Czasopismo

Tytuł artykułu

Autorzy

Treść / Zawartość

Warianty tytułu

Języki publikacji

Abstrakty

Kategorie tematyczne

Wydawca

Czasopismo

Rocznik

Tom

Strony

151-163

Opis fizyczny

Daty

otrzymano

2012-09-28

zaakceptowano

2013-04-29

online

2013-07-05

Twórcy

Bibliografia

- [1] J. Antosiewicz, J. A. McCammon, and M. K. Gilson, “Prediction of pH-dependent properties of proteins.,” Journal ofMolecular Biology, vol. 238, no. 3, pp. 415–436, 1994.
- [2] D. Bashford and M. Karplus, “pKa’s of ionizable groups in proteins: atomic detail from a continuum electrostaticmodel.,” Biochemistry, vol. 29, no. 44, pp. 10219–10225, 1990.
- [3] S. Bhakdi and J. Tranum-Jensen, “Alpha-toxin of Staphylococcus aureus.,” Microbiological reviews, vol. 55, no. 4,pp. 733–751, 1991.
- [4] P. M. De Biase, C. J. F. Solano, S. Markosyan, L. Czapla, and S. Y. Noskov, “BROMOC-D: BrownianDynamics/Monte-Carlo Program Suite to Study Ion and DNA Permeation in Nanopores.,” Journal of ChemicalTheory and Computation, vol. 8, no. 7, pp. 2540–2551, 2012.
- [5] N. Carrascal and D. F. Green, “Energetic decomposition with the generalized-born and Poisson-Boltzmann solventmodels: lessons from association of G-protein components.,” The Journal of Physical Chemistry B, vol. 114, no. 15,pp. 5096–5116, 2010.[WoS]
- [6] I.-L. Chern, J.-G. Liu, and W.-C. Wang, “Accurate evaluation of electrostatics for macromolecules in solution,” Methodsand Applications of Analysis, vol. 10, no. 2, pp. 309–328, 2003.
- [7] R. D. Coalson and M. G. Kurnikova, “Poisson-Nernst-Planck theory approach to the calculation of current throughbiological ion channels.,” IEEE Transactions on NanoBioscience, vol. 4, no. 1, pp. 81–93, 2005.
- [8] M. L. Connolly, “Molecular Surfaces 5. Solvent Accessible Surfaces,” Network Science Corporation. [Online]. Available:http://www.netsci.org/Science/Compchem/feature14e.html.
- [9] B. Eisenberg, “From Structure to Function in Open Ionic Channels,” The Journal of membrane biology, vol. 171, no.1, pp. 1–24, 2010.
- [10] M. K. Gilson and B. H. Honig, “Energetics of charge-charge interactions in proteins.,” Proteins, vol. 3, no. 1, pp.32–52, Jan. 1988.[WoS]
- [11] D. F. Green and B. Tidor, “Evaluation of electrostatic interactions.,” Current protocols in bioinformatics editoralboard Andreas D Baxevanis et al, vol. Chapter 8, p. Unit 8.3, 2003.
- [12] J. G. Kirkwood, “Theory of solutions of molecules containing widely separated charges with special application tozwitterions,” Journal of Chemical Physics, vol. 2, no. 7, pp. 351–361, 1934.[Crossref]
- [13] I. Klapper, R. Hagstrom, R. Fine, K. Sharp, and B. Honig, “Focusing of electric fields in the active site of Cu-Znsuperoxide dismutase: effects of ionic strength and amino-acid modification.,” Proteins, vol. 1, no. 1, pp. 47–59,1986.
- [14] V. Krishnamurthy and S.-H. C. S.-H. Chung, “Brownian dynamics simulation for modeling ion permeation acrossbionanotubes.,” IEEE Transactions on NanoBioscience, vol. 4, no. 1, pp. 102–111, 2005.[Crossref]
- [15] B. Kuhn and P. A. Kollman, “Binding of a Diverse Set of Ligands to Avidin and Streptavidin: An AccurateQuantitative Prediction of Their Relative Affinities by a Combination of Molecular Mechanics and Continuum SolventModels,” Journal of Medicinal Chemistry, vol. 43, no. 20, pp. 3786–3791, Oct. 2000.
