메뉴 건너뛰기




Volumn 12, Issue 4, 2016, Pages 1401-1407

Optimizing Solute-Solute Interactions in the GLYCAM06 and CHARMM36 Carbohydrate Force Fields Using Osmotic Pressure Measurements

Author keywords

[No Author keywords available]

Indexed keywords

CARBOHYDRATE; DEXTRAN; GLUCOSE; SUCROSE;

EID: 84964624195     PISSN: 15499618     EISSN: 15499626     Source Type: Journal    
DOI: 10.1021/acs.jctc.5b01136     Document Type: Article
Times cited : (50)

References (35)
  • 2
    • 0004106191 scopus 로고    scopus 로고
    • Cold Spring Harbor Laboratory Press: Cold Spring Harbor, NY, USA
    • Varki, A., et al., Eds. Essentials of glycobiology. Cold Spring Harbor Laboratory Press: Cold Spring Harbor, NY, USA, 2009.
    • (2009) Essentials of Glycobiology
    • Varki, A.1
  • 5
    • 73349137333 scopus 로고    scopus 로고
    • CHARMM additive all-atom force field for glycosidic linkages between hexopyranoses
    • Guvench, O.; Hatcher, E.; Venable, R. M.; Pastor, R. W.; MacKerell, A. D., Jr. CHARMM additive all-atom force field for glycosidic linkages between hexopyranoses J. Chem. Theory Comput. 2009, 5, 2353-2370 10.1021/ct900242e
    • (2009) J. Chem. Theory Comput. , vol.5 , pp. 2353-2370
    • Guvench, O.1    Hatcher, E.2    Venable, R.M.3    Pastor, R.W.4    MacKerell, A.D.5
  • 6
    • 70349125512 scopus 로고    scopus 로고
    • CHARMM additive all-atom force field for aldopentofuranoses, methyl-aldopentofuranosides, and fructofuranose
    • Hatcher, E.; Guvench, O.; Mackerell, A. D., Jr. CHARMM additive all-atom force field for aldopentofuranoses, methyl-aldopentofuranosides, and fructofuranose J. Phys. Chem. B 2009, 113, 12466-76 10.1021/jp905496e
    • (2009) J. Phys. Chem. B , vol.113 , pp. 12466-12476
    • Hatcher, E.1    Guvench, O.2    Mackerell, A.D.3
  • 9
    • 84882643757 scopus 로고    scopus 로고
    • CHARMM36 all-atom additive protein force field: Validation based on comparison to NMR data
    • Huang, J.; MacKerell, A. D., Jr. CHARMM36 all-atom additive protein force field: Validation based on comparison to NMR data J. Comput. Chem. 2013, 34, 2135-2145 10.1002/jcc.23354
    • (2013) J. Comput. Chem. , vol.34 , pp. 2135-2145
    • Huang, J.1    MacKerell, A.D.2
  • 10
    • 0242593434 scopus 로고    scopus 로고
    • Development and current status of the CHARMM force field for nucleic acids
    • MacKerell, A. D., Jr.; Banavali, N.; Foloppe, N. Development and current status of the CHARMM force field for nucleic acids Biopolymers 2000, 56, 257-265 10.1002/1097-0282(2000)56:4<257::AID-BIP10029>3.0.CO;2-W
    • (2000) Biopolymers , vol.56 , pp. 257-265
    • MacKerell, A.D.1    Banavali, N.2    Foloppe, N.3
  • 11
    • 79960182810 scopus 로고    scopus 로고
    • Development of the CHARMM force field for lipids
    • Pastor, R.; MacKerell, A. D., Jr. Development of the CHARMM force field for lipids J. Phys. Chem. Lett. 2011, 2, 1526-1532 10.1021/jz200167q
    • (2011) J. Phys. Chem. Lett. , vol.2 , pp. 1526-1532
    • Pastor, R.1    MacKerell, A.D.2
  • 13
    • 77955476492 scopus 로고    scopus 로고
    • Molecular simulations of carbohydrates and protein-carbohydrate interactions: Motivation, issues and prospects
    • Fadda, E.; Woods, R. J. Molecular simulations of carbohydrates and protein-carbohydrate interactions: motivation, issues and prospects Drug Discovery Today 2010, 15, 596-609 10.1016/j.drudis.2010.06.001
