DOI QR코드

DOI QR Code

Interaction at the nanoscale of fundamental biological molecules with minerals

  • Valdre, Giovanni (Interdisciplinary Research Centre of Biomineralogy, Crystallography and Biomaterials, Department of Biological, Geological and Environmental Sciences, Alma Mater Studiorum University of Bologna) ;
  • Moro, Daniele (Interdisciplinary Research Centre of Biomineralogy, Crystallography and Biomaterials, Department of Biological, Geological and Environmental Sciences, Alma Mater Studiorum University of Bologna) ;
  • Ulian, Gianfranco (Interdisciplinary Research Centre of Biomineralogy, Crystallography and Biomaterials, Department of Biological, Geological and Environmental Sciences, Alma Mater Studiorum University of Bologna)
  • 투고 : 2013.06.19
  • 심사 : 2013.10.01
  • 발행 : 2013.09.25

초록

The availability of advanced nanotechnological methodologies (experimental and theoretical) has widened the investigation of biological/organic matter in interaction with substrates. Minerals are good candidates as substrates because they may present a wide variety of physico-chemical properties and surface nanostructures that can be used to actively condense and manipulate the biomolecules. Scanning Probe Microscopy (SPM) is one of the best suited techniques used to investigate at a single molecule level the surface interactions. In addition, the recent availability of high performance computing has increased the possibility to study quantum mechanically the interaction phenomena extending the number of atoms involved in the simulation. In the present paper, firstly we will briefly introduce new SPM technological developments and applications to investigate mineral surfaces and mineral-biomolecule interaction, then we will present results on the specific RNA-mineral interaction and recent basics and applicative achievements in the field of the interactions between other fundamental biological molecules and mineral surfaces from both an experimental and theoretical point of view.

키워드

참고문헌

  1. Antognozzi, M., Wotherspoon, A., Hayes, J.M., Miles, M.J., Szczelkun, M.D. and Valdre, G. (2006), "A chlorite mineral surface actively drives the deposition of DNA molecules in stretched conformations", Nanotechnology, 17, 3897-3902. https://doi.org/10.1088/0957-4484/17/15/047
  2. Asthagiri, A. and Hazen, R.M. (2007a), "An ab initio study of adsorption of alanine on the chiral calcite(2131) surface", Mol. Simulat., 33, 343-351. https://doi.org/10.1080/08927020601155485
  3. Asthagiri, A.R. and Hazen, R.M. (2007b), "First-principle studies of amino acid adsorption on chiral mineral surfaces", Proceedings of the 2007 AIChE Annual Meeting, Salt Lake City, UT, USA, November.
  4. Bankston, T.E., Dattolo, L. and Carta, G. (2010), "pH Transients in hydroxyapatite chromatography columns-Experimental evidence and phenomenological modeling", J. Chromatogr. A, 1217, 2123-2131. https://doi.org/10.1016/j.chroma.2010.02.004
  5. Bocchi, G. and Valdre, G. (1993), "Physical, chemical, and mineralogical characterization of carbonate-hydroxyapatite concretions of the human pineal-gland", J. Inorg. Biochem., 49, 209-220. https://doi.org/10.1016/0162-0134(93)80006-U
  6. Borgia, G.C., Brown, R.J.S., Fantazzini, P., Mesini, E. and Valdre, G. (1992), "Diffusion-weighted spatial information from H-1 relaxation in restricted geometries", Nuovo Cimento, 14, 745-759. https://doi.org/10.1007/BF02451721
  7. Bosetti, M., Lloyd, A.W., Santin, M., Denyer, S.P. and Cannas, M. (2005), "Effects of phosphatidylserine coatings on titanium on inflammatory cells and cell-induced mineralisation in vitro", Biomaterials, 26, 7572-7578. https://doi.org/10.1016/j.biomaterials.2005.05.033
