메뉴 건너뛰기




Volumn 8, Issue 2, 2012, Pages 554-562

Automated parametrization of AMBER force field terms from vibrational analysis with a focus on functionalizing dinuclear zinc(II) scaffolds

Author keywords

[No Author keywords available]

Indexed keywords


EID: 84857078912     PISSN: 15499618     EISSN: 15499626     Source Type: Journal    
DOI: 10.1021/ct2007742     Document Type: Article
Times cited : (43)

References (49)
  • 1
    • 0037439997 scopus 로고    scopus 로고
    • Structural classification of zinc fingers
    • DOI 10.1093/nar/gkg161
    • Krishna, S. S.; Majumdar, I.; Grishin, N. V. Structural classification of zinc fingers Nucleic Acids Res. 2003, 31 (2) 532-550 (Pubitemid 36175942)
    • (2003) Nucleic Acids Research , vol.31 , Issue.2 , pp. 532-550
    • Krishna, S.S.1    Majumdar, I.2    Grishin, N.V.3
  • 2
    • 0032835617 scopus 로고    scopus 로고
    • De novo design and structural characterization of proteins and metalloproteins
    • DOI 10.1146/annurev.biochem.68.1.779
    • DeGrado, W. F.; Summa, C. M.; Pavone, V.; Nastri, F.; Lombardi, A. De novo design and structural characterization of proteins and metalloproteins Annu. Rev. Biochem. 1999, 68, 779-819 (Pubitemid 29449209)
    • (1999) Annual Review of Biochemistry , vol.68 , pp. 779-819
    • DeGrado, W.F.1    Summa, C.M.2    Pavone, V.3    Nastri, F.4    Lombardi, A.5
  • 3
    • 1642307125 scopus 로고    scopus 로고
    • Dinuclear Zn2+ complexes in the hydrolysis of the phosphodiester linkage in a diribonucleoside monophosphate diester
    • Yashiro, M.; Kaneiwa, H.; Onaka, K.; Komiyama, M. Dinuclear Zn2+ complexes in the hydrolysis of the phosphodiester linkage in a diribonucleoside monophosphate diester Dalton Trans. 2004, 4, 605-610
    • (2004) Dalton Trans. , vol.4 , pp. 605-610
    • Yashiro, M.1    Kaneiwa, H.2    Onaka, K.3    Komiyama, M.4
  • 4
    • 37049084241 scopus 로고
    • Preparation and Study of Dinuclear Zinc(Ii) Complex for the Efficient Hydrolysis of the Phosphodiester Linkage in a Diribonucleotide
    • Yashiro, M.; Ishikubo, A.; Komiyama, M. Preparation and Study of Dinuclear Zinc(Ii) Complex for the Efficient Hydrolysis of the Phosphodiester Linkage in a Diribonucleotide J. Chem. Soc., Chem. Commun. 1995, 17, 1793-1794
    • (1995) J. Chem. Soc., Chem. Commun. , vol.17 , pp. 1793-1794
    • Yashiro, M.1    Ishikubo, A.2    Komiyama, M.3
  • 5
    • 2342589413 scopus 로고    scopus 로고
    • Recognition of phosphate monoester dianion by an alkoxide-bridged dinuclear zinc(II) complex
    • Kinoshita, E.; Takahashi, M.; Takeda, H.; Shiro, M.; Koike, T. Recognition of phosphate monoester dianion by an alkoxide-bridged dinuclear zinc(II) complex Dalton Trans. 2004, 8, 1189-1193
    • (2004) Dalton Trans. , vol.8 , pp. 1189-1193
    • Kinoshita, E.1    Takahashi, M.2    Takeda, H.3    Shiro, M.4    Koike, T.5
  • 6
    • 79952270966 scopus 로고    scopus 로고
    • Dinuclear Zn(II) Complex Catalyzed Phosphodiester Cleavage Proceeds via a Concerted Mechanism: A Density Functional Theory Study
    • Gao, H.; Ke, Z.; DeYonker, N. J.; Wang, J.; Xu, H.; Mao, Z.-W.; Phillips, D. L.; Zhao, C. Dinuclear Zn(II) Complex Catalyzed Phosphodiester Cleavage Proceeds via a Concerted Mechanism: A Density Functional Theory Study. J. Am. Chem. Soc. 2011, 133 (9), 2904-2915.
