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Original Articles

3D-RISM-KH approach for biomolecular modelling at nanoscale: thermodynamics of fibril formation and beyond

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Pages 718-728 | Received 24 Sep 2010, Accepted 28 Nov 2010, Published online: 25 Mar 2011

References

  • Karplus , M. 2002 . Molecular dynamics simulations of biomolecules . Acc. Chem. Res. , 35 : 321 – 323 .
  • Still , W.C. , Tempczyk , A. , Hawley , R.C. and Hendrickson , T. 1990 . Semianalytical treatment of solvation for molecular mechanics and dynamics . J. Am. Chem. Soc. , 112 : 6127 – 6129 .
  • Sigalov , G. , Fenley , A. and Onufriev , A. 2006 . Analytical electrostatics for biomolecules: Beyond the generalized Born approximation . J. Chem. Phys. , 124 124902, 14 pages
  • Wagoner , J.A. and Baker , N.A. 2006 . Assessing implicit models for nonpolar mean solvation forces: The importance of dispersion and volume terms . Proc. Natl Acad. Sci. USA , 103 : 8331 – 8336 .
  • Levy , R.M. , Zhang , L.Y. , Gallicchio , E. and Felts , A.K. 2003 . On the nonpolar hydration free energy of proteins: Surface area and continuum solvent models for the solute-solvent interaction energy . J. Am. Chem. Soc. , 125 : 9523 – 9530 .
  • Kovalenko , A. 2003 . “ Three-dimensional RISM theory for molecular liquids and solid–liquid interfaces ” . In Molecular Theory of Solvation, Understanding Chemical Reactivity , Edited by: Hirata , F. 169 – 275 . Dordrecht : Kluwer Academic Publishers .
  • Hansen , J.P. and McDonald , I.R. 1986 . Theory of Simple Liquids , 2nd ed. , London : Academic Press .
  • Pettitt , B.M. and Karplus , M. 1985 . The potential of mean force surface for the alanine dipeptide in aqueous solution: A theoretical approach . Chem. Phys. Lett. , 121 : 194 – 201 .
  • Pettitt , B.M. and Karplus , M. 1987 . Structure of water surrounding a peptide: A theoretical approach . Chem. Phys. Lett. , 136 : 383 – 386 .
  • Yu , H.A. , Roux , B. and Karplus , M. 1990 . Solvation thermodynamics: An approach from analytic temperature derivatives . J. Chem. Phys. , 92 : 5020 – 5033 .
  • Boresch , S. , Archontis , G. and Karplus , M. 1994 . Free energy simulations: The meaning of the individual contributions from a component analysis . Proteins: Struct. Funct. Genet. , 20 : 25 – 33 .
  • Imai , T. , Ohyama , S. , Kovalenko , A. and Hirata , F. 2007 . Theoretical study of the partial molar volume change associated with the pressure-induced structural transition of ubiquitin . Protein Sci. , 16 : 1927 – 1933 .
  • Imai , T. , Hiraoka , R. , Kovalenko , A. and Hirata , F. 2007 . Locating missing water molecules in protein cavities by the three-dimensional reference interaction site model theory of molecular solvation . Proteins: Struct. Funct. Bioinf. , 66 : 804 – 813 .
  • Imai , T. , Hiraoka , R. , Seto , T. , Kovalenko , A. and Hirata , F. 2007 . Three-dimensional distribution function theory for the prediction of protein-ligand binding sites and affinities: Application to the binding of noble gases to hen egg-white lysozyme in aqueous solution . J. Phys. Chem. B. , 111 : 11585 – 11591 .
  • Imai , T. , Harano , Y. , Kinoshita , M. , Kovalenko , A. and Hirata , F. 2007 . Theoretical analysis on changes in thermodynamic quantities upon protein folding: Essential role of hydration . J. Chem. Phys. , 126 : 225102 9 pages
  • Imai , T. , Harano , Y. , Kinoshita , M. , Kovalenko , A. and Hirata , F. 2006 . A theoretical analysis on hydration thermodynamics of proteins . J. Chem. Phys. , 125 : 024911 7 pages
  • Harano , Y. , Imai , T. , Kovalenko , A. , Kinoshita , M. and Hirata , F. 2001 . Theoretical study for partial molar volume of amino acids and polypeptides by the three-dimensional reference interaction site model . J. Chem. Phys. , 114 : 9506 – 9511 .
  • Drabik , P. , Gusarov , S. and Kovalenko , A. 2007 . Microtubule stability studied by three-dimensional molecular theory of solvation . Biophys. J. , 92 : 394 – 403 .
  • Imai , T. , Isogai , H. , Seto , T. , Kovalenko , A. and Hirata , F. 2006 . Theoretical study of volume changes accompanying xenon-lysozyme binding: Implications for the molecular mechanism of pressure reversal of anesthesia . J. Phys. Chem. B. , 110 : 12149 – 12154 .
