On the protein crystal formation as an interface-controlled process with prototype ion-channeling effect

Journal of Biological Physics

Volumn 33, Issue 4, 2007, Pages 313-329

  Siódmiak, Jacek ^a   Uher, Jan J ^b   Santamaría Holek, Ivan ^c   Kruszewska, Natalia ^a   Gadomski, Adam ^a  

^a UNIVERSITY OF TECHNOLOGY AND LIFE SCIENCES   (Poland)

^b ZSMiO   (Poland)

^c UNIVERSIDAD NACIONAL AUTÓNOMA DE MÉXICO   (Mexico)

Author keywords

Electrostatic double layer; Enhanced diffusion; Ion channel; Protein crystal; Protein solution

Indexed keywords

ION CHANNEL;

ARTICLE; COMPUTER INTERFACE; DIFFUSION COEFFICIENT; ELECTRICITY; HYDROPHOBICITY; MATHEMATICAL COMPUTING; PARTICLE SIZE; PRIORITY JOURNAL; PROTEIN AGGREGATION; QUANTITATIVE ANALYSIS; THERMODYNAMICS; VELOCITY;

EID: 46449111362     PISSN: 00920606     EISSN: None     Source Type: Journal    
DOI: 10.1007/s10867-008-9076-1     Document Type: Article

References (45)

