메뉴 건너뛰기




Volumn 96, Issue 3, 2009, Pages 831-839

Sequence-specific size, structure, and stability of tight protein knots

Author keywords

[No Author keywords available]

Indexed keywords

GLYCINE; PEPTIDE; WATER;

EID: 61549130600     PISSN: 00063495     EISSN: 15420086     Source Type: Journal    
DOI: 10.1016/j.bpj.2008.10.019     Document Type: Article
Times cited : (43)

References (59)
  • 1
    • 0028421135 scopus 로고
    • Are there knots in proteins?
    • Mansfield, M. L. 1994. Are there knots in proteins? Nat. Struct. Biol. 1:213-214.
    • (1994) Nat. Struct. Biol , vol.1 , pp. 213-214
    • Mansfield, M.L.1
  • 2
    • 0037413604 scopus 로고    scopus 로고
    • A tangled problem
    • Taylor, W. R., and K. Lin. 2003. A tangled problem. Nature. 421:25.
    • (2003) Nature , vol.421 , pp. 25
    • Taylor, W.R.1    Lin, K.2
  • 3
    • 33646904782 scopus 로고    scopus 로고
    • Statistics of knots, geometry of conformations, and evolution of proteins
    • Lua, R. C., and A. Y. Grosberg. 2006. Statistics of knots, geometry of conformations, and evolution of proteins. PLOS Computational Biology. 2:e45.
    • (2006) PLOS Computational Biology , vol.2
    • Lua, R.C.1    Grosberg, A.Y.2
  • 4
    • 33749347406 scopus 로고    scopus 로고
    • Intricate knots in proteins: Function and evolution
    • Virnau, P., L. A. Mirny, and M. Kardar. 2006. Intricate knots in proteins: function and evolution. PLOS Comput. Biol. 2:e122.
    • (2006) PLOS Comput. Biol , vol.2
    • Virnau, P.1    Mirny, L.A.2    Kardar, M.3
  • 5
    • 85031347277 scopus 로고    scopus 로고
    • Reference deleted in proof
    • Reference deleted in proof.
  • 7
    • 85031366953 scopus 로고    scopus 로고
    • Reference deleted in proof
    • Reference deleted in proof.
  • 8
    • 34248570354 scopus 로고    scopus 로고
    • Protein knots and fold complexity: Some new twists
    • Taylor, W. R. 2007. Protein knots and fold complexity: some new twists. Comput. Biol. Chem. 31:151-162.
    • (2007) Comput. Biol. Chem , vol.31 , pp. 151-162
    • Taylor, W.R.1
  • 9
    • 0037157105 scopus 로고    scopus 로고
    • The importance of being knotted: Effects of the C-terminal knot structure on enzymatic and mechanical properties of bovine carbonic anhydrase II
    • Alam, M. T., T. Yamada, U. Carlsson, and A. Ikai. 2002. The importance of being knotted: effects of the C-terminal knot structure on enzymatic and mechanical properties of bovine carbonic anhydrase II. FEBS Lett. 519:35-40.
    • (2002) FEBS Lett , vol.519 , pp. 35-40
    • Alam, M.T.1    Yamada, T.2    Carlsson, U.3    Ikai, A.4
  • 10
  • 12
    • 34548575206 scopus 로고    scopus 로고
    • Identification of rare slipknots in proteins and their implications for stability and folding
    • King, N. P., E. O. Yeates, and T. O. Yeates. 2007. Identification of rare slipknots in proteins and their implications for stability and folding. J. Mol. Biol. 373:153-166.
    • (2007) J. Mol. Biol , vol.373 , pp. 153-166
    • King, N.P.1    Yeates, E.O.2    Yeates, T.O.3
  • 13
    • 0037424506 scopus 로고    scopus 로고
    • Twists, knots, and rings in proteins: Structural definition of the cyclotide framework
    • Rosengren, K. J., N. L. Daly, M. R. Plan, C. Waine, and D. J. Craik. 2002. Twists, knots, and rings in proteins: structural definition of the cyclotide framework. J. Biol. Chem. 278:8606-8616.
    • (2002) J. Biol. Chem , vol.278 , pp. 8606-8616
