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Volumn 86, Issue 4, 2004, Pages 2383-2391

Dynamic Properties of the N-Terminal Swapped Dimer of Ribonuclease A

Author keywords

[No Author keywords available]

Indexed keywords

DIMER; ENZYME; RIBONUCLEASE A;

EID: 1942519384     PISSN: 00063495     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0006-3495(04)74295-2     Document Type: Article
Times cited : (49)

References (47)
  • 1
    • 0342980331 scopus 로고    scopus 로고
    • Characterization of the unfolding pathway of the cell-cycle protein p13suc1 by molecular dynamics simulations: Implications for domain swapping
    • Alonso, D. O., E. Alm, and V. Daggett. 2000. Characterization of the unfolding pathway of the cell-cycle protein p13suc1 by molecular dynamics simulations: implications for domain swapping. Structure. 8:101-110.
    • (2000) Structure , vol.8 , pp. 101-110
    • Alonso, D.O.1    Alm, E.2    Daggett, V.3
  • 2
    • 0032802062 scopus 로고    scopus 로고
    • On the convergence of the conformational coordinates basis set obtained by the essential dynamics analysis of proteins' molecular dynamics simulations
    • Amadei, A., M. A. Ceruso, and A. Di Nola. 1999. On the convergence of the conformational coordinates basis set obtained by the essential dynamics analysis of proteins' molecular dynamics simulations. Proteins Struct. Funct. Gen. 36:419-424.
    • (1999) Proteins Struct. Funct. Gen. , vol.36 , pp. 419-424
    • Amadei, A.1    Ceruso, M.A.2    Di Nola, A.3
  • 4
    • 0028865843 scopus 로고
    • Three-dimensional domain swapping: A mechanism for oligomer assembly
    • Bennett, M. J., M. P. Schlunegger, and D. Eisenberg. 1995. Three-dimensional domain swapping: a mechanism for oligomer assembly. Protein Sci. 4:2455-2468.
    • (1995) Protein Sci. , vol.4 , pp. 2455-2468
    • Bennett, M.J.1    Schlunegger, M.P.2    Eisenberg, D.3
  • 5
    • 0002775934 scopus 로고
    • Interaction models for water in relation to protein hydration
    • B. Pullman, editor. Reidel Publishing Company, Dordrecht, The Netherlands
    • Berendsen, H. J. C., J. P. M. Postma, W. F. van Gusteren, and J. Hermans. 1981. Interaction models for water in relation to protein hydration. In Intermolecular Forces. B. Pullman, editor. Reidel Publishing Company, Dordrecht, The Netherlands. 331-342.
    • (1981) Intermolecular Forces , pp. 331-342
    • Berendsen, H.J.C.1    Postma, J.P.M.2    Van Gusteren, W.F.3    Hermans, J.4
  • 10
    • 0034793735 scopus 로고    scopus 로고
    • The structure of an engineered domain-swapped ribonuclease dimer and its implications for the evolution of proteins toward oligomerization
    • Canals, A., J. Pous, A. Guasch, A. Benito, M. Ribo, M. Vilanova, and M. Coll. 2001. The structure of an engineered domain-swapped ribonuclease dimer and its implications for the evolution of proteins toward oligomerization. Structure. 9:967-976.
    • (2001) Structure , vol.9 , pp. 967-976
    • Canals, A.1    Pous, J.2    Guasch, A.3    Benito, A.4    Ribo, M.5    Vilanova, M.6    Coll, M.7
  • 11
    • 0032901423 scopus 로고    scopus 로고
    • Mechanics and dynamics of B1 domain of protein G: Role of packing and surface hydrophobic residues
    • Ceruso, M. A., A. Amadei, and A. Di Nola. 1999a. Mechanics and dynamics of B1 domain of protein G: role of packing and surface hydrophobic residues. Protein Sci. 8:147-160.
    • (1999) Protein Sci. , vol.8 , pp. 147-160
    • Ceruso, M.A.1    Amadei, A.2    Di Nola, A.3
  • 12
    • 0032808843 scopus 로고    scopus 로고
    • Effects of core-packing on the structure, function, and mechanics of a four-helix-bundle protein ROP
    • Ceruso, M. A., A. Grottesi, and A. Di Nola. 1999b. Effects of core-packing on the structure, function, and mechanics of a four-helix-bundle protein ROP. Proteins Struct. Funct. Gen. 36:436-446.