    • (2011) J. Am. Chem. Soc. , vol.133 , Issue.9 , pp. 2904-2915
    • Gao, H.1    Ke, Z.2    Deyonker, N.J.3    Wang, J.4    Xu, H.5    Mao, Z.-W.6    Phillips, D.L.7    Zhao, C.8
  • 7
    • 13644255254 scopus 로고    scopus 로고
    • Solvent deuterium isotope effects on phosphodiester cleavage catalyzed by an extraordinarily active Zn(II) complex
    • DOI 10.1021/ja044617i
    • Yang, M. Y.; Iranzo, O.; Richard, J. P.; Morrow, J. R. Solvent deuterium isotope effects on phosphodiester cleavage catalyzed by an extraordinarily active Zn(II) complex J. Am. Chem. Soc. 2005, 127 (4) 1064-1065 (Pubitemid 40228656)
    • (2005) Journal of the American Chemical Society , vol.127 , Issue.4 , pp. 1064-1065
    • Yang, M.-Y.1    Iranzo, O.2    Richard, J.P.3    Morrow, J.R.4
  • 8
    • 0037024162 scopus 로고    scopus 로고
    • First artificial receptors and chemosensors toward phosphorylated peptide in aqueous solution
    • DOI 10.1021/ja025761b
    • Ojida, A.; Mito-oka, Y.; Inoue, M.; Hamachi, I. First artificial receptors and chemosensors toward phosphorylated peptide in aqueous solution J. Am. Chem. Soc. 2002, 124 (22) 6256-6258 (Pubitemid 34579375)
    • (2002) Journal of the American Chemical Society , vol.124 , Issue.22 , pp. 6256-6258
    • Ojida, A.1    Mito-Oka, Y.2    Inoue, M.-A.3    Hamachi, I.4
  • 9
    • 78649906409 scopus 로고    scopus 로고
    • Recent advances in biosensory and medicinal therapeutic applications of zinc(II) and copper(II) coordination complexes
    • Drewry, J. A.; Gunning, P. T. Recent advances in biosensory and medicinal therapeutic applications of zinc(II) and copper(II) coordination complexes. Coord. Chem. Rev. 2011, 255 (3-4), 459-472.
    • (2011) Coord. Chem. Rev. , vol.255 , Issue.3-4 , pp. 459-472
    • Drewry, J.A.1    Gunning, P.T.2
  • 11
    • 74549185979 scopus 로고    scopus 로고
    • Molecular disruption of oncogenic signal transducer and activator of transcription 3 (STAT3) protein
    • Fletcher, S.; Drewry, J. A.; Shahani, V. M.; Page, B. D. G.; Gunning, P. T. Molecular disruption of oncogenic signal transducer and activator of transcription 3 (STAT3) protein Biochem. Cell Biol. 2009, 87 (6) 825-833
    • (2009) Biochem. Cell Biol. , vol.87 , Issue.6 , pp. 825-833
    • Fletcher, S.1    Drewry, J.A.2    Shahani, V.M.3    Page, B.D.G.4    Gunning, P.T.5
  • 12
    • 72549104819 scopus 로고    scopus 로고
    • Novel asymmetrically functionalized bis-dipicolylamine metal complexes: Peripheral decoration of a potent anion recognition scaffold
    • Drewry, J. A.; Fletcher, S.; Hassan, H.; Gunning, P. T. Novel asymmetrically functionalized bis-dipicolylamine metal complexes: peripheral decoration of a potent anion recognition scaffold Org. Biomol. Chem. 2009, 7 (24) 5074-5077
    • (2009) Org. Biomol. Chem. , vol.7 , Issue.24 , pp. 5074-5077
    • Drewry, J.A.1    Fletcher, S.2    Hassan, H.3    Gunning, P.T.4
  • 13
    • 0000419771 scopus 로고
    • Molecular-Dynamics Simulation Study of Lanthanide Ions Ln(3+) in Aqueous-Solution Including Water Polarization - Change in Coordination-Number from 9 to 8 Along the Series
