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Volumn 21, Issue 8, 2013, Pages 1317-1324

Mechanistic explanation of different unfolding behaviors observed for transmembrane and soluble β-barrel proteins

Author keywords

[No Author keywords available]

Indexed keywords

GREEN FLUORESCENT PROTEIN; MEMBRANE PROTEIN; OUTER MEMBRANE PROTEIN; OUTER MEMBRANE PROTEIN G; UNCLASSIFIED DRUG; WATER;

EID: 84881476212     PISSN: 09692126     EISSN: 18784186     Source Type: Journal    
DOI: 10.1016/j.str.2013.06.001     Document Type: Article
Times cited : (14)

References (64)
  • 3
    • 0030999097 scopus 로고    scopus 로고
    • Molecular dynamics simulations of a fluid bilayer of dipalmitoylphosphatidylcholine at full hydration, constant pressure, and constant temperature
    • O. Berger, O. Edholm, and F. Jähnig Molecular dynamics simulations of a fluid bilayer of dipalmitoylphosphatidylcholine at full hydration, constant pressure, and constant temperature Biophys. J. 72 1997 2002 2013
    • (1997) Biophys. J. , vol.72 , pp. 2002-2013
    • Berger, O.1    Edholm, O.2    Jähnig, F.3
  • 6
    • 54249156909 scopus 로고    scopus 로고
    • Navigating the folding energy landscape of green fluorescent protein
    • M. Bertz, A. Kunfermann, and M. Rief Navigating the folding energy landscape of green fluorescent protein Angew. Chem. Int. Ed. Engl. 47 2008 8192 8195
    • (2008) Angew. Chem. Int. Ed. Engl. , vol.47 , pp. 8192-8195
    • Bertz, M.1    Kunfermann, A.2    Rief, M.3
  • 7
    • 79961064868 scopus 로고    scopus 로고
    • High-resolution atomic force microscopy and spectroscopy of native membrane proteins
    • C.A. Bippes, and D.J. Muller High-resolution atomic force microscopy and spectroscopy of native membrane proteins Rep. Prog. Phys. 74 2011 086601
    • (2011) Rep. Prog. Phys. , vol.74 , pp. 086601
    • Bippes, C.A.1    Muller, D.J.2
  • 8
    • 84857650478 scopus 로고    scopus 로고
    • Hydrogen bond dynamics in membrane protein function
    • A.-N. Bondar, and S.H. White Hydrogen bond dynamics in membrane protein function Biochim. Biophys. Acta 1818 2012 942 950
    • (2012) Biochim. Biophys. Acta , vol.1818 , pp. 942-950
    • Bondar, A.-N.1    White, S.H.2
  • 11
    • 84855769023 scopus 로고    scopus 로고
    • The transmembrane protein KpOmpA anchoring the outer membrane of Klebsiella pneumoniae unfolds and refolds in response to tensile load
    • P.D. Bosshart, I. Iordanov, C. Garzon-Coral, P. Demange, A. Engel, A. Milon, and D.J. Müller The transmembrane protein KpOmpA anchoring the outer membrane of Klebsiella pneumoniae unfolds and refolds in response to tensile load Structure 20 2012 121 127
    • (2012) Structure , vol.20 , pp. 121-127
    • Bosshart, P.D.1    Iordanov, I.2    Garzon-Coral, C.3    Demange, P.4    Engel, A.5    Milon, A.6    Müller, D.J.7
  • 12
    • 79551683006 scopus 로고    scopus 로고
    • Membrane protein folding: How important are hydrogen bonds?