    • (1999) Proteins Struct. Funct. Gen. , vol.36 , pp. 436-446
    • Ceruso, M.A.1    Grottesi, A.2    Di Nola, A.3
  • 13
    • 0037295565 scopus 로고    scopus 로고
    • Dynamic effects of mutations within two loops of cytochrome c551 from Pseudomonas aeruginosa
    • Ceruso, M. A., A. Grottesi, and A. Di Nola. 2003. Dynamic effects of mutations within two loops of cytochrome c551 from Pseudomonas aeruginosa. Proteins Struct. Funct. Gen. 50:222-229.
    • (2003) Proteins Struct. Funct. Gen. , vol.50 , pp. 222-229
    • Ceruso, M.A.1    Grottesi, A.2    Di Nola, A.3
  • 15
    • 33846823909 scopus 로고
    • Particle mesh Ewald: An N-log (N) method for Ewald sums in large systems
    • Darden, T., D. York, and L. Pedersen. 1993. Particle mesh Ewald: an N-log (N) method for Ewald sums in large systems. J. Chem. Phys. 98:10089-10092.
    • (1993) J. Chem. Phys. , vol.98 , pp. 10089-10092
    • Darden, T.1    York, D.2    Pedersen, L.3
  • 16
    • 0036923039 scopus 로고    scopus 로고
    • Molecular dynamics simulation of the SH3 domain aggregation suggests a generic amyloidogenesis mechanism
    • Ding, F., N. V. Dokholyan, S. V. Buldyrev, H. E. Stanley, and E. I. Shakhnovich. 2002. Molecular dynamics simulation of the SH3 domain aggregation suggests a generic amyloidogenesis mechanism. J. Mol. Biol. 324:851-857.
    • (2002) J. Mol. Biol. , vol.324 , pp. 851-857
    • Ding, F.1    Dokholyan, N.V.2    Buldyrev, S.V.3    Stanley, H.E.4    Shakhnovich, E.I.5
  • 18
    • 0001970541 scopus 로고    scopus 로고
    • Crystallographic studies of ribonuclease complexes
    • G. D'Alessio and J. F. Riordan, editors. Academic Press, New York
    • Gilliland, G. 1997. Crystallographic studies of ribonuclease complexes. In Ribonuclease: Structures and Functions. G. D'Alessio and J. F. Riordan, editors. Academic Press, New York. 306-341.
    • (1997) Ribonuclease: Structures and Functions , pp. 306-341
    • Gilliland, G.1
  • 19
    • 0034029144 scopus 로고    scopus 로고
    • Proteins with similar architecture exhibit similar large-scale dynamic behavior
    • Keskin, O., R. L. Jernigan, and I. Bahar. 2000. Proteins with similar architecture exhibit similar large-scale dynamic behavior. Biophys. J. 78:2093-2106.
    • (2000) Biophys. J. , vol.78 , pp. 2093-2106
    • Keskin, O.1    Jernigan, R.L.2    Bahar, I.3
  • 20
    • 0036108484 scopus 로고    scopus 로고
    • Three-dimensional domain swapping: As domains continue to swap
    • Liu, Y., and D. Eisenberg. 2002. Three-dimensional domain swapping: as domains continue to swap. Protein Sci. 11:1285-1299.
    • (2002) Protein Sci. , vol.11 , pp. 1285-1299
    • Liu, Y.1    Eisenberg, D.2
  • 21
    • 0035127031 scopus 로고    scopus 로고
    • A domain-swapped RNase A dimer with implications for amyloid formation
    • Liu, Y., G. Gotte, M. Libonati, and D. Eisenberg. 2001. A domain-swapped RNase A dimer with implications for amyloid formation. Nat. Struct. Biol. 8:211-214.