  8. Bosetti, M., Santin, M., Lloyd, A.W., Denyer, S.P., Sabbatini, M. and Cannas, M. (2007), "Cell behaviour on phospholipids-coated surfaces", J. Mater. Sci. Mater. Med., 18, 611-617. https://doi.org/10.1007/s10856-007-2309-1
  9. Cagnasso, M., Boero, V., Franchini, M.A. and Chorover, J. (2010), "ATR-FTIR studies of phospholipid vesicle interactions with alpha-FeOOH and alpha-Fe(2)O(3) surfaces", Colloid Surf. B-Biointerfaces, 76, 456-467. https://doi.org/10.1016/j.colsurfb.2009.12.005
  10. Case, D.A., Cheatham, T.E., Darden, T., Gohlke, H., Luo, R., Merz, K.M., Onufriev, A., Simmerling, C., Wang, B. and Woods, R. (2005), "The Amber biomolecular simulation programs", J. Computat. Chem., 26, 1668-1688. https://doi.org/10.1002/jcc.20290
  11. Chen, W.Y., Lin, M.S., Lin, P.H., Tasi, P.S., Chang, Y. and Yamamoto, S. (2007), "Studies of the interaction mechanism between single strand and double-strand DNA with hydroxyapatite by microcalorimetry and isotherm measurements", Colloid Surface A, 295, 274-283. https://doi.org/10.1016/j.colsurfa.2006.09.013
  12. Churchill, H., Teng, H. and Hazen, R.M. (2004), "Correlation of pH-dependent surface interaction forces to amino acid adsorption: Implications for the origin of life", Am. Mineral., 89, 1048-1055. https://doi.org/10.2138/am-2004-0716
  13. Collins, J.R., Loew, G.H., Luke, B.T. and White, D.H. (1988), "Theoretical investigation of the role of clay edges in prebiotic peptide-bond formation. II. Structures and thermodynamics of the activated complex species", Origins Life Evol. B, 18, 107-119. https://doi.org/10.1007/BF01808785
  14. Corno, M., Rimola, A., Bolis, V. and Ugliengo, P. (2010), "Hydroxyapatite as a key biomaterial: quantum-mechanical simulation of its surfaces in interaction with biomolecules", Phys. Chem. Chem. Phys., 12, 6309-6329. https://doi.org/10.1039/c002146f
  15. Cygan, R.T., Greathouse, J.A., Heinz, H. and Kalinichev, A.G. (2009), "Molecular models and simulations of layered materials", J. Mater. Chem., 19, 2470-2481. https://doi.org/10.1039/b819076c
  16. Dangaria, S.J., Ito, Y., Yin, L.L., Valdre, G., Luan, X.H. and Diekwisch, T.G.H. (2011), "Apatite Microtopographies Instruct Signaling Tapestries for Progenitor-Driven New Attachment of Teeth", Tissue Eng. Part A, 17, 279-290. https://doi.org/10.1089/ten.tea.2010.0264
  17. de Duve, C. and Miller, D.L. (1991), "Two-dimensional life?", Proc. Natl. Acad. Sci. U.S.A., 88, 10014-10017. https://doi.org/10.1073/pnas.88.22.10014
  18. Dovesi, R., Civalleri, B., Orlando, R., Roetti, C. and Saunders, V.R. (2005), Ab Initio Quantum Simulation in Solid State Chemistry, Eds. K.B. Lipkowitz, R. Larter and T.R. Cundari, Reviews in Computational Chemistry, Wiley, New York, USA.
  19. Dovesi, R., Saunders, V.R., Roetti, C., Orlando, R., Zicovich-Wilson, C.M., Pascale, F., Civalleri, B., Doll, K., Harrison, N.M., Bush, I.J., D‟Arco, P. and Llunell, M. (2009), CRYSTAL09 User's Manual, University of Torino, Torino, Italy.
  20. Downs, R.T. and Hazen, R.M. (2004), "Chiral indices of crystalline surfaces as a measure enantioselective potential", J. Mol. Catal. a-Chem., 216, 273-285. https://doi.org/10.1016/j.molcata.2004.03.026
  21. Dubey, D.K. and Tomar, V. (2009), "Understanding the influence of structural hierarchy and its coupling with chemical environment on the strength of idealized tropocollagen-hydroxyapatite biomaterials", J. Mech. Phys. Solids, 57, 1702-1717. https://doi.org/10.1016/j.jmps.2009.07.002
  22. Eanes, E.D. (1989), "Biophysical aspects of lipid interaction with mineral - liposome model studies", Anat. Rec., 224, 220-225. https://doi.org/10.1002/ar.1092240211
  23. Elings, V.B. and Gurley, J.A. (1994), "Scanning probe microscope using stored data for vertical probe positioning", Patent, US5308974.
