crc press - E-Lib FK UWKS

Structure Prediction of CPPs and Iterative Development of Novel CPPs 221
39. Sankararamakrishnan, R. and Weinstein, H., Molecular dynamics simulations predict
a tilted orientation for the helical region of dynorphin A(1-17) in dimyristoylphosphatidylcholine
bilayers, Biophys. J., 79, 2331, 2000.
40. Milik, M. and Skolnick, J., Insertion of peptide chains into lipid membranes: an offlattice
Monte Carlo dynamics model, Proteins, 15, 10, 1993.
41. White, S.H., Hydropathy plots and the prediction of membrane topology, in Membrane
Protein Structure: Experimental Approaches, White, S.H., Eds., Oxford University
Press, New York, 1994.
42. Popot, J.L., De Vitry, C., and Atteia, A., Folding and assembly of integral membrane
proteins: an introduction, in Membrane Protein Structure: Experimental Approaches,
White, S.H., Eds., Oxford University Press, New York, 2001.
43. Shrake, A. and Rupley J.A., Environment and exposure to solvent of proteins atoms.
Lysozyme and insulin, J. Mol. Biol., 79, 351, 1973.
44. Flower, D.R., SERF: a program for accessible surface area calculations, J. Mol.
Graph. Model., 15, 238, 1997.
45. Brasseur, R., Differentiation of lipid-associating helices by use of three- dimensional
molecular hydrophobicity potential calculations, J. Biol. Chem., 266, 16120, 1991.
46. Eisenberg, D. and McLachlan, A.D., Solvation energy in protein folding and binding,
Nature, 319, 199, 1986.
47. Fauchère, J.L. and Pliska, V., Hydrophobicity parameter π of amino acid side chains
from the partitioning of N-acetyl-amino-acid-amides, Eur. J. Med. Chem, 18, 369, 1983.
48. Rees, D.C. et al., Membrane protein structure and stability: implications of the first
crystallographic analysis, in Membrane Protein Structure: Experimental Approaches,
White, S.H., Ed., Oxford University Press, New York, 1994.
49. Heller, H., Shaefer, M., and Shulten, K., Molecular dynamics simulation of a bilayer
of 200 lipids in the gel and in the liquid crystal phase, J. Phys. Chem., 97, 8343, 1993.
50. Flewelling, R.F. and Hubbell, W.L., The membrane dipole potential in a total membrane
potential model. Applications to hydrophobic ion interactions with membranes,
Biophys. J., 49, 541, 1986.
51. Press, W.H. et al., Numerical recipes in FORTRAN, in The Art of Scientific Computing,
Cambridge University Press, 1992.
52. Thomas, A. et al., Pex, analytical tools for PDB files. I. GF-Pex: basic file to describe
a protein, Proteins, 43, 28, 2001.
53. Rahman, M. and Brasseur, R., WinMGM: a fast CPK molecular graphics program
for analyzing molecular structure, J. Mol. Graph., 12, 212, 1994.
54. Tanford, C., The Hydrophobic Effect: Formation of Micelles and Biological Membranes,
1st ed., John Wiley & Sons, New York, 1973.
55. Lins, L. et al., Computational study of lipid-destabilizing protein fragments: towards
a comprehensive view of tilted peptides, Proteins, 44, 435, 2001.
56. Lund-Katz, S. et al., Nuclear magnetic resonance investigation of the interactions
with phospholipid of an amphipathic alpha-helix-forming peptide of the apolipoprotein
class, J. Biol. Chem., 265, 12217, 1990.
57. Kersh, G.J., Tomich, J.M., and Montal, M., The M2 delta transmembrane domain of
the nicotinic cholinergic receptor forms ion channels in human erythrocyte membranes,
Biochem. Biophys. Res. Commun., 162, 352, 1989.
58. Martin, I. et al., Fusogenic activity of SIV (simian immunodeficiency virus) peptides
located in the GP32 NH2 terminal domain, Biochem. Biophys. Res. Commun., 175,
872, 1991.