메뉴 건너뛰기




Volumn 9, Issue 2, 2014, Pages

Role of tryptophan side chain dynamics on the Trp-cage mini-protein folding studied by molecular dynamics simulations

Author keywords

[No Author keywords available]

Indexed keywords

PROTEIN; TRP CAGE MINIPROTEIN; TRYPTOPHAN; UNCLASSIFIED DRUG;

EID: 84895509709     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0088383     Document Type: Article
Times cited : (27)

References (51)
  • 2
    • 0037032225 scopus 로고    scopus 로고
    • Smaller and faster: The 20-residue Trp-cage protein folds in 4 micros
    • Qiu L, Pabit SA, Roitberg AE, Hagen SJ (2002) Smaller and faster: the 20-residue Trp-cage protein folds in 4 micros. J. Am. Chem. Soc. 124: 12952- 12953.
    • (2002) J. Am. Chem. Soc. , vol.124 , pp. 12952-12953
    • Qiu, L.1    Pabit, S.A.2    Roitberg, A.E.3    Hagen, S.J.4
  • 3
    • 84864507797 scopus 로고    scopus 로고
    • Crystal and NMR structures of a Trp-cage mini-protein benchmark for computational fold prediction
    • Scian M, Lin JC, Le Trong I, Makhatadze GI, Stenkamp RE, et al. (2012) Crystal and NMR structures of a Trp-cage mini-protein benchmark for computational fold prediction. Proc. Natl. Acad. Sci. USA. 109: 12521-12525.
    • (2012) Proc. Natl. Acad. Sci. USA. , vol.109 , pp. 12521-12525
    • Scian, M.1    Lin, J.C.2    Le Trong, I.3    Makhatadze, G.I.4    Stenkamp, R.E.5
  • 4
    • 33947209951 scopus 로고    scopus 로고
    • Unfolding thermodynamics of Trp-cage, a 20 residue miniprotein, studied by differential scanning calorimetry and circular dichroism spectroscopy
    • DOI 10.1021/bi602424x
    • Streicher WW, Makhatadze GI (2007) Unfolding thermodynamics of Trp-cage, a 20 residue miniprotein, studied by differential scanning calorimetry and circular dichroism spectroscopy. Biochemistry. 46: 2876-2880. (Pubitemid 46417925)
    • (2007) Biochemistry , vol.46 , Issue.10 , pp. 2876-2880
    • Streicher, W.W.1    Makhatadze, G.I.2
  • 6
    • 23744503388 scopus 로고    scopus 로고
    • UV-resonance Raman thermal unfolding study of Trp-cage shows that it is not a simple two-state miniprotein
    • DOI 10.1021/ja050664e
    • Ahmed Z, Beta IA, Mikhonin AV, Asher SA (2005) UV-resonance Raman thermal unfolding study of Trp-cage shows that it is not a simple two-state miniprotein. J. Am. Chem. Soc. 127: 10943-10950. (Pubitemid 41129869)
    • (2005) Journal of the American Chemical Society , vol.127 , Issue.31 , pp. 10943-10950
    • Ahmed, Z.1    Beta, I.A.2    Mikhonin, A.V.3    Asher, S.A.4
  • 7
    • 34247577665 scopus 로고    scopus 로고
    • A pre-existing hydrophobic collapse in the unfolded state of an ultrafast folding protein
    • DOI 10.1038/nature05728, PII NATURE05728
    • Mok KH, Kuhn LT, Goez M, Day IJ, Lin JC, et al. (2007) A pre-existing hydrophobic collapse in the unfolded state of an ultrafast folding protein. Nature. 447: 106-109. (Pubitemid 46685836)
    • (2007) Nature , vol.447 , Issue.7140 , pp. 106-109
    • Mok, K.H.1    Kuhn, L.T.2    Goez, M.3    Day, I.J.4    Lin, J.C.5    Andersen, N.H.6    Hore, P.J.7
  • 8
    • 80855133540 scopus 로고    scopus 로고
    • Achieving secondary structural resolution in kinetic measurements of protein folding: A case study of the folding mechanism of Trp-cage
    • Culik RM, Serrano AL, Bunagan MR, Gai F (2011) Achieving secondary structural resolution in kinetic measurements of protein folding: a case study of the folding mechanism of Trp-cage. Angew. Chem. Int. Ed. Engl. 50: 10884-10887.