  24. Fukuma, T. (2009), "Subnanometer-Resolution Frequency Modulation Atomic Force Microscopy in Liquid for Biological Applications", Jpn. J. Appl. Phys., 48, 08JA01.
  25. Gambino, G.L., Lombardo, G.M., Grassi, A. and Marletta, G. (2004), "Molecular modeling of interactions between L-lysine and a hydroxylated quartz surface", J. Phys. Chem. B, 108, 2600-2607. https://doi.org/10.1021/jp035991s
  26. Gambino, G.L., Grassi, A. and Marletta, G. (2006), "Molecular modeling of interactions between L-lysine and a functionalized quartz surface", J. Phys. Chem. B, 110, 4836-4845. https://doi.org/10.1021/jp0508610
  27. Gatti, A.M., Valdre, G. and Tombesi, A. (1996), "Importance of microanalysis in understanding mechanism of transformation in active glassy biomaterials", J. Biomed. Mater. Res., 31, 475-480. https://doi.org/10.1002/(SICI)1097-4636(199608)31:4<475::AID-JBM6>3.0.CO;2-I
  28. Giessibl, F.J. (2003), "Advances in atomic force microscopy", Rev. Mod. Phys., 75, 949-983. https://doi.org/10.1103/RevModPhys.75.949
  29. Giro, A., Bergia, A., Zuccheri, G., Bink, H.H.J., Pleij, C.W.A. and Samori, B. (2004), "Single molecule studies of RNA secondary structure: AFM of TYMV viral RNA", Microsc. Res. Techniq., 65, 235-245. https://doi.org/10.1002/jemt.20123
  30. Goldberg, M. and Boskey, A.L. (1996), "Lipids and biomineralizations - Introduction", Prog. Histochem. Cytochem., 31, 1-39.
  31. Gromelski, S., Saraiva, A.M., Krastev, R. and Brezesinki, G. (2009), "The formation of lipid bilayers on surfaces", Colloid Surf. B-Biointerfaces, 74, 477-483. https://doi.org/10.1016/j.colsurfb.2009.08.006
  32. Gromovoy, T.Y., Basiuk, V.A. and Chuiko, A.A. (1991), "Growth of Peptide Chains on Silica in Absence of Amino-Acid Access from Without", Origins Life Evol. B, 21, 119-128. https://doi.org/10.1007/BF01809441
  33. Gross, L., Mohn, F., Moll, N., Liljeroth, P. and Meyer, G. (2009), "The Chemical Structure of a Molecule Resolved by Atomic Force Microscopy", Science, 325, 1110-1114. https://doi.org/10.1126/science.1176210
  34. Gross, L., Mohn, F., Moll, N., Meyer, G., Ebel, R., Abdel-Mageed, W.M. and Jaspars, M. (2010), "Organic structure determination using atomic-resolution scanning probe microscopy", Nat. Chem., 2, 821-825. https://doi.org/10.1038/nchem.765
  35. Hanczyc, M.M., Mansy, S.S. and Szostak, J.W. (2007), "Mineral surface directed membrane assembly", Origins Life Evol. B, 37, 67-82. https://doi.org/10.1007/s11084-006-9018-5
  36. Hazen, R.M. and Sverjensky, D.A. (2010), "Mineral surfaces, feochemical complexities, and the origins of life", Csh. Perspect. Biol., 2, a002162.