    • J.U. Bowie Membrane protein folding: how important are hydrogen bonds? Curr. Opin. Struct. Biol. 21 2011 42 49
    • (2011) Curr. Opin. Struct. Biol. , vol.21 , pp. 42-49
    • Bowie, J.U.1
  • 13
    • 33846086933 scopus 로고    scopus 로고
    • Canonical sampling through velocity rescaling
    • G. Bussi, D. Donadio, and M. Parrinello Canonical sampling through velocity rescaling J. Chem. Phys. 126 2007 014101
    • (2007) J. Chem. Phys. , vol.126 , pp. 014101
    • Bussi, G.1    Donadio, D.2    Parrinello, M.3
  • 14
    • 80855133525 scopus 로고    scopus 로고
    • Cell membranes: The lipid perspective
    • Ü. Coskun, and K. Simons Cell membranes: the lipid perspective Structure 19 2011 1543 1548
    • (2011) Structure , vol.19 , pp. 1543-1548
    • Coskun, Ü.1    Simons, K.2
  • 15
    • 78649652074 scopus 로고    scopus 로고
    • Dual energy landscape: The functional state of the β-barrel outer membrane protein G molds its unfolding energy landscape
    • M. Damaghi, K.T. Sapra, S. Köster, O. Yildiz, W. Kühlbrandt, and D.J. Muller Dual energy landscape: the functional state of the β-barrel outer membrane protein G molds its unfolding energy landscape Proteomics 10 2010 4151 4162
    • (2010) Proteomics , vol.10 , pp. 4151-4162
    • Damaghi, M.1    Sapra, K.T.2    Köster, S.3    Yildiz, O.4    Kühlbrandt, W.5    Muller, D.J.6
  • 16
    • 77950021500 scopus 로고    scopus 로고
    • PH-dependent interactions guide the folding and gate the transmembrane pore of the β-barrel membrane protein OmpG
    • M. Damaghi, C. Bippes, S. Köster, O. Yildiz, S.A. Mari, W. Kühlbrandt, and D.J. Muller pH-dependent interactions guide the folding and gate the transmembrane pore of the β-barrel membrane protein OmpG J. Mol. Biol. 397 2010 878 882
    • (2010) J. Mol. Biol. , vol.397 , pp. 878-882
    • Damaghi, M.1    Bippes, C.2    Köster, S.3    Yildiz, O.4    Mari, S.A.5    Kühlbrandt, W.6    Muller, D.J.7
  • 17
    • 79960917538 scopus 로고    scopus 로고
    • One β hairpin follows the other: Exploring refolding pathways and kinetics of the transmembrane β-barrel protein OmpG
    • M. Damaghi, S. Köster, C.A. Bippes, O. Yildiz, and D.J. Müller One β hairpin follows the other: exploring refolding pathways and kinetics of the transmembrane β-barrel protein OmpG Angew. Chem. Int. Ed. Engl. 50 2011 7422 7424
    • (2011) Angew. Chem. Int. Ed. Engl. , vol.50 , pp. 7422-7424
    • Damaghi, M.1    Köster, S.2    Bippes, C.A.3    Yildiz, O.4    Müller, D.J.5
  • 18
    • 33846823909 scopus 로고
    • Particle mesh Ewald - An N.Log(N) method for ewald sums in large systems
    • T. Darden, D. York, and L. Pedersen Particle mesh Ewald - An N.Log(N) method for ewald sums in large systems J. Chem. Phys. 98 1993 10089 10092
    • (1993) J. Chem. Phys. , vol.98 , pp. 10089-10092
    • Darden, T.1    York, D.2    Pedersen, L.3
  • 19
    • 9244234443 scopus 로고    scopus 로고
    • Exploring the energy landscape of GFP by single-molecule mechanical experiments
    • H. Dietz, and M. Rief Exploring the energy landscape of GFP by single-molecule mechanical experiments Proc. Natl. Acad. Sci. USA 101 2004 16192 16197
    • (2004) Proc. Natl. Acad. Sci. USA , vol.101 , pp. 16192-16197
    • Dietz, H.1    Rief, M.2
  • 20
    • 31944436148 scopus 로고    scopus 로고
    • Protein structure by mechanical triangulation
    • H. Dietz, and M. Rief Protein structure by mechanical triangulation Proc. Natl. Acad. Sci. USA 103 2006 1244 1247
    • (2006) Proc. Natl. Acad. Sci. USA , vol.103 , pp. 1244-1247
