulation of biological water
    • Despa F, Fernández A, Berry RS. Dielectric modulation of biological water. Phys Rev Lett 2004;93:228104.
    • (2004) Phys Rev Lett , vol.93 , pp. 228104
    • Despa, F.1    Fernández, A.2    Berry, R.S.3
  • 9
    • 26944481188 scopus 로고    scopus 로고
    • Interfaces and the driving force of hydrophobic assembly
    • Chandler D. Interfaces and the driving force of hydrophobic assembly. Nature 2005;437:640-647.
    • (2005) Nature , vol.437 , pp. 640-647
    • Chandler, D.1
  • 10
    • 24344448662 scopus 로고    scopus 로고
    • Observation of a dewetting transition in the collapse of the melittin tetramer
    • Liu P, Huang X, Zhou R, Berne BJ. Observation of a dewetting transition in the collapse of the melittin tetramer. Nature 2005;437:159-162.
    • (2005) Nature , vol.437 , pp. 159-162
    • Liu, P.1    Huang, X.2    Zhou, R.3    Berne, B.J.4
  • 11
    • 0037038372 scopus 로고    scopus 로고
    • Absolute comparison of simulated and experimental protein-folding dynamics
    • Snow CD, Nguyen H, Pande VS, Gruebele M. Absolute comparison of simulated and experimental protein-folding dynamics. Nature 2003;420:102-106.
    • (2003) Nature , vol.420 , pp. 102-106
    • Snow, C.D.1    Nguyen, H.2    Pande, V.S.3    Gruebele, M.4
  • 12
    • 0032561237 scopus 로고    scopus 로고
    • Pathways to a protein folding intermediate observed in a 1-microsecond simulation in aqueous solution
    • Duan Y, Kollmann PA. Pathways to a protein folding intermediate observed in a 1-microsecond simulation in aqueous solution. Science 1998;282:740-747.
    • (1998) Science , vol.282 , pp. 740-747
    • Duan, Y.1    Kollmann, P.A.2
  • 13
    • 18744371588 scopus 로고    scopus 로고
    • Molecular dynamics and protein function
    • Karplus M, Kuriyan J. Molecular dynamics and protein function. Proc Natl Acad Sci USA 2005;102:6679-6685.
    • (2005) Proc Natl Acad Sci USA , vol.102 , pp. 6679-6685
    • Karplus, M.1    Kuriyan, J.2
  • 14
    • 4544386044 scopus 로고    scopus 로고
    • Carbopeptoid folding: Effects of stereochemistry, chain length, and solvent
    • Baron R, Bakowies D, van Gunsteren WF. Carbopeptoid folding: effects of stereochemistry, chain length, and solvent. Angew Chem Int Ed 2004;43:4055-4059.
    • (2004) Angew Chem Int Ed , vol.43 , pp. 4055-4059
    • Baron, R.1    Bakowies, D.2    van Gunsteren, W.F.3
  • 16
    • 0029151245 scopus 로고
    • First-principles calculation of the folding free energy of a three-helix bundle protein
    • Boczko EM, Brooks CL, III. First-principles calculation of the folding free energy of a three-helix bundle protein. Science 1995;269:393-396.
    • (1995) Science , vol.269 , pp. 393-396
    • Boczko, E.M.1    Brooks III, C.L.2
  • 17
    • 0042171838 scopus 로고    scopus 로고
    • Parallel tempering simulations of HP-36
    • Lin CY, Hu CK, Hansmann UHE. Parallel tempering simulations of HP-36. Proteins 2003;52:436-445.
    • (2003) Proteins , vol.52 , pp. 436-445
    • Lin, C.Y.1    Hu, C.K.2    Hansmann, U.H.E.3
  • 18
    • 0026095584 scopus 로고
    • Determination of macromolecular structures from anomalous diffraction of synchrotron radiation
    • Hendrickson WA. Determination of macromolecular structures from anomalous diffraction of synchrotron radiation. Science 1991;254:51-58.
    • (1991) Science , vol.254 , pp. 51-58
    • Hendrickson, W.A.1
  • 19
    • 0034764117 scopus 로고    scopus 로고
    • The way to NMR structures of proteins
    • Wüthrich K. The way to NMR structures of proteins. Nat Struct Biol 2001;8:923-925.
