Bovine pancreatic trypsin inhibitor crystals with different morphologies: a molecular dynamics simulation study

References

• Margolin , A.L. and Navia , M.A. 2001 . Protein crystals as novel catalytic materials . Angew. Chem. Int. Ed. , 40 : 2205 – 2222 .
   Google Scholar
• Marquart , M. , Walter , J. , Deisenhofer , J. , Bode , W. and Huber , R. 1983 . The geometry of the reactive site and of the peptide groups in trypsin, trypsinogen and its complexes with inhibitors . Acta Crystallogr. Sect. B , 39 : 480 – 490 .
   Google Scholar
• Wlodawer , A. , Walter , J. , Huber , R. and Sjolin , L. 1984 . Structure of bovine pancreatic trypsin-inhibitor – results of joint neutron and x-ray refinement of crystal form-II . J. Mol. Biol. , 180 : 301 – 329 .
   PubMed Web of Science ®Google Scholar
• Wlodawer , A. , Nachman , J. , Gilliland , G.L. , Gallagher , W. and Woodward , C. 1987 . Structure of form-III crystals of bovine pancreatic trypsin-inhibitor . J. Mol. Biol. , 198 : 469 – 480 .
   Google Scholar
• McPherson , A. 1982 . “ Chapter 5: The nature of crystals ” . In Preparation and Analysis of Protein Crystals , Edited by: McPherson , A. New York : John Wiley & Sons .
   Google Scholar
• Cvetkovic , A. , Straathof , A.J.J. , Krishna , R. and van der Wielen , L.A.M. 2005 . Adsorption of xanthene dyes by lysozyme crystals . Langmuir , 21 : 1475 – 1480 .
   PubMed Web of Science ®Google Scholar
• Morozova , T.Y. , Kachalova , G.S. , Lanina , N.F. , Evtodienko , V.U. , Botin , A.S. , Shlyapnikova , E.A. and Morozov , V.N. 1996 . Ionic conductivity, transference numbers, composition and mobility of ions in cross-linked lysozyme crystals . Biophys. Chem. , 60 : 1 – 16 .
   Google Scholar
• Cvetkovic , A. , Picioreanu , C. , Straathof , A.J.J. , Krishna , R. and van der Wielent , L.A.M. 2005 . Relation between pore sizes of protein crystals and anisotropic solute diffusivities . J. Am. Chem. Soc. , 127 : 875 – 879 .
   Google Scholar
• Merzel , F. and Smith , J.C. 2002 . Is the first hydration shell of lysozyme of higher density than bulk water? . Proc. Natl Acad. Sci. USA , 99 : 5378 – 5383 .
   PubMed Web of Science ®Google Scholar
• Heiner , A.P. , Berendsen , H.J.C. and van Gunsteren , W.F. 1992 . Molecular dynamics simulation of subtilisin BPN' in a crystal environment . Proteins , 14 : 451 – 464 .
   Google Scholar
• York , D.M. , Darden , T.A. , Pedersen , L.G. and Anderson , M.W. 1993 . Molecular dynamics simulation of HIV-1 protease in a crystalline environment and in solution . Biochemistry , 32 : 1443 – 1453 .
   Google Scholar
• Ceccarelli , M. and Marchi , M. 1997 . Simulation of a protein crystal at constant pressure . J. Phys. Chem. B , 101 : 2105 – 2108 .
   Web of Science ®Google Scholar
• Marchi , M. and Akasaka , K. 2001 . Simulation of hydrated BPTI at high pressure: Changes in hydrogen bonding and its relation with NMR experiments . J. Phys. Chem. B , 105 : 711 – 714 .
   Google Scholar
• Geremia , S. , Campagnolo , M. , Demitri , N. and Johnson , L.N. 2006 . Simulation of diffusion time of small molecules in protein crystals . Structures , 14 : 393 – 400 .
   PubMed Web of Science ®Google Scholar
• Cerutti , D.S. , Trong , I.L. , Stenkamp , R.E. and Lybrand , T.P. 2008 . Simulations of a protein crystal: Explicit treatment of crystallization conditions links theory and experiment in the streptavidin-biotin complex . Biochemistry , 47 : 12065 – 12077 .
   PubMed Web of Science ®Google Scholar
• Hu , Z.Q. and Jiang , J.W. 2008 . Molecular dynamics simulations for water and ions in protein crystals . Langmuir , 24 : 4215 – 4223 .
   Google Scholar
• Hu , Z.Q. and Jiang , J.W. 2008 . Electrophoresis in protein crystal: Nonequilibrium molecular dynamics simulations . Biophys. J. , 95 : 4148 – 4156 .
   PubMed Web of Science ®Google Scholar
• Hu , Z.Q. and Jiang , J.W. 2009 . Separation of amino acids in glucose isomerase crystal: Insight from molecular dynamics simulations . J. Chromatogr. A , 1216 : 5122 – 5129 .
   Google Scholar
• Hu , Z.Q. and Jiang , J.W. 2009 . Chiral separation of racemic phenylglycines in thermolysin crystal: A molecular simulation study . J. Phys. Chem. B , 113 : 15851 – 15857 .
   Google Scholar
• Schuler , L.D. , Daura , X. and van Gunsteren , W.F. 2001 . An improved GROMOS96 force field for aliphatic hydrocarbons in the condensed phase . J. Comput. Chem. , 22 : 1205 – 1218 .
   Web of Science ®Google Scholar
• Berendsen , H.J.C. , Postma , J.P.M. , van Gunsteren , W.F. and Hermans , J. 1981 . “ Interaction models for water in relation to protein hydration ” . In Intermolecular Forces , Edited by: Pullman , B. Dordrecht : D. Reidel Publishing Company .
   Google Scholar
• Van der Spoel , D. , Lindahl , E. , Hess , B. , Groenhof , G. , Mark , A.E. and Berendsen , H.J.C. 2005 . GROMCAS: Fast, flexible, and free . J. Comput. Chem. , 26 : 1701 – 1718 .
   PubMed Web of Science ®Google Scholar
• Darden , T. , York , D. and Pedersen , L. 1993 . Particle mesh Ewald: An N Log(N) method for Ewald sums in large systems . J. Chem. Phys. , 98 : 10089 – 10092 .
   Web of Science ®Google Scholar
• Hess , B. , Bekker , H. , Berendsen , H.J.C. and Fraaije , J. 1997 . LINCS: A linear constraint solver for molecular simulations . J. Comput. Chem. , 18 : 1463 – 1472 .
   Web of Science ®Google Scholar
• Miyamoto , S. and Kollman , P.A. 1992 . SETTLE: An analytical version of the shake and rattle algorithm for rigid water models . J. Comput. Chem. , 13 : 952 – 962 .
   Web of Science ®Google Scholar
• Berendsen , H.J.C. , Postma , J.P.M. , van Gunsteren , W.F. , DiNola , A. and Haak , J.R. 1984 . Molecular dynamics with coupling to an external bath . J. Chem. Phys. , 81 : 3684 – 3690 .
   Web of Science ®Google Scholar
• Kabsch , W. and Sander , C. 1983 . Dictionary of protein secondary structure pattern recognition of hydrogen-bonded and geometrical features . Biopolymers , 22 : 2577 – 2637 .
   PubMed Web of Science ®Google Scholar
• Lins , L. , Thomas , A. and Brasseur , R. 2003 . Analysis of accessible surface of residues in proteins . Protein Sci. , 12 : 1406 – 1417 .
   PubMedGoogle Scholar
• 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 .
   Web of Science ®Google Scholar