메뉴 건너뛰기




Volumn 91, Issue 2, 2006, Pages 694-704

Testing simplified proteins models of the hPin1 WW domain

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID; PROTEIN; PROTEIN HPIN1; UNCLASSIFIED DRUG;

EID: 33745714381     PISSN: 00063495     EISSN: None     Source Type: Journal    
DOI: 10.1529/biophysj.105.069138     Document Type: Article
Times cited : (25)

References (57)
  • 1
    • 0035818471 scopus 로고    scopus 로고
    • Ultrafast folding of WW domains without structured aromatic clusters in the denatured state
    • Ferguson, N., C. M. Johnson, M. Macias, H. Oschkinat, and A. R. Fersht. 2001. Ultrafast folding of WW domains without structured aromatic clusters in the denatured state. Proc. Natl. Acad. Sci. USA. 98:13002-13007.
    • (2001) Proc. Natl. Acad. Sci. USA , vol.98 , pp. 13002-13007
    • Ferguson, N.1    Johnson, C.M.2    Macias, M.3    Oschkinat, H.4    Fersht, A.R.5
  • 2
    • 0037386699 scopus 로고    scopus 로고
    • Structural basis for biphasic kinetics in the folding of the WW domain from a formin-binding protein: Lessons for protein design?
    • Karanicolas, J., and C. L. Brooks III. 2003. Structural basis for biphasic kinetics in the folding of the WW domain from a formin-binding protein: lessons for protein design? Proc. Natl. Acad. Sci. USA 100:3954-3959.
    • (2003) Proc. Natl. Acad. Sci. USA , vol.100 , pp. 3954-3959
    • Karanicolas, J.1    Brooks III, C.L.2
  • 4
    • 0038448924 scopus 로고    scopus 로고
    • Structural analysis of the mitotic regulator hPin1 in solution: Insights into domain architecture and substrate binding
    • Bayer, E., S. Goettsch, J. W. Mueller, B. Griewel, E. Guiberman, L. M. Mayr, and P. Bayer. 2003. Structural analysis of the mitotic regulator hPin1 in solution: insights into domain architecture and substrate binding. J. Biol. Chem. 278:26183-26193.
    • (2003) J. Biol. Chem. , vol.278 , pp. 26183-26193
    • Bayer, E.1    Goettsch, S.2    Mueller, J.W.3    Griewel, B.4    Guiberman, E.5    Mayr, L.M.6    Bayer, P.7
  • 6
    • 14744267933 scopus 로고    scopus 로고
    • Analysis of Pin1 WW domain through a simple statistical mechanics model
    • Bruscolini, P., and F. Cecconi. 2005. Analysis of Pin1 WW domain through a simple statistical mechanics model. Biophys. Chem. 115:153-158.
    • (2005) Biophys. Chem. , vol.115 , pp. 153-158
    • Bruscolini, P.1    Cecconi, F.2
  • 8
    • 0030424581 scopus 로고    scopus 로고
    • Structure and function of the WW domain
    • Sudol, M. 1996. Structure and function of the WW domain. Prog. Biophys. Mol. Biol. 65:113-132.
    • (1996) Prog. Biophys. Mol. Biol. , vol.65 , pp. 113-132
    • Sudol, M.1
  • 9
    • 18344362394 scopus 로고
    • On the use of classical statistical mechanics in the treatment of polymer chain conformations
    • Gō, N., and H. A. Scheraga. 1976. On the use of classical statistical mechanics in the treatment of polymer chain conformations. Macromolecules. 9:535-542.
    • (1976) Macromolecules , vol.9 , pp. 535-542
    • Go, N.1    Scheraga, H.A.2
  • 10
    • 0033693141 scopus 로고    scopus 로고
    • Matching simulation and experiment: A new simplified model for simulating protein folding
    • Sorenson, J. M., and T. Head-Gordon. 2000. Matching simulation and experiment: a new simplified model for simulating protein folding. J. Comp. Biol. 7:469-481.
