PROTEİN DİNAMİĞİ

[1] Henzler-Wildman, K. and Kern, D., Dynamic personalities of proteins, Nature, 13:450
(7172):964-72, 2007.
[2] Oltvai, Z. N. and Barabasi, A.-L., Life's Complexity Pyramid, Science, 298, 763-764,
2002.
[3] Baker, D. and Lim, W.A., From folding towards function, Current Opinion in Structural
Biology, 12, 11-13, 2002.
[4] Clarke, J. and Schreiber, J., Folding and binding - new technologies and new perspectives,
Current Opinion in Structural Biology, 13, 71-74, 2003.
[5] Azároff, L. V., Kaplow R., Kato N., Weiss R. J., Wilson A. J. C. and Young R.A., X-ray
diffraction. McGraw-Hill, 1974
[6] Martin, G. E. and Zekter, A. S., Two-Dimensional NMR Methods for Establishing
Molecular Connectivity. VCH Publishers, New York, p. 59, 1988.
[7] Frank, J., Three-Dimensional Electron Microscopy of Macromolecular Assemblies.
Oxford University Press, New York, 2006.
[8] Zhang, Y., Progress and challenges in protein structure prediction, Current Opinion in
Structural Biology 18 (3): 342-348, 2008
[9] Zhang, Y. and Skolnick, J., The protein structure prediction problem could be solved
using the current PDB library, Proc Natl Acad Sci USA 102 (4): 1029-1034, 2005.
[10] Bradley, P., Misura, K. M. S. and Baker, D., Toward High-Resolution de Novo Structure
Prediction for Small Proteins, Science, 309 (5742): 1868 – 1871, 2005.
[11] Teilum K., Olsen J. G. and Kragelund B. B., Functional aspects of protein flexibility,
Cellular and Molecular Life Sciences, 66:14, 2231-2247, 2009.
[12] Smock, R. G. and Gierasch, L. M., Sending signals dynamically. Science,
10;324(5924):198-203, 2009.
[13] Vinson V. V., Proteins in Motion, Science, 324 (5924): 197, 2009.
[14] Tokuriki, N. and Tawfik, D. S., Protein Dynamism and Evolvability, Science 324, 5924,
203 – 207, 2009.
[15] Pervushin, K., Riek, R., Wider, G. and Wuthrich, K., Attenuated T-2 relaxation by mutual
cancellation of dipole–dipole coupling and chemical shift anisotropy indicates an avenue
to NMR structures of very large biological macromolecules in solution. Proc. Natl Acad.
Sci. USA 94, 12366–12371, 1997.
[16] Sprangers, R., Gribun, A., Hwang, P. M., Houry, W. A. and Kay, L. E., Quantitative
NMR spectroscopy of supramolecular complexes: dynamic side pores in ClpP are
important for product release. Proc. Natl Acad. Sci. USA 102, 16678–16683, 2005.
[17] Palmer, A. G., Grey, M. J. and Wang, C. Y., Solution NMR spin relaxation methods for
characterizing chemical exchange in high-molecular-weight systems. Methods Enzymol.
394, 430–465, 2005.
[18] Tugarinov, V. and Kay, L. E., Quantitative C-13 and H-2 NMR relaxation studies of the
723- residue enzyme malate synthase G reveal a dynamic binding interface. Biochemistry
44, 15970–15977, 2005.
[19] Sprangers, R. and Kay, L. E., Quantitative dynamics and binding studies of the 20S
proteasome by NMR. Nature, 445, 618–622, 2007.
[20] Horst, R. et al. Direct NMR observation of a substrate protein bound to the chaperonin
GroEL. Proc. Natl Acad. Sci. USA 102, 12748–12753, 2005.
[21] Christodoulou, J. et al. Heteronuclear NMR investigations of dynamic regions of intact
Escherichia coli ribosomes. Proc. Natl Acad. Sci. USA 101, 10949–10954, 2004.
[22] Förster, T., Zwischenmolekulare Energiewanderung und Fluoreszenz, Ann. Physik 437,
55, 1948
[23] Diez, M. et al. Proton-powered subunit rotation in single membrane-bound F0F1-ATP
synthase. Nature Struct. Mol. Biol. 11, 135–141, 2004
[24] Cui, Q. and Bahar, I., Normal Mode Analysis: Theory and applications to biological and
chemical systems, Chapman&Hall/CRC, 2005
[25] Case, D. A., Normal mode analysis of protein dynamics. Curr Opin Struct Biol. 4:285–
290, 1994
[26] Kitao, A. and Go, N., Investigating protein dynamics in collective coordinate space. Curr
Opin Struct Biol. 9:164–169,1999.
[27] Bahar, I., Atilgan, A. R. and Erman, B., Direct evaluation of thermal fluctuations in
proteins using a single parameter harmonic potential, Folding & Design, 2, 173-181,
1997.
[28] Haliloglu, T., Bahar, I. and Erman, B. Gaussian dynamics of folded proteins. Phys. Rev.
Lett. 79, 3090–3093, 1997.
[29] Atilgan, A. R., Durell, S. R. , Jernigan, R. L., Demirel, M. C., Keskin, O. and Bahar, I.,
Anisotropy of fluctuation dynamics of proteins with an elastic network model. Biophys J.
80:505–515, 2001
[30] Jacobs, D. J., Rader, A. J., Kuhn, L. A. and Thorpe, M. F., Protein flexibility predictions
using graph theory. Proteins 44, 150–165, 2001.
[31] Wells, S., Menor, S., Hespenheide, B. and Thorpe, M. F., Constrained geometric
simulation of diffusive motion in proteins. Phys. Biol. 2, S127–S136, 2005.
[32] Scheraga, H. A., Khalili, M. and Liwo, A., Protein-folding dynamics: overview of
molecular simulation techniques. Annu. Rev. Phys. Chem. 58, 57–83, 2007.
[33] Leach, A.R., Molecular Modelling 2nd, Prentice Hall, 2001.
[34] Larsson, G., Schleucher, J., Onions, J., Hermann, S., Grundstrom T. and Wijmenga, S.S.,
A novel target recognition revealed by calmodulin in complex with the basic helix-loophelix transcription factor SEF2-1/E2-2, Protein Sci. 10, 169-186, 2001.
[35] Elshorst, B., Hennig, M., Forsterling, H., Diener, A., Maurer M., Schulte, P., Schwalbe,
H., Griesinger, C., Krebs, J., Schmid, H., Vorherr, T. and Carafoli, E., NMR Solution
Structure of a Complex of Calmodulin with a Binding Peptide of the Ca2+ Pump.
Biochemistry 38, 12320-32, 1999.
[36] Emekli, U., Schneidman-Duhovny, D., Wolfson, H. J , Nussinov, R. and Haliloglu, T.,
HingeProt: Automated Prediction of Hinges in Protein Structures. Proteins 70:1219-27,
2008.
[37] Kurt, N., Scott, W. R., Schiffer, C. A. and Haliloglu, T., Cooperative fluctuations of
unliganded and substrate-bound HIV-1 protease: a structure-based analysis on a variety of
conformations from crystallography and molecular dynamics simulations, 15;51(3): 409-
22, 2003.
[38] Haliloglu T. and Ben-Tal N., Cooperative Transition between Open and Closed
Conformations in Potassium Channels. PLoS Comput Biol 4(8), 2008.
[39] Kessel, A., Haliloglu, T. and Ben-Tal, N., Interaction of Hydrophobic Peptides with Lipid
Bilayers: Monte Carlo Simulations with M2d, Biophysical Journal, 85, 3431-3444, 2003.