    • (2001) Nat. Struct. Biol. , vol.8 , pp. 211-214
    • Liu, Y.1    Gotte, G.2    Libonati, M.3    Eisenberg, D.4
  • 22
    • 0032584210 scopus 로고    scopus 로고
    • The crystal structure of a three-dimensional domain-swapped dimer of RNase A at a 2.1-Å resolution
    • Liu, Y., P. J. Hart, M. P. Schlunegger, and D. Eisenberg. 1998. The crystal structure of a three-dimensional domain-swapped dimer of RNase A at a 2.1-Å resolution. Proc. Natl. Acad. Sci. USA. 95:3437-3442.
    • (1998) Proc. Natl. Acad. Sci. USA , vol.95 , pp. 3437-3442
    • Liu, Y.1    Hart, P.J.2    Schlunegger, M.P.3    Eisenberg, D.4
  • 24
    • 0029041305 scopus 로고
    • Swapping structural determinants of ribonucleases: An energetic analysis of the hinge peptide 16-22
    • Mazzarella, L., L. Vitagliano, and A. Zagari. 1995. Swapping structural determinants of ribonucleases: an energetic analysis of the hinge peptide 16-22. Proc. Natl. Acad. Sci. USA. 92:3799-3803.
    • (1995) Proc. Natl. Acad. Sci. USA , vol.92 , pp. 3799-3803
    • Mazzarella, L.1    Vitagliano, L.2    Zagari, A.3
  • 25
  • 26
    • 0042821730 scopus 로고    scopus 로고
    • Subtle functional collective motions in pancreatic-like ribonucleases: From ribonuclease A to angiogenin
    • Merlino, A., L. Vitagliano, M. A. Ceruso, and L. Mazzarella. 2003. Subtle functional collective motions in pancreatic-like ribonucleases: from ribonuclease A to angiogenin. Proteins Struct. Funct. Gen. 53:101-110.
    • (2003) Proteins Struct. Funct. Gen. , vol.53 , pp. 101-110
    • Merlino, A.1    Vitagliano, L.2    Ceruso, M.A.3    Mazzarella, L.4
  • 27
    • 0031260211 scopus 로고    scopus 로고
    • Effects of substrate binding on the dynamics of RNase A: Molecular dynamics simulations of UpA bound and Native RNase A
    • Nadig, G., and S. Vishveshwara. 1997. Effects of substrate binding on the dynamics of RNase A: molecular dynamics simulations of UpA bound and Native RNase A. Biopolymers. 42:505-520.
    • (1997) Biopolymers , vol.42 , pp. 505-520
    • Nadig, G.1    Vishveshwara, S.2
  • 28
    • 0035830749 scopus 로고    scopus 로고
    • Different susceptibility of the two dimers of ribonuclease A to subtilisin. Implications for their structure
    • Nenci, A., G. Gotte, B. Maras, and M. Libonati. 2001. Different susceptibility of the two dimers of ribonuclease A to subtilisin. Implications for their structure. Biochim. Biophys. Acta. 1545:255-262.
    • (2001) Biochim. Biophys. Acta , vol.1545 , pp. 255-262
    • Nenci, A.1    Gotte, G.2    Maras, B.3    Libonati, M.4
  • 29
    • 0033080367 scopus 로고    scopus 로고
    • Glutamine repeats and neurodegenerative diseases: Molecular aspects
    • Perutz, M. 1999. Glutamine repeats and neurodegenerative diseases: molecular aspects. Trends Biochem. Sci. 24:58-63.
    • (1999) Trends Biochem. Sci. , vol.24 , pp. 58-63
    • Perutz, M.1
  • 30
    • 0021359166 scopus 로고
    • Relationships between nonhyperbolic kinetics and dimeric structure in ribonucleases
    • Piccoli, R., and G. D'Alessio. 1984. Relationships between nonhyperbolic kinetics and dimeric structure in ribonucleases. J. Biol. Chem. 259:693-695.
    • (1984) J. Biol. Chem. , vol.259 , pp. 693-695
    • Piccoli, R.1    D'Alessio, G.2
  • 32
    • 0037339403 scopus 로고    scopus 로고
    • Selective excitation of native fluctuations during thermal unfolding simulations: Horse heart cytochrome C as a case study
    • Roccatano, D., I. Daidone, M. A. Ceruso, C. Bossa, and A. Di Nola. 2003. Selective excitation of native fluctuations during thermal unfolding simulations: horse heart cytochrome C as a case study. Biophys. J. 84:1876-1883.
