메뉴 건너뛰기




Volumn 386, Issue 4, 2009, Pages 920-928

ψ-Constrained Simulations of Protein Folding Transition States: Implications for Calculating ϕ

Author keywords

Langevin dynamics; metal binding; phi analysis; psi analysis

Indexed keywords

HISTIDINE DERIVATIVE;

EID: 60149100982     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmb.2009.01.010     Document Type: Article
Times cited : (11)

References (25)
  • 1
    • 33646935188 scopus 로고    scopus 로고
    • Characterizing the protein folding transition state using psi analysis
    • Sosnick T.R., Krantz B.A., Dothager R.S., and Baxa M. Characterizing the protein folding transition state using psi analysis. Chem. Rev. 106 (2006) 1862-1876
    • (2006) Chem. Rev. , vol.106 , pp. 1862-1876
    • Sosnick, T.R.1    Krantz, B.A.2    Dothager, R.S.3    Baxa, M.4
  • 2
  • 3
    • 48249086517 scopus 로고    scopus 로고
    • Kinetic barriers and the role of topology in protein and RNA folding
    • Sosnick T.R. Kinetic barriers and the role of topology in protein and RNA folding. Protein Sci. 17 (2008) 1308-1318
    • (2008) Protein Sci. , vol.17 , pp. 1308-1318
    • Sosnick, T.R.1
  • 4
    • 1442348207 scopus 로고    scopus 로고
    • Discerning the structure and energy of multiple transition states in protein folding using psi-analysis
    • Krantz B.A., Dothager R.S., and Sosnick T.R. Discerning the structure and energy of multiple transition states in protein folding using psi-analysis. J. Mol. Biol. 337 (2004) 463-475
    • (2004) J. Mol. Biol. , vol.337 , pp. 463-475
    • Krantz, B.A.1    Dothager, R.S.2    Sosnick, T.R.3
  • 5
    • 0035191642 scopus 로고    scopus 로고
    • Engineered metal binding sites map the heterogeneous folding landscape of a coiled coil
    • Krantz B.A., and Sosnick T.R. Engineered metal binding sites map the heterogeneous folding landscape of a coiled coil. Nat. Struct. Biol. 8 (2001) 1042-1047
    • (2001) Nat. Struct. Biol. , vol.8 , pp. 1042-1047
    • Krantz, B.A.1    Sosnick, T.R.2
  • 6
    • 33746828217 scopus 로고    scopus 로고
    • Small proteins fold through transition states with native-like topologies
    • Pandit A.D., Jha A., Freed K.F., and Sosnick T.R. Small proteins fold through transition states with native-like topologies. J. Mol. Biol. 361 (2006) 755-770
    • (2006) J. Mol. Biol. , vol.361 , pp. 755-770
    • Pandit, A.D.1    Jha, A.2    Freed, K.F.3    Sosnick, T.R.4
  • 7
    • 48749087319 scopus 로고    scopus 로고
    • Quantifying the structural requirements of the folding transition state of protein A and other systems
    • Baxa M., Freed K.F., and Sosnick T.R. Quantifying the structural requirements of the folding transition state of protein A and other systems. J. Mol. Biol. 381 (2008) 1362-1381
    • (2008) J. Mol. Biol. , vol.381 , pp. 1362-1381
    • Baxa, M.1    Freed, K.F.2    Sosnick, T.R.3
  • 8
    • 10644295536 scopus 로고    scopus 로고
    • φ{symbol} value versus ψ analysis
    • Fersht A.R. φ{symbol} value versus ψ analysis. Proc. Natl Acad. Sci. USA 101 (2004) 17327-17328
    • (2004) Proc. Natl Acad. Sci. USA , vol.101 , pp. 17327-17328
    • Fersht, A.R.1
  • 9
    • 22444441276 scopus 로고    scopus 로고
    • Interpretation of protein folding psi values
    • Bodenreider C., and Kiefhaber T. Interpretation of protein folding psi values. J. Mol. Biol. 351 (2005) 393-401
    • (2005) J. Mol. Biol. , vol.351 , pp. 393-401
    • Bodenreider, C.1    Kiefhaber, T.2
  • 10
    • 10644261303 scopus 로고    scopus 로고
    • Differences in the folding transition state of ubiquitin indicated by phi and psi analyses
    • Sosnick T.R., Dothager R.S., and Krantz B.A. Differences in the folding transition state of ubiquitin indicated by phi and psi analyses. Proc. Natl Acad. Sci. USA 101 (2004) 17377-17382
    • (2004) Proc. Natl Acad. Sci. USA , vol.101 , pp. 17377-17382
    • Sosnick, T.R.1    Dothager, R.S.2    Krantz, B.A.3
  • 11
    • 84979853222 scopus 로고    scopus 로고
    • Erratum to Discerning the structure and energy of multiple transition states in protein folding using psi-analysis
    • Krantz B.A., Dothager R.S., and Sosnick T.R. Erratum to Discerning the structure and energy of multiple transition states in protein folding using psi-analysis. J. Mol. Biol. 347 (2004) 889-1109
    • (2004) J. Mol. Biol. , vol.347 , pp. 889-1109
    • Krantz, B.A.1    Dothager, R.S.2    Sosnick, T.R.3
  • 12
    • 40049091818 scopus 로고    scopus 로고
    • Determination of the transition state ensemble for the folding of ubiquitin from a combination of phi and psi analyses