    • Kowall, T.; Foglia, F.; Helm, L.; Merbach, A. E. Molecular-Dynamics Simulation Study of Lanthanide Ions Ln(3+) in Aqueous-Solution Including Water Polarization-Change in Coordination-Number from 9 to 8 Along the Series J. Am. Chem. Soc. 1995, 117 (13) 3790-3799
    • (1995) J. Am. Chem. Soc. , vol.117 , Issue.13 , pp. 3790-3799
    • Kowall, T.1    Foglia, F.2    Helm, L.3    Merbach, A.E.4
  • 14
    • 0029115487 scopus 로고
    • Zinc-Binding in Proteins and Solution - A Simple but Accurate Nonbonded Representation
    • Stote, R. H.; Karplus, M. Zinc-Binding in Proteins and Solution-a Simple but Accurate Nonbonded Representation Proteins: Struct., Funct., Genet. 1995, 23 (1) 12-31
    • (1995) Proteins: Struct., Funct., Genet. , vol.23 , Issue.1 , pp. 12-31
    • Stote, R.H.1    Karplus, M.2
  • 15
    • 0025158237 scopus 로고
    • A New Force-Field for Modeling Metalloproteins
    • Vedani, A.; Huhta, D. W. A New Force-Field for Modeling Metalloproteins J. Am. Chem. Soc. 1990, 112 (12) 4759-4767
    • (1990) J. Am. Chem. Soc. , vol.112 , Issue.12 , pp. 4759-4767
    • Vedani, A.1    Huhta, D.W.2
  • 16
    • 0035889687 scopus 로고    scopus 로고
    • Successful molecular dynamics simulation of two zinc complexes bridged by a hydroxide in phosphotriesterase using the cationic dummy atom method
    • Pang, Y. P. Successful molecular dynamics simulation of two zinc complexes bridged by a hydroxide in phosphotriesterase using the cationic dummy atom method Proteins: Struct., Funct., Genet. 2001, 45 (3) 183-189
    • (2001) Proteins: Struct., Funct., Genet. , vol.45 , Issue.3 , pp. 183-189
    • Pang, Y.P.1
  • 18
    • 0001474977 scopus 로고    scopus 로고
    • Automated molecular mechanics parameterization with simultaneous utilization of experimental and quantum mechanical data
    • Norrby, P. O.; Liljefors, T. Automated molecular mechanics parameterization with simultaneous utilization of experimental and quantum mechanical data J. Comput. Chem. 1998, 19 (10) 1146-1166
    • (1998) J. Comput. Chem. , vol.19 , Issue.10 , pp. 1146-1166
    • Norrby, P.O.1    Liljefors, T.2
  • 19
    • 0035125739 scopus 로고    scopus 로고
    • Deriving force field parameters for coordination complexes
    • Norrby, P. O.; Brandt, P. Deriving force field parameters for coordination complexes Coord. Chem. Rev. 2001, 212, 79-109
    • (2001) Coord. Chem. Rev. , vol.212 , pp. 79-109
    • Norrby, P.O.1    Brandt, P.2
  • 20
    • 0034647681 scopus 로고    scopus 로고
    • Selectivity in asymmetric synthesis from QM-guided molecular mechanics
    • Norrby, P. O. Selectivity in asymmetric synthesis from QM-guided molecular mechanics THEOCHEM 2000, 506, 9-16
    • (2000) Theochem , vol.506 , pp. 9-16
    • Norrby, P.O.1
  • 21
    • 0001185199 scopus 로고    scopus 로고
    • The Hessian biased singular value decomposition method for optimization and analysis of force fields
    • Dasgupta, S.; Yamasaki, T.; Goddard, W. A. The Hessian biased singular value decomposition method for optimization and analysis of force fields J. Chem. Phys. 1996, 104 (8) 2898-2920 (Pubitemid 126747620)
    • (1996) Journal of Chemical Physics , vol.104 , Issue.8 , pp. 2898-2920
    • Dasgupta, S.1    Yamasaki, T.2    Goddard III, W.A.3
  • 22
    • 14844330742 scopus 로고    scopus 로고
    • AFMM: A molecular mechanics force field vibrational parametrization program