    • Dietz, H.1    Rief, M.2
  • 21
    • 0141816804 scopus 로고    scopus 로고
    • Beyond the conventional description of dynamic force spectroscopy of adhesion bonds
    • O.K. Dudko, A.E. Filippov, J. Klafter, and M. Urbakh Beyond the conventional description of dynamic force spectroscopy of adhesion bonds Proc. Natl. Acad. Sci. USA 100 2003 11378 11381
    • (2003) Proc. Natl. Acad. Sci. USA , vol.100 , pp. 11378-11381
    • Dudko, O.K.1    Filippov, A.E.2    Klafter, J.3    Urbakh, M.4
  • 22
    • 33645004171 scopus 로고    scopus 로고
    • Intrinsic rates and activation free energies from single-molecule pulling experiments
    • O.K. Dudko, G. Hummer, and A. Szabo Intrinsic rates and activation free energies from single-molecule pulling experiments Phys. Rev. Lett. 96 2006 108101
    • (2006) Phys. Rev. Lett. , vol.96 , pp. 108101
    • Dudko, O.K.1    Hummer, G.2    Szabo, A.3
  • 23
    • 50649125304 scopus 로고    scopus 로고
    • Structure and mechanics of membrane proteins
    • A. Engel, and H.E. Gaub Structure and mechanics of membrane proteins Annu. Rev. Biochem. 77 2008 127 148
    • (2008) Annu. Rev. Biochem. , vol.77 , pp. 127-148
    • Engel, A.1    Gaub, H.E.2
  • 24
    • 28444437064 scopus 로고    scopus 로고
    • Membranes are more mosaic than fluid
    • D.M. Engelman Membranes are more mosaic than fluid Nature 438 2005 578 580
    • (2005) Nature , vol.438 , pp. 578-580
    • Engelman, D.M.1
  • 26
    • 0032227720 scopus 로고    scopus 로고
    • Energy landscapes of biomolecular adhesion and receptor anchoring at interfaces explored with dynamic force spectroscopy
    • E. Evans Energy landscapes of biomolecular adhesion and receptor anchoring at interfaces explored with dynamic force spectroscopy Faraday Discuss. 111 1998 1 16
    • (1998) Faraday Discuss. , vol.111 , pp. 1-16
    • Evans, E.1
  • 27
    • 0034979287 scopus 로고    scopus 로고
    • Probing the relation between force - Lifetime - and chemistry in single molecular bonds
    • E. Evans Probing the relation between force - lifetime - and chemistry in single molecular bonds Annu. Rev. Biophys. Biomol. Struct. 30 2001 105 128
    • (2001) Annu. Rev. Biophys. Biomol. Struct. , vol.30 , pp. 105-128
    • Evans, E.1
  • 28
    • 0031001349 scopus 로고    scopus 로고
    • Dynamic strength of molecular adhesion bonds
    • E. Evans, and K. Ritchie Dynamic strength of molecular adhesion bonds Biophys. J. 72 1997 1541 1555
    • (1997) Biophys. J. , vol.72 , pp. 1541-1555
    • Evans, E.1    Ritchie, K.2
  • 29
    • 18844398202 scopus 로고    scopus 로고
    • Mechanically induced titin kinase activation studied by force-probe molecular dynamics simulations
    • F. Gräter, J. Shen, H. Jiang, M. Gautel, and H. Grubmüller Mechanically induced titin kinase activation studied by force-probe molecular dynamics simulations Biophys. J. 88 2005 790 804
    • (2005) Biophys. J. , vol.88 , pp. 790-804
    • Gräter, F.1    Shen, J.2    Jiang, H.3    Gautel, M.4    Grubmüller, H.5
  • 30
    • 0030059225 scopus 로고    scopus 로고
    • Ligand binding: Molecular mechanics calculation of the streptavidin-biotin rupture force
    • H. Grubmüller, B. Heymann, and P. Tavan Ligand binding: molecular mechanics calculation of the streptavidin-biotin rupture force Science 271 1996 997 999
    • (1996) Science , vol.271 , pp. 997-999
    • Grubmüller, H.1    Heymann, B.2    Tavan, P.3
  • 31
    • 80054068982 scopus 로고    scopus 로고
    • Mechanosensitive channels: What can they do and how do they do it?
