[BAKE75] Baker, H. N., A. M. Gotto, Jr., and R. L. Jackson. 1975. The primary structure of human plasma high density apolipoprotein glutamine I (ApoA-I). J. Biol. Chem. 250:2725--2738.

[BERG95a] Bergeron, J., P. G. Frank, D. Scales, Q.-H. Meng, G. Castro, and Y. L. Marcel. 1995. Apolipoprotein A-I conformation in reconstituted discoidal lipoproteins varying in phospholipid and cholesterol content. J. Biol. Chem. 270:27429--27438.

[BOGU86] Boguski, M. S., M. Freeman, N. A. Elshourbagy, J. M. Taylor, and J. I. Gordon. 1986. On computer-assisted analysis of biological sequences: proline punctuation, consensus sequences, and apolipoprotein repeats. J. Lipid. Res. 27:1011--1034.

[BORH97] Borhani, D. W., D. P. Rogers, J. A. Engler, and C. G. Brouillette. 1997. Crystal structure of truncated human apolipoprotein A-I suggests a lipid-bound conformation. Proc. Natl. Acad. Sci. USA. Submitted.

[BRAS90a] Brasseur, R., J. D. Meutter, B. Vanloo, E. Goormaghtigh, J.-M. Ruysschaert, and M. Rosseneu. 1990. Mode of assembly of amphipathic helical segments in model high-density lipoproteins. Biochim. Biophys. Acta 1043:245--252.

[BRAS92] Brasseur, R., L. Lins, B. Vanloo, J.-M. Ruysschaert, and M. Rosseneu. 1992. Molecular modeling of the amphipathic helices of the plasma apolipoproteins. Proteins: Structure, Function, and Genetics 13:246--257.

[BROO83] Brooks, B. R., R. E. Bruccoleri, B. D. Olafson, D. J. States, S. Swaminathan, and M. Karplus. 1983. CHARMm: A program for macromolecular energy, minimization, and dynamics calculations. J. Comp. Chem. 4:187--217.

[BRUN91B] Br\"unger, A. 1991. Simulated annealing in crystallography. Ann. Rev. Phys. Chem. 42:197--223.

[BRUN90b] Br\"unger, A. T., A. Krukowski, and J. Erickson. 1990. Slow-cooling protocols for crystallographic refinement by simulated annealing. \it Acta Cryst. A46:585--593.

[BRUN92b] Br\"unger, A. T. 1992. X-PLOR, Version 3.1: A System for X-ray Crystallography and NMR. The Howard Hughes Medical Institute and Department of Molecular Biophysics and Biochemistry, Yale University.

[CALA97] Calabresi, L., G. Franceschini, A. Burkybile, and A. Jonas. 1997. Activation of lecithin cholesterol acyltransferase by a disulfide-linked apolipoprotein A-I dimer. Biochem. Biophys. Res. Commun. 232:345--349.

[DAGG93] Daggett, V., and M. Levitt. 1993. Realistic simulations of native-protein dynamics in solution and beyond. Ann. Rev. Biophys. Biomol. Struct. 22:353--380.

[DAVI94] Davidson, W. S., D. L. Sparks, S. Lund-Katz, and M. C. Phillips. 1994. The molecular basis for the difference in charge between pre-$\beta$- and $\alpha$-migrating high density lipoproteins. J. Biol. Chem. 269:8959--8965.

[DAVI96] Davidson, W. S., T. Hazlett, W. W. Mantulin, and A. Jonas. 1996. The role of apolipoprotein A-I domains in lipid binding. Proc. Natl. Acad. Sci. USA 93:13605--13610.

[GARN78] Garnier, J., D. Osguthorpe, and B. Robson. 1978. Analysis of the accuracy and implications of simple methods for predicting the secondary structure of globular proteins. Journal of Molecular Biology 120:97.

[FRAU91] H. Frauenfelder, S. G. Sligar, P. G. W. 1991. The energy landscapes and motions of proteins. Science 254:1598--1603.

[HELL93] Heller, H., M. Schaefer, and K. Schulten. 1993. Molecular dynamics simulation of a bilayer of 200 lipids in the gel and in the liquid crystal-phases. J. Phys. Chem. 97:8343--8360.

[HOLL89] Holley, L. H., and M. Karplus. 1989. Protein secondary structure prediction with a neural network. Proc. Natl. Acad. Sci. USA 86:152--156.