    • DOI 10.1016/j.cpc.2004.12.005, PII S0010465504005624
    • Vaiana, A. C.; Cournia, Z.; Costescu, I. B.; Smith, J. C. AFMM: A molecular mechanics force field vibrational parametrization program Comput. Phys. Commun. 2005, 167 (1) 34-42 (Pubitemid 40340045)
    • (2005) Computer Physics Communications , vol.167 , Issue.1 , pp. 34-42
    • Vaiana, A.C.1    Cournia, Z.2    Costescu, I.B.3    Smith, J.C.4
  • 23
    • 0001348690 scopus 로고    scopus 로고
    • Parameter analysis and refinement toolkit system and its application in MM3 parameterization for phosphine and its derivatives
    • Liang, G. Y.; Fox, P. C.; Bowen, J. P. Parameter analysis and refinement toolkit system and its application in MM3 parameterization for phosphine and its derivatives J. Comput. Chem. 1996, 17 (8) 940-953 (Pubitemid 126572054)
    • (1996) Journal of Computational Chemistry , vol.17 , Issue.8 , pp. 940-953
    • Liang, G.1    Fox, P.C.2    Bowen, J.P.3
  • 24
  • 25
    • 0035451865 scopus 로고    scopus 로고
    • Automatic parameterization of force field by systematic search and genetic algorithms
    • DOI 10.1002/jcc.1079
    • Wang, J. M.; Kollman, P. A. Automatic parameterization of force field by systematic search and genetic algorithms J. Comput. Chem. 2001, 22 (12) 1219-1228 (Pubitemid 32763388)
    • (2001) Journal of Computational Chemistry , vol.22 , Issue.12 , pp. 1219-1228
    • Wang, J.1    Kollman, P.A.2
  • 26
    • 61949237711 scopus 로고    scopus 로고
    • Systematic First Principles Parameterization of Force Fields for Metal-Organic Frameworks using a Genetic Algorithm Approach
    • Tafipolsky, M.; Schmid, R. Systematic First Principles Parameterization of Force Fields for Metal-Organic Frameworks using a Genetic Algorithm Approach J. Phys. Chem. B 2009, 113 (5) 1341-1352
    • (2009) J. Phys. Chem. B , vol.113 , Issue.5 , pp. 1341-1352
    • Tafipolsky, M.1    Schmid, R.2
  • 27
    • 80051645750 scopus 로고    scopus 로고
    • Comparison of Methods to Obtain Force-Field Parameters for Metal Sites
    • Hu, L. H.; Ryde, U. Comparison of Methods to Obtain Force-Field Parameters for Metal Sites. J. Chem. Theory Comput. 2011, 7 (8), 2452-2463.
    • (2011) J. Chem. Theory Comput. , vol.7 , Issue.8 , pp. 2452-2463
    • Hu, L.H.1    Ryde, U.2
  • 28
    • 3743152989 scopus 로고    scopus 로고
    • Calculation of intramolecular force fields from second-derivative tensors
    • Seminario, J. M. Calculation of intramolecular force fields from second-derivative tensors Int. J. Quantum Chem. 1996, 60 (7) 1271-1277 (Pubitemid 126534861)
    • (1996) International Journal of Quantum Chemistry , vol.60 , Issue.7 , pp. 1271-1277
    • Seminario, J.M.1
  • 29
    • 0000730887 scopus 로고    scopus 로고
    • Application of the RESP methodology in the parametrization of organic solvents
    • Fox, T.; Kollman, P. A. Application of the RESP methodology in the parametrization of organic solvents J. Phys. Chem. B 1998, 102 (41) 8070-8079 (Pubitemid 128578425)
    • (1998) Journal of Physical Chemistry B , vol.102 , Issue.41 , pp. 8070-8079
    • Fox, T.1    Kollman, P.A.2
  • 30
    • 0034829463 scopus 로고    scopus 로고
    • Molecular dynamics simulations of the mononuclear: Zinc-β-lactamase from Bacillus cereus