1. Ducruix, A., Giege, R.: Crystallization of Nucleic Acids and Proteins, a Practical Approach. Oxford University Press, New York (1992)
2. McPherson, A.: Crystallization of Biological Macromolecules. Cold Spring Harbor Laboratory Press, New York (1999)
3. Miyazawa, S., Jernigan, R.L.: Estimation of effective interresidue contact energies from protein crystal structures: quasi-chemical approximation. Macromolecules 18, 534-552 (1985)
4. Nicolis, G., Basios, V., Nicolis, C.: Pattern formation and fluctuation-induced transitions in protein crystallization. J. Chem. Phys. 120, 7708-7719 (2004)
5. Vekilov, P.G., Lin, H., Rosenberger, F.: Unsteady crystal growth due to step-bunch cascading. Phys. Rev. E 55, 3202-3214 (1997)
6. Hołyst, R.: Some features of soft matter systems. Soft Matter 1, 329-333 (2005)
7. Gadomski, A., Siódmiak, J.: Kinetics of protein crystal growth in mass convection regime. Cryst. Res. Technol. 37, 281-291 (2002)
8. Łuczka, J., Niemiec, M., Rudnicki, R.: Kinetics of growth process controlled by convective fluctuations. Phys. Rev. E 65, 051401.1-9 (2002)
9. α noise in membrane channel currents. Phys. Rev. Lett. 89, 158101.1-4 (2002)
10. Bezrukov, S.M., Winterhalter, M.: Examining noise sources at the single-molecule level: 1/f noise of an open Maltoporin channel. Phys. Rev. Lett. 85, 202-205 (2000)
11. Fuliński, A., Grzywna, Z., Mellor, I., Siwy, Z., Usherwood, P.N.R.: Non-Markovian character of ionic current fluctuations in membrane channels. Phys. Rev. E 58, 919-924 (1998)
12. Siódmiak, J., Gadomski, A.: Computer model of biopolymer crystal growth and aggregation by addition of macromolecular units-a comparative study. Int. J. Mod. Phys. C 17, 1037-1054 (2006)
13. Gadomski, A., Siódmiak, J.: On the elastic contribution to crystal growth in complex environments. Phys. Status Solidi B 242, 538-549 (2005)
14. Chernov, A.A.: Crystal growth science between the centuries. J. Mater. Sci. Mater. Electron. 12, 437-449 (2001)
15. Gadomski, A., Grzywna, Z., Łuczka, J.: An evolution equation applied to the perturbed sphere growth. Chem. Eng. Sci. 48, 3713-3721 (1993)
16. Cabrera, N., Levine, M.M.: On the dislocation theory of evaporation of crystals. Philos. Mag. 1, 450-458 (1956)
17. Gadomski, A., Łuczka, J.: Some remarks concerning spherulitic growth. Int. J. Quant. Chem. 52, 301-308 (1994)
18. Tolman, R.C.: The effect of droplet size on surface tension. J. Chem. Phys. 17, 333-337 (1949)
19. Gadomski, A., Łuczka, J.: Convection-driven growth in fluctuating velocity field. Acta Phys. Pol. B 24, 725-731 (1993)
20. Kurzynski, M.: The Thermodynamic Machinery of Life. Frontiers Collection. Springer, Berlin (2006)
21. Reguera, D., Rubí, J.M.: Nonequilibrium translational-rotational effects in nucleation. J. Chem. Phys. 115, 7100-7106 (2001)
22. Gadomski, A., Rubí, J.M.: On the two principal curvatures as potential barriers in a model of complex matter agglomeration. Chem. Phys. 293, 169-177 (2003)
23. Chernov, A.A.: Modern Crystallography III: Crystal Growth. Springer, Berlin (1984)
24. Chernov, A.A.: Crystals built of biological macromolecules. Phys. Rep. 288, 61-75 (1997)
25. Pimpinelli, D.K., Villain, J.: Physics of Crystal Growth. Cambridge University Press, New York (1998)
26. Vainstein, M.H., Costa, I.V.L., Morgado, R., Oliveira, F.A.: Non-exponential relaxation for anomalous diffusion. Europhys. Lett. 73, 726-732 (2006)
27. Gadomski, A., Łuczka, J.: Kinetics of temperature or pressure field induced phase transformation in lipid bilayers. Acta Phys. Pol. B 28, 1827-1842 (1997)
28. Málaga, C., Mandujano, F., Santamaría-Holek, I.: Mesoscopic constitutive relations for dilute polymer solutions. Physica A 369, 291-300 (2006)
29. Kosińska, I.D., Fuliński, A.: Asymmetries and anomalous phenomena in ionic transport through nanochannels. Acta Phys. Pol. B 38, 1631-1645 (2007)
30. Liu, X.Y., Boek, E.S., Briels, W.J., Bennema, P.: Prediction of crystal growth morphology based on structural analysis of the solid-fluid interface. Nature 374, 342-345 (1995)
31. Heinemann, S.H., Sigworth, F.J.: Open channel noise V. Fluctuating barriers to ion entry in gramicidin A channels. Biophys. J. 57, 499-514 (1990)
32. Jia, Y.W., Liu. X.Y.: Self-assembly of protein at aqueous solution surface in correlation to protein crystallization. Appl. Phys. Lett. 86, 023903-024100 (2005)
33. Jia, Y.W., Liu. X.Y.: From surface self-assembly to crystallization: prediction of protein crystallization conditions. J. Phys. Chem. B 110, 6949-6955 (2006)
34. Santamaría-Holek, I., Rubí, J.M., Gadomski, A.: Thermokinetic approach of single particles and clusters involving anomalous diffusion under viscoelastic response. J. Phys. Chem. B 111, 2293-2298 (2007)
35. Sakmann, B., Neher, E.: Patch clamp techniques for studying ionic channels in excitable membranes. Annu. Rev. Physiol. 46, 455-472 (1984)
36. Karle, J.: Some developments in anomalous dispersion for the structural investigation of macromolecular systems in biology. Int. J. Quant. Chem. 7, 357-367 (1980)
37. Li, H., Perozzo, M.A., Konnert, J.H., Nadarajah, A., Pusey, M.L.: Determining the molecular-packing arrangements on protein crystal faces by atomic force microscopy. Acta Crystallogr. D 55, 1023-1035 (1999)
38. Kruszewska, N., Gadomski, A.: Towards a 2D model biopolymer polycrystalline aggregation based on Smoluchowski dynamics supplemented by computer experiment. Acta Phys. Pol. B 38, 1819-1835 (2007)
39. Stauffer, D., Aharony, A.: Introduction to Percolation Theory. Taylor and Francis, London (1994)
40. Siwy, Z., Apel, P., Baur, D., Dobrev, D.D., Korchev, Y.E., Neumann, R., Spohr, R., Trautmann, C., Voss, K.: Preparation of synthetic nanopores with transport properties analogous to biological channels. Surf. Sci. 532-535, 1061-1066 (2003)
41. Pechkova, E., Nicolini, C.: Accelerated protein crystal growth by protein thin film template. J. Cryst. Growth 231, 599-602 (2001)
42. Buff, F.P.: The spherical interface. I. Thermodynamics. J. Chem. Phys. 19, 1591-1594 (1951)
43. Babin, V., Holyst, R.: Evaporation of a sub-micrometer droplet. J. Phys. Chem. B 109 11367-11372 (2005)
44. Gadomski, A.: Diffusion-reaction approach applied to the ionic wave propagation through biomembrane channels. Cell. Mol. Biol. Lett. 1, 273-289 (1996)
45. Liebovitch, L.S., Fischbarg, J., Koniarek, J.P., Todorova, I., Wang, M.: Fractal model of ion-channel kinetics. Biochim. Biophys. Acta Biomembr. 896, 173-180 (1987)