    • Varnai P., Dobson C.M., and Vendruscolo M. Determination of the transition state ensemble for the folding of ubiquitin from a combination of phi and psi analyses. J. Mol. Biol. 377 (2008) 575-588
    • (2008) J. Mol. Biol. , vol.377 , pp. 575-588
    • Varnai, P.1    Dobson, C.M.2    Vendruscolo, M.3
  • 13
    • 0032843763 scopus 로고    scopus 로고
    • Transition state heterogeneity in GCN4 coiled coil folding studied by using multisite mutations and crosslinking
    • Moran L.B., Schneider J.P., Kentsis A., Reddy G.A., and Sosnick T.R. Transition state heterogeneity in GCN4 coiled coil folding studied by using multisite mutations and crosslinking. Proc. Natl Acad. Sci. USA 96 (1999) 10699-10704
    • (1999) Proc. Natl Acad. Sci. USA , vol.96 , pp. 10699-10704
    • Moran, L.B.1    Schneider, J.P.2    Kentsis, A.3    Reddy, G.A.4    Sosnick, T.R.5
  • 14
    • 44949274272 scopus 로고
    • Crystal radii and effective ionic radii of the rare earth ions
    • Jia Y.Q. Crystal radii and effective ionic radii of the rare earth ions. J. Solid State Chem. 95 (1991) 184
    • (1991) J. Solid State Chem. , vol.95 , pp. 184
    • Jia, Y.Q.1
  • 16
    • 33751283357 scopus 로고    scopus 로고
    • Long time dynamics of met-enkephalin: explicit and model solvent simulations and mode-coupling theory studies
    • Shen M.Y., and Freed K.F. Long time dynamics of met-enkephalin: explicit and model solvent simulations and mode-coupling theory studies. Abstr. Pap.-Am. Chem. Soc. 222 (2001) U361-U362
    • (2001) Abstr. Pap.-Am. Chem. Soc. , vol.222
    • Shen, M.Y.1    Freed, K.F.2
  • 17
    • 0036892356 scopus 로고    scopus 로고
    • All-atom fast protein folding simulations: the villin headpiece
    • Shen M.Y., and Freed K.F. All-atom fast protein folding simulations: the villin headpiece. Proteins 49 (2002) 439-445
    • (2002) Proteins , vol.49 , pp. 439-445
    • Shen, M.Y.1    Freed, K.F.2
  • 18
    • 17844392069 scopus 로고    scopus 로고
    • A simple method for faster nonbonded force evaluations
    • Shen M.Y., and Freed K.F. A simple method for faster nonbonded force evaluations. J. Comput. Chem. 26 (2005) 691-698
    • (2005) J. Comput. Chem. , vol.26 , pp. 691-698
    • Shen, M.Y.1    Freed, K.F.2
  • 20
    • 0037022662 scopus 로고    scopus 로고
    • alpha-Helical stabilization by side chain shielding of backbone hydrogen bonds
    • Garcia A.E., and Sanbonmatsu K.Y. alpha-Helical stabilization by side chain shielding of backbone hydrogen bonds. Proc. Natl Acad. Sci. USA 99 (2002) 2782-2787
    • (2002) Proc. Natl Acad. Sci. USA , vol.99 , pp. 2782-2787
    • Garcia, A.E.1    Sanbonmatsu, K.Y.2
  • 21
    • 0035913529 scopus 로고    scopus 로고
    • Evaluation and reparametrization of the OPLS-AA force field for proteins via comparison with accurate quantum chemical calculations on peptides
    • Kaminski G.A., Friesner R.A., Tirado-Rives J., and Jorgensen W.L. Evaluation and reparametrization of the OPLS-AA force field for proteins via comparison with accurate quantum chemical calculations on peptides. J. Phys. Chem. B 105 (2001) 6474-6487
    • (2001) J. Phys. Chem. B , vol.105 , pp. 6474-6487
    • Kaminski, G.A.1    Friesner, R.A.2    Tirado-Rives, J.3    Jorgensen, W.L.4
  • 23
    • 20844443079 scopus 로고    scopus 로고
    • Ubiquitin folds through a highly polarized transition state
    • Went H.M., and Jackson S.E. Ubiquitin folds through a highly polarized transition state. Protein Eng. Des. Sel. 18 (2005) 229-237
    • (2005) Protein Eng. Des. Sel. , vol.18 , pp. 229-237
    • Went, H.M.1    Jackson, S.E.2
  • 24
    • 24944542708 scopus 로고    scopus 로고
    • Statistical coil model of the unfolded state: resolving the reconciliation problem
    • Jha A.K., Colubri A., Freed K.F., and Sosnick T.R. Statistical coil model of the unfolded state: resolving the reconciliation problem. Proc. Natl Acad. Sci. USA 102 (2005) 13099-13104
    • (2005) Proc. Natl Acad. Sci. USA , vol.102 , pp. 13099-13104
    • Jha, A.K.1    Colubri, A.2    Freed, K.F.3    Sosnick, T.R.4
  • 25
    • 0035066647 scopus 로고    scopus 로고
    • Phi-values for BPTI folding intermediates and implications for transition state analysis
    • Bulaj G., and Goldenberg D.P. Phi-values for BPTI folding intermediates and implications for transition state analysis. Nat. Struct. Biol. 8 (2001) 326-330
    • (2001) Nat. Struct. Biol. , vol.8 , pp. 326-330
    • Bulaj, G.1    Goldenberg, D.P.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.