    • (2000) J. Comp. Biol. , vol.7 , pp. 469-481
    • Sorenson, J.M.1    Head-Gordon, T.2
  • 11
    • 0141480046 scopus 로고    scopus 로고
    • Coarse-grained sequences for protein folding and design
    • Brown, S., N. J. Fawzi, and T. Head-Gordon. 2003. Coarse-grained sequences for protein folding and design. Proc. Natl. Acad. Sci. USA. 100:10712-10717.
    • (2003) Proc. Natl. Acad. Sci. USA , vol.100 , pp. 10712-10717
    • Brown, S.1    Fawzi, N.J.2    Head-Gordon, T.3
  • 12
    • 18344391877 scopus 로고    scopus 로고
    • Protein structures and optimal folding from a geometrical variational principle
    • Micheletti, C., J. R. Banavar, A. Maritan, and F. Seno. 1999. Protein structures and optimal folding from a geometrical variational principle. Phys. Rev. Lett. 82:3372-3375.
    • (1999) Phys. Rev. Lett. , vol.82 , pp. 3372-3375
    • Micheletti, C.1    Banavar, J.R.2    Maritan, A.3    Seno, F.4
  • 14
    • 0033613255 scopus 로고    scopus 로고
    • Prediction of protein-folding mechanisms from free-energy landscapes derived from native structures
    • Alm, E., and D. Baker. 1999. Prediction of protein-folding mechanisms from free-energy landscapes derived from native structures. Proc. Natl. Acad. Sci. USA. 96:11305-11310.
    • (1999) Proc. Natl. Acad. Sci. USA , vol.96 , pp. 11305-11310
    • Alm, E.1    Baker, D.2
  • 15
    • 0034652206 scopus 로고    scopus 로고
    • Transition-state structure as a unifying basis in protein-folding mechanisms: Contact order, chain topology, stability, and the extended nucleus mechanism
    • Fersht, A. R. 2000. Transition-state structure as a unifying basis in protein-folding mechanisms: contact order, chain topology, stability, and the extended nucleus mechanism. Proc. Natl. Acad. Sci. USA. 97:1525-1529.
    • (2000) Proc. Natl. Acad. Sci. USA , vol.97 , pp. 1525-1529
    • Fersht, A.R.1
  • 16
    • 0034604105 scopus 로고    scopus 로고
    • A surprising simplicity to protein folding
    • Baker, D. 2000. A surprising simplicity to protein folding. Nature. 405:39-42.
    • (2000) Nature , vol.405 , pp. 39-42
    • Baker, D.1
  • 17
    • 0031825181 scopus 로고    scopus 로고
    • Obligatory steps in protein folding and the conformational diversity of the transition state
    • Martinez, J. C., M. T. Pisabarro, and L. Serrano. 1998. Obligatory steps in protein folding and the conformational diversity of the transition state. Nat. Struct. Biol. 5:721-729.
    • (1998) Nat. Struct. Biol. , vol.5 , pp. 721-729
    • Martinez, J.C.1    Pisabarro, M.T.2    Serrano, L.3
  • 18
    • 0032750509 scopus 로고    scopus 로고
    • The folding transition state between SH3 domains is conformationally restricted and evolutionarily conserved
    • Martinez, J. C., and L. Serrano. 1999. The folding transition state between SH3 domains is conformationally restricted and evolutionarily conserved. Nat. Struct. Biol. 6:1010-1016.
    • (1999) Nat. Struct. Biol. , vol.6 , pp. 1010-1016
    • Martinez, J.C.1    Serrano, L.2
  • 20
    • 0032708771 scopus 로고    scopus 로고
    • Mutational analysis of acylphosphatase suggests the importance of topology and contact order in protein folding
    • Chiti, F., N. Taddei, P. M. White, M. Bucciantini, F. Magherini, M. Stefani, and C. M. Dobson. 1999. Mutational analysis of acylphosphatase suggests the importance of topology and contact order in protein folding. Nat. Struct. Biol. 6:1005-1009.
