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Volumn 373, Issue 1, 2007, Pages 153-166

Identification of Rare Slipknots in Proteins and Their Implications for Stability and Folding

Author keywords

alkaline phosphatase; protein folding; protein knots; protein topology; thermophilic proteins

Indexed keywords

ALKALINE PHOSPHATASE;

EID: 34548575206     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmb.2007.07.042     Document Type: Article
Times cited : (129)

References (56)
  • 1
    • 0016077291 scopus 로고
    • Topology of globular proteins
    • Crippen G.M. Topology of globular proteins. J. Theor. Biol. 45 (1974) 327-338
    • (1974) J. Theor. Biol. , vol.45 , pp. 327-338
    • Crippen, G.M.1
  • 2
  • 4
    • 0032502839 scopus 로고    scopus 로고
    • Contact order, transition state placement and the refolding rates of single domain proteins
    • Plaxco K.W., Simons K.T., and Baker D. Contact order, transition state placement and the refolding rates of single domain proteins. J. Mol. Biol. 277 (1998) 985-994
    • (1998) J. Mol. Biol. , vol.277 , pp. 985-994
    • Plaxco, K.W.1    Simons, K.T.2    Baker, D.3
  • 5
    • 0036678120 scopus 로고    scopus 로고
    • Experimental evaluation of topological parameters determining protein-folding rates
    • Miller E.J., Fischer K.F., and Marqusee S. Experimental evaluation of topological parameters determining protein-folding rates. Proc. Natl. Acad. Sci. USA 99 (2002) 10359-10363
    • (2002) Proc. Natl. Acad. Sci. USA , vol.99 , pp. 10359-10363
    • Miller, E.J.1    Fischer, K.F.2    Marqusee, S.3
  • 7
    • 34247215529 scopus 로고    scopus 로고
    • Discovery of a thermophilic protein complex stabilized by topologically interlinked chains
    • Boutz D.R., Cascio D., Whitelegge J., Perry L.J., and Yeates T.O. Discovery of a thermophilic protein complex stabilized by topologically interlinked chains. J. Mol. Biol. 368 (2007) 1332-1344
    • (2007) J. Mol. Biol. , vol.368 , pp. 1332-1344
    • Boutz, D.R.1    Cascio, D.2    Whitelegge, J.3    Perry, L.J.4    Yeates, T.O.5
  • 10
    • 0034710671 scopus 로고    scopus 로고
    • A deeply knotted protein structure and how it might fold
    • Taylor W.R. A deeply knotted protein structure and how it might fold. Nature 406 (2000) 916-919
    • (2000) Nature , vol.406 , pp. 916-919
    • Taylor, W.R.1
  • 11
    • 27844461604 scopus 로고    scopus 로고
    • A light-sensing knot revealed by the structure of the chromophore-binding domain of phytochrome
    • Wagner J.R., Brunzelle J.S., Forest K.T., and Vierstra R.D. A light-sensing knot revealed by the structure of the chromophore-binding domain of phytochrome. Nature 438 (2005) 325-331
    • (2005) Nature , vol.438 , pp. 325-331
    • Wagner, J.R.1    Brunzelle, J.S.2    Forest, K.T.3    Vierstra, R.D.4
  • 13
    • 0028421135 scopus 로고
    • Are there knots in proteins?