    • Rosengren, K.J.1    Daly, N.L.2    Plan, M.R.3    Waine, C.4    Craik, D.J.5
  • 17
    • 27544511752 scopus 로고    scopus 로고
    • Knots in globule and coil phases of a model polyethylene
    • Virnau, P., V. Kantor, and M. Kardar. 2005. Knots in globule and coil phases of a model polyethylene. J. Am. Chem. Soc. 127:15102-15106.
    • (2005) J. Am. Chem. Soc , vol.127 , pp. 15102-15106
    • Virnau, P.1    Kantor, V.2    Kardar, M.3
  • 18
    • 36849002753 scopus 로고    scopus 로고
    • The tangled web of self-tying knots
    • Belmonte, A. 2007. The tangled web of self-tying knots. Proc. Natl. Acad. Sci. USA. 104:17243-17244.
    • (2007) Proc. Natl. Acad. Sci. USA , vol.104 , pp. 17243-17244
    • Belmonte, A.1
  • 19
    • 53149132042 scopus 로고    scopus 로고
    • The elusiveness of polymer knots
    • Kardar, M. 2007. The elusiveness of polymer knots. Eur. PhysJ. B. 64:519-523.
    • (2007) Eur. PhysJ. B , vol.64 , pp. 519-523
    • Kardar, M.1
  • 22
    • 36248974307 scopus 로고    scopus 로고
    • Metastable tight knots in a wormlike polymer
    • Grosberg, A. Y., and Y. Rabin. 2007. Metastable tight knots in a wormlike polymer. Phys. Rev. Lett. 99:217801.
    • (2007) Phys. Rev. Lett , vol.99 , pp. 217801
    • Grosberg, A.Y.1    Rabin, Y.2
  • 26
    • 0033519644 scopus 로고    scopus 로고
    • Tying a molecular knot with optical tweezers
    • Arai, Y., et al. 1999. Tying a molecular knot with optical tweezers. Nature. 399:446-448.
    • (1999) Nature , vol.399 , pp. 446-448
    • Arai, Y.1
  • 27
    • 1042300668 scopus 로고    scopus 로고
    • Behavior of complex knots in single DNA molecules
    • Bao, X. R., H. J. Lee, and S. R. Quake. 2003. Behavior of complex knots in single DNA molecules. Phys. Rev. Lett. 91:265506.
    • (2003) Phys. Rev. Lett , vol.91 , pp. 265506
    • Bao, X.R.1    Lee, H.J.2    Quake, S.R.3
  • 28
    • 0035538383 scopus 로고    scopus 로고
    • The study of molecular interactions by AFM force spectroscopy
    • Hugel, T., and M. Seitz. 2001. The study of molecular interactions by AFM force spectroscopy. Macromol. Rapid Commun. 22: 989-1016.
    • (2001) Macromol. Rapid Commun , vol.22 , pp. 989-1016
    • Hugel, T.1    Seitz, M.2
  • 29
    • 62649138263 scopus 로고    scopus 로고
    • Tightening the knot in phytochrome by single molecule atomic force microscopy
    • In press
    • Bornschlögl, T., D. Anstrom, J. Dzubiella, M. Rief, and K. T. Forest. 2009. Tightening the knot in phytochrome by single molecule atomic force microscopy. Biophys. J. In press.
    • (2009) Biophys. J
    • Bornschlögl, T.1    Anstrom, D.2    Dzubiella, J.3    Rief, M.4    Forest, K.T.5
  • 30
    • 0033529081 scopus 로고    scopus 로고
    • Influence of a knot on the strength of a polymer strand
    • Saitta, A. M., P. D. Soper, E. Wasserman, and M. L. Klein. 1999. Influence of a knot on the strength of a polymer strand. Nature. 399:46-48.
    • (1999) Nature , vol.399 , pp. 46-48
    • Saitta, A.M.1    Soper, P.D.2    Wasserman, E.3    Klein, M.L.4
  • 31
    • 0032094933 scopus 로고    scopus 로고
    • Tight knots in polymers
    • Mansfield, M. L. 1997. Tight knots in polymers. Macromolecules. 31:4030-4032.
    • (1997) Macromolecules , vol.31 , pp. 4030-4032
    • Mansfield, M.L.1
  • 33
    • 34548439786 scopus 로고    scopus 로고
    • Externally steered relaxation of tight polyethylene tangles with different initial knot topologies
