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Volumn 5, Issue 10, 2009, Pages

Mechanical strength of 17 134 model proteins and cysteine slipknots

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACIDS; MOLECULAR DYNAMICS; SULFUR COMPOUNDS;

EID: 73549110486     PISSN: 1553734X     EISSN: 15537358     Source Type: Journal    
DOI: 10.1371/journal.pcbi.1000547     Document Type: Article
Times cited : (107)

References (73)
  • 1
    • 73549120339 scopus 로고    scopus 로고
    • Protein mechanics at the single-molecule level
    • Editor-in-chief R. A. Meyers, Springer, New York, ISBN: 978-0-387-75888-6
    • Carrion-Vazquez M, Cieplak M, Oberhauser AF (2009) Protein mechanics at the single-molecule level. In Encyclopedia of Complexity and Systems Science: 7026-7050. Editor-in-chief R. A. Meyers, Springer, New York, ISBN: 978-0-387-75888-6.
    • (2009) Encyclopedia of Complexity and Systems Science , pp. 7026-7050
    • Carrion-Vazquez, M.1    Cieplak, M.2    Oberhauser, A.F.3
  • 2
    • 0033445338 scopus 로고    scopus 로고
    • Steered molecular dynamics simulation of conformational changes of immunoglobulin domain I27 interpret atomic force microscopy observations
    • Lu H, Schulten K (1999) Steered molecular dynamics simulation of conformational changes of immunoglobulin domain I27 interpret atomic force microscopy observations. J Chem Phys 247: 141-153.
    • (1999) J Chem Phys , vol.247 , pp. 141-153
    • Lu, H.1    Schulten, K.2
  • 3
    • 0033531973 scopus 로고    scopus 로고
    • Forced Unfolding of Fibronectin Type 3 Modules: An Analysis by Biased Molecular Dynamics Simulations
    • Paci E, Karplus M (1999) Forced Unfolding of Fibronectin Type 3 Modules: An Analysis by Biased Molecular Dynamics Simulations. J Mol Biol 288: 441-459.
    • (1999) J Mol Biol , vol.288 , pp. 441-459
    • Paci, E.1    Karplus, M.2
  • 5
    • 0019571422 scopus 로고
    • Noninteracting local-structure model of folding and unfolding transition in globular proteins. II. Application to two-dimensional lattice proteins
    • Abe H, Go N (1981) Noninteracting local-structure model of folding and unfolding transition in globular proteins. II. Application to two-dimensional lattice proteins. Biopolymers 20: 1013-1031.
    • (1981) Biopolymers , vol.20 , pp. 1013-1031
    • Abe, H.1    Go, N.2
  • 6
    • 0030624384 scopus 로고    scopus 로고
    • Protein folding kinetics: Time scales, pathways, and energy landscapes in terms of sequence-dependent properties
    • Veitshans T, Klimov D, Thirumalai D (1997) Protein folding kinetics: time scales, pathways, and energy landscapes in terms of sequence-dependent properties. Folding Des 2: 1-22.
    • (1997) Folding Des , vol.2 , pp. 1-22
    • Veitshans, T.1    Klimov, D.2    Thirumalai, D.3
  • 7
    • 0034319711 scopus 로고    scopus 로고
    • Sequencing of folding events in Go-like proteins
    • Hoang TX, Cieplak M (2000) Sequencing of folding events in Go-like proteins. J Chem Phys 113: 8319-8328.
    • (2000) J Chem Phys , vol.113 , pp. 8319-8328
    • Hoang, T.X.1    Cieplak, M.2
  • 8
    • 0034685604 scopus 로고    scopus 로고
    • Topological and energetic factors: What determines the structural details of the transition state ensemble and "onroute" intermediates for protein folding? An investigation for small globular proteins
    • Clementi C, Nymeyer H, Onuchic JN (2000) Topological and energetic factors: what determines the structural details of the transition state ensemble and "onroute" intermediates for protein folding? An investigation for small globular proteins. J Mol Biol 298: 937-953.