    • E.S. Haswell, R. Phillips, and D.C. Rees Mechanosensitive channels: what can they do and how do they do it? Structure 19 2011 1356 1369
    • (2011) Structure , vol.19 , pp. 1356-1369
    • Haswell, E.S.1    Phillips, R.2    Rees, D.C.3
  • 32
    • 0000388705 scopus 로고    scopus 로고
    • LINCS: A linear constraint solver for molecular simulations
    • B. Hess, H. Bekker, H. Berendsen, and J. Fraaije LINCS: A linear constraint solver for molecular simulations J. Comput. Chem. 18 1997 1463 1472
    • (1997) J. Comput. Chem. , vol.18 , pp. 1463-1472
    • Hess, B.1    Bekker, H.2    Berendsen, H.3    Fraaije, J.4
  • 33
    • 46249092554 scopus 로고    scopus 로고
    • GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable molecular simulation
    • B. Hess, C. Kutzner, D. van der Spoel, and E. Lindahl GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable molecular simulation J. Chem. Theory Comput. 4 2008 435 447
    • (2008) J. Chem. Theory Comput. , vol.4 , pp. 435-447
    • Hess, B.1    Kutzner, C.2    Van Der Spoel, D.3    Lindahl, E.4
  • 34
    • 0030442990 scopus 로고    scopus 로고
    • Positioning hydrogen atoms by optimizing hydrogen-bond networks in protein structures
    • R.W.W. Hooft, C. Sander, and G. Vriend Positioning hydrogen atoms by optimizing hydrogen-bond networks in protein structures Proteins 26 1996 363 376
    • (1996) Proteins , vol.26 , pp. 363-376
    • Hooft, R.W.W.1    Sander, C.2    Vriend, G.3
  • 35
    • 0001538909 scopus 로고
    • Canonical dynamics: Equilibrium phase-space distributions
    • W.G. Hoover Canonical dynamics: Equilibrium phase-space distributions Phys. Rev. A 31 1985 1695 1697
    • (1985) Phys. Rev. A , vol.31 , pp. 1695-1697
    • Hoover, W.G.1
  • 36
    • 0030834853 scopus 로고    scopus 로고
    • Binding pathway of retinal to bacterio-opsin: A prediction by molecular dynamics simulations
    • B. Isralewitz, S. Izrailev, and K. Schulten Binding pathway of retinal to bacterio-opsin: a prediction by molecular dynamics simulations Biophys. J. 73 1997 2972 2979
    • (1997) Biophys. J. , vol.73 , pp. 2972-2979
    • Isralewitz, B.1    Izrailev, S.2    Schulten, K.3
  • 38
    • 33645941402 scopus 로고
    • The OPLS potential functions for proteins - Energy minimizations for crystals of cyclic peptides and crambin
    • W. Jorgensen, and J. Tiradorives The OPLS potential functions for proteins - energy minimizations for crystals of cyclic peptides and crambin J. Am. Chem. Soc. 110 1988 1657 1666
    • (1988) J. Am. Chem. Soc. , vol.110 , pp. 1657-1666
    • Jorgensen, W.1    Tiradorives, J.2
  • 39
    • 0020997912 scopus 로고
    • Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features
    • W. Kabsch, and C. Sander Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features Biopolymers 22 1983 2577 2637
    • (1983) Biopolymers , vol.22 , pp. 2577-2637
    • Kabsch, W.1    Sander, C.2
  • 40
    • 34347259478 scopus 로고    scopus 로고
    • Deciphering molecular interactions of native membrane proteins by single-molecule force spectroscopy
    • A. Kedrov, H. Janovjak, K.T. Sapra, and D.J. Müller Deciphering molecular interactions of native membrane proteins by single-molecule force spectroscopy Annu. Rev. Biophys. Biomol. Struct. 36 2007 233 260
    • (2007) Annu. Rev. Biophys. Biomol. Struct. , vol.36 , pp. 233-260
    • Kedrov, A.1    Janovjak, H.2    Sapra, K.T.3    Müller, D.J.4
  • 41