  37. Ikhsan, J., Johnson, B.B., Wells, J.D. and Angove, M.J. (2004), "Adsorption of aspartic acid on kaolinite", J. Colloid Interf. Sci., 273, 1-5. https://doi.org/10.1016/j.jcis.2004.01.061
  38. Kim, H.J., Roh, Y. and Hong, B. (2010), "Selective formation of a latticed nanostructure with the precise alignment of DNA-templated gold nanowires", Langmuir, 26, 18315-18319. https://doi.org/10.1021/la101086h
  39. Kirkham, J., Zhang, J., Brookes, S.J., Shore, R.C., Wood, S.R., Smith, D.A., Wallwork, M.L., Ryu, O.H. and Robinson, C. (2000), "Evidence for charge domains on developing enamel crystal surfaces", J. Dent. Res., 79, 1943-1947. https://doi.org/10.1177/00220345000790120401
  40. Kirkham, J., Brookes, S.J., Shore, R.C., Wood, S.R., Smith, D.A., Zhang, J., Chen, H.F. and Robinson, C. (2002), "Physico-chemical properties of crystal surfaces in matrix-mineral interactions during mammalian biomineralisation", Curr. Opin. Colloid. In., 7, 124-132. https://doi.org/10.1016/S1359-0294(02)00017-1
  41. Kresse, G. and Furthmuller, J. (1996), "Efficiency of ab-initio total energy calculations for metals and semiconductors using a plane-wave basis set", Comput. Mater. Sci., 6, 15-50. https://doi.org/10.1016/0927-0256(96)00008-0
  42. Kresse, G. and Hafner, J. (1993), "Ab-initio molecular-dynamics for open-shell transition-metals", Phys. Rev. B, 48, 13115-13118. https://doi.org/10.1103/PhysRevB.48.13115
  43. Kresse, G. and Joubert, D. (1999), "From ultrasoft pseudopotentials to the projector augmented-wave method", Phys. Rev. B, 59, 1758-1775. https://doi.org/10.1103/PhysRevB.59.1758
  44. Lambert, J.F. (2008), "Adsorption and polymerization of amino acids on mineral surfaces: a review", Origins Life Evol. B, 38, 211-242. https://doi.org/10.1007/s11084-008-9128-3
  45. Lee, M.H. and Jhe, W.H. (2006), "General theory of amplitude-modulation atomic force microscopy", Phys. Rev. Lett., 97, 036104. https://doi.org/10.1103/PhysRevLett.97.036104
  46. Lee, J.S., Lee, J.S., Wagoner-Johnson, A. and Murphy, W.L. (2009), "Modular peptide growth factors for substrate-mediated stem cell differentiation", Angew. Chem. Int. Edit., 48, 6266-6269. https://doi.org/10.1002/anie.200901618
  47. Li, P.R., Wei, J.C., Chiu, Y.F., Su, H.L., Peng, F.C. and Lin, J.J. (2010), "Evaluation on cytotoxicity and genotoxicity of the exfoliated silicate nanoclay", ACS Appl. Mater. Interfaces, 2, 1608-1613. https://doi.org/10.1021/am1001162
  48. Lin, H.Y., Tsai, L.C. and Chen, C.D. (2007), "Assembly of nanoparticle patterns with single-particle resolution using DNA-mediated charge trapping technique: method and applications", Adv. Funct. Mater., 17, 3182-3186. https://doi.org/10.1002/adfm.200601180
  49. Lins, R.D. and Straatsma, T.P. (2001), "Computer simulation of the rough lipopolysaccharide membrane of Pseudomonas aeruginosa", Biophys. J., 81, 1037-1046. https://doi.org/10.1016/S0006-3495(01)75761-X
  50. McConnell, H.M., Watts, T.H., Weis, R.M. and Brian, A.A. (1986), "Supported planar membranes in studies of cell-cell recognition in the immune-system", Biochim. Biophys. Acta, 864, 95-106. https://doi.org/10.1016/0304-4157(86)90016-X
  51. Merolli, A., Bosetti, M., Giannotta, L., Lloyd, A.W., Denyer, S.P., Rhys-Williams, W., Love, W.G., Gabbi, C., Cacchioli, A., Tranquilli Leali, P., Cannas, M. and Santin, M. (2006), "In vivo assessment of the osteointegrative potential of phospatidylserine-based coatings", J. Mater. Sci.-Mater. Med., 17, 789-794. https://doi.org/10.1007/s10856-006-9836-z
  52. Michalkova, A., Robinson, T.L. and Leszczynski, J. (2011), "Adsorption of thymine and uracil on 1: 1 clay mineral surfaces: comprehensive ab initio study on influence of sodium cation and water", Phys. Chem. Chem. Phys., 13, 7862-7881. https://doi.org/10.1039/c1cp00008j
  53. Mignon, P., Ugliengo, P. and Sodupe, M. (2009), "Theoretical study of the adsorption of RNA/DNA bases on the external surfaces of $Na^{+}$-montmorillonite", J. Phys. Chem. C, 113, 13741-13749. https://doi.org/10.1021/jp901699q
  54. Muscatello, U., Valdre, G. and Valdre, U. (1996), "Atomic force microscopy observations of acyl chains in phospholipids", J. Microsc., 182, 200-207.