    • (2003) Biophys. J. , vol.84 , pp. 1876-1883
    • Roccatano, D.1    Daidone, I.2    Ceruso, M.A.3    Bossa, C.4    Di Nola, A.5
  • 33
    • 0037337270 scopus 로고    scopus 로고
    • The unfolding story of the three-dimensional domain swapping
    • Rousseau, F., J. W. H. Schymkovitz, and L. S. Itzhaki. 2003. The unfolding story of the three-dimensional domain swapping. Structure. 11:243-251.
    • (2003) Structure , vol.11 , pp. 243-251
    • Rousseau, F.1    Schymkovitz, J.W.H.2    Itzhaki, L.S.3
  • 34
    • 33646940952 scopus 로고
    • Numerical integration of the Cartesian equations of motion of a system with constraints: Molecular dynamics simulations of n-alkanes
    • Ryckaert, J. P., G. Ciccotti, and H. J. C. Berendsen. 1977. Numerical integration of the Cartesian equations of motion of a system with constraints: molecular dynamics simulations of n-alkanes. J. Comput. Phys. 23:327-341.
    • (1977) J. Comput. Phys. , vol.23 , pp. 327-341
    • Ryckaert, J.P.1    Ciccotti, G.2    Berendsen, H.J.C.3
  • 35
    • 0027511809 scopus 로고
    • High-resolution three-dimensional structure of ribonuclease A in solution by nuclear magnetic resonance spectroscopy
    • Santoro, J., C. Gonzalez, M. Bruix, J. L. Neira, J. L. Nieto, J. Herranz, and M. Rico. 1993. High-resolution three-dimensional structure of ribonuclease A in solution by nuclear magnetic resonance spectroscopy. J. Mol. Biol. 229:722-734.
    • (1993) J. Mol. Biol. , vol.229 , pp. 722-734
    • Santoro, J.1    Gonzalez, C.2    Bruix, M.3    Neira, J.L.4    Nieto, J.L.5    Herranz, J.6    Rico, M.7
  • 36
    • 0030770294 scopus 로고    scopus 로고
    • Oligomer formation by three-dimensional domain swapping: A model for protein assembly and misassembly
    • Schlunegger, M. P., M. J. Bennett, and D. Eisenberg. 1997. Oligomer formation by three-dimensional domain swapping: a model for protein assembly and misassembly. Adv. Protein Chem. 50:61-122.
    • (1997) Adv. Protein Chem. , vol.50 , pp. 61-122
    • Schlunegger, M.P.1    Bennett, M.J.2    Eisenberg, D.3
  • 37
    • 0041843693 scopus 로고    scopus 로고
    • Molecular dynamics simulation of dimeric and monomeric forms of human prion protein: Insight into dynamics and properties
    • Sekijima, M., C. Motono, S. Yamasaki, K. Kaneko, and Y. Akiyama. 2003. Molecular dynamics simulation of dimeric and monomeric forms of human prion protein: insight into dynamics and properties. Biophys. J. 85:1176-1185.
    • (2003) Biophys. J. , vol.85 , pp. 1176-1185
    • Sekijima, M.1    Motono, C.2    Yamasaki, S.3    Kaneko, K.4    Akiyama, Y.5
  • 38
    • 0028568249 scopus 로고
    • Characterization of substrate UpA binding to RNase A-computer modelling and energetics approach
    • Seshadri, K., V. S. Rao, and S. Vishveshwara. 1994. Characterization of substrate UpA binding to RNase A-computer modelling and energetics approach. J. Biomol. Struct. Dyn. 12:581-603.
    • (1994) J. Biomol. Struct. Dyn. , vol.12 , pp. 581-603
    • Seshadri, K.1    Rao, V.S.2    Vishveshwara, S.3
  • 39
    • 0035037143 scopus 로고    scopus 로고
    • A proposed structural model for amyloid fibril elongation: Domain swapping forms an interdigitating beta-structure polymer
    • Sinha, N., C. J. Tsai, and R. Nussinov. 2001. A proposed structural model for amyloid fibril elongation: domain swapping forms an interdigitating beta-structure polymer. Protein Eng. 14:93-103.