    • 79955901803 scopus 로고    scopus 로고
    • Keep it flexible: Driving macromolecular rotary motions in atomistic simulations with GROMACS
    • C. Kutzner, J. Czub, and H. Grubmüller Keep it flexible: Driving macromolecular rotary motions in atomistic simulations with GROMACS J. Chem. Theory Comput. 7 2011 1381 1393
    • (2011) J. Chem. Theory Comput. , vol.7 , pp. 1381-1393
    • Kutzner, C.1    Czub, J.2    Grubmüller, H.3
  • 45
    • 74849118341 scopus 로고    scopus 로고
    • Lipid rafts as a membrane-organizing principle
    • D. Lingwood, and K. Simons Lipid rafts as a membrane-organizing principle Science 327 2010 46 50
    • (2010) Science , vol.327 , pp. 46-50
    • Lingwood, D.1    Simons, K.2
  • 46
    • 77949316155 scopus 로고    scopus 로고
    • PH-induced conformational change of the beta-barrel-forming protein OmpG reconstituted into native E. Coli lipids
    • S.A. Mari, S. Köster, C.A. Bippes, O. Yildiz, W. Kühlbrandt, and D.J. Muller pH-induced conformational change of the beta-barrel-forming protein OmpG reconstituted into native E. coli lipids J. Mol. Biol. 396 2010 610 616
    • (2010) J. Mol. Biol. , vol.396 , pp. 610-616
    • Mari, S.A.1    Köster, S.2    Bippes, C.A.3    Yildiz, O.4    Kühlbrandt, W.5    Muller, D.J.6
  • 47
    • 38049119865 scopus 로고    scopus 로고
    • Revealing the bifurcation in the unfolding pathways of GFP by using single-molecule experiments and simulations
    • M. Mickler, R.I. Dima, H. Dietz, C. Hyeon, D. Thirumalai, and M. Rief Revealing the bifurcation in the unfolding pathways of GFP by using single-molecule experiments and simulations Proc. Natl. Acad. Sci. USA 104 2007 20268 20273
    • (2007) Proc. Natl. Acad. Sci. USA , vol.104 , pp. 20268-20273
    • Mickler, M.1    Dima, R.I.2    Dietz, H.3    Hyeon, C.4    Thirumalai, D.5    Rief, M.6
  • 48
    • 84986440341 scopus 로고
    • SETTLE - An analytical version of the SHAKE and RATTLE algorithm for rigid water models
    • S. Miyamoto, and P. Kollman SETTLE - an analytical version of the SHAKE and RATTLE algorithm for rigid water models J. Comput. Chem. 13 1992 952 962
    • (1992) J. Comput. Chem. , vol.13 , pp. 952-962
    • Miyamoto, S.1    Kollman, P.2
  • 49
    • 84943502952 scopus 로고
    • A molecular dynamics method for simulations in the canonical ensemble
    • S. Nosé A molecular dynamics method for simulations in the canonical ensemble Mol. Physiol. 52 1984 255 268
    • (1984) Mol. Physiol. , vol.52 , pp. 255-268
    • Nosé, S.1
  • 52
    • 0019707626 scopus 로고
    • Polymorphic transitions in single crystals: A new molecular dynamics method
    • M. Parrinello Polymorphic transitions in single crystals: A new molecular dynamics method J. Appl. Physiol. 52 1981 7182 7190
    • (1981) J. Appl. Physiol. , vol.52 , pp. 7182-7190
    • Parrinello, M.1
  • 54
    • 70350036095 scopus 로고    scopus 로고
    • One beta hairpin after the other: Exploring mechanical unfolding pathways of the transmembrane beta-barrel protein OmpG
    • K.T. Sapra, M. Damaghi, S. Köster, O. Yildiz, W. Kühlbrandt, and D.J. Muller One beta hairpin after the other: exploring mechanical unfolding pathways of the transmembrane beta-barrel protein OmpG Angew. Chem. Int. Ed. Engl. 48 2009 8306 8308
    • (2009) Angew. Chem. Int. Ed. Engl. , vol.48 , pp. 8306-8308
    • Sapra, K.T.1    Damaghi, M.2    Köster, S.3    Yildiz, O.4    Kühlbrandt, W.5    Muller, D.J.6
  • 55