    • (2000) J Mol Biol , vol.298 , pp. 937-953
    • Clementi, C.1    Nymeyer, H.2    Onuchic, J.N.3
  • 9
    • 0036785556 scopus 로고    scopus 로고
    • The origins of asymmetry in the folding transition states of protein L and protein G
    • Karanicolas J, Brooks CL III (2002) The origins of asymmetry in the folding transition states of protein L and protein G. Protein Science 11: 2351-2361.
    • (2002) Protein Science , vol.11 , pp. 2351-2361
    • Karanicolas, J.1    Brooks III, C.L.2
  • 11
    • 0037216990 scopus 로고    scopus 로고
    • Universality classes in folding times of proteins
    • Cieplak M, Hoang TX (2003) Universality classes in folding times of proteins. Biophys J 84: 475-488.
    • (2003) Biophys J , vol.84 , pp. 475-488
    • Cieplak, M.1    Hoang, T.X.2
  • 13
    • 33847116895 scopus 로고    scopus 로고
    • Flap opening dynamics in HIV-1 protease explored with a coarse-grained model
    • Tozzini V, Trylska J, Chang C, McCammon JA (2007) Flap opening dynamics in HIV-1 protease explored with a coarse-grained model. J Struct Biol 157: 606-615.
    • (2007) J Struct Biol , vol.157 , pp. 606-615
    • Tozzini, V.1    Trylska, J.2    Chang, C.3    McCammon, J.A.4
  • 14
    • 55949109149 scopus 로고    scopus 로고
    • Selection of optimal variants of Go-like models of proteins through studies of stretching
    • Sułkowska JI, Cieplak M (2008) Selection of optimal variants of Go-like models of proteins through studies of stretching. Biophys J 95: 3174-3191.
    • (2008) Biophys J , vol.95 , pp. 3174-3191
    • Sułkowska, J.I.1    Cieplak, M.2
  • 15
    • 0033516705 scopus 로고    scopus 로고
    • The packing density in proteins: Standard radii and volumes
    • Tsai J, Taylor R, Chothia C, Gerstein M (1999) The packing density in proteins: Standard radii and volumes. J Mol Biol 290: 253-266.
    • (1999) J Mol Biol , vol.290 , pp. 253-266
    • Tsai, J.1    Taylor, R.2    Chothia, C.3    Gerstein, M.4
  • 18
    • 34547673274 scopus 로고    scopus 로고
    • Mechanical stretching of proteins - a theoretical survey of the Protein Data Bank
    • Sułkowska JI, Cieplak M (2007) Mechanical stretching of proteins - a theoretical survey of the Protein Data Bank. J Phys Cond Mat 19: 283201.
    • (2007) J Phys Cond Mat , vol.19 , pp. 283201
    • Sułkowska, J.I.1    Cieplak, M.2
  • 19
    • 37749024809 scopus 로고    scopus 로고
    • Stretching to understand proteins - A survey of the Protein Data Bank
    • Sułkowska JI, Cieplak M (2008) Stretching to understand proteins - A survey of the Protein Data Bank. Biophys J 94: 6-13.
    • (2008) Biophys J , vol.94 , pp. 6-13
    • Sułkowska, J.I.1    Cieplak, M.2
  • 20
    • 63549137892 scopus 로고    scopus 로고
    • Cieplak M, Su?kowska JI (2009) Tests of the Structure-based models of proteins. Acta Phys Polonica 115: 441-445.
    • Cieplak M, Su?kowska JI (2009) Tests of the Structure-based models of proteins. Acta Phys Polonica 115: 441-445.
  • 21
    • 0031011695 scopus 로고    scopus 로고
    • Reversible unfolding of individual titin immunoglobulin domains by AFM
    • Rief M, Gautel M, Oesterhelt F, Fernandez JM, Gaub HE (1997) Reversible unfolding of individual titin immunoglobulin domains by AFM. Science 276: 1109-1112.
    • (1997) Science , vol.276 , pp. 1109-1112
    • Rief, M.1    Gautel, M.2    Oesterhelt, F.3    Fernandez, J.M.4    Gaub, H.E.5
  • 25
    • 13444272079 scopus 로고    scopus 로고
    • The CATH Domain Structure Database and related resources Gene3D and DHS provide comprehensive domain family information for genome analysis
    • Pearl F, Todd A, Sillitoe I, Dibley M, Redfern O, et al. (2005) The CATH Domain Structure Database and related resources Gene3D and DHS provide comprehensive domain family information for genome analysis. Nucl Acid Res 33: D247-51.
