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Volumn 8, Issue 4, 2013, Pages

Plasticity of 150-Loop in Influenza Neuraminidase Explored by Hamiltonian Replica Exchange Molecular Dynamics Simulations

Author keywords

[No Author keywords available]

Indexed keywords

VIRUS SIALIDASE;

EID: 84876041941     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0060995     Document Type: Article
Times cited : (26)

References (41)
  • 2
    • 0344395604 scopus 로고    scopus 로고
    • Are we ready for pandemic influenza?
    • Webby RJ, Webster RG, (2003) Are we ready for pandemic influenza? Science 302: 1519-1522.
    • (2003) Science , vol.302 , pp. 1519-1522
    • Webby, R.J.1    Webster, R.G.2
  • 3
    • 31344462092 scopus 로고    scopus 로고
    • Pandemic influenza threat and preparedness
    • Fauci AS, (2006) Pandemic influenza threat and preparedness. Emerg Infect Dis 12: 73-77.
    • (2006) Emerg Infect Dis , vol.12 , pp. 73-77
    • Fauci, A.S.1
  • 4
    • 33847044691 scopus 로고    scopus 로고
    • The evolution of epidemic influenza
    • Nelson MI, Holmes EC, (2007) The evolution of epidemic influenza. Nat Rev Genet 8: 196-205.
    • (2007) Nat Rev Genet , vol.8 , pp. 196-205
    • Nelson, M.I.1    Holmes, E.C.2
  • 5
    • 67649297821 scopus 로고    scopus 로고
    • Emergence and pandemic potential of swine-origin H1N1 influenza virus
    • Neumann G, Noda T, Kawaoka Y, (2009) Emergence and pandemic potential of swine-origin H1N1 influenza virus. Nature 459: 931-939.
    • (2009) Nature , vol.459 , pp. 931-939
    • Neumann, G.1    Noda, T.2    Kawaoka, Y.3
  • 6
    • 70449127983 scopus 로고    scopus 로고
    • New prospects for the rational design of antivirals
    • Nistal-Villan E, Garcia-Sastre A, (2009) New prospects for the rational design of antivirals. Nat Med 15: 1253-1254.
    • (2009) Nat Med , vol.15 , pp. 1253-1254
    • Nistal-Villan, E.1    Garcia-Sastre, A.2
  • 7
    • 77951976539 scopus 로고    scopus 로고
    • Structures of influenza A proteins and insights into antiviral drug targets
    • Das K, Aramini JM, Ma LC, Krug RM, Arnold E, (2010) Structures of influenza A proteins and insights into antiviral drug targets. Nat Strut Mol Biol 17: 530-538.
    • (2010) Nat Strut Mol Biol , vol.17 , pp. 530-538
    • Das, K.1    Aramini, J.M.2    Ma, L.C.3    Krug, R.M.4    Arnold, E.5
  • 8
    • 0031048319 scopus 로고    scopus 로고
    • Influenza neuraminidase inhibitors possessing a novel hydrophobic interaction in the enzyme active site: design, synthesis, and structural analysis of carbocyclic sialic acid analogues with potent anti-influenza activity
    • Kim CU, Lew W, Williams MA, Liu H, Zhang L, et al. (1997) Influenza neuraminidase inhibitors possessing a novel hydrophobic interaction in the enzyme active site: design, synthesis, and structural analysis of carbocyclic sialic acid analogues with potent anti-influenza activity. J Am Chem Soc 119: 681-690.
    • (1997) J Am Chem Soc , vol.119 , pp. 681-690
    • Kim, C.U.1    Lew, W.2    Williams, M.A.3    Liu, H.4    Zhang, L.5
  • 9
    • 0027287506 scopus 로고
    • Rational Design of Potent Sialidase-Based Inhibitors of Influenza-Virus Replication
    • von Itzstein M, Wu WY, Kok GB, Pegg MS, Dyason JC, et al. (1993) Rational Design of Potent Sialidase-Based Inhibitors of Influenza-Virus Replication. Nature 363: 418-423.
    • (1993) Nature , vol.363 , pp. 418-423
    • von Itzstein, M.1    Wu, W.Y.2    Kok, G.B.3    Pegg, M.S.4    Dyason, J.C.5
  • 10
    • 0034699492 scopus 로고    scopus 로고
    • BCX-1812 (RWJ-270201): Discovery of a novel, highly potent, orally active, and selective influenza neuraminidase inhibitor through structure-based drug design
    • Babu YS, Chand P, Bantia S, Kotian P, Dehghani A, et al. (2000) BCX-1812 (RWJ-270201): Discovery of a novel, highly potent, orally active, and selective influenza neuraminidase inhibitor through structure-based drug design. J Med Chem 43: 3482-3486.