[HOLV95] Holvoet, P., Z. Zhao, B. Vanloo, R. Vos, E. Deridder, A. Dhoest, J. Taveirne, E. Brouwers, E. Demarsin, Y. Engelborghs, M. Rosseneu, D. Collen, and R. Brasseur. 1995. Phospholipid binding and lecithin-cholesterol acyltransferase activation properties of apolipoprotein A-I mutants. Biochemistry 34:13334--13342.

[HU95] Hu, X., D. Xu, K. Hamer, K. Schulten, J. K\"opke, and H. Michel. 1995. Predicting the structure of the light-harvesting complex II of Rhodospirillum molischianum. Protein Science 4:1670--1682.

[HUMP96] Humphrey, W. F., A. Dalke, and K. Schulten. 1996. VMD -- Visual molecular dynamics. J. Mol. Graphics 14:33--38.

[JI95] Ji, Y., and A. Jonas. 1995. Properties of an N-terminal proteolytic fragment of apolipoprotein A-I in solution and in reconstituted high density lipoproteins. J. Biol. Chem. 270:11290--11297.

[JOHN94] Johnson, M. S., N. Srinivasan, R. Sowdhamini, and T. L. Blundell. 1994. Knowledge-based protein modeling. Critical Reviews in Biochemistry and Molecular Biology 29:1--68.

[JONA86B] Jonas, A. 1986. Reconstitution of high-density lipoproteins. Methods Enzymol. 128:553.

[JONA89] Jonas, A., K. E. Kezdy, and J. H. Wald. 1989. Defined apolipoprotein A-I conformations in reconstituted high density lipoprotein discs. J. Biol. Chem. 264:4818--4824.

[JONA90] Jonas, A., J. H. Wald, K. L. H. Toohill, E. S. Krul, and K. E. Kezdy. 1990. Apolipoprotein A-I structure and lipid properties in homogeneous reconstituted spherical and discoidal high density lipoproteins. J. Biol. Chem. 265:22123--22129.

[JONA92] Jonas, A. 1992. Lipid-binding properties of apolipoproteins. In Structure and Function of Apolipoproteins, M. Rosseneu, editor. \newblock

[JORG83] Jorgensen, W. L., J. Chandrasekhar, J. D. Madura, R. W. Impey, and M. L. Klein. 1983. Comparison of simple potential functions for simulating liquid water. J. Chem. Phys. 79:926--935.

[KYTE82b] Kyte, J., and R. F. Doolittle. 1982. A simple method for displaying the hydropathic character of a protein. J. Mol. Biol. 157:105--132.

[LASK93] Laskowski, R. A., M. W. MacArthur, D. S. Moss, and J. M. Thornton. 1993. PROCHECK: a program to check the stereochemical quality of protein structures. J. Appl. Cryst. 26:283--291.

[LUCH94] Luchoomun, J., N. Theret, V. Clavey, P. Duchateau, M. Rosseneu, R. Brasseur, P. Denefle, J.-C. Fruchart, and G. R. Castro. 1994. Structural domain of apolipoprotein A-I involved in its interaction with cells. Biochim. Biophys. Acta 1212:319--326.

[MARC91] Marcel, Y. L., P. R. Prevost, H. Kao, E. Raffai, N. VuDac, J.-C. Fruchart, and E. Rassart. 1991. The epitopes of apolipoprotein A-I define distinct structural domains including a mobile middle region. J. Biol. Chem. 266:3644--3653.

[MATZ82] Matz, C. E., and A. Jonas. 1982. Micellar complexes of human apolipoprotein A-I with phosphatidylcholines and cholesterol prepared from cholate-lipid dispersions. J. Biol. Chem. 257:4535--4540.

[ARNV96] McGuire, K. A., W. S. Davidson, and A. Jonas. 1996. High yield overexpression and characterization of human recombinant proapolipoprotein A-I. J. Lipid. Res. 37:1519.

[MERR94] Merritt, E. A., and M. E. P. Murphy. 1994. Raster3D version 2.0 - a program for photorealistic molecular graphics. Acta Cryst. D 50:869--873.