    • (2001) Protein Eng. , vol.14 , pp. 93-103
    • Sinha, N.1    Tsai, C.J.2    Nussinov, R.3
  • 41
    • 0032454903 scopus 로고    scopus 로고
    • Binding of a substrate analog to a domain swapping protein: X-ray structure of the complex of bovine seminal ribonuclease with uridylyl(2′,5′)adenosine
    • Vitagliano, L., S. Adinolfi, A. Riccio, F. Sica, A. Zagari, and L. Mazzarella. 1998. Binding of a substrate analog to a domain swapping protein: x-ray structure of the complex of bovine seminal ribonuclease with uridylyl(2′,5′)adenosine. Protein Sci. 7:1691-1699.
    • (1998) Protein Sci. , vol.7 , pp. 1691-1699
    • Vitagliano, L.1    Adinolfi, S.2    Riccio, A.3    Sica, F.4    Zagari, A.5    Mazzarella, L.6
  • 42
    • 0032714439 scopus 로고    scopus 로고
    • A potential allosteric subsite generated by domain swapping in bovine seminal ribonuclease
    • Vitagliano, L., S. Adinolfi, F. Sica, A. Merlino, A. Zagari, and L. Mazzarella. 1999. A potential allosteric subsite generated by domain swapping in bovine seminal ribonuclease. J. Mol. Biol. 293:569-577.
    • (1999) J. Mol. Biol. , vol.293 , pp. 569-577
    • Vitagliano, L.1    Adinolfi, S.2    Sica, F.3    Merlino, A.4    Zagari, A.5    Mazzarella, L.6
  • 43
    • 0033933352 scopus 로고    scopus 로고
    • Productive and nonproductive binding to ribonuclease A: X-ray structure of two complexes with uridylyl(2′,5′)guanosine
    • Vitagliano, L., A. Merlino, A. Zagari, and L. Mazzarella. 2000. Productive and nonproductive binding to ribonuclease A: x-ray structure of two complexes with uridylyl(2′,5′)guanosine. Protein Sci. 9:1217-1225.
    • (2000) Protein Sci. , vol.9 , pp. 1217-1225
    • Vitagliano, L.1    Merlino, A.2    Zagari, A.3    Mazzarella, L.4
  • 45
    • 0020772531 scopus 로고
    • Active site of RNase: Neutron diffraction study of a complex with uridine vanadate, a transitionstate analog
    • Wlodawer, A., M. Miller, and L. Sjolin. 1983. Active site of RNase: neutron diffraction study of a complex with uridine vanadate, a transitionstate analog. Proc. Natl. Acad. Sci. USA. 80:3628-3631.
    • (1983) Proc. Natl. Acad. Sci. USA , vol.80 , pp. 3628-3631
    • Wlodawer, A.1    Miller, M.2    Sjolin, L.3
  • 46
    • 0024291642 scopus 로고
    • Structure of phosphate-free ribonuclease A refined at 1.26 Å
    • Wlodawer, A., L. A. Svensson, L. Sjolin, and G. Gilliland. 1988. Structure of phosphate-free ribonuclease A refined at 1.26 Å. Biochemistry. 27:2705-2717.
    • (1988) Biochemistry , vol.27 , pp. 2705-2717
    • Wlodawer, A.1    Svensson, L.A.2    Sjolin, L.3    Gilliland, G.4
  • 47
    • 0028564999 scopus 로고
    • The structures of RNase A complexed with 3′-CMP and d(CpA): Active site conformation and conserved water molecules
    • Zegers, I., D. Maes, M. H. Dao-Thi, F. Poortmans, R. Palmer, and L. Wyns. 1994. The structures of RNase A complexed with 3′-CMP and d(CpA): active site conformation and conserved water molecules. Protein Sci. 3:2322-2339.
    • (1994) Protein Sci. , vol.3 , pp. 2322-2339
    • Zegers, I.1    Maes, D.2    Dao-Thi, M.H.3    Poortmans, F.4    Palmer, R.5    Wyns, L.6


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