    • (2011) Angew. Chem. Int. Ed. Engl. , vol.50 , pp. 10884-10887
    • Culik, R.M.1    Serrano, A.L.2    Bunagan, M.R.3    Gai, F.4
  • 9
    • 84885138820 scopus 로고    scopus 로고
    • Folding Dynamics of the Trp-cage Miniprotein: Evidence for a Native-like Intermediate from combined Time-Resolved Vibrational Spectroscopy and Molecular Dynamics Simulations
    • Meuzelaar H, Marino KA, Huerta-Viga A, Panman MR, Smeenk LEJ, et al. (2013) Folding Dynamics of the Trp-cage Miniprotein: Evidence for a Native-like Intermediate from combined Time-Resolved Vibrational Spectroscopy and Molecular Dynamics Simulations. J Phys. Chem. B. 117: 11490-11501.
    • (2013) J Phys. Chem. B. , vol.117 , pp. 11490-11501
    • Meuzelaar, H.1    Marino, K.A.2    Huerta-Viga, A.3    Panman, M.R.4    Smeenk, L.E.J.5
  • 13
    • 38349097833 scopus 로고    scopus 로고
    • Cooperation between a Salt Bridge and the Hydrophobic Core Triggers Fold Stabilization in a Trp-Cage Miniprotein
    • Hudky P, Strner P, Farkas V, Váradi G, Tóth G, et al. (2008) Cooperation between a Salt Bridge and the Hydrophobic Core Triggers Fold Stabilization in a Trp-Cage Miniprotein. Biochemistry. 47: 1007-1016.
    • (2008) Biochemistry. , vol.47 , pp. 1007-1016
    • Hudky, P.1    Strner, P.2    Farkas, V.3    Váradi, G.4    Tóth, G.5
  • 14
    • 84862274056 scopus 로고    scopus 로고
    • Conformational dynamics of the trp-cage miniprotein at its folding temperature
    • Halabis A, Zmudzinska W, Liwo A, Oldziej S (2012) Conformational dynamics of the trp-cage miniprotein at its folding temperature. J. Phys. Chem. B. 116: 6898-6907.
    • (2012) J. Phys. Chem. B. , vol.116 , pp. 6898-6907
    • Halabis, A.1    Zmudzinska, W.2    Liwo, A.3    Oldziej, S.4
  • 15
    • 84876748955 scopus 로고    scopus 로고
    • Monitoring the folding of Trp-cage peptide by two-dimensional infrared (2DIR) spectroscopy
    • Lai Z, Preketes NK, Mukamel S, Wang J (2013) Monitoring the folding of Trp-cage peptide by two-dimensional infrared (2DIR) spectroscopy. J. Phys. Chem. B. 117: 4661-4669.
    • (2013) J. Phys. Chem. B. , vol.117 , pp. 4661-4669
    • Lai, Z.1    Preketes, N.K.2    Mukamel, S.3    Wang, J.4
  • 16
    • 0037174385 scopus 로고    scopus 로고
    • All-atom structure prediction and folding simulations of a stable protein
    • Simmerling C, Strockbine B, Roitberg AE (2002) All-atom structure prediction and folding simulations of a stable protein. J. Am. Chem. Soc. 124: 11258-11259.