    • (1999) Nat. Struct. Biol. , vol.6 , pp. 1005-1009
    • Chiti, F.1    Taddei, N.2    White, P.M.3    Bucciantini, M.4    Magherini, F.5    Stefani, M.6    Dobson, C.M.7
  • 21
    • 0032502839 scopus 로고    scopus 로고
    • Contact order, transition state placement and the refolding rates of single domain proteins
    • Plaxco, K. W., K. T. Simons, and D. Baker. 1998. Contact order, transition state placement and the refolding rates of single domain proteins. J. Mol. Biol. 277:985-994.
    • (1998) J. Mol. Biol. , vol.277 , pp. 985-994
    • Plaxco, K.W.1    Simons, K.T.2    Baker, D.3
  • 22
    • 0034685604 scopus 로고    scopus 로고
    • Topological and energetic factors: What determines the structural details of the transition state ensemble and "en-route" intermediates for protein folding?
    • Clementi, C., H. Nymeyer, and J. N. Onuchic. 2000. Topological and energetic factors: what determines the structural details of the transition state ensemble and "en-route" intermediates for protein folding? 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
  • 23
    • 0033613131 scopus 로고    scopus 로고
    • A theoretical search for folding/unfolding nuclei in three-dimensional protein structures
    • Galzitskaya, O. V., and A. V. Finkelstein. 1999. A theoretical search for folding/unfolding nuclei in three-dimensional protein structures. Proc. Natl. Acad. Sci. USA. 96:11299-11304.
    • (1999) Proc. Natl. Acad. Sci. USA , vol.96 , pp. 11299-11304
    • Galzitskaya, O.V.1    Finkelstein, A.V.2
  • 24
    • 0033527768 scopus 로고    scopus 로고
    • Folding of a model three-helix bundle protein: A thermodynamic and kinetic analysis
    • Zhou, Y., and M. Karplus. 1999. Folding of a model three-helix bundle protein: a thermodynamic and kinetic analysis. J. Mol. Biol. 293:917-951.
    • (1999) J. Mol. Biol. , vol.293 , pp. 917-951
    • Zhou, Y.1    Karplus, M.2
  • 25
    • 0036927818 scopus 로고    scopus 로고
    • Direct molecular dynamics observation of protein folding transition state ensemble
    • Ding, F., N. V. Dokholyan, S. V. Buldyrev, H. E. Stanley, and E. I. Shakhnovich. 2002. Direct molecular dynamics observation of protein folding transition state ensemble. Biophys. J. 83:3525-3532.
    • (2002) Biophys. J. , vol.83 , pp. 3525-3532
    • Ding, F.1    Dokholyan, N.V.2    Buldyrev, S.V.3    Stanley, H.E.4    Shakhnovich, E.I.5
  • 26
    • 0346003771 scopus 로고    scopus 로고
    • Computing the transition state populations in simple protein model
    • Ozkan, S. B., K. A. Dill, and I. Bahar. 2003. Computing the transition state populations in simple protein model. Biopolymers. 68:35-46.
    • (2003) Biopolymers , vol.68 , pp. 35-46
    • Ozkan, S.B.1    Dill, K.A.2    Bahar, I.3
  • 28
    • 0001022344 scopus 로고    scopus 로고
    • The fast protein folding problem
    • Gruebele, M. 1999. The fast protein folding problem. Annu. Rev. Phys. Chem. 50:485-516.
    • (1999) Annu. Rev. Phys. Chem. , vol.50 , pp. 485-516
    • Gruebele, M.1
  • 29
    • 33845377127 scopus 로고
    • Estimation of effective interresidue contact energies from protein crystal structures: Quasichemical approximation
    • Miyazawa, S., and R. L. Jernigan. 1985. Estimation of effective interresidue contact energies from protein crystal structures: quasichemical approximation. Macromolecules. 18:534-552.
    • (1985) Macromolecules , vol.18 , pp. 534-552
    • Miyazawa, S.1    Jernigan, R.L.2
  • 30
    • 3042677501 scopus 로고    scopus 로고
    • The effects of nonnative interactions on protein folding rates: Theory and simulations
    • Clementi, C., and S. S. Plotkin. 2004. The effects of nonnative interactions on protein folding rates: theory and simulations. Protein Sci. 13:1750-1766.