    • 0035344650 scopus 로고    scopus 로고
    • Cell control by membrane-cytoskeleton adhesion
    • M.P. Sheetz Cell control by membrane-cytoskeleton adhesion Nat. Rev. Mol. Cell Biol. 2 2001 392 396
    • (2001) Nat. Rev. Mol. Cell Biol. , vol.2 , pp. 392-396
    • Sheetz, M.P.1
  • 56
    • 84869138346 scopus 로고    scopus 로고
    • Molecular force transduction by ion channels: Diversity and unifying principles
    • S. Sukharev, and F. Sachs Molecular force transduction by ion channels: diversity and unifying principles J. Cell Sci. 125 2012 3075 3083
    • (2012) J. Cell Sci. , vol.125 , pp. 3075-3083
    • Sukharev, S.1    Sachs, F.2
  • 57
    • 84870513294 scopus 로고    scopus 로고
    • Out but not in: The large transmembrane β-barrel protein FhuA unfolds but cannot refold via β-hairpins
    • J. Thoma, P. Bosshart, M. Pfreundschuh, and D.J. Müller Out but not in: the large transmembrane β-barrel protein FhuA unfolds but cannot refold via β-hairpins Structure 20 2012 2185 2190
    • (2012) Structure , vol.20 , pp. 2185-2190
    • Thoma, J.1    Bosshart, P.2    Pfreundschuh, M.3    Müller, D.J.4
  • 59
    • 0025398721 scopus 로고
    • WHAT IF: A molecular modeling and drug design program
    • 29
    • G. Vriend WHAT IF: a molecular modeling and drug design program J. Mol. Graph. 8 1990 52 56 29
    • (1990) J. Mol. Graph. , vol.8 , pp. 52-56
    • Vriend, G.1
  • 60
    • 0032987478 scopus 로고    scopus 로고
    • Membrane protein folding and stability: Physical principles
    • S.H. White, and W.C. Wimley Membrane protein folding and stability: physical principles Annu. Rev. Biophys. Biomol. Struct. 28 1999 319 365
    • (1999) Annu. Rev. Biophys. Biomol. Struct. , vol.28 , pp. 319-365
    • White, S.H.1    Wimley, W.C.2
  • 61
    • 36549047363 scopus 로고    scopus 로고
    • Wolfram Research, Inc. Wolfram Research, Inc. Champaign, IL
    • Wolfram Research, Inc. Mathematica Edition: Version 8.0 2010 Wolfram Research, Inc. Champaign, IL
    • (2010) Mathematica Edition: Version 8.0
  • 62
    • 77954256616 scopus 로고    scopus 로고
    • G-membed: Efficient insertion of a membrane protein into an equilibrated lipid bilayer with minimal perturbation
    • M.G. Wolf, M. Hoefling, C. Aponte-Santamaría, H. Grubmüller, and G. Groenhof g-membed: Efficient insertion of a membrane protein into an equilibrated lipid bilayer with minimal perturbation J. Comput. Chem. 31 2010 2169 2174
    • (2010) J. Comput. Chem. , vol.31 , pp. 2169-2174
    • Wolf, M.G.1    Hoefling, M.2    Aponte-Santamaría, C.3    Grubmüller, H.4    Groenhof, G.5
  • 63
    • 0029780351 scopus 로고    scopus 로고
    • The molecular structure of green fluorescent protein
    • F. Yang, L.G. Moss, and G.N. Phillips Jr. The molecular structure of green fluorescent protein Nat. Biotechnol. 14 1996 1246 1251
    • (1996) Nat. Biotechnol. , vol.14 , pp. 1246-1251
    • Yang, F.1    Moss, L.G.2    Phillips, Jr.G.N.3
  • 64
    • 33747623998 scopus 로고    scopus 로고
    • Structure of the monomeric outer-membrane porin OmpG in the open and closed conformation
    • O. Yildiz, K.R. Vinothkumar, P. Goswami, and W. Kühlbrandt Structure of the monomeric outer-membrane porin OmpG in the open and closed conformation EMBO J. 25 2006 3702 3713
    • (2006) EMBO J , vol.25 , pp. 3702-3713
    • Yildiz, O.1    Vinothkumar, K.R.2    Goswami, P.3    Kühlbrandt, W.4


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