    • DOI 10.1021/ja003796a
    • Suarez, D.; Merz, K. M. Molecular dynamics simulations of the mononuclear zinc-beta-lactamase from Bacillus cereus J. Am. Chem. Soc. 2001, 123 (16) 3759-3770 (Pubitemid 32879538)
    • (2001) Journal of the American Chemical Society , vol.123 , Issue.16 , pp. 3759-3770
    • Suarez, D.1    Merz Jr., K.M.2
  • 31
    • 0028815118 scopus 로고
    • Molecular-Dynamics Simulations of Alcohol-Dehydrogenase with a 4-Coordinate or 5-Coordinate Catalytic Zinc Ion
    • Ryde, U. Molecular-Dynamics Simulations of Alcohol-Dehydrogenase with a 4-Coordinate or 5-Coordinate Catalytic Zinc Ion Proteins: Struct., Funct., Genet. 1995, 21 (1) 40-56
    • (1995) Proteins: Struct., Funct., Genet. , vol.21 , Issue.1 , pp. 40-56
    • Ryde, U.1
  • 32
    • 0001067597 scopus 로고
    • Force-Field Design for Metalloproteins
    • Hoops, S. C.; Anderson, K. W.; Merz, K. M. Force-Field Design for Metalloproteins J. Am. Chem. Soc. 1991, 113 (22) 8262-8270
    • (1991) J. Am. Chem. Soc. , vol.113 , Issue.22 , pp. 8262-8270
    • Hoops, S.C.1    Anderson, K.W.2    Merz, K.M.3
  • 34
    • 77953305723 scopus 로고    scopus 로고
    • Systematic Derivation of AMBER Force Field Parameters Applicable to Zinc-Containing Systems
    • Lin, F.; Wang, R. Systematic Derivation of AMBER Force Field Parameters Applicable to Zinc-Containing Systems. J. Chem. Theory Comput. 2010, 6 (6), 1852-1870.
    • (2010) J. Chem. Theory Comput. , vol.6 , Issue.6 , pp. 1852-1870
    • Lin, F.1    Wang, R.2
  • 35
    • 77956608400 scopus 로고    scopus 로고
    • Structural Survey of Zinc-Containing Proteins and Development of the Zinc AMBER Force Field (ZAFF)
    • Peters, M. B.; Yang, Y.; Wang, B.; Fuesti-Molnar, L.; Weaver, M. N.; Merz, K. M., Jr. Structural Survey of Zinc-Containing Proteins and Development of the Zinc AMBER Force Field (ZAFF). J. Chem. Theory Comput. 2010, 6 (9), 2935-2947.
    • (2010) J. Chem. Theory Comput. , vol.6 , Issue.9 , pp. 2935-2947
    • Peters, M.B.1    Yang, Y.2    Wang, B.3    Fuesti-Molnar, L.4    Weaver, M.N.5    Merz Jr., K.M.6
  • 36
    • 0037159980 scopus 로고    scopus 로고
    • The efficient optimization of molecular geometries using redundant internal coordinates
    • Bakken, V.; Helgaker, T. The efficient optimization of molecular geometries using redundant internal coordinates J. Chem. Phys. 2002, 117 (20) 9160-9174
    • (2002) J. Chem. Phys. , vol.117 , Issue.20 , pp. 9160-9174
    • Bakken, V.1    Helgaker, T.2
  • 38
    • 33748538349 scopus 로고    scopus 로고
    • Automatic atom type and bond type perception in molecular mechanical calculations
    • DOI 10.1016/j.jmgm.2005.12.005, PII S1093326305001737
    • Wang, J. M.; Wang, W.; Kollman, P. A.; Case, D. A. Automatic atom type and bond type perception in molecular mechanical calculations J. Mol. Graphics Modell. 2006, 25 (2) 247-260 (Pubitemid 44363172)
    • (2006) Journal of Molecular Graphics and Modelling , vol.25 , Issue.2 , pp. 247-260
    • Wang, J.1    Wang, W.2    Kollman, P.A.3    Case, D.A.4
  • 40
    • 0001861542 scopus 로고
    • Some Mathematical Methods for the Study of Molecular Vibrations
    • Wilson, E. B. Some Mathematical Methods for the Study of Molecular Vibrations J. Chem. Phys. 1941, 9, 76-84