    • (2000) J Med Chem , vol.43 , pp. 3482-3486
    • Babu, Y.S.1    Chand, P.2    Bantia, S.3    Kotian, P.4    Dehghani, A.5
  • 11
    • 59749091876 scopus 로고    scopus 로고
    • CS-8958, a Prodrug of the New Neuraminidase Inhibitor R-125489, Shows Long-Acting Anti-Influenza Virus Activity
    • Yamashita M, Tomozawa T, Kakuta M, Tokumitsu A, Nasu H, et al. (2009) CS-8958, a Prodrug of the New Neuraminidase Inhibitor R-125489, Shows Long-Acting Anti-Influenza Virus Activity. Antimicrob Agents and Chemother 53: 186-192.
    • (2009) Antimicrob Agents and Chemother , vol.53 , pp. 186-192
    • Yamashita, M.1    Tomozawa, T.2    Kakuta, M.3    Tokumitsu, A.4    Nasu, H.5
  • 12
    • 33748437791 scopus 로고    scopus 로고
    • The structure of H5N1 avian influenza neuraminidase suggests new opportunities for drug design
    • Russell RJ, Haire LF, Stevens DJ, Collins PJ, Lin YP, et al. (2006) The structure of H5N1 avian influenza neuraminidase suggests new opportunities for drug design. Nature 443: 45-49.
    • (2006) Nature , vol.443 , pp. 45-49
    • Russell, R.J.1    Haire, L.F.2    Stevens, D.J.3    Collins, P.J.4    Lin, Y.P.5
  • 13
    • 36749056771 scopus 로고    scopus 로고
    • The war against influenza: discovery and development of sialidase inhibitors
    • von Itzstein M, (2007) The war against influenza: discovery and development of sialidase inhibitors. Nat Rev Drug Discov 6: 967-974.
    • (2007) Nat Rev Drug Discov , vol.6 , pp. 967-974
    • von Itzstein, M.1
  • 14
    • 78650045655 scopus 로고    scopus 로고
    • Novel sialic acid derivatives lock open the 150-loop of an influenza A virus group-1 sialidase
    • Rudrawar S, Dyason JC, Rameix-Welti MA, Rose FJ, Kerry PS, et al. (2010) Novel sialic acid derivatives lock open the 150-loop of an influenza A virus group-1 sialidase. Nat Commun 1: 113.
    • (2010) Nat Commun , vol.1 , pp. 113
    • Rudrawar, S.1    Dyason, J.C.2    Rameix-Welti, M.A.3    Rose, F.J.4    Kerry, P.S.5
  • 15
    • 77957767268 scopus 로고    scopus 로고
    • The 2009 pandemic H1N1 neuraminidase N1 lacks the 150-cavity in its active site
    • Li Q, Qi JX, Zhang W, Vavricka CJ, Shi Y, et al. (2010) The 2009 pandemic H1N1 neuraminidase N1 lacks the 150-cavity in its active site. Nat Struct Mol Biol 17: 1266-1268.
    • (2010) Nat Struct Mol Biol , vol.17 , pp. 1266-1268
    • Li, Q.1    Qi, J.X.2    Zhang, W.3    Vavricka, C.J.4    Shi, Y.5
  • 17
    • 34347230817 scopus 로고    scopus 로고
    • Remarkable loop flexibility in avian influenza N1 and its implications for antiviral drug design
    • Amaro RE, Minh DD, Cheng LS, Lindstrom WM Jr, Olson AJ, et al. (2007) Remarkable loop flexibility in avian influenza N1 and its implications for antiviral drug design. J Am Chem Soc 129: 7764-7765.
    • (2007) J Am Chem Soc , vol.129 , pp. 7764-7765
    • Amaro, R.E.1    Minh, D.D.2    Cheng, L.S.3    Lindstrom Jr., W.M.4    Olson, A.J.5
  • 18
    • 79961185765 scopus 로고    scopus 로고
    • Influenza A virus N5 neuraminidase has an extended 150-cavity
    • Wang M, Qi J, Liu Y, Vavricka CJ, Wu Y, et al. (2011) Influenza A virus N5 neuraminidase has an extended 150-cavity. J Virol 85: 8431-8435.
    • (2011) J Virol , vol.85 , pp. 8431-8435
    • Wang, M.1    Qi, J.2    Liu, Y.3    Vavricka, C.J.4    Wu, Y.5
  • 19
    • 67949124553 scopus 로고    scopus 로고
    • Characterizing loop dynamics and ligand recognition in human- and avian-type influenza neuraminidases via generalized born molecular dynamics and end-point free energy calculations
    • Amaro RE, Cheng X, Ivanov I, Xu D, McCammon JA, (2009) Characterizing loop dynamics and ligand recognition in human- and avian-type influenza neuraminidases via generalized born molecular dynamics and end-point free energy calculations. J Am Chem Soc 131: 4702-4709.
    • (2009) J Am Chem Soc , vol.131 , pp. 4702-4709