    • (2004) Protein Sci. , vol.13 , pp. 1750-1766
    • Clementi, C.1    Plotkin, S.S.2
  • 31
    • 0036172116 scopus 로고    scopus 로고
    • Hydrophobic core packing in the Sh3 domain folding transition state
    • Northey, J. G. B., A. A. D. Nardo, and A. R. Davidson. 2002. Hydrophobic core packing in the Sh3 domain folding transition state. Nat. Struct. Biol. 9:126-130.
    • (2002) Nat. Struct. Biol. , vol.9 , pp. 126-130
    • Northey, J.G.B.1    Nardo, A.A.D.2    Davidson, A.R.3
  • 33
    • 19444381093 scopus 로고    scopus 로고
    • Chevron behavior and isostable enthalpic barriers in protein folding: Successes and limitation of simple Gō-like modeling
    • Kaya, H., Z. Liu, and H. S. Chan. 2005. Chevron behavior and isostable enthalpic barriers in protein folding: successes and limitation of simple Gō-like modeling. Biophys. J. 89:520-535.
    • (2005) Biophys. J. , vol.89 , pp. 520-535
    • Kaya, H.1    Liu, Z.2    Chan, H.S.3
  • 34
    • 0026643094 scopus 로고
    • The nature of folded states of globular proteins
    • Honeycutt, J. D., and D. Thirumalai. 1992. The nature of folded states of globular proteins. Biopolymers. 32:695-709.
    • (1992) Biopolymers , vol.32 , pp. 695-709
    • Honeycutt, J.D.1    Thirumalai, D.2
  • 35
    • 0030624384 scopus 로고    scopus 로고
    • Protein folding kinetics: Timescales, pathways and energy landscapes in terms of sequence-dependent properties
    • Veitshans, T., D. Klimov, and D. Thirumalai. 1996. Protein folding kinetics: timescales, pathways and energy landscapes in terms of sequence-dependent properties. Fold. Des. 2:1-22.
    • (1996) Fold. Des. , vol.2 , pp. 1-22
    • Veitshans, T.1    Klimov, D.2    Thirumalai, D.3
  • 36
    • 0032726519 scopus 로고    scopus 로고
    • Redesigning the hydrophobic core of a model β-sheet protein: Destabilizing traps through a threading approach
    • Sorenson, J. M., and T. Head-Gordon. 1999. Redesigning the hydrophobic core of a model β-sheet protein: destabilizing traps through a threading approach. Proteins Struct. Funct. Gen. 37:582-591.
    • (1999) Proteins Struct. Funct. Gen. , vol.37 , pp. 582-591
    • Sorenson, J.M.1    Head-Gordon, T.2
  • 37
    • 0031745665 scopus 로고    scopus 로고
    • Protein design: A perspective from simple tractable models
    • Shakhnovich, E. I. 1998. Protein design: a perspective from simple tractable models. Fold. Des. 3:R45-R58.
    • (1998) Fold. Des. , vol.3
    • Shakhnovich, E.I.1
  • 38
    • 0001412505 scopus 로고
    • Non-equilibrium molecular dynamics via Gauss's principle of least constraint
    • Evans, D. J., W. G. Hoover, B. H. Failor, B. Moran, and A. J. C. Ladd. 1983. Non-equilibrium molecular dynamics via Gauss's principle of least constraint. Phys. Rev. A. 28:1016-1021.
    • (1983) Phys. Rev. A , vol.28 , pp. 1016-1021
    • Evans, D.J.1    Hoover, W.G.2    Failor, B.H.3    Moran, B.4    Ladd, A.J.C.5
  • 39
    • 84893482610 scopus 로고
    • Solution for best rotation to relate two sets of vectors
    • Kabsch, W. 1976. Solution for best rotation to relate two sets of vectors. Acta Crystallogr. 32:922-923.
    • (1976) Acta Crystallogr. , vol.32 , pp. 922-923
    • Kabsch, W.1
  • 40
    • 33646987405 scopus 로고
    • Optimized Monte Carlo data analysis
    • Ferrenberg, A. M., and R. H. Swendsen. 1989. Optimized Monte Carlo data analysis. Phys. Rev. Lett. 63:1195-1198.