    • (2005) Nucl Acid Res , vol.33
    • Pearl, F.1    Todd, A.2    Sillitoe, I.3    Dibley, M.4    Redfern, O.5
  • 27
    • 0028961335 scopus 로고
    • SCOP: A structural classification of proteins database for the investigation of sequences and structures
    • Murzin AG, Brenner SE, Hubbard T, Chothia C (1995) SCOP: a structural classification of proteins database for the investigation of sequences and structures. J Mol Biol 247: 536-40.
    • (1995) J Mol Biol , vol.247 , pp. 536-540
    • Murzin, A.G.1    Brenner, S.E.2    Hubbard, T.3    Chothia, C.4
  • 30
    • 61349104703 scopus 로고    scopus 로고
    • Stretching to understand proteins - a survey of the Protein Data Bank (Retraction)
    • Sułkowska JI, Cieplak M (2008) Stretching to understand proteins - a survey of the Protein Data Bank (Retraction). Biophys J 95: 5487-5487.
    • (2008) Biophys J , vol.95 , pp. 5487-5487
    • Sułkowska, J.I.1    Cieplak, M.2
  • 31
    • 0034069495 scopus 로고    scopus 로고
    • gene ontology: Tool for the unification of biology
    • The Gene Ontology Consortium
    • The Gene Ontology Consortium (2000) gene ontology: tool for the unification of biology. Nat Genet 25: 25-29.
    • (2000) Nat Genet , vol.25 , pp. 25-29
  • 33
    • 33645770767 scopus 로고    scopus 로고
    • Stepwise unfolding of ankyrin repeats in a single protein revealed by atomic force microscopy
    • Li LW, Wetzel S, Pluckthun A, Fernandez JM (2006) Stepwise unfolding of ankyrin repeats in a single protein revealed by atomic force microscopy. Biophys J 90: 30-32.
    • (2006) Biophys J , vol.90 , pp. 30-32
    • Li, L.W.1    Wetzel, S.2    Pluckthun, A.3    Fernandez, J.M.4
  • 34
    • 0035239222 scopus 로고    scopus 로고
    • The cysteine knot motif in toxins and implications for drug design
    • Craik DJ, Dally NL, Waine C (2001) The cysteine knot motif in toxins and implications for drug design. Toxicon 39: 43-60.
    • (2001) Toxicon , vol.39 , pp. 43-60
    • Craik, D.J.1    Dally, N.L.2    Waine, C.3
  • 35
    • 33847385325 scopus 로고    scopus 로고
    • Insecticidal plant cyclotides and related cysteine knot toxins
    • Gruber CW, Cemazar M, Anderson MA, Craik DJ (2007) Insecticidal plant cyclotides and related cysteine knot toxins. Toxicon 49: 561-575.
    • (2007) Toxicon , vol.49 , pp. 561-575
    • Gruber, C.W.1    Cemazar, M.2    Anderson, M.A.3    Craik, D.J.4
  • 36
    • 0033579483 scopus 로고    scopus 로고
    • Plant cyclotides: A unique family of cyclic and knotted proteins that defines the cyclic cystine knot structural motif
    • Craik DJ, Daly NL, Bond TJ, Waine C (1999) Plant cyclotides: A unique family of cyclic and knotted proteins that defines the cyclic cystine knot structural motif. J Mol Biol 294: 1327-1336.
    • (1999) J Mol Biol , vol.294 , pp. 1327-1336
    • Craik, D.J.1    Daly, N.L.2    Bond, T.J.3    Waine, C.4
  • 37
    • 0037424506 scopus 로고    scopus 로고
    • Rosengren KJ, Daly NL, Plan MR, Waine C, Craik DJ (2003) Twists, knots, and rings in proteins - Structural definition of the cyclotide framework. J Biol Chem 278: 8606-8616.
    • Rosengren KJ, Daly NL, Plan MR, Waine C, Craik DJ (2003) Twists, knots, and rings in proteins - Structural definition of the cyclotide framework. J Biol Chem 278: 8606-8616.