    • (2010) Drug Discovery Today , vol.15 , pp. 596-609
    • Fadda, E.1    Woods, R.J.2
  • 16
    • 33748940468 scopus 로고    scopus 로고
    • Swelling behavior of the cellulose Iβ crystal models by molecular dynamics
    • Yui, T.; Nishimura, S.; Akiba, S.; Hayashi, S. Swelling behavior of the cellulose Iβ crystal models by molecular dynamics Carbohydr. Res. 2006, 341, 2521-2530 10.1016/j.carres.2006.04.051
    • (2006) Carbohydr. Res. , vol.341 , pp. 2521-2530
    • Yui, T.1    Nishimura, S.2    Akiba, S.3    Hayashi, S.4
  • 18
    • 79953780010 scopus 로고    scopus 로고
    • Analysis of twisting of cellulose nanofibrils in atomistic molecular dynamics simulations
    • Paavilainen, S.; Róg, T.; Vattulainen, I. Analysis of twisting of cellulose nanofibrils in atomistic molecular dynamics simulations J. Phys. Chem. B 2011, 115, 3747-3755 10.1021/jp111459b
    • (2011) J. Phys. Chem. B , vol.115 , pp. 3747-3755
    • Paavilainen, S.1    Róg, T.2    Vattulainen, I.3
  • 20
    • 84881187926 scopus 로고    scopus 로고
    • Unraveling cellulose microfibrils: A twisted tale
    • Hadden, J. A.; French, A. D.; Woods, R. J. Unraveling cellulose microfibrils: A twisted tale Biopolymers 2013, 99, 746-756 10.1002/bip.22279
    • (2013) Biopolymers , vol.99 , pp. 746-756
    • Hadden, J.A.1    French, A.D.2    Woods, R.J.3
  • 21
    • 84927928234 scopus 로고    scopus 로고
    • Solution properties of hemicellulose polysaccharides with four common carbohydrate force fields
    • Sauter, J.; Grafmüller, A. Solution properties of hemicellulose polysaccharides with four common carbohydrate force fields J. Chem. Theory Comput. 2015, 11, 1765-1774 10.1021/ct500924f
    • (2015) J. Chem. Theory Comput. , vol.11 , pp. 1765-1774
    • Sauter, J.1    Grafmüller, A.2
  • 24
    • 80053479096 scopus 로고    scopus 로고
    • A Kirkwood-Buff force field for the aromatic amino acids
    • Ploetz, E. A.; Smith, P. E. A Kirkwood-Buff force field for the aromatic amino acids Phys. Chem. Chem. Phys. 2011, 13, 18154-67 10.1039/c1cp21883b
    • (2011) Phys. Chem. Chem. Phys. , vol.13 , pp. 18154-18167
    • Ploetz, E.A.1    Smith, P.E.2
  • 25
    • 0000016785 scopus 로고
    • A computer simulation of the classic experiment on osmosis and osmotic pressure
    • Murad, S.; Powles, J. A computer simulation of the classic experiment on osmosis and osmotic pressure J. Chem. Phys. 1993, 99, 7271-7272 10.1063/1.465421
    • (1993) J. Chem. Phys. , vol.99 , pp. 7271-7272
    • Murad, S.1    Powles, J.2
  • 26
    • 0344621730 scopus 로고
    • Osmosis and reverse osmosis in solutions: Monte Carlo simulations and van der Waals one-fluid theory
    • Murad, S.; Powles, J. G.; Holtz, B. Osmosis and reverse osmosis in solutions: Monte Carlo simulations and van der Waals one-fluid theory Mol. Phys. 1995, 86, 1473-1483 10.1080/00268979500102861
    • (1995) Mol. Phys. , vol.86 , pp. 1473-1483
    • Murad, S.1    Powles, J.G.2    Holtz, B.3
  • 27
    • 0030266187 scopus 로고    scopus 로고
    • Molecular simulations of osmosis and reverse osmosis in aqueous electrolyte solutions
    • Paritosh, F.; Murad, S. Molecular simulations of osmosis and reverse osmosis in aqueous electrolyte solutions AIChE J. 1996, 42, 2984-2986 10.1002/aic.690421026