    • (1989) Phys. Rev. Lett. , vol.63 , pp. 1195-1198
    • Ferrenberg, A.M.1    Swendsen, R.H.2
  • 41
    • 0002689652 scopus 로고    scopus 로고
    • Thermodynamics of protein folding: A statistical mechanical study of a small all-β protein
    • Guo, Z., and C. L. Brooks III. 1997. Thermodynamics of protein folding: a statistical mechanical study of a small all-β protein. Biopolymers. 42:745-757.
    • (1997) Biopolymers , vol.42 , pp. 745-757
    • Guo, Z.1    Brooks III, C.L.2
  • 42
    • 0035371215 scopus 로고    scopus 로고
    • The structural basis of antiviral drug resistance and role of folding pathways in HIV-1 protease
    • Cecconi, F., C. Micheletti, P. Carloni, and A. Maritan. 2001. The structural basis of antiviral drug resistance and role of folding pathways in HIV-1 protease. Proteins Struct. Funct. Gen. 43:365-372.
    • (2001) Proteins Struct. Funct. Gen. , vol.43 , pp. 365-372
    • Cecconi, F.1    Micheletti, C.2    Carloni, P.3    Maritan, A.4
  • 43
    • 0036073320 scopus 로고    scopus 로고
    • Crucial stages of protein folding through a solvable model: Predicting target sites for enzyme-inhibiting drugs
    • Micheletti, C., F. Cecconi, A. Flammini, and A. Maritan. 2002. Crucial stages of protein folding through a solvable model: predicting target sites for enzyme-inhibiting drugs. Protein Sci. 11:1878-1887.
    • (2002) Protein Sci. , vol.11 , pp. 1878-1887
    • Micheletti, C.1    Cecconi, F.2    Flammini, A.3    Maritan, A.4
  • 44
    • 0035278121 scopus 로고    scopus 로고
    • Thermodynamically important contacts in folding of model proteins
    • Scala, A., N. V. Dokholyan, S. V. Buldyrev, and H. E. Stanley. 2001. Thermodynamically important contacts in folding of model proteins. Phys. Rev. E. 63:032901.
    • (2001) Phys. Rev. E , vol.63 , pp. 032901
    • Scala, A.1    Dokholyan, N.V.2    Buldyrev, S.V.3    Stanley, H.E.4
  • 45
    • 0035252350 scopus 로고    scopus 로고
    • Three key residues form a critical contact network in a protein folding transition state
    • Vendruscolo, M., E. Paci, C. M. Dobson, and M. Karplus. 2001. Three key residues form a critical contact network in a protein folding transition state. Nature. 409:641-645.
    • (2001) Nature , vol.409 , pp. 641-645
    • Vendruscolo, M.1    Paci, E.2    Dobson, C.M.3    Karplus, M.4
  • 46
    • 0028024928 scopus 로고
    • Specific nucleus as the transition state for protein folding: Evidence from the lattice model
    • Abkevich, V. I., A. M. Gutin, and E. I. Shakhnovich. 1994. Specific nucleus as the transition state for protein folding: evidence from the lattice model. Biochemistry. 33:10026-10036.
    • (1994) Biochemistry , vol.33 , pp. 10026-10036
    • Abkevich, V.I.1    Gutin, A.M.2    Shakhnovich, E.I.3
  • 47
    • 0034581317 scopus 로고    scopus 로고
    • The energy landscape theory of protein folding: Insights into folding mechanisms and scenarios
    • Onuchic, J. N., H. Nymeyer, A. E. Garcia, J. Chahine, and N. D. Socci. 2000. The energy landscape theory of protein folding: insights into folding mechanisms and scenarios. Adv. Protein Chem. 53:87-152.