[MINI92] Minnich, A., X. Collet, A. Roghani, C. Cladaras, R. L. Hamilton, C. J. Fielding, and V. I. Zannis. 1992. Site-directed mutagenesis and structure-function analysis of the human apolipoprotein A-I. J. Biol. Chem. 267:16553--16560.

[MSI94] MSI. 1994. QUANTA 4.0. Molecular Simulations Inc., Burlington, Massachusetts.

[NELS96] Nelson, M., W. Humphrey, A. Gursoy, A. Dalke, L. Kal\'e, R. D. Skeel, and K. Schulten. 1996. NAMD--- A parallel, object-oriented molecular dynamics program. J. Supercomputing App. 10:251--268.

[NICH84] Nichols, A. V., E. L. Gong, P. J. Blanche, T. M. Forte, and V. G. Shore. 1984. Interaction of model discoidal complexes of phosphatidylcholine and apolipoprotein A-I plasma components. Biochim. Biophys. Acta 793:325--337.

[POWN92] Pownall, H. J., and A. M. Gotto, Jr. 1992. Human plasma apolipoproteins. In Biology and medicine in structure and function of apolipoproteins M. Rosseneu, editor. CRC Press, Boca Raton, FL.

[ROGE97] Rogers, D. P., C. G. Brouillette, J. A. Engler, S. W. Tendian, L. Roberts, V. K. Mishra, G. M. Anantharamaiah, S. Lund-Katz, M. C. Phillips, and M. J. Ray. 1997. Truncation of the amino terminus of human apolipoprotein A-I] substantially alters only the lipid-free conformation. Biochemistry 36:288--300.

[SEGR92] Segrest, J. P., M. K. Jones, H. DeLoof, C. G. Brouillette, Y. V. Venkatachalapathi, and G. M. Anantharamaiah. 1992. The amphipathic helix in the exchangeable apolipoproteins: A review of secondary structure and function. J. Lipid. Res. 33:141--166.

[SORC93] Sorci-Thomas, M., M. W. Kearns, and J. P. Lee. 1993. Apolipoprotein A-I domains involved in lecithin-cholesterol acyltransferase activation. J. Biol. Chem. 268:21403--21409.

[STEI93] Steinbach, P. J., and B. R. Brooks. 1993. Protein hydration elucidated by molecular dynamics simulation. Proc. Natl. Acad. Sci. USA 90:9135--9139.

[TEET91] Teeter, M. M. 1991. Water-protein interactions: Theory and experiment. Ann. Rev. Biophys. Biophys. Chem. 20:577--600.

[TuBM92] Tuckerman, M., B. J. Berne, and G. J. Martyna. 1992. Reversible multiple time scale molecular dynamics. J. Chem. Phys 97:1990--2001.

[LAAR87] van Laarhoven, P. J. M., and E. H. L. Aarts. 1987. Simulated Annealing: Theory and Application. D. Reidel, Dordrecht.

[HEFE90b] Wald, J. H., E. Goormaghtigh, J. D. Meutter, J.-M. Ruysschaert, and A. Jonas. 1990a. Investigation of the lipid domains and apolipoprotein orientation in reconstituted high density lipoproteins by fluorescence and IR methods. J. Biol. Chem. 265:20044--20050.

[HEFE90a] Wald, J. H., E. S. Krul, and A. Jonas. 1990b. Structure of apolipoprotein A-I in three homogeneous reconstituted high density lipoprotein particles. J. Biol. Chem. 265:20037--20043.

[WATA95] Watanabe, M., and M. Karplus. 1995. Simulation of macromolecules by multiple-time-step methods. J. Phys. Chem. 99:5680--5697.

[WILS91] Wilson, C., M. R. Wardell, K. H. Weisgraber, R. W. Mahley, and D. A. Agard. 1991. Three-dimensional structure of the LDL receptor-binding domain of human apolipoprotein E. Science 252:1817--1822.

[WLOD79] Wlodawer, A., J. P. Segrest, B. H. Chung, R. Chiovetti, Jr., and J. N. Weinstein. 1979. High-density lipoprotein recombinants: Evidence for a bicycle tire micelle structure obtained by neutron scattering and electron microscopy. FEBS Lett. 104:231--235.

[XU95C] Xu, D., M. Sheves, and K. Schulten. 1995. Molecular dynamics study of the M412 intermediate of bacteriorhodopsin. Biophys. J. 69:2745--2760.