    • Mansfield M.L. Are there knots in proteins?. Nat. Struct. Biol. 1 (1994) 213-214
    • (1994) Nat. Struct. Biol. , vol.1 , pp. 213-214
    • Mansfield, M.L.1
  • 16
    • 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 A resolution
    • Biou V., Dumas R., Cohen-Addad C., Douce R., Job D., and Pebay-Peyroula E. The crystal structure of plant acetohydroxy acid isomeroreductase complexed with NADPH, two magnesium ions and a herbicidal transition state analog determined at 1.65 A resolution. EMBO J. 16 (1997) 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    Pebay-Peyroula, E.6
  • 17
    • 33747883688 scopus 로고    scopus 로고
    • Rapid knot detection and application to protein structure prediction
    • Khatib F., Weirauch M.T., and Rohl C.A. Rapid knot detection and application to protein structure prediction. Bioinformatics 22 (2006) e252-e259
    • (2006) Bioinformatics , vol.22
    • Khatib, F.1    Weirauch, M.T.2    Rohl, C.A.3
  • 18
    • 33646904782 scopus 로고    scopus 로고
    • Statistics of knots, geometry of conformations, and evolution of proteins
    • Lua R.C., and Grosberg A.Y. Statistics of knots, geometry of conformations, and evolution of proteins. PLoS Comput. Biol. 2 (2006) e45
    • (2006) PLoS Comput. Biol. , vol.2
    • Lua, R.C.1    Grosberg, A.Y.2
  • 19
    • 33749347406 scopus 로고    scopus 로고
    • Intricate knots in proteins: function and evolution
    • Virnau P., Mirny L.A., and Kardar M. Intricate knots in proteins: function and evolution. PLoS Comput. Biol. 2 (2006) e122
    • (2006) PLoS Comput. Biol. , vol.2
    • Virnau, P.1    Mirny, L.A.2    Kardar, M.3
  • 20
    • 13844255609 scopus 로고    scopus 로고
    • Folding studies on a knotted protein
    • Mallam A.L., and Jackson S.E. Folding studies on a knotted protein. J. Mol. Biol. 346 (2005) 1409-1421
    • (2005) J. Mol. Biol. , vol.346 , pp. 1409-1421
    • Mallam, A.L.1    Jackson, S.E.2
  • 21
    • 33745163582 scopus 로고    scopus 로고
    • Probing nature's knots: the folding pathway of a knotted homodimeric protein
    • Mallam A.L., and Jackson S.E. Probing nature's knots: the folding pathway of a knotted homodimeric protein. J. Mol. Biol. 359 (2006) 1420-1436
    • (2006) J. Mol. Biol. , vol.359 , pp. 1420-1436
    • Mallam, A.L.1    Jackson, S.E.2
  • 22
    • 0344010492 scopus 로고    scopus 로고
    • The refined structure of a protein catenane: the HK97 bacteriophage capsid at 3.44 A resolution
    • Helgstrand C., Wikoff W.R., Duda R.L., Hendrix R. W., Johnson J.E., and Liljas L. The refined structure of a protein catenane: the HK97 bacteriophage capsid at 3.44 A resolution. J. Mol. Biol. 334 (2003) 885-899
    • (2003) J. Mol. Biol. , vol.334 , pp. 885-899
    • Helgstrand, C.1    Wikoff, W.R.2    Duda, R.L.3    Hendrix, R. W.4    Johnson, J.E.5    Liljas, L.6
  • 23
    • 0037459237 scopus 로고    scopus 로고
    • Thermodynamics of a designed protein catenane
    • Blankenship J.W., and Dawson P.E. Thermodynamics of a designed protein catenane. J. Mol. Biol. 327 (2003) 537-548
    • (2003) J. Mol. Biol. , vol.327 , pp. 537-548
    • Blankenship, J.W.1    Dawson, P.E.2
  • 24
    • 33748123253 scopus 로고    scopus 로고
    • A framework for describing topological frustration in models of protein folding
    • Norcross T.S., and Yeates T.O. A framework for describing topological frustration in models of protein folding. J. Mol. Biol. 362 (2006) 605-621
    • (2006) J. Mol. Biol. , vol.362 , pp. 605-621