- [16] B. Lu, M. J. Holst, J. A. McCammon, and Y. C. Zhou, “Poisson-Nernst-Planck equations for simulating biomoleculardiffusion-reaction processes I: Finite element solutions,” Journal of Computational Physics, vol. 229, no. 19, pp.6979–6994, 2010.
- [17] A. Nicholls and B. Honig, “A rapid finite difference algorithm, utilizing successive over-relaxation to solve thePoisson-Boltzmann equation,” Journal of Computational Chemistry, vol. 12, no. 4, pp. 435–445, 1991.[Crossref]
- [18] NVIDIA, NVIDIA CUDA C Programming Guide, PG-02829-001_v5.0, no. 350. NVIDIA Corporation, 2012.
- [19] G. Prévost, L. Mourey, D. A. Colin, and G. Menestrina, “Staphylococcal pore-forming toxins.,” Current Topics inMicrobiology and Immunology, vol. 257, pp. 53–83, 2001.
- [20] M. Ramanadham, L. C. Sieker, and L. H. Jensen, “Refinement of triclinic lysozyme: II. The method of stereochemicallyrestrained least squares.,” Acta Crystallographica Section B Structural Science, vol. 46, no. 1, pp. 63–69, 1990.
- [21] W. Rocchia, S. Sridharan, A. Nicholls, E. Alexov, A. Chiabrera, and B. Honig, “Rapid grid-based construction of themolecular surface and the use of induced surface charge to calculate reaction field energies: applications to themolecular systems and geometric objects.,” Journal of Computational Chemistry, vol. 23, no. 1, pp. 128–137, 2002.[Crossref]
- [22] B. Roux, “Theoretical and computational models of ion channels.,” Current Opinion in Structural Biology, vol. 12,no. 2, pp. 182–189, 2002.[Crossref]
- [23] N. A. Simakov and M. G. Kurnikova, “Soft wall ion channel in continuum representation with application to modelingion currents in α-hemolysin.,” The journal of physical chemistry. B, vol. 114, no. 46, pp. 15180–90, Dec. 2010.
- [24] D. Sitkoff, K. A. Sharp, and B. Honig, “Accurate Calculation of Hydration Free Energies Using Macroscopic SolventModels,” Journal of Physical Chemistry, vol. 98, no. 7, pp. 1978–1988, 1994.
- [25] L. Song, M. R. Hobaugh, C. Shustak, S. Cheley, H. Bayley, and J. E. Gouaux, “Structure of staphylococcal alphahemolysin,a heptameric transmembrane pore.,” Science, vol. 274, no. 5294, pp. 1859–1866, 1996.
- [26] Y. Song, J. Mao, and M. R. Gunner, “MCCE2: Improving protein pKa calculations with extensive side chain rotamersampling,” Journal of Computational Chemistry, vol. 30, no. 14, pp. 2231–2247, 2009.[WoS]
- [27] J. Srinivasan, T. E. Cheatham, P. Cieplak, P. A. Kollman, and D. A. Case, “Continuum Solvent Studies of the Stabilityof Continuum Solvent Studies of the Stability of DNA , RNA , and Phosphoramidate-DNA Helices,” Structure, vol.120, no. 37, pp. 9401–9409, 1998.
- [28] D. J. Vocadlo, G. J. Davies, R. Laine, and S. G. Withers, “Catalysis by hen egg-white lysozyme proceeds via acovalent intermediate,” Nature, vol. 412, no. 6849, pp. 835–838, 2001.
- [29] Y. C. Zhou, M. Feig, and G. W. Wei, “Highly accurate biomolecular electrostatics in continuum dielectric environments.,”Journal of Computational Chemistry, vol. 29, no. 1, pp. 87–97, 2008.[WoS]

Typ dokumentu

Bibliografia

Identyfikatory

Identyfikator YADDA

bwmeta1.element.doi-10_2478_mlbmb-2013-0008