    • Amaro, R.E.1    Cheng, X.2    Ivanov, I.3    Xu, D.4    McCammon, J.A.5
  • 20
    • 0025895628 scopus 로고
    • 3-Dimensional Structure of the Neuraminidase of Influenza Virus-a/Tokyo/3/67 at 2.2-a Resolution
    • Varghese JN, Colman PM, (1991) 3-Dimensional Structure of the Neuraminidase of Influenza Virus-a/Tokyo/3/67 at 2.2-a Resolution. J Mol Biol 221: 473-486.
    • (1991) J Mol Biol , vol.221 , pp. 473-486
    • Varghese, J.N.1    Colman, P.M.2
  • 21
    • 65149096011 scopus 로고    scopus 로고
    • Dissociation aided and side chain sampling enhanced Hamiltonian replica exchange
    • Mu Y, (2009) Dissociation aided and side chain sampling enhanced Hamiltonian replica exchange. J Chem Phys 130: 164107.
    • (2009) J Chem Phys , vol.130 , pp. 164107
    • Mu, Y.1
  • 22
    • 43149126349 scopus 로고    scopus 로고
    • Reversible folding simulation by hybrid Hamiltonian replica exchange
    • Xu W, Lai T, Yang Y, Mu Y, (2008) Reversible folding simulation by hybrid Hamiltonian replica exchange. J Chem Phys 128: 175105.
    • (2008) J Chem Phys , vol.128 , pp. 175105
    • Xu, W.1    Lai, T.2    Yang, Y.3    Mu, Y.4
  • 23
    • 32144432437 scopus 로고    scopus 로고
    • The SWISS-MODEL workspace: a web-based environment for protein structure homology modelling
    • Arnold K, Bordoli L, Kopp J, Schwede T, (2006) The SWISS-MODEL workspace: a web-based environment for protein structure homology modelling. Bioinformatics 22: 195-201.
    • (2006) Bioinformatics , vol.22 , pp. 195-201
    • Arnold, K.1    Bordoli, L.2    Kopp, J.3    Schwede, T.4
  • 24
    • 84866902241 scopus 로고    scopus 로고
    • H1N1 2009 Pandemic Influenza Virus: Resistance of the I223R Neuraminidase Mutant Explained by Kinetic and Structural Analysis
    • van der Vries E, Collins PJ, Vachieri SG, Xiong XL, Liu JF, et al. (2012) H1N1 2009 Pandemic Influenza Virus: Resistance of the I223R Neuraminidase Mutant Explained by Kinetic and Structural Analysis. Plos Pathogens 8: e1002914.
    • (2012) Plos Pathogens , vol.8
    • van der Vries, E.1    Collins, P.J.2    Vachieri, S.G.3    Xiong, X.L.4    Liu, J.F.5
  • 27
    • 46249092554 scopus 로고    scopus 로고
    • GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable molecular simulation
    • Hess B, Kutzner C, van der Spoel D, Lindahl E, (2008) GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable molecular simulation. J Chem Theory Comput 4: 435-447.
    • (2008) J Chem Theory Comput , vol.4 , pp. 435-447
    • Hess, B.1    Kutzner, C.2    van der Spoel, D.3    Lindahl, E.4
  • 28
    • 33748518255 scopus 로고    scopus 로고
    • Comparison of multiple amber force fields and development of improved protein backbone parameters
    • Hornak V, Abel R, Okur A, Strockbine B, Roitberg A, et al. (2006) Comparison of multiple amber force fields and development of improved protein backbone parameters. Proteins: Struct Funct and Bioinform 65: 712-725.
    • (2006) Proteins: Struct Funct and Bioinform , vol.65 , pp. 712-725
    • Hornak, V.1    Abel, R.2    Okur, A.3    Strockbine, B.4    Roitberg, A.5
  • 30
    • 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
  • 33
    • 10844292652 scopus 로고    scopus 로고
    • Energy landscape of a small peptide revealed by dihedral angle principal component analysis
    • Mu Y, Nguyen PH, Stock G, (2005) Energy landscape of a small peptide revealed by dihedral angle principal component analysis. Proteins: Struct Funct and Bioinform 58: 45-52.
    • (2005) Proteins: Struct Funct and Bioinform , vol.58 , pp. 45-52
    • Mu, Y.1    Nguyen, P.H.2    Stock, G.3
  • 34
    • 79956114933 scopus 로고    scopus 로고
    • Chapter 5-Proteins MOVE! Protein dynamics and long-range allostery in cell signaling
    • In: Rossen D, editor, Academic Press