    • Norcross, T.S.1    Yeates, T.O.2
  • 25
    • 0025777694 scopus 로고
    • Reaction mechanism of alkaline phosphatase based on crystal structures. Two-metal ion catalysis
    • Kim E.E., and Wyckoff H.W. Reaction mechanism of alkaline phosphatase based on crystal structures. Two-metal ion catalysis. J. Mol. Biol. 218 (1991) 449-464
    • (1991) J. Mol. Biol. , vol.218 , pp. 449-464
    • Kim, E.E.1    Wyckoff, H.W.2
  • 26
    • 0033613255 scopus 로고    scopus 로고
    • Prediction of protein-folding mechanisms from free-energy landscapes derived from native structures
    • Alm E., and Baker D. Prediction of protein-folding mechanisms from free-energy landscapes derived from native structures. Proc. Natl. Acad. Sci. USA 96 (1999) 11305-11310
    • (1999) Proc. Natl. Acad. Sci. USA , vol.96 , pp. 11305-11310
    • Alm, E.1    Baker, D.2
  • 27
    • 34248576501 scopus 로고    scopus 로고
    • Protein folds, knots and tangles
    • JA C., KC M., and EJ R. (Eds), World Scientific, Singapore
    • Taylor W. Protein folds, knots and tangles. In: JA C., KC M., and EJ R. (Eds). Physical and Numerical Models in Knot Theory (2005), World Scientific, Singapore 171-202
    • (2005) Physical and Numerical Models in Knot Theory , pp. 171-202
    • Taylor, W.1
  • 28
    • 0042924171 scopus 로고    scopus 로고
    • A knot or not a knot? SETting the record 'straight' on proteins
    • Taylor W.R., Xiao B., Gamblin S.J., and Lin K. A knot or not a knot? SETting the record 'straight' on proteins. Comput. Biol. Chem. 27 (2003) 11-15
    • (2003) Comput. Biol. Chem. , vol.27 , pp. 11-15
    • Taylor, W.R.1    Xiao, B.2    Gamblin, S.J.3    Lin, K.4
  • 29
    • 0642361805 scopus 로고
    • Topological invariants of knots and links
    • Alexander J.W. Topological invariants of knots and links. Trans. Am. Math. Soc. 30 (1928) 275-306
    • (1928) Trans. Am. Math. Soc. , vol.30 , pp. 275-306
    • Alexander, J.W.1
  • 30
    • 84968518084 scopus 로고
    • A polynomial invariant for knots via von Neumann algebras
    • Jones V. A polynomial invariant for knots via von Neumann algebras. Bull. Am. Math. Soc. 12 (1985) 103-111
    • (1985) Bull. Am. Math. Soc. , vol.12 , pp. 103-111
    • Jones, V.1
  • 31
    • 0043180474 scopus 로고    scopus 로고
    • PISCES: a protein sequence culling server
    • Wang G., and Dunbrack Jr. R.L. PISCES: a protein sequence culling server. Bioinformatics 19 (2003) 1589-1591
    • (2003) Bioinformatics , vol.19 , pp. 1589-1591
    • Wang, G.1    Dunbrack Jr., R.L.2
  • 32
    • 13444307044 scopus 로고    scopus 로고
    • Secondary-structure matching (SSM), a new tool for fast protein structure alignment in three dimensions
    • Krissinel E., and Henrick K. Secondary-structure matching (SSM), a new tool for fast protein structure alignment in three dimensions. Acta Crystallogr. D 60 (2004) 2256-2268
    • (2004) Acta Crystallogr. D , vol.60 , pp. 2256-2268
    • Krissinel, E.1    Henrick, K.2
  • 33
    • 20444390656 scopus 로고    scopus 로고
    • Metal specificity is correlated with two crucial active site residues in Escherichia coli alkaline phosphatase
    • Wang J., Stieglitz K.A., and Kantrowitz E.R. Metal specificity is correlated with two crucial active site residues in Escherichia coli alkaline phosphatase. Biochemistry 44 (2005) 8378-8386
    • (2005) Biochemistry , vol.44 , pp. 8378-8386
    • Wang, J.1    Stieglitz, K.A.2    Kantrowitz, E.R.3
  • 34
    • 0141594761 scopus 로고    scopus 로고