    • (1941) J. Chem. Phys. , vol.9 , pp. 76-84
    • Wilson, E.B.1
  • 43
    • 84986513567 scopus 로고
    • Determining Atom-Centered Monopoles from Molecular Electrostatic Potentials - The Need for High Sampling Density in Formamide Conformational-Analysis
    • Breneman, C. M.; Wiberg, K. B. Determining Atom-Centered Monopoles from Molecular Electrostatic Potentials-the Need for High Sampling Density in Formamide Conformational-Analysis J. Comput. Chem. 1990, 11 (3) 361-373
    • (1990) J. Comput. Chem. , vol.11 , Issue.3 , pp. 361-373
    • Breneman, C.M.1    Wiberg, K.B.2
  • 44
    • 7544222355 scopus 로고    scopus 로고
    • Harmonic vibrational frequencies: Scaling factors for HF, B3LYP, and MP2 methods in combination with correlation consistent basis sets
    • Sinha, P.; Boesch, S. E.; Gu, C. M.; Wheeler, R. A.; Wilson, A. K. Harmonic vibrational frequencies: Scaling factors for HF, B3LYP, and MP2 methods in combination with correlation consistent basis sets J. Phys. Chem. A 2004, 108 (42) 9213-9217
    • (2004) J. Phys. Chem. A , vol.108 , Issue.42 , pp. 9213-9217
    • Sinha, P.1    Boesch, S.E.2    Gu, C.M.3    Wheeler, R.A.4    Wilson, A.K.5
  • 45
    • 0012927513 scopus 로고    scopus 로고
    • Leontes, N. B. SantaLucia, J. American Chemical Society: Washington, DC
    • Case, T. M. a. D. A. Molecular Modeling of Nucleic Acids; Leontes, N. B.,; SantaLucia, J., Ed.; American Chemical Society: Washington, DC, 1998; pp 379-393.
    • (1998) Molecular Modeling of Nucleic Acids , pp. 379-393
    • Case, A.M.T.D.A.1
  • 46
    • 84857073882 scopus 로고    scopus 로고
    • (accessed Aug. 18).
    • Verstraelen, T. MolMod. http://molmod.ugent.be/code/wiki/MolMod (accessed Aug. 18, 2011).
    • (2011)
    • Verstraelen, T.M.1
  • 47
    • 84857078342 scopus 로고    scopus 로고
    • Ayers Group Software. (accessed Dec. 1)
    • Ayers Group Software. http://www.chemistry.mcmaster.ca/ayers/projects. html (accessed Dec. 1, 2011)
    • (2011)
  • 48
    • 33644753023 scopus 로고    scopus 로고
    • AMBER force-field parameters for phosphorylated amino acids in different protonation states: Phosphoserine, phosphothreonine, phosphotyrosine, and phosphohistidine
    • DOI 10.1007/s00894-005-0028-4
    • Homeyer, N.; Horn, A. H. C.; Lanig, H.; Sticht, H. AMBER force-field parameters for phosphorylated amino acids in different protonation states: phosphoserine, phosphothreonine, phosphotyrosine, and phosphohistidine J. Mol. Model. 2006, 12 (3) 281-289 (Pubitemid 43337197)
    • (2006) Journal of Molecular Modeling , vol.12 , Issue.3 , pp. 281-289
    • Homeyer, N.1    Horn, A.H.C.2    Lanig, H.3    Sticht, H.4
  • 49
    • 3042524904 scopus 로고
    • A Well-Behaved Electrostatic Potential Based Method Using Charge Restraints for Deriving Atomic Charges - The Resp Model
    • Bayly, C. I.; Cieplak, P.; Cornell, W. D.; Kollman, P. A. A Well-Behaved Electrostatic Potential Based Method Using Charge Restraints for Deriving Atomic Charges-the Resp Model J. Phys. Chem. 1993, 97 (40) 10269-10280
    • (1993) J. Phys. Chem. , vol.97 , Issue.40 , pp. 10269-10280
    • Bayly, C.I.1    Cieplak, P.2    Cornell, W.D.3    Kollman, P.A.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.