  55. Muscatello, U., Alessandrini, A., Valdre, G., Vannini, V. and Valdre, U. (2000), "Lipid oxidation deletes the nanodomain organization of artificial membranes", Biochem. Biophys. Res. Commun., 270, 448-452. https://doi.org/10.1006/bbrc.2000.2445
  56. Noy, A., Vezenov, D.V. and Lieber, C.M. (1997), "Chemical force microscopy", Annu. Rev. Mater. Sci., 27, 381-421. https://doi.org/10.1146/annurev.matsci.27.1.381
  57. Phillips, J.C., Braun, R., Wang, W., Gumbart, J., Tajkhorshid, E., Villa, E., Chipot, C., Skeel, R.D., Kale, L. and Schulten, K. (2005), "Scalable molecular dynamics with NAMD", J. Computat. Chem., 26, 1781-1802. https://doi.org/10.1002/jcc.20289
  58. Rimola, A., Sodupe, M., Tosoni, S., Civalleri, B. and Ugliengo, P. (2006a), "Interaction of glycine with isolated hydroxyl groups at the silica surface: First principles B3LYP periodic simulation", Langmuir, 22, 6593-6604. https://doi.org/10.1021/la0610203
  59. Rimola, A., Tosoni, S., Sodupe, M. and Ugliengo, P. (2006b), "Does silica surface catalyse peptide bond formation-New insights from first-principles calculations", Chemphyschem, 7, 157-163. https://doi.org/10.1002/cphc.200500401
  60. Robinson, T.L., Michalkova, A., Gorb, L. and Leszczynski, J. (2007), "Hydrogen bonding of thymine and uracil with surface of dickite: an ab initio study", J. Mol. Struct., 844, 48-58.
  61. Sackmann, E. (1996), "Supported membranes: Scientific and practical applications", Science, 271, 43-48. https://doi.org/10.1126/science.271.5245.43
  62. Santin, M., Rhys-Williams, W., O'Reilly, J., Davies, M.C., Shakesheff, K., Love, W.G., Lloyd, A.W. and Denyer, S.P. (2006), "Calcium-binding phospholipids as a coating material for implant osteointegration", J. R. Soc. Interface, 3, 277-281. https://doi.org/10.1098/rsif.2005.0088
  63. Spanos, N., Klepetsanis, P.G. and Koutsoukos, P.G. (2001), "Model studies on the interaction of amino acids with biominerals: the effect of L-serine at the hydroxyapatite-water interface", J. Colloid Interf. Sci., 236, 260-265. https://doi.org/10.1006/jcis.2000.7396
  64. Stievano, L., Piao, L.Y., Lopes, I., Meng, M., Costa, D. and Lambert, J.F. (2007), "Glycine and lysine adsorption and reactivity on the surface of amorphous silica", Eur. J. Mineral., 19, 321-331. https://doi.org/10.1127/0935-1221/2007/0019-1731
  65. Sugimoto, Y., Pou, P., Abe, M., Jelinek, P., Perez, R., Morita, S. and Custance, O. (2007), "Chemical identification of individual surface atoms by atomic force microscopy", Nature, 446, 64-67. https://doi.org/10.1038/nature05530
  66. Swart, I., Gross, L. and Liljeroth, P. (2011), "Single-molecule chemistry and physics explored by low-temperature scanning probe microscopy", Chem. Commun., 47, 9011-9023. https://doi.org/10.1039/c1cc11404b
  67. Tiselius, A., Hjerten, S. and Levin, O. (1956), "Protein chromatography on calcium phosphate columns", Arch. Biochem. Biophys., 65, 132-155. https://doi.org/10.1016/0003-9861(56)90183-7
  68. Valdre, G., Antognozzi, M., Wotherspoon, A. and Miles, M.J. (2004), "Influence of properties of layered silicate minerals on adsorbed DNA surface affinity, self-assembly and nanopatterning", Phil. Mag. Lett., 84, 539-545. https://doi.org/10.1080/09500830512331325082
  69. Valdre, G. and Fabbrizioli, S. (2006), "The role of layer silicate substrates on immobilization of red blood cells", Scanning, 28, 72-73.