    • Structural basis for the dual thymidine and thymidylate kinase activity of herpes thymidine kinases
    • Gardberg A., Shuvalova L., Monnerjahn C., Konrad M., and Lavie A. Structural basis for the dual thymidine and thymidylate kinase activity of herpes thymidine kinases. Structure 11 (2003) 1265-1277
    • (2003) Structure , vol.11 , pp. 1265-1277
    • Gardberg, A.1    Shuvalova, L.2    Monnerjahn, C.3    Konrad, M.4    Lavie, A.5
  • 36
    • 0025330038 scopus 로고
    • lac permease of Escherichia coli: topology and sequence elements promoting membrane insertion
    • Calamia J., and Manoil C. lac permease of Escherichia coli: topology and sequence elements promoting membrane insertion. Proc. Natl. Acad. Sci. USA 87 (1990) 4937-4941
    • (1990) Proc. Natl. Acad. Sci. USA , vol.87 , pp. 4937-4941
    • Calamia, J.1    Manoil, C.2
  • 37
    • 0026052185 scopus 로고
    • Membrane topology analysis of Escherichia coli mannitol permease by using a nested-deletion method to create mtlA-phoA fusions
    • Sugiyama J.E., Mahmoodian S., and Jacobson G.R. Membrane topology analysis of Escherichia coli mannitol permease by using a nested-deletion method to create mtlA-phoA fusions. Proc. Natl. Acad. Sci. USA 88 (1991) 9603-9607
    • (1991) Proc. Natl. Acad. Sci. USA , vol.88 , pp. 9603-9607
    • Sugiyama, J.E.1    Mahmoodian, S.2    Jacobson, G.R.3
  • 38
    • 34248570354 scopus 로고    scopus 로고
    • Protein knots and fold complexity: some new twists
    • Taylor W.R. Protein knots and fold complexity: some new twists. Comput. Biol. Chem. 31 (2007) 151-162
    • (2007) Comput. Biol. Chem. , vol.31 , pp. 151-162
    • Taylor, W.R.1
  • 39
    • 33846505059 scopus 로고    scopus 로고
    • Coupling substrate and ion binding to extracellular gate of a sodium-dependent aspartate transporter
    • Boudker O., Ryan R.M., Yernool D., Shimamoto K., and Gouaux E. Coupling substrate and ion binding to extracellular gate of a sodium-dependent aspartate transporter. Nature 445 (2007) 387-393
    • (2007) Nature , vol.445 , pp. 387-393
    • Boudker, O.1    Ryan, R.M.2    Yernool, D.3    Shimamoto, K.4    Gouaux, E.5
  • 41
    • 0017662230 scopus 로고
    • Differential scanning calorimetry of apo-, apophosphoryl, and metalloalkaline phosphatases
    • Chlebowski J.F., and Mabrey S. Differential scanning calorimetry of apo-, apophosphoryl, and metalloalkaline phosphatases. J. Biol. Chem. 252 (1977) 7042-7052
    • (1977) J. Biol. Chem. , vol.252 , pp. 7042-7052
    • Chlebowski, J.F.1    Mabrey, S.2
  • 42
    • 0018786919 scopus 로고
    • Calorimetry of alkaline phosphatase. Stability of the monomer and effect of metal ion and phosphate binding on dimer stability
    • Chlebowski J.F., Mabrey S., and Falk M.C. Calorimetry of alkaline phosphatase. Stability of the monomer and effect of metal ion and phosphate binding on dimer stability. J. Biol. Chem. 254 (1979) 5745-5753
    • (1979) J. Biol. Chem. , vol.254 , pp. 5745-5753
    • Chlebowski, J.F.1    Mabrey, S.2    Falk, M.C.3
  • 43
    • 0035908887 scopus 로고    scopus 로고
    • 2+ binding to alkaline phosphatase correlates with slow changes in protein lability
    • 2+ binding to alkaline phosphatase correlates with slow changes in protein lability. Biochemistry 40 (2001) 11219-11226
    • (2001) Biochemistry , vol.40 , pp. 11219-11226
    • Dirnbach, E.1    Steel, D.G.2    Gafni, A.3
  • 46
    • 0037413604 scopus 로고    scopus 로고
    • Protein knots: a tangled problem