    • Arteca, G. A. 2007. Externally steered relaxation of tight polyethylene tangles with different initial knot topologies. Theor. Chem. Acc. 118:549-556.
    • (2007) Theor. Chem. Acc , vol.118 , pp. 549-556
    • Arteca, G.A.1
  • 34
    • 33646131847 scopus 로고    scopus 로고
    • Brownian dynamics simulation of knot diffusion along a stretched DNA molecule
    • Vologodskii, A. 2006. Brownian dynamics simulation of knot diffusion along a stretched DNA molecule. Biophys. J. 90:1594-1597.
    • (2006) Biophys. J , vol.90 , pp. 1594-1597
    • Vologodskii, A.1
  • 35
    • 35948963619 scopus 로고    scopus 로고
    • Langevin dynamics simulations of the diffusion of molecular knots in tensioned polymer chains
    • Huang, L., and D. E. Makarov. 2007. Langevin dynamics simulations of the diffusion of molecular knots in tensioned polymer chains. J. Phys. Chem. A. 111:10338-10344.
    • (2007) J. Phys. Chem. A , vol.111 , pp. 10338-10344
    • Huang, L.1    Makarov, D.E.2
  • 39
    • 0036725277 scopus 로고    scopus 로고
    • Molecular dynamics simulations ofmacromolecules: Aperspective
    • Karplus, M., and J. A. McCammon. 2002. Molecular dynamics simulations ofmacromolecules: aperspective. Nat. Struct. Mol. Biol. 9:646-652.
    • (2002) Nat. Struct. Mol. Biol , vol.9 , pp. 646-652
    • Karplus, M.1    McCammon, J.A.2
  • 40
    • 85031359795 scopus 로고    scopus 로고
    • Case, D. A., T. Darden, T. E. Cheatham, III, C. Simmerling, J. Wang, et al. 2006. AMBER9.0. University of California, San Francisco.
    • Case, D. A., T. Darden, T. E. Cheatham, III, C. Simmerling, J. Wang, et al. 2006. AMBER9.0. University of California, San Francisco.
  • 42
    • 0037375572 scopus 로고    scopus 로고
    • Structure of the YibK methyltransferase from Haemophilus influenzae (HI0766): A cofactor bound at a site formed by a knot
    • Lim, K., H. Zhang, A. Tempczyk, W. Krajewski, N. Bonander, et al. 2003. Structure of the YibK methyltransferase from Haemophilus influenzae (HI0766): a cofactor bound at a site formed by a knot. Proteins Struct. Funct. Genet. 51:56-67.
    • (2003) Proteins Struct. Funct. Genet , vol.51 , pp. 56-67
    • Lim, K.1    Zhang, H.2    Tempczyk, A.3    Krajewski, W.4    Bonander, N.5
  • 43
    • 0030996769 scopus 로고    scopus 로고
    • The crystal structure of plant acetohydroxy acid isomeroreductase complexed with NADPH, two magnesium ions and a herbicidal transition state analog determined at 1.65 Å resolution
    • Biou, V., R. Dumas, C. Cohen-Addad, R. Douce, D. Job, et al. 1997. The crystal structure of plant acetohydroxy acid isomeroreductase complexed with NADPH, two magnesium ions and a herbicidal transition state analog determined at 1.65 Å resolution. EMBO J. 16:3405-3415.
    • (1997) EMBO J , vol.16 , pp. 3405-3415
    • Biou, V.1    Dumas, R.2    Cohen-Addad, C.3    Douce, R.4    Job, D.5
  • 46
    • 0035883960 scopus 로고    scopus 로고
    • Modified atomic force microscope applied to the measurement of elastic modulus for a single peptide molecule
    • Ptak, A., S. Takeda, C. Nakamura, J. M. M. Kageshima, S. P. Jarvis, et al. 2001. Modified atomic force microscope applied to the measurement of elastic modulus for a single peptide molecule. J. Appl. Phys. 90:3095-3099.
    • (2001) J. Appl. Phys , vol.90 , pp. 3095-3099
    • Ptak, A.1    Takeda, S.2    Nakamura, C.3    Kageshima, J.M.M.4    Jarvis, S.P.5
  • 49
    • 34250744647 scopus 로고    scopus 로고