    • (2002) J. Am. Chem. Soc. , vol.124 , pp. 11258-11259
    • Simmerling, C.1    Strockbine, B.2    Roitberg, A.E.3
  • 17
    • 0037065310 scopus 로고    scopus 로고
    • The Trp cage: Folding kinetics and unfolded state topology via molecular dynamics simulations
    • DOI 10.1021/ja028604l
    • Snow CD, Zagrovic B, Pande VS (2002) The Trp cage: folding kinetics and unfolded state topology via molecular dynamics simulations. J. Am. Chem. Soc. 124: 14548-14549. (Pubitemid 35425023)
    • (2002) Journal of the American Chemical Society , vol.124 , Issue.49 , pp. 14548-14549
    • Snow, C.D.1    Zagrovic, B.2    Pande, V.S.3
  • 18
    • 0037470691 scopus 로고    scopus 로고
    • Ab initio folding simulation of the Trp-cage mini-protein approaches NMR resolution
    • DOI 10.1016/S0022-2836(03)00177-3
    • Chowdhury S, Lee MC, Xiong G, Duan Y (2003) Ab initio folding simulation of the Trp-cage mini-protein approaches NMR resolution. J. Mol. Biol. 327: 711-717. (Pubitemid 36300811)
    • (2003) Journal of Molecular Biology , vol.327 , Issue.3 , pp. 711-717
    • Chowdhury, S.1    Lee, M.C.2    Xiong, G.3    Duan, Y.4
  • 19
    • 4544223597 scopus 로고    scopus 로고
    • Characterizing the rate-limiting step of Trp-Cage folding by all-atom molecular dynamics simulations
    • Chowdhury S, Lee MC, Duan Y (2004) Characterizing the rate-limiting step of Trp-Cage folding by all-atom molecular dynamics simulations. J. Phys. Chem. B. 108: 13855-13865.
    • (2004) J. Phys. Chem. B. , vol.108 , pp. 13855-13865
    • Chowdhury, S.1    Lee, M.C.2    Duan, Y.3
  • 22
    • 63449088579 scopus 로고    scopus 로고
    • Folding of Trp-cage mini protein using temperature and biasing potential replica-exchange molecular dynamics simulations
    • Kannan S, Zacharias M (2009) Folding of Trp-cage mini protein using temperature and biasing potential replica-exchange molecular dynamics simulations. Int. J. Mol. Sci. 10: 1121-1137.
    • (2009) Int. J. Mol. Sci. , vol.10 , pp. 1121-1137
    • Kannan, S.1    Zacharias, M.2
  • 23
    • 0344824394 scopus 로고    scopus 로고
    • Trp-cage: Folding free energy landscape in explicit water
    • Zhou R (2003) Trp-cage: folding free energy landscape in explicit water. Proc. Natl. Acad. Sci. USA. 100: 13280-13285.
    • (2003) Proc. Natl. Acad. Sci. USA. , vol.100 , pp. 13280-13285
    • Zhou, R.1
  • 25
    • 33847201903 scopus 로고    scopus 로고
    • Exploring the energy landscape of protein folding using replica-exchange and conventional molecular dynamics simulations
    • Beck DA, White GW, Daggett V (2007) Exploring the energy landscape of protein folding using replica-exchange and conventional molecular dynamics simulations. J. Struct. Biol. 157: 514-523.
    • (2007) J. Struct. Biol. , vol.157 , pp. 514-523
    • Beck, D.A.1    White, G.W.2    Daggett, V.3
  • 26
    • 33847254549 scopus 로고    scopus 로고
    • Replica exchange simulation of reversible folding/unfolding of the Trp-cage miniprotein in explicit solvent: On the structure and possible role of internal water
    • DOI 10.1016/j.jsb.2006.10.031, PII S1047847706003297, Advanced in Molecular Dynamics Simulations
    • Paschek D, Nymeyer H, Garcia AE (2007) Replica exchange simulation of reversible folding/unfolding of the Trp-cage miniprotein in explicit solvent: on the structure and possible role of internal water. J. Struct. Biol. 157: 524-533. (Pubitemid 46321518)
    • (2007) Journal of Structural Biology , vol.157 , Issue.3 , pp. 524-533
    • Paschek, D.1    Nymeyer, H.2    Garcia, A.E.3
  • 27
    • 56649083699 scopus 로고    scopus 로고
    • Computing the stability diagram of the Trp-cage miniprotein
    • Paschek D, Hempel S, Garcia AE (2008) Computing the stability diagram of the Trp-cage miniprotein. Proc. Natl. Acad. Sci. USA. 105: 17754-17759.
    • (2008) Proc. Natl. Acad. Sci. USA. , vol.105 , pp. 17754-17759
    • Paschek, D.1    Hempel, S.2    Garcia, A.E.3
  • 28
    • 45849116879 scopus 로고    scopus 로고
    • Key residue-dominated protein folding dynamics
    • Yao XQ, She ZS (2008) Key residue-dominated protein folding dynamics. Biochem. Biophys. Res. Commun. 373: 64-68.