    • Taylor W.R., and Lin K. Protein knots: a tangled problem. Nature 421 (2003) 25
    • (2003) Nature , vol.421 , pp. 25
    • Taylor, W.R.1    Lin, K.2
  • 47
    • 0023430560 scopus 로고
    • Enhanced protein thermostability from site-directed mutations that decrease the entropy of unfolding
    • Matthews B.W., Nicholson H., and Becktel W.J. Enhanced protein thermostability from site-directed mutations that decrease the entropy of unfolding. Proc. Natl. Acad. Sci. USA 84 (1987) 6663-6667
    • (1987) Proc. Natl. Acad. Sci. USA , vol.84 , pp. 6663-6667
    • Matthews, B.W.1    Nicholson, H.2    Becktel, W.J.3
  • 48
    • 0027155577 scopus 로고
    • Engineered disulfide bonds as probes of the folding pathway of barnase: increasing the stability of proteins against the rate of denaturation
    • Clarke J., and Fersht A.R. Engineered disulfide bonds as probes of the folding pathway of barnase: increasing the stability of proteins against the rate of denaturation. Biochemistry 32 (1993) 4322-4329
    • (1993) Biochemistry , vol.32 , pp. 4322-4329
    • Clarke, J.1    Fersht, A.R.2
  • 49
    • 0024116932 scopus 로고
    • Function of arginine-166 in the active site of Escherichia coli alkaline phosphatase
    • Chaidaroglou A., Brezinski D.J., Middleton S.A., and Kantrowitz E.R. Function of arginine-166 in the active site of Escherichia coli alkaline phosphatase. Biochemistry 27 (1988) 8338-8343
    • (1988) Biochemistry , vol.27 , pp. 8338-8343
    • Chaidaroglou, A.1    Brezinski, D.J.2    Middleton, S.A.3    Kantrowitz, E.R.4
  • 50
    • 0014949207 scopus 로고
    • Cleavage of structural proteins during the assembly of the head of bacteriophage T4
    • Laemmli U.K. Cleavage of structural proteins during the assembly of the head of bacteriophage T4. Nature 227 (1970) 680-685
    • (1970) Nature , vol.227 , pp. 680-685
    • Laemmli, U.K.1
  • 51
    • 0034705337 scopus 로고    scopus 로고
    • A revised mechanism for the alkaline phosphatase reaction involving three metal ions
    • Stec B., Holtz K.M., and Kantrowitz E.R. A revised mechanism for the alkaline phosphatase reaction involving three metal ions. J. Mol. Biol. 299 (2000) 1303-1311
    • (2000) J. Mol. Biol. , vol.299 , pp. 1303-1311
    • Stec, B.1    Holtz, K.M.2    Kantrowitz, E.R.3
  • 52
    • 0017184389 scopus 로고
    • A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding
    • Bradford M.M. A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding. Anal. Biochem. 72 (1976) 248-254
    • (1976) Anal. Biochem. , vol.72 , pp. 248-254
    • Bradford, M.M.1
  • 53
    • 0014690182 scopus 로고
    • Escherichia coli co (II) alkaline phosphatase
    • Applebury M.L., and Coleman J.E. Escherichia coli co (II) alkaline phosphatase. J. Biol. Chem. 244 (1969) 709-718
    • (1969) J. Biol. Chem. , vol.244 , pp. 709-718
    • Applebury, M.L.1    Coleman, J.E.2
  • 54
    • 0021099043 scopus 로고
    • 113Cd nuclear magnetic resonance of Cd(II) alkaline phosphatases
    • Gettins P., and Coleman J.E. 113Cd nuclear magnetic resonance of Cd(II) alkaline phosphatases. J. Biol. Chem. 258 (1983) 396-407
    • (1983) J. Biol. Chem. , vol.258 , pp. 396-407
    • Gettins, P.1    Coleman, J.E.2
  • 55
    • 4944244701 scopus 로고    scopus 로고
    • Harvard Univ. Press, Cambridge, Massachusetts
    • Sossinsky A. Knots (2002), Harvard Univ. Press, Cambridge, Massachusetts
    • (2002) Knots
    • Sossinsky, A.1


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