  • Imai , T. , Kovalenko , A. and Hirata , F. 2006 . Hydration structure, thermodynamics, and functions of protein studied by the 3D-RISM theory . Mol. Simul. , 32 : 817 – 824 .
  • Imai , T. , Hiraoka , R. , Kovalenko , A. and Hirata , F. 2005 . Water molecules in a protein cavity detected by a statistical-mechanical theory . J. Am. Chem. Soc. , 127 : 15334 – 15335 .
  • Prusiner , S.B. 1998 . Prions . Proc. Natl Acad. Sci. USA , 95 : 13363 – 13383 .
  • Lansbury , P.T. 1999 . Evolution of amyloid: What normal protein folding may tell us about fibrillogenesis and disease . Proc. Natl Acad. Sci. USA , 96 : 3342 – 3344 .
  • Chiti , F. and Dobson , C.M. 2006 . Protein misfolding, functional amyloid, and human disease . Annu. Rev. Biochem. , 75 : 333 – 366 .
  • Dobson , C.M. 2001 . The structural basis of protein folding and its links with human disease . Philos. Trans. Biol. Sci. , 356 : 133 – 145 .
  • Jahn , T.R. and Radford , S.E. 2008 . Folding versus aggregation: Polypeptide conformations on competing pathways . Arch. Biochem. Biophys. , 469 : 100 – 117 .
  • Aguzzi , A. and Heikenwalder , M. 2006 . Pathogenesis of prion diseases: Current status and future outlook . Nat. Rev. Micro. , 4 : 765 – 775 .
  • Caughey , B. and Lansbury , P.T. 2003 . Protofibrils, pores, fibrils, and neurodegeneration: Separating the responsible protein aggregates from the innocent bystanders . Annu. Rev. Neurosci. , 26 : 267 – 298 .
  • Sipe , J.D. and Cohen , A.S. 2000 . Review: History of the amyloid fibril . J. Struct. Biol. , 130 : 88 – 98 .
  • Case , D.A. , Cheatham , T.E. III , Darden , T. , Gohlke , H. , Luo , R. , Merz , K.M. Jr , Onufriev , A. , Simmerling , C. , Wang , B. and Woods , R.J. 2005 . The amber biomolecular simulation programs . J. Comput. Chem. , 26 : 1668 – 1688 .
  • Blinov , N. , Dorosh , L. , Wishart , D. and Kovalenko , A. 2010 . Association thermodynamics and conformational stability of β-sheet amyloid β(17-42) oligomers: Effects of E22Q (Dutch) mutation and charge neutralization . Biophys. J. , 98 : 282 – 296 .
  • Kinoshita , M. 2003 . “ Conformational stability of biomolecules in solution ” . In Molecular Theory of Solvation, Understanding Chemical Reactivity , Edited by: Hirata , F. 101 – 168 . Dordrecht : Kluwer Academic Publishers .
  • Miyata , T. and Hirata , F. 2008 . Combination of molecular dynamics method and 3D-RISM theory for conformational sampling of large flexible molecules in solution . J. Comput. Chem. , 29 : 871 – 882 .
  • Luchko , T. , Gusarov , S. , Roe , D.R. , Simmerling , C. , Case , D.A. , Tuszynski , J. and Kovalenko , A. 2010 . Three-dimensional molecular theory of solvation coupled with molecular dynamics in Amber . J. Chem. Theory Comput. , 6 : 607 – 624 .
  • Perutz , M.F. , Finch , J.T. , Berriman , J. and Lesk , A. 2002 . Amyloid fibers are water-filled nanotubes . Proc. Natl Acad. Sci. USA , 99 : 5591 – 5595 .
  • Imai , T. , Oda , K. , Kovalenko , A. , Hirata , F. and Kidera , A. 2009 . Ligand mapping on protein surfaces by the 3D-RISM theory: Toward computational fragment-based drug design . J. Am. Chem. Soc. , 131 : 12430 – 12440 .
  • Kuwata , K. , Nishida , N. , Matsumoto , T. , Kamatari , Y.O. , Hosokawa-Muto , J. , Kodama , K. , Nakamura , H.K. , Kimura , K. , Kawasaki , M. , Takakura , Y. , Shirabe , S. , Takata , J. , Kataoka , Y. and Katamine , S. 2007 . Hot spots in prion protein for pathogenic conversion . Proc. Natl Acad. Sci. USA , 104 : 11921 – 11926 .
  • Beglov , D. and Roux , B. 1997 . An integral equation to describe the solvation of polar molecules in liquid water . J. Phys. Chem. B. , 101 : 7821 – 7826 .
  • Chandler , D. and Andersen , H.C. 1972 . Optimized cluster expansions for classical fluids. II. Theory of molecular liquids . J. Chem. Phys. , 57 : 1930 – 1937 .