    • (2008) Biochem. Biophys. Res. Commun. , vol.373 , pp. 64-68
    • Yao, X.Q.1    She, Z.S.2
  • 29
    • 51649103970 scopus 로고    scopus 로고
    • Ab initio folding simulation of Trpcage by replica exchange with hybrid Hamiltonian
    • Xu W, Mu Y (2008) Ab initio folding simulation of Trpcage by replica exchange with hybrid Hamiltonian. Biophys. Chem. 137: 116-125.
    • (2008) Biophys. Chem. , vol.137 , pp. 116-125
    • Xu, W.1    Mu, Y.2
  • 30
    • 67650230368 scopus 로고    scopus 로고
    • Folding simulations of Trp-cage mini protein in explicit solvent using biasing potential replica-exchange molecular dynamics simulations
    • Kannan S, Zacharias M (2009) Folding simulations of Trp-cage mini protein in explicit solvent using biasing potential replica-exchange molecular dynamics simulations. Proteins. 76: 448-460.
    • (2009) Proteins. , vol.76 , pp. 448-460
    • Kannan, S.1    Zacharias, M.2
  • 31
    • 69049099679 scopus 로고    scopus 로고
    • A kinetic models of Trp-cage folding from multiple biased molecular dynamics simulations
    • doi: 10.1371/journal.pcbi.1000452
    • Marinelli F, Pietrucci F, Laio A, Piana S (2009) A kinetic models of Trp-cage folding from multiple biased molecular dynamics simulations. PLoS Comput. Biol. 5(8): e1000452. doi: 10.1371/journal.pcbi.1000452.
    • (2009) PLoS Comput. Biol. , vol.5 , Issue.8
    • Marinelli, F.1    Pietrucci, F.2    Laio, A.3    Piana, S.4
  • 32
    • 84883607162 scopus 로고    scopus 로고
    • Following easy slope paths on a free energy landscape: The case study of the Trp-cage folding mechanism
    • Marinelli F (2013) Following easy slope paths on a free energy landscape: The case study of the Trp-cage folding mechanism. Biophys J. 105: 1236-1247.
    • (2013) Biophys J. , vol.105 , pp. 1236-1247
    • Marinelli, F.1
  • 33
    • 84867027679 scopus 로고    scopus 로고
    • Enhanced sampling molecular dynamics simulation captures experimentally suggested intermediate and unfolded states in the folding pathway of Trp-cage miniprotein
    • Shao Q, Shi J, Zhu W (2012) Enhanced sampling molecular dynamics simulation captures experimentally suggested intermediate and unfolded states in the folding pathway of Trp-cage miniprotein. J. Chem. Phys. 137: 125103.
    • (2012) J. Chem. Phys. , vol.137 , pp. 125103
    • Shao, Q.1    Shi, J.2    Zhu, W.3
  • 35
    • 79951523268 scopus 로고    scopus 로고
    • Kinetic network study of the diversity and temperature dependence of Trp-Cage folding pathways: Combining transition path theory with stochastic simulations
    • Zheng W, Gallicchio E, Deng M, Andrec M, Levy RM (2011) Kinetic network study of the diversity and temperature dependence of Trp-Cage folding pathways: combining transition path theory with stochastic simulations. J. Phys. Chem. B. 115: 1512-1523.
    • (2011) J. Phys. Chem. B. , vol.115 , pp. 1512-1523
    • Zheng, W.1    Gallicchio, E.2    Deng, M.3    Andrec, M.4    Levy, R.M.5
  • 36
    • 77953508894 scopus 로고    scopus 로고
    • Microsecond simulations of the folding/unfolding thermodynamics of the Trp-cage miniprotein
    • Day R, Paschek D, Garcia AE (2010) Microsecond simulations of the folding/unfolding thermodynamics of the Trp-cage miniprotein. Proteins. 78: 1889-1899.