    • Bu Z, Callaway DJE (2011) Chapter 5-Proteins MOVE! Protein dynamics and long-range allostery in cell signaling. In: Rossen D, editor. Advances in Protein Chemistry and Structural Biology: Academic Press. pp. 163-221.
    • (2011) Advances in Protein Chemistry and Structural Biology , pp. 163-221
    • Bu, Z.1    Callaway, D.J.E.2
  • 35
    • 0032540692 scopus 로고    scopus 로고
    • Use of Locally Enhanced Sampling in Free Energy Calculations: Testing and Application to the α → β Anomerization of Glucose
    • Simmerling C, Fox T, Kollman PA, (1998) Use of Locally Enhanced Sampling in Free Energy Calculations: Testing and Application to the α → β Anomerization of Glucose. J Am Chem Soc 120: 5771-5782.
    • (1998) J Am Chem Soc , vol.120 , pp. 5771-5782
    • Simmerling, C.1    Fox, T.2    Kollman, P.A.3
  • 36
    • 80052834610 scopus 로고    scopus 로고
    • Novel Genotyping and Quantitative Analysis of Neuraminidase Inhibitor Resistance-Associated Mutations in Influenza A Viruses by Single-Nucleotide Polymorphism Analysis
    • Duan S, Boltz DA, Li J, Oshansky CM, Marjuki H, et al. (2011) Novel Genotyping and Quantitative Analysis of Neuraminidase Inhibitor Resistance-Associated Mutations in Influenza A Viruses by Single-Nucleotide Polymorphism Analysis. Antimicrob Agents Chemother 55: 4718-4727.
    • (2011) Antimicrob Agents Chemother , vol.55 , pp. 4718-4727
    • Duan, S.1    Boltz, D.A.2    Li, J.3    Oshansky, C.M.4    Marjuki, H.5
  • 37
    • 57749118013 scopus 로고    scopus 로고
    • Origins of Resistance Conferred by the R292K Neuraminidase Mutation via Molecular Dynamics and Free Energy Calculations
    • Chachra R, Rizzo RC, (2008) Origins of Resistance Conferred by the R292K Neuraminidase Mutation via Molecular Dynamics and Free Energy Calculations. J Chem Theory Comput 4: 1526-1540.
    • (2008) J Chem Theory Comput , vol.4 , pp. 1526-1540
    • Chachra, R.1    Rizzo, R.C.2
  • 38
    • 84866106043 scopus 로고    scopus 로고
    • Exploring the Mechanism of Zanamivir Resistance in a Neuraminidase Mutant: A Molecular Dynamics Study
    • Han N, Liu X, Mu Y, (2012) Exploring the Mechanism of Zanamivir Resistance in a Neuraminidase Mutant: A Molecular Dynamics Study. PLoS ONE 7: e44057.
    • (2012) PLoS ONE , vol.7
    • Han, N.1    Liu, X.2    Mu, Y.3
  • 39
    • 38549150173 scopus 로고    scopus 로고
    • Novel druggable hot spots in avian influenza neuraminidase H5N1 revealed by computational solvent mapping of a reduced and representative receptor ensemble
    • Landon MR, Amaro RE, Baron R, Ngan CH, Ozonoff D, et al. (2008) Novel druggable hot spots in avian influenza neuraminidase H5N1 revealed by computational solvent mapping of a reduced and representative receptor ensemble. Chem Biol Drug Des 71: 106-116.
    • (2008) Chem Biol Drug Des , vol.71 , pp. 106-116
    • Landon, M.R.1    Amaro, R.E.2    Baron, R.3    Ngan, C.H.4    Ozonoff, D.5
  • 40
    • 46849105028 scopus 로고    scopus 로고
    • Ensemble-based virtual screening reveals potential novel antiviral compounds for avian influenza neuraminidase
    • Cheng LS, Amaro RE, Xu D, Li WW, Arzberger PW, et al. (2008) Ensemble-based virtual screening reveals potential novel antiviral compounds for avian influenza neuraminidase. J Med Chem 51: 3878-3894.
    • (2008) J Med Chem , vol.51 , pp. 3878-3894
    • Cheng, L.S.1    Amaro, R.E.2    Xu, D.3    Li, W.W.4    Arzberger, P.W.5
  • 41
    • 77249115238 scopus 로고    scopus 로고
    • Antiviral Potential and Molecular Insight into Neuraminidase Inhibiting Diarylheptanoids from Alpinia katsumadai
    • Grienke U, Schmidtke M, Kirchmair J, Pfarr K, Wutzler P, et al. (2010) Antiviral Potential and Molecular Insight into Neuraminidase Inhibiting Diarylheptanoids from Alpinia katsumadai. J Med Chem 53: 778-786.
    • (2010) J Med Chem , vol.53 , pp. 778-786
    • Grienke, U.1    Schmidtke, M.2    Kirchmair, J.3    Pfarr, K.4    Wutzler, P.5


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