  • Hirata , F. 2003 . “ Theory of molecular liquids ” . In Molecular Theory of Solvation, Understanding Chemical Reactivity , Edited by: Hirata , F. 1 – 60 . Dordrecht : Kluwer Academic Publishers .
  • Perkyns , J.S. and Pettitt , B.M. 1992 . A dielectrically consistent interaction site theory for solvent-electrolyte mixtures . Chem. Phys. Lett. , 190 : 626 – 630 .
  • Kovalenko , A. and Hirata , F. 2000 . Potentials of mean force of simple ions in ambient aqueous solution. I. Three-dimensional reference interaction site model approach . J. Chem. Phys. , 112 : 10391 – 10402 .
  • Smith , D.E. and Haymet , A.D.J. 1993 . Free energy, entropy, and internal energy of hydrophobic interactions: Computer simulations . J. Chem. Phys. , 98 : 6445 – 6454 .
  • Wang , L. , Duan , Y. , Shortle , R. , Imperiali , B. and Kollman , P. 1999 . Study of the stability and unfolding mechanism of BBA1 by molecular dynamics simulations at different temperatures . Protein Sci. , 8 : 1292 – 1304 .
  • Berendsen , H.J.C. , Grigera , J.R. and Straatsma , T.P. 1987 . The missing term in effective pair potentials . J. Phys. Chem. , 91 : 6269 – 6271 .
  • Jorgensen , W.L. and Tirado-Rives , J. 1988 . The OPLS potential functions for proteins, energy minimizations for crystals of cyclic peptides and crambin . J. Am. Chem. Soc. , 110 : 1657 – 1666 .
  • Allen , M.P. and Tildesley , D.J. 1989 . Computer Simulation of Liquids , New York, USA : Clarendon Press .
  • James , T. , Liu , H. , Ulyanov , N. , Farr-Jones , S. , Zhang , H. , Donne , D. , Kaneko , K. , Groth , D. , Mehlhorn , I. , Prusiner , S. and Cohen , F. 1997 . Solution structure of a 142-residue recombinant prion protein corresponding to the infectious fragment of the scrapie isoform (NMR structure/conformational change) . Proc. Natl Acad. Sci. USA , 94 : 10086 – 10091 .
  • Ilc , G. , Giachin , G. , Jaremko , M. , Jaremko , L. , Benetti , F. , Plavec , J. , Zhukov , I. and Legname , G. 2010 . NMR structure of the human prion protein with the pathological Q212P mutation reveals unique structural features . Plos One. , 5 : e11715
  • Bae , S. , Legname , G. , Serban , A. , Prusiner , S. , Wright , P. and Dyson , H. 2009 . Prion proteins with pathogenic and protective mutations show similar structure and dynamics . Biochemistry , 48 : 8120 – 8128 .
  • Christen , B. , Hornemann , S. , Damberger , F. and Wuthrich , K. 2009 . Prion protein NMR structure from Tammar Wallaby (Macropus eugenii) shows that the beta 2-alpha 2 loop is modulated by long-range sequence effects . J. Mol. Biol. , 389 : 833 – 845 .
  • Christen , B. , Perez , D. , Hornemann , S. and Wuthrich , K. 2008 . NMR structure of the bank vole prion protein at 20 degrees C contains a structured loop of residues 165-171 . J. Mol. Biol. , 383 : 306 – 312 .
  • Gossert , A. , Bonjour , S. , Lysek , D. , Fiorito , F. and Wuthrich , K. 2005 . Prion protein NMR structures of elk and of mouse/elk hybrids . Proc. Natl Acad. Sci. USA , 102 : 646 – 650 .
  • Prusiner , S.B. 1982 . Novel proteinaceous infectious particles cause scrapie . Science , 216 : 136 – 144 .
  • Caughey , B. 2001 . Prion protein interconversions . Philos. Trans. Biol. Sci. , 356 : 197 – 202 .
  • Pan , K. , Baldwin , M. , Nguyen , J. , Gasset , M. , Serban , A. , Groth , D. , Mehlhorn , I. , Huang , Z. , Fletterick , R.J. , Cohen , F.E. and Prusiner , S.B. 1993 . Conversion of alpha-helices into beta-sheets features in the formation of the scrapie prion proteins . Proc. Natl Acad. Sci. USA , 90 : 10962 – 10966 .
  • Cobb , N.J. and Surewicz , W.K. 2009 . Prion diseases and their biochemical mechanisms . Biochemistry , 48 : 2574 – 2585 .
  • Zahn , R. , Liu , A. , Lührs , T. , Riek , R. , Schroettervon , C. , Lopez Garcia , F. , Billeter , M. , Calzolai , L. , Wider , G. and Wuthrich , K. 2000 . NMR solution structure of the human prion protein . Proc. Natl Acad. Sci. USA. , 97 : 145 – 150 .