    • (1996) AIChE J. , vol.42 , pp. 2984-2986
    • Paritosh, F.1    Murad, S.2
  • 28
    • 0001228466 scopus 로고
    • A novel osmotic pressure route to the activity coefficient of a molecule in a solution
    • Powles, J. G.; Murad, S.; Holtz, B. A novel osmotic pressure route to the activity coefficient of a molecule in a solution Chem. Phys. Lett. 1995, 245, 178-182 10.1016/0009-2614(95)00977-C
    • (1995) Chem. Phys. Lett. , vol.245 , pp. 178-182
    • Powles, J.G.1    Murad, S.2    Holtz, B.3
  • 29
    • 77149136136 scopus 로고    scopus 로고
    • Simulation of osmotic pressure in concentrated aqueous salt solutions
    • Luo, Y.; Roux, B. Simulation of osmotic pressure in concentrated aqueous salt solutions J. Phys. Chem. Lett. 2010, 1, 183-189 10.1021/jz900079w
    • (2010) J. Phys. Chem. Lett. , vol.1 , pp. 183-189
    • Luo, Y.1    Roux, B.2
  • 30
    • 84855431691 scopus 로고    scopus 로고
    • 2+ ions for all-atom molecular dynamics simulations of nucleic acid systems
    • 2+ ions for all-atom molecular dynamics simulations of nucleic acid systems J. Phys. Chem. Lett. 2012, 3, 45-50 10.1021/jz201501a
    • (2012) J. Phys. Chem. Lett. , vol.3 , pp. 45-50
    • Yoo, J.1    Aksimentiev, A.2
  • 31
    • 84954438464 scopus 로고    scopus 로고
    • Improved parameterization of amine-carboxylate and amine-phosphate interactions for molecular dynamics simulations using the CHARMM and AMBER force fields
    • Yoo, J.; Aksimentiev, A. Improved parameterization of amine-carboxylate and amine-phosphate interactions for molecular dynamics simulations using the CHARMM and AMBER force fields J. Chem. Theory Comput. 2016, 12, 430-443 10.1021/acs.jctc.5b00967
    • (2016) J. Chem. Theory Comput. , vol.12 , pp. 430-443
    • Yoo, J.1    Aksimentiev, A.2
  • 32
    • 0035868723 scopus 로고    scopus 로고
    • Molecular dynamics of carbohydrate aqueous solutions. Dielectric relaxation as a function of glucose and fructose concentration
    • Fuchs, K.; Kaatze, U. Molecular dynamics of carbohydrate aqueous solutions. Dielectric relaxation as a function of glucose and fructose concentration J. Phys. Chem. B 2001, 105, 2036-2042 10.1021/jp0030084
    • (2001) J. Phys. Chem. B , vol.105 , pp. 2036-2042
    • Fuchs, K.1    Kaatze, U.2
  • 33
    • 84944484425 scopus 로고
    • Ueber die Anwendung des Satzes vom Virial in der kinetischen Theorie der Gase
    • Lorentz, H. A. Ueber die Anwendung des Satzes vom Virial in der kinetischen Theorie der Gase Ann. Phys. 1881, 248, 127-136 10.1002/andp.18812480110
    • (1881) Ann. Phys. , vol.248 , pp. 127-136
    • Lorentz, H.A.1
  • 34
    • 0000499903 scopus 로고
    • Sur le mélange des gaz
    • Berthelot, D. Sur le mélange des gaz Comptes Rendus 1898, 126, 1703-1706
    • (1898) Comptes Rendus , vol.126 , pp. 1703-1706
    • Berthelot, D.1
  • 35
    • 33947334590 scopus 로고
    • Interactions in aqueous nonelectrolyte solutions. I. Solute-solvent equilibria
    • Stokes, R.; Robinson, R. Interactions in aqueous nonelectrolyte solutions. I. Solute-solvent equilibria J. Phys. Chem. 1966, 70, 2126-2131 10.1021/j100879a010
    • (1966) J. Phys. Chem. , vol.70 , pp. 2126-2131
    • Stokes, R.1    Robinson, R.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.