    • (2010) Proteins. , vol.78 , pp. 1889-1899
    • Day, R.1    Paschek, D.2    Garcia, A.E.3
  • 38
    • 84886686981 scopus 로고    scopus 로고
    • Characterization of Folding Mechanisms of Trp-Cage and WW-Domain by Network Analysis of Simulations with a Hybrid-Resolution Model
    • doi:10.1021/jp404331d
    • Han W, Schulten K (2013) Characterization of Folding Mechanisms of Trp-Cage and WW-Domain by Network Analysis of Simulations with a Hybrid-Resolution Model. J. Phys. Chem. B. doi:10.1021/jp404331d.
    • (2013) J. Phys. Chem. B.
    • Han, W.1    Schulten, K.2
  • 39
    • 84886690260 scopus 로고    scopus 로고
    • How Kinetics within the Unfolded State Affects Protein Folding: An Analysis Based on Markov State Models and an Ultra-Long MD Trajectory
    • doi:10.1021/jp401962k
    • Deng NJ, Dai W, Levy RM (2013) How Kinetics within the Unfolded State Affects Protein Folding: An Analysis Based on Markov State Models and an Ultra-Long MD Trajectory. J. Phys. Chem. B. doi:10.1021/jp401962k.
    • (2013) J. Phys. Chem. B.
    • Deng, N.J.1    Dai, W.2    Levy, R.M.3
  • 41
    • 33846227108 scopus 로고    scopus 로고
    • Enhanced sampling of peptide and protein conformations using replica exchange simulations with a peptide backbone biasing-potential
    • DOI 10.1002/prot.21258
    • Kannan S, Zacharias M (2007) Enhanced sampling of peptide and protein conformations using replica exchange simulations with a peptide backbone biasing-potential. Proteins. 66: 697-706. (Pubitemid 46106774)
    • (2007) Proteins: Structure, Function and Genetics , vol.66 , Issue.3 , pp. 697-706
    • Kannan, S.1    Zacharias, M.2
  • 43
    • 0242663237 scopus 로고    scopus 로고
    • A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations
    • Duan Y, Wu A, Chowdhury CS, Lee MC, Xiong G, et al. (2003) A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations. J. Comput. Chem. 24: 1999-2012.
    • (2003) J. Comput. Chem. , vol.24 , pp. 1999-2012
    • Duan, Y.1    Wu, A.2    Chowdhury, C.S.3    Lee, M.C.4    Xiong, G.5
  • 45
    • 77953513118 scopus 로고    scopus 로고
    • Improved side-chain torsion potentials for the Amber ff99SB protein force field
    • Lindorff-Larsen K, Piana S, Palmo K, Maragakis P, Klepeis JL, et al. (2010) Improved side-chain torsion potentials for the Amber ff99SB protein force field. Proteins. 78: 1950-1958.
    • (2010) Proteins. , vol.78 , pp. 1950-1958
    • Lindorff-Larsen, K.1    Piana, S.2    Palmo, K.3    Maragakis, P.4    Klepeis, J.L.5
  • 47
    • 33846823909 scopus 로고
    • Particle mesh Ewald: An N·log(N) method for Ewald sums in large systems
    • Darden T, York D, Pedersen L (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
  • 48
    • 84986440341 scopus 로고
    • Settle: An analytical version of the SHAKE and RATTLE algorithm for rigid water models
    • Miyamoto S, Kollman PA (1992) Settle: an analytical version of the SHAKE and RATTLE algorithm for rigid water models. J. Comput. Chem. 13: 952-962.
    • (1992) J. Comput. Chem. , vol.13 , pp. 952-962
    • Miyamoto, S.1    Kollman, P.A.2
  • 51
    • 0036324483 scopus 로고    scopus 로고
    • Determinants of miniprotein stability: Can anything replace a buried H-bonded Trp sidechain?
    • DOI 10.1023/A:1016252324134
    • Barua B, Andersen NH (2002) Determinants of Miniprotein Stability: Can anything replace a buried H-bonded Trp sidechain. Lett. Pept. Sci. 8: 221-226. (Pubitemid 34836496)
    • (2002) Letters in Peptide Science , vol.8 , Issue.3-5 , pp. 221-226
    • Barua, B.1    Andersen, N.H.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.