  • Lindahl , E. , Hess , B. and Spoelvan der , D. 2001 . GROMACS 3.0: A package for molecular simulation and trajectory analysis . J. Mol. Model. , 7 : 306 – 317 .
  • Anfinsen , C. 1973 . Principles that govern the folding of protein chains . Science , 181 : 223 – 230 .
  • Sunde , M. , Serpell , L.C. , Bartlam , M. , Fraser , P.E. , Pepys , M.B. and Blake , C.C.F. 1997 . Common core structure of amyloid fibrils by synchrotron X-ray diffraction . J. Mol. Biol. , 273 : 729 – 739 .
  • Nelson , R. , Sawaya , M.R. , Balbirnie , M. , Madsen , A.O. , Riekel , C. , Grothe , R. and Eisenberg , D. 2005 . Structure of the cross-β spine of amyloid-like fibrils . Nature , 435 : 773 – 778 .
  • Sawaya , M.R. , Sambashivan , S. , Nelson , R. , Ivanova , M.I. , Sievers , S.A. , Apostol , M.I. , Thompson , M.J. , Balbirnie , M. , Wiltzius , J.J.W. , McFarlane , H.T. , Madsen , A.O. , Riekel , C. and Eisenberg , D. 2007 . Atomic structures of amyloid cross-β spines reveal varied steric zippers . Nature , 447 : 453 – 457 .
  • Petkova , A.T. , Ishii , Y. , Balbach , J.J. , Antzutkin , O.N. , Leapman , R.D. , Delaglio , F. and Tycko , R. 2002 . A structural model for Alzheimer's β-amyloid fibrils based on experimental constraints from solid state NMR . Proc. Natl Acad. Sci. USA , 99 : 16742 – 16747 .
  • Lührs , T. , Ritter , C. , Adrian , M. , Riek-Loher , D. , Bohrmann , B. , Dobeli , H. , Schubert , D. and Riek , R. 2005 . 3D structure of Alzheimer's amyloid-β(1-42) fibrils . Proc. Natl Acad. Sci. USA , 102 : 17342 – 17347 .
  • Wasmer , C. , Lange , A. , Van Melckebeke , H. , Siemer , A.B. , Riek , R. and Meier , B.H. 2008 . Amyloid fibrils of the HET-s(218-289) prion form a β solenoid with a triangular hydrophobic core . Science , 319 : 1523 – 1526 .
  • Cobb , N.J. , Sonnichsen , F.D. , Mchaourab , H. and Surewicz , W.K. 2007 . Molecular architecture of human prion protein amyloid: A parallel, in-register β-structure . Proc. Natl Acad. Sci. USA , 104 : 18946 – 18951 .
  • Lu , X. , Wintrode , P.L. and Surewicz , W.K. 2007 . β-Sheet core of human prion protein amyloid fibrils as determined by hydrogen/deuterium exchange . Proc. Natl Acad. Sci. USA , 104 : 1510 – 1515 .
  • Auer , S. , Dobson , C.M. and Vendruscolo , M. 2007 . Characterization of the nucleation barriers for protein aggregation and amyloid formation . HFSP J. , 1 : 137 – 146 .
  • Grant , M.A. , Lazo , N.D. , Lomakin , A. , Condron , M.M. , Arai , H. , Yamin , G. , Rigby , A.C. and Teplow , D.B. 2007 . Familial Alzheimer's disease mutations alter the stability of the amyloid β-protein monomer folding nucleus . Proc. Natl Acad. Sci. USA , 104 : 16522 – 16527 .
  • Blinov , N. , Dorosh , L. , Wishart , D. and Kovalenko , A. 2011 . Desolvation effects and thermodynamic stability of amyloid fibrils , to be submitted
  • De Simone , A. , Dodson , G.G. , Verma , C.S. , Zagari , A. and Fraternali , F. 2005 . Prion and water: Tight and dynamical hydration sites have a key role in structural stability . Proc. Natl Acad. Sci. USA , 102 : 7535 – 7540 .
  • Buchete , N.V. , Tycko , R. and Hummer , G. 2005 . Molecular dynamics simulations of Alzheimer's β-amyloid protofilaments . J. Mol. Biol. , 353 : 804 – 821 .
  • Zheng , J. , Jang , H. , Ma , B. , Tsai , C.J. and Nussinov , R. 2007 . Modeling the Alzheimer Aβ17-42 fibril architecture: Tight intermolecular sheet-sheet association and intramolecular hydrated cavities . Biophys. J. , 93 : 3046 – 3057 .
  • Humphrey , W. , Dalke , A. and Schulten , K. 1996 . VMD: Visual molecular dynamics . J. Mol. Graph. , 14 : 33 – 38 .

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