    • The molecular structure of human tissue type XV presents a unique conformation among the collagens
    • Myers, J. C., P. S. Amenta, A. S. Dion, J. P. Sciancalepore, C. Nagaswami, et al. 2007. The molecular structure of human tissue type XV presents a unique conformation among the collagens. Biochem. J. 404:535-544.
    • (2007) Biochem. J , vol.404 , pp. 535-544
    • Myers, J.C.1    Amenta, P.S.2    Dion, A.S.3    Sciancalepore, J.P.4    Nagaswami, C.5
  • 51
    • 0002335699 scopus 로고
    • Solvent interactions with proteins as revealed by X-ray crystallographic studies
    • Interactions. R. B. Gregroy, editor. Marcel Dekker, New York, pp
    • Baker, E. N. 1995. Solvent interactions with proteins as revealed by X-ray crystallographic studies. In Protein-Solvent Interactions. R. B. Gregroy, editor. Marcel Dekker, New York, pp. 143-189.
    • (1995) Protein-Solvent , pp. 143-189
    • Baker, E.N.1
  • 52
    • 0029994817 scopus 로고    scopus 로고
    • Using buried water molecules to explore the energy landscape of proteins
    • Denisov, V. P., J. Peters, H. D. Horlein, and B. Halle. 1996. Using buried water molecules to explore the energy landscape of proteins. Nat. Struct. Biol. 3:505-509.
    • (1996) Nat. Struct. Biol , vol.3 , pp. 505-509
    • Denisov, V.P.1    Peters, J.2    Horlein, H.D.3    Halle, B.4
  • 53
    • 42149186359 scopus 로고    scopus 로고
    • Solvent molecules bridge the mechanical unfolding transition state of a protein
    • Dougan, L., G. F. H. Lu, and J. M. Fernandez. 2008. Solvent molecules bridge the mechanical unfolding transition state of a protein. Proc. Natl. Acad. Sci. USA. 105:3185-3190.
    • (2008) Proc. Natl. Acad. Sci. USA , vol.105 , pp. 3185-3190
    • Dougan, L.1    Lu, G.F.H.2    Fernandez, J.M.3
  • 54
    • 38849196324 scopus 로고    scopus 로고
    • Water as an active constituent in cell biology
    • Ball, P. 2008. Water as an active constituent in cell biology. Chem. Rev. 108:74-108.
    • (2008) Chem. Rev , vol.108 , pp. 74-108
    • Ball, P.1
  • 55
    • 0033578333 scopus 로고    scopus 로고
    • Binding of buried structural water increases the flexibility of proteins
    • Fischer, S., and C. S. Verma. 1999. Binding of buried structural water increases the flexibility of proteins. Proc. Natl. Acad. Sci. USA. 96:9613-9615.
    • (1999) Proc. Natl. Acad. Sci. USA , vol.96 , pp. 9613-9615
    • Fischer, S.1    Verma, C.S.2
  • 56
    • 0024278757 scopus 로고
    • Hydrophobicity of the peptide C=OH-N hydrogen-bonded group
    • Roseman, M. A. 1988. Hydrophobicity of the peptide C=OH-N hydrogen-bonded group. J. Mol. Biol. 201:621-623.
    • (1988) J. Mol. Biol , vol.201 , pp. 621-623
    • Roseman, M.A.1
  • 58
    • 36549032188 scopus 로고    scopus 로고
    • Knotted and topologically complex proteins as models for studying folding and stability
    • Yeates, T., S. Norcross, and N. P. King. 2007. Knotted and topologically complex proteins as models for studying folding and stability. Curr. Opin. Chem. Biol. 11:595-603.
    • (2007) Curr. Opin. Chem. Biol , vol.11 , pp. 595-603
    • Yeates, T.1    Norcross, S.2    King, N.P.3
  • 59
    • 34248351114 scopus 로고    scopus 로고
    • Solid-state nanopores
    • Dekker, C. 2007. Solid-state nanopores. Nat. Nanotechnol. 2:209-215.
    • (2007) Nat. Nanotechnol , vol.2 , pp. 209-215
    • Dekker, C.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.