  • 38
    • 36549032188 scopus 로고    scopus 로고
    • Knotted and topologically complex proteins as models for studying folding and stability
    • Yeates TO, Norcross TS, King NP (2007) Knotted and topologically complex proteins as models for studying folding and stability. Curr Opinion in Chem Biol 11: 595-603.
    • (2007) Curr Opinion in Chem Biol , vol.11 , pp. 595-603
    • Yeates, T.O.1    Norcross, T.S.2    King, N.P.3
  • 39
    • 34248570354 scopus 로고    scopus 로고
    • Protein knots and fold complexity: Some new twists
    • Taylor WR (2007) Protein knots and fold complexity: Some new twists. Comp Biol and Chem 31: 151.
    • (2007) Comp Biol and Chem , vol.31 , pp. 151
    • Taylor, W.R.1
  • 40
    • 73549125388 scopus 로고    scopus 로고
    • Jamming proteins with slipknots and their free energy landscapes
    • submitted
    • Sułkowska JI, Sulkowski P, Onuchic JN, Jamming proteins with slipknots and their free energy landscapes. submitted (2009).
    • (2009)
    • Sułkowska, J.I.1    Sulkowski, P.2    Onuchic, J.N.3
  • 41
    • 33749347406 scopus 로고    scopus 로고
    • Intricate Knots in Proteins: Function and Evolution. PLOS
    • Virnau P, Mirny LA, Kardar M (2006) Intricate Knots in Proteins: Function and Evolution. PLOS Comp Biol 2: 1074-1079.
    • (2006) Comp Biol , vol.2 , pp. 1074-1079
    • Virnau, P.1    Mirny, L.A.2    Kardar, M.3
  • 44
    • 0037044749 scopus 로고    scopus 로고
    • The cystine knot promotes folding and not thermodynamic stability in vascular endothelial growth factor
    • Muller YA, Heiring C, Misselwitz R, Welfle K, Welfle H (2002) The cystine knot promotes folding and not thermodynamic stability in vascular endothelial growth factor. J Biol Chem 277: 43410.
    • (2002) J Biol Chem , vol.277 , pp. 43410
    • Muller, Y.A.1    Heiring, C.2    Misselwitz, R.3    Welfle, K.4    Welfle, H.5
  • 49
    • 33646185640 scopus 로고    scopus 로고
    • Crystal Structure of Human Vascular Endothelial Growth Factor-B: Identification of Amino Acids Important for Receptor Binding
    • Iyer S, Scotney PD, Nash AD, Acharya KR (2006) Crystal Structure of Human Vascular Endothelial Growth Factor-B: Identification of Amino Acids Important for Receptor Binding. J Mol Biol 359: 76.
    • (2006) J Mol Biol , vol.359 , pp. 76
    • Iyer, S.1    Scotney, P.D.2    Nash, A.D.3    Acharya, K.R.4
  • 50
    • 2442716797 scopus 로고    scopus 로고
    • Mechanistic Diversity of Cytokine Receptor Signaling Across Cell
    • Stroud RM, Wells JA (2004) Mechanistic Diversity of Cytokine Receptor Signaling Across Cell Membranes. Sci STKE 231: re7.
    • (2004) Membranes. Sci , vol.STKE 231
    • Stroud, R.M.1    Wells, J.A.2
  • 51
    • 0037351880 scopus 로고    scopus 로고
    • The BMP7/ActRII Extracellular Domain Complex Provides New Insights into the Cooperative Nature of Receptor Assembly
    • Greenwald J, Groppe J, Gray P, Wiater E, Kwiatkowski W, Vale W, Choe S (2003) The BMP7/ActRII Extracellular Domain Complex Provides New Insights into the Cooperative Nature of Receptor Assembly. Mol Cell 11: 605.