    • (2000) Adv. Protein Chem. , vol.53 , pp. 87-152
    • Onuchic, J.N.1    Nymeyer, H.2    Garcia, A.E.3    Chahine, J.4    Socci, N.D.5
  • 49
    • 14144255497 scopus 로고    scopus 로고
    • Phi-value analysis by molecular dynamics simulations of reversible folding
    • Settanni, G., F. Rao, and A. Caflisch. 2005. Phi-value analysis by molecular dynamics simulations of reversible folding. Proc. Natl. Acad. Sci. USA. 102:628-633.
    • (2005) Proc. Natl. Acad. Sci. USA , vol.102 , pp. 628-633
    • Settanni, G.1    Rao, F.2    Caflisch, A.3
  • 50
    • 18844421130 scopus 로고    scopus 로고
    • Robustness of downhill folding: Guidelines for the analysis of equilibrium folding experiments on small proteins
    • Naganathan, A. N., R. Perez-Jimenez, J. M. Sanchez-Ruiz, and V. Munoz. 2005. Robustness of downhill folding: guidelines for the analysis of equilibrium folding experiments on small proteins. Biochemistry. 44:7435-7449.
    • (2005) Biochemistry , vol.44 , pp. 7435-7449
    • Naganathan, A.N.1    Perez-Jimenez, R.2    Sanchez-Ruiz, J.M.3    Munoz, V.4
  • 51
    • 17844386576 scopus 로고    scopus 로고
    • Comparison of sequence-based and structure-based energy functions for the reversible folding of a peptide
    • Cavalli, A., M. Vendruscolo, and E. Paci. 2005. Comparison of sequence-based and structure-based energy functions for the reversible folding of a peptide. Biophys. J. 88:3158-3166.
    • (2005) Biophys. J. , vol.88 , pp. 3158-3166
    • Cavalli, A.1    Vendruscolo, M.2    Paci, E.3
  • 52
    • 0001764256 scopus 로고    scopus 로고
    • Energy landscape of a model protein
    • Miller, M. A., and D. J. Wales. 1999. Energy landscape of a model protein. J. Chem. Phys. 111:6610-6616.
    • (1999) J. Chem. Phys. , vol.111 , pp. 6610-6616
    • Miller, M.A.1    Wales, D.J.2
  • 53
    • 0034284060 scopus 로고    scopus 로고
    • Polymer principles of protein calorimetric two-state cooperativity
    • Kaya, H., and H. S. Chan. 2000. Polymer principles of protein calorimetric two-state cooperativity. Proteins Struct. Funct. Gen. 40:637-661.
    • (2000) Proteins Struct. Funct. Gen. , vol.40 , pp. 637-661
    • Kaya, H.1    Chan, H.S.2
  • 54
    • 0347753598 scopus 로고    scopus 로고
    • Energetic of protein thermodynamic cooperativity: Contributions of local and nonlocal interactions
    • Knott, M., H. Kaya, and H. S. Chan. 2004. Energetic of protein thermodynamic cooperativity: contributions of local and nonlocal interactions. Polymers. 45:623-632.
    • (2004) Polymers , vol.45 , pp. 623-632
    • Knott, M.1    Kaya, H.2    Chan, H.S.3
  • 55
    • 0034284366 scopus 로고    scopus 로고
    • Modeling protein density of states: Additive hydrophobic effects are insufficient for calorimetric two-state cooperativity
    • Chan, H. S. 2000. Modeling protein density of states: Additive hydrophobic effects are insufficient for calorimetric two-state cooperativity. Proteins Struct. Funct. Gen. 40:543-571.
    • (2000) Proteins Struct. Funct. Gen. , vol.40 , pp. 543-571
    • Chan, H.S.1
  • 56
    • 0032568599 scopus 로고    scopus 로고
    • Folding funnels and frustration in off-lattice minimalist protein landscapes
    • Nymeyer, H., A. E. García, and J. N. Onuchic. 1998. Folding funnels and frustration in off-lattice minimalist protein landscapes. Proc. Natl. Acad. Sci. USA. 95:5921-5928.
    • (1998) Proc. Natl. Acad. Sci. USA , vol.95 , pp. 5921-5928
    • Nymeyer, H.1    García, A.E.2    Onuchic, J.N.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.