    • (2001) Nat Struct Biol , vol.8 , pp. 923-925
    • Wüthrich, K.1
  • 21
    • 0025077695 scopus 로고
    • 2D NMR and structural model for a mitochondrial signal peptide bound to a micelle
    • Karslake C, Piotto ME, Pak YK, Weiner H, Gorenstein DG. 2D NMR and structural model for a mitochondrial signal peptide bound to a micelle. Biochemistry 1990;29:9872-9878.
    • (1990) Biochemistry , vol.29 , pp. 9872-9878
    • Karslake, C.1    Piotto, M.E.2    Pak, Y.K.3    Weiner, H.4    Gorenstein, D.G.5
  • 22
    • 0027295559 scopus 로고
    • Import, process-ing, and two-dimensional NMR structure of a linker-deleted signal peptide of rat liver mitochondrial aldehyde dehydrogenase
    • Thornton K, Wang Y, Weiner H, Gorenstein DG. Import, process-ing, and two-dimensional NMR structure of a linker-deleted signal peptide of rat liver mitochondrial aldehyde dehydrogenase. J Biol Chem 1993;268:19906-19914.
    • (1993) J Biol Chem , vol.268 , pp. 19906-19914
    • Thornton, K.1    Wang, Y.2    Weiner, H.3    Gorenstein, D.G.4
  • 23
    • 0035979713 scopus 로고    scopus 로고
    • Topogenesis of membrane proteins: Determinants and dynamics
    • Goder V, Spiess M. Topogenesis of membrane proteins: determinants and dynamics. FEBS Lett 2001;504:87-93.
    • (2001) FEBS Lett , vol.504 , pp. 87-93
    • Goder, V.1    Spiess, M.2
  • 24
    • 28544445590 scopus 로고    scopus 로고
    • RNA-mediated interaction between the peptide-binding and GTPase domains of the signal recognition particle
    • Spanggord RJ, Siu F, Ke A, Doudna JA. RNA-mediated interaction between the peptide-binding and GTPase domains of the signal recognition particle Nat Struct Mol Biol 2005;12:1116-1122.
    • (2005) Nat Struct Mol Biol , vol.12 , pp. 1116-1122
    • Spanggord, R.J.1    Siu, F.2    Ke, A.3    Doudna, J.A.4
  • 25
    • 0034637111 scopus 로고    scopus 로고
    • The complete atomic structure of the large ribosomal subunit at 2.4 A resolution
    • Ban N, Nissen P, Hansen J, Moore PB, Steitz TA. The complete atomic structure of the large ribosomal subunit at 2.4 A resolution. Science 2000;289:905-920.
    • (2000) Science , vol.289 , pp. 905-920
    • Ban, N.1    Nissen, P.2    Hansen, J.3    Moore, P.B.4    Steitz, T.A.5
  • 26
    • 0031578972 scopus 로고    scopus 로고
    • Parallel tempering algorithm for conformational studies of biological molecules
    • Hansmann UHE. Parallel tempering algorithm for conformational studies of biological molecules. Chem Phys Lett 1997;281:140-150.
    • (1997) Chem Phys Lett , vol.281 , pp. 140-150
    • Hansmann, U.H.E.1
  • 27
    • 34447502366 scopus 로고    scopus 로고
    • Ponder JW. TINKER software tools for molecular design, Version 4.2. Copyright 1990-2004, Jay William Ponder, 2004
    • Ponder JW. TINKER software tools for molecular design, Version 4.2. Copyright 1990-2004, Jay William Ponder, 2004.
  • 29
    • 0033963034 scopus 로고    scopus 로고
    • Molden: A pre- and post-processing program for molecular and electronic structures
    • Schaftenaar G, Noordik JH. Molden: a pre- and post-processing program for molecular and electronic structures. J Comput Aided Mol Des 2000;14:123-134.
    • (2000) J Comput Aided Mol Des , vol.14 , pp. 123-134
    • Schaftenaar, G.1    Noordik, J.H.2
  • 31
    • 84946450438 scopus 로고
    • Algorithms for macromolecular dynamics and constraint dynamics
    • van Gunsteren WF, Berendsen HJC. Algorithms for macromolecular dynamics and constraint dynamics. Mol Phys 1977;34:1311-1327.
    • (1977) Mol Phys , vol.34 , pp. 1311-1327
    • van Gunsteren, W.F.1    Berendsen, H.J.C.2
  • 33
    • 0037934616 scopus 로고    scopus 로고
    • Understanding folding and design: Replicaexchange simulations of "Trp-cage" miniproteins
    • Pitera JW, Swope W. Understanding folding and design: replicaexchange simulations of "Trp-cage" miniproteins. Proc Natl Acad Sci USA 2003;100:7587-7592.