    • (2003) Mol Cell , vol.11 , pp. 605
    • Greenwald, J.1    Groppe, J.2    Gray, P.3    Wiater, E.4    Kwiatkowski, W.5    Vale, W.6    Choe, S.7
  • 52
    • 34249821932 scopus 로고    scopus 로고
    • Backbone building from quadrilaterals. A fast and accurate algorithm for protein backbone reconstruction from alpha carbon coordinates
    • Gront D, Kmiecik S, Kolinski A (2007) Backbone building from quadrilaterals. A fast and accurate algorithm for protein backbone reconstruction from alpha carbon coordinates. J Comput Chemistry 28: 1593-1597.
    • (2007) J Comput Chemistry , vol.28 , pp. 1593-1597
    • Gront, D.1    Kmiecik, S.2    Kolinski, A.3
  • 53
    • 33750453758 scopus 로고    scopus 로고
    • Stretching of proteins in a uniform flow
    • Szymczak P, Cieplak M (2006) Stretching of proteins in a uniform flow. J Chem Phys 125: 164903.
    • (2006) J Chem Phys , vol.125 , pp. 164903
    • Szymczak, P.1    Cieplak, M.2
  • 54
    • 0032988663 scopus 로고    scopus 로고
    • Strength of Weak Bond Connecting Flexible Polymer Chains
    • Evans E, Ritchie K (1999) Strength of Weak Bond Connecting Flexible Polymer Chains. Biophys J 76: 2439-2447.
    • (1999) Biophys J , vol.76 , pp. 2439-2447
    • Evans, E.1    Ritchie, K.2
  • 55
    • 0034688856 scopus 로고    scopus 로고
    • Rupture of multiple parallel molecular binds under dynamic loading
    • Seifert U (2000) Rupture of multiple parallel molecular binds under dynamic loading. Phys Rev Lett 84: 2750-2753.
    • (2000) Phys Rev Lett , vol.84 , pp. 2750-2753
    • Seifert, U.1
  • 57
    • 10044290957 scopus 로고    scopus 로고
    • Reversible mechanical unfolding of single ubiquitin molecules
    • Chyan CL, Lin FC, Peng H, Yuan JM, Chang CH, et al. (2003) Reversible mechanical unfolding of single ubiquitin molecules. Biophys J 87: 3995-4006.
    • (2003) Biophys J , vol.87 , pp. 3995-4006
    • Chyan, C.L.1    Lin, F.C.2    Peng, H.3    Yuan, J.M.4    Chang, C.H.5
  • 58
    • 33748046806 scopus 로고    scopus 로고
    • Anisotropic deformation response of single protein molecules
    • Dietz H, Berkemeier F, Bertz M, Rief M (2006) Anisotropic deformation response of single protein molecules. Proc Natl Acad Sci U S A 103: 12724-12728.
    • (2006) Proc Natl Acad Sci U S A , vol.103 , pp. 12724-12728
    • Dietz, H.1    Berkemeier, F.2    Bertz, M.3    Rief, M.4
  • 59
    • 18744374455 scopus 로고    scopus 로고
    • Different molecular mechanics displayed by titin's constitutively and differentially expressed tandem Ig segment
    • Watanabe K, Muhle-Goll C, Kellermayer MSZ, Labeit S, Granzier HL (2002) Different molecular mechanics displayed by titin's constitutively and differentially expressed tandem Ig segment. Struct Biol J 137: 248-258.
    • (2002) Struct Biol , vol.J 137 , pp. 248-258
    • Watanabe, K.1    Muhle-Goll, C.2    Kellermayer, M.S.Z.3    Labeit, S.4    Granzier, H.L.5
  • 60
    • 0037192845 scopus 로고    scopus 로고
    • Molecular mechanics of cardiac titins PEVK and N2B spring elements
    • Watanabe K, Nair P, Labeit D, Kellermayer MSZ, Greaser M, et al. (2002) Molecular mechanics of cardiac titins PEVK and N2B spring elements. J Biol Chem 277: 11549-11558.
    • (2002) J Biol Chem , vol.277 , pp. 11549-11558
    • Watanabe, K.1    Nair, P.2    Labeit, D.3    Kellermayer, M.S.Z.4    Greaser, M.5
  • 61
    • 0142195769 scopus 로고    scopus 로고
    • Mechanical design of the first proximal Ig domain of hman cardiac titin revealed by single molecule force spectroscopy
    • Li HB, Fernandez JM (2003) Mechanical design of the first proximal Ig domain of hman cardiac titin revealed by single molecule force spectroscopy. J Mol Biol 334: 75-86.