  70. Valdre, G. (2007), "Natural nanoscale surface potential of clinochlore and its ability to align nucleotides and drive DNA conformational change", Eur. J. Mineral., 19, 309-319. https://doi.org/10.1127/0935-1221/2007/0019-1732
  71. Valdre, G. and Moro, D. (2008a), "3D finite element analysis of electrostatic deflection of commercial and FIB-modified cantilevers for electric and Kelvin force microscopy: I. Triangular shaped cantilevers with symmetric pyramidal tips", Nanotechnology, 19, 405501. https://doi.org/10.1088/0957-4484/19/40/405501
  72. Valdre, G. and Moro, D. (2008b), "3D finite element analysis of electrostatic deflection and shielding of commercial and FIB-modified cantilevers for electric and Kelvin force microscopy: II. Rectangular shaped cantilevers with asymmetric pyramidal tips", Nanotechnology, 19, 405502. https://doi.org/10.1088/0957-4484/19/40/405502
  73. Valdre, G., Malferrari, D. and Brigatti, M.F. (2009), "Crystallographic features and cleavage nanomorphology of chlinochlore: specific applications", Clay Clay Miner., 57, 183-193. https://doi.org/10.1346/CCMN.2009.0570205
  74. Valdre, G., Tosoni, S. and Moro, D. (2011), "Zeolitic-type Brønsted-Lowry sites distribution observed on clinochlore", Am. Mineral., 96, 1461-1466. https://doi.org/10.2138/am.2011.3774
  75. Vandiver, J., Dean, D., Patel, N., Bonfield, W. and Ortiz, C. (2005), "Nanoscale variation in surface charge of synthetic hydroxyapatite detected by chemically and spatially specific high-resolution force spectroscopy", Biomaterials, 26, 271-283. https://doi.org/10.1016/j.biomaterials.2004.02.053
  76. Vlasova, N.N. and Golovkova, L.P. (2004), "The adsorption of amino acids on the surface of highly dispersed silica", Colloid J+, 66, 657-662. https://doi.org/10.1007/s10595-005-0042-3
  77. Vogel, J.J. and Boyan-Salyers, B.D. (1976), "Acidic lipids associated with the local mechanism of calcification: a review", Clin. Orthop. Rel. Res., 118, 231-241.
  78. Walsh, T.R. (2008), "Modelling the nanoscale patterning of nucleic acid base pairs deposited on graphite", Mol. Phys., 106, 1613-1619. https://doi.org/10.1080/00268970802225533
  79. Ziegler, D., Rychen, J., Naujoks, N. and Stemmer, A. (2007), "Compensating electrostatic forces by single-scan Kelvin probe force microscopy", Nanotechnology, 18, 225505. https://doi.org/10.1088/0957-4484/18/22/225505

피인용 문헌

  1. Nano‐atomic scale hydrophobic/philic confinement of peptides on mineral surfaces by cross‐correlated SPM and quantum mechanical DFT analysis vol.280, pp.3, 2013, https://doi.org/10.1111/jmi.12923
  2. Layer-by-Layer technique as a versatile tool for gene delivery applications vol.18, pp.8, 2013, https://doi.org/10.1080/17425247.2021.1879790