    • (2003) Proc Natl Acad Sci USA , vol.100 , pp. 7587-7592
    • Pitera, J.W.1    Swope, W.2
  • 34
    • 0035909921 scopus 로고    scopus 로고
    • The free energy landscape for beta hairpin folding in explicit water
    • Zhou R, Berne BJ, Germain R. The free energy landscape for beta hairpin folding in explicit water. Proc Natl Acad Sci USA 2001;98:14931-14936.
    • (2001) Proc Natl Acad Sci USA , vol.98 , pp. 14931-14936
    • Zhou, R.1    Berne, B.J.2    Germain, R.3
  • 35
    • 34547139358 scopus 로고    scopus 로고
    • Optimized parallel tempring simulations of proteins
    • Trebst S, Troyer M, Hansmann UHE. Optimized parallel tempring simulations of proteins. J Chem Phys 2006;124:174903.
    • (2006) J Chem Phys , vol.124 , pp. 174903
    • Trebst, S.1    Troyer, M.2    Hansmann, U.H.E.3
  • 36
    • 0022596727 scopus 로고
    • Solvation energy in protein folding and binding
    • Eisenberg D, McLachlan AD. Solvation energy in protein folding and binding. Nature 1986;319:199-203.
    • (1986) Nature , vol.319 , pp. 199-203
    • Eisenberg, D.1    McLachlan, A.D.2
  • 37
    • 0027080909 scopus 로고
    • Atomic solvation parameters applied to molecular dynamics of proteins in solution
    • Wesson L, Eisenberg D. Atomic solvation parameters applied to molecular dynamics of proteins in solution. Protein Sci 1992;1:227-235.
    • (1992) Protein Sci , vol.1 , pp. 227-235
    • Wesson, L.1    Eisenberg, D.2
  • 38
    • 0023338543 scopus 로고
    • Accessible surface areas as a measure of the thermodynamic parameters of hydration of peptides
    • Ooi T, Oobatake G, Nemethy G, Scheraga HA. Accessible surface areas as a measure of the thermodynamic parameters of hydration of peptides. Proc Natl Acad Sci USA 1987;84:3086-3090.
    • (1987) Proc Natl Acad Sci USA , vol.84 , pp. 3086-3090
    • Ooi, T.1    Oobatake, G.2    Nemethy, G.3    Scheraga, H.A.4
  • 39
    • 0344778061 scopus 로고
    • A semiempirical treatment of solvation for molecular mechanics and dynamics
    • Still WC, Tempczyk A, Hawley RC, Hendrickson T. A semiempirical treatment of solvation for molecular mechanics and dynamics. J Am Chem Soc 1990;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
  • 40
    • 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. The GB/SA continuum model for solvation. A fast analytical method for the calculation of approximate born radii. J Phys Chem A 1997;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
  • 41
    • 33748390341 scopus 로고    scopus 로고
    • Parametrized models of aqueous free energies of solvation based on pairwise descreening of solute atomic charges from a dielectric medium
    • Hawkins GD, Cramer CJ, Truhlar DG. Parametrized models of aqueous free energies of solvation based on pairwise descreening of solute atomic charges from a dielectric medium. J Phys Chem 1996;100:19824-19839.
    • (1996) J Phys Chem , vol.100 , pp. 19824-19839
    • Hawkins, G.D.1    Cramer, C.J.2    Truhlar, D.G.3
  • 42
    • 0020997912 scopus 로고
    • Dictionary of protein secondary structure: Pattern recognition of hydrogen bonded and geometrical features
    • Kabsch W, Sander C. Dictionary of protein secondary structure: pattern recognition of hydrogen bonded and geometrical features. Biopolymers 1983;22:2577-2637.
    • (1983) Biopolymers , vol.22 , pp. 2577-2637
    • Kabsch, W.1    Sander, C.2
  • 43
    • 0345133287 scopus 로고    scopus 로고
    • Folding a protein in a computer: An atomic description of the folding/unfolding of protein A
    • Garcia AE, Onuchic JN. Folding a protein in a computer: An atomic description of the folding/unfolding of protein A. Proc Natl Acad Sci USA 2003:100:13898-13903.
    • (2003) Proc Natl Acad Sci USA , vol.100 , pp. 13898-13903
    • Garcia, A.E.1    Onuchic, J.N.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.