    • (2003) J Mol Biol , vol.334 , pp. 75-86
    • Li, H.B.1    Fernandez, J.M.2
  • 65
    • 0034804341 scopus 로고    scopus 로고
    • Can non-mechanical proteins withstand force? Stretching barnase by atomic force microscopy and molecular dynamics simulation
    • Best RB, Li B, Steward A, Daggett V, Clarke J (2001) Can non-mechanical proteins withstand force? Stretching barnase by atomic force microscopy and molecular dynamics simulation. Biophys J 81: 2344-2356.
    • (2001) Biophys J , vol.81 , pp. 2344-2356
    • Best, R.B.1    Li, B.2    Steward, A.3    Daggett, V.4    Clarke, J.5
  • 66
    • 23244441268 scopus 로고    scopus 로고
    • Mechanically unfolding small topologically simple protein L
    • Brockwell DJ, Godfrey S, Beddard S, Paci E, West DK, et al. (2005) Mechanically unfolding small topologically simple protein L. Biophys J 89: 506-519.
    • (2005) Biophys J , vol.89 , pp. 506-519
    • Brockwell, D.J.1    Godfrey, S.2    Beddard, S.3    Paci, E.4    West, D.K.5
  • 67
    • 9244234443 scopus 로고    scopus 로고
    • Exploring the energy landscape of the GFP by single-molecule mechanical experiments
    • Dietz H, Rief M (2004) Exploring the energy landscape of the GFP by single-molecule mechanical experiments. Proc Natl Acad Sci U S A 101: 16192-16197.
    • (2004) Proc Natl Acad Sci U S A , vol.101 , pp. 16192-16197
    • Dietz, H.1    Rief, M.2
  • 68
    • 31944436148 scopus 로고    scopus 로고
    • Protein structure by mechanical triangulation
    • Dietz H, Rief M (2006) Protein structure by mechanical triangulation. Proc Natl Acad Sci U S A 103: 1244-1247.
    • (2006) Proc Natl Acad Sci U S A , vol.103 , pp. 1244-1247
    • Dietz, H.1    Rief, M.2
  • 69
    • 10044247452 scopus 로고    scopus 로고
    • Mechanical unfolding intermediates observed by single-molecule spectroscopy in fibronectin type III module
    • Li L, Han-Li Huang H, Badilla CL, Fernandez JM (2005) Mechanical unfolding intermediates observed by single-molecule spectroscopy in fibronectin type III module. J Mol Biol 345: 817-826.
    • (2005) J Mol Biol , vol.345 , pp. 817-826
    • Li, L.1    Han-Li Huang, H.2    Badilla, C.L.3    Fernandez, J.M.4
  • 71
    • 0038368702 scopus 로고    scopus 로고
    • Conformational analysis of native fibronectin by means of force spectroscopy
    • Oberdorfer Y, Fuchs H, Janshoff A (2000) Conformational analysis of native fibronectin by means of force spectroscopy. Langmuir 16: 9955-9958.
    • (2000) Langmuir , vol.16 , pp. 9955-9958
    • Oberdorfer, Y.1    Fuchs, H.2    Janshoff, A.3
  • 72
    • 0032516205 scopus 로고    scopus 로고
    • The molecular elasticity of the extracellular matrix protein tenascin
    • Oberhauser AF, Marszalek PE, Erickson HP, Fernandez JM (1998) The molecular elasticity of the extracellular matrix protein tenascin. Nature 14: 181-185.
    • (1998) Nature , vol.14 , pp. 181-185
    • Oberhauser, A.F.1    Marszalek, P.E.2    Erickson, H.P.3    Fernandez, J.M.4
  • 73
    • 33846666463 scopus 로고    scopus 로고
    • Polyprotein of GB1 is an ideal artificial elastomeric protein
    • Cao Y, Li HB (2007) Polyprotein of GB1 is an ideal artificial elastomeric protein. Nature Mat 6: 109-114.
    • (2007) Nature Mat , vol.6 , pp. 109-114
    • Cao, Y.1    Li, H.B.2


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