User:Johnsy/Lipoprotein Modelling/References

Books & Papers

1. ISBN:071673706X
2. ISBN:047119350X
3. ISBN:0713144378

Lipoproteins

4. Adiels M, Packard C, Caslake MJ, Stewart P, Soro A, Westerbacka J, Wennberg B, Olofsson SO, Taskinen MR, and Borén J. A new combined multicompartmental model for apolipoprotein B-100 and triglyceride metabolism in VLDL subfractions. J Lipid Res. 2005 Jan;46(1):58-67. DOI:10.1194/jlr.M400108-JLR200 |
5. Brown MS and Goldstein JL. Receptor-mediated endocytosis: insights from the lipoprotein receptor system. Proc Natl Acad Sci U S A. 1979 Jul;76(7):3330-7. DOI:10.1073/pnas.76.7.3330 |
6. Brown MS and Goldstein JL. A receptor-mediated pathway for cholesterol homeostasis. Science. 1986 Apr 4;232(4746):34-47. DOI:10.1126/science.3513311 |
7. Goldstein JL and Brown MS. The low-density lipoprotein pathway and its relation to atherosclerosis. Annu Rev Biochem. 1977;46:897-930. DOI:10.1146/annurev.bi.46.070177.004341 |
8. Dietschy JM, Turley SD, and Spady DK. Role of liver in the maintenance of cholesterol and low density lipoprotein homeostasis in different animal species, including humans. J Lipid Res. 1993 Oct;34(10):1637-59.
9. Goldstein JL and Brown MS. Regulation of the mevalonate pathway. Nature. 1990 Feb 1;343(6257):425-30. DOI:10.1038/343425a0 |
10. Hussain MM. A proposed model for the assembly of chylomicrons. Atherosclerosis. 2000 Jan;148(1):1-15. DOI:10.1016/s0021-9150(99)00397-4 |
11. Johnson WJ, Mahlberg FH, Chacko GK, Phillips MC, and Rothblat GH. The influence of cellular and lipoprotein cholesterol contents on the flux of cholesterol between fibroblasts and high density lipoprotein. J Biol Chem. 1988 Oct 5;263(28):14099-106.
12. Khan B, Wilcox HG, and Heimberg M. Cholesterol is required for secretion of very-low-density lipoprotein by rat liver. Biochem J. 1989 Mar 15;258(3):807-16. DOI:10.1042/bj2580807 |
13. Lewis GF and Rader DJ. New insights into the regulation of HDL metabolism and reverse cholesterol transport. Circ Res. 2005 Jun 24;96(12):1221-32. DOI:10.1161/01.RES.0000170946.56981.5c |
14. Meddings JB and Dietschy JM. Regulation of plasma levels of low-density lipoprotein cholesterol: interpretation of data on low-density lipoprotein turnover in man. Circulation. 1986 Oct;74(4):805-14. DOI:10.1161/01.cir.74.4.805 |
15. Mineo C, Deguchi H, Griffin JH, and Shaul PW. Endothelial and antithrombotic actions of HDL. Circ Res. 2006 Jun 9;98(11):1352-64. DOI:10.1161/01.RES.0000225982.01988.93 |
16. Packard CJ, Demant T, Stewart JP, Bedford D, Caslake MJ, Schwertfeger G, Bedynek A, Shepherd J, and Seidel D. Apolipoprotein B metabolism and the distribution of VLDL and LDL subfractions. J Lipid Res. 2000 Feb;41(2):305-18.
17. Rye KA, Clay MA, and Barter PJ. Remodelling of high density lipoproteins by plasma factors. Atherosclerosis. 1999 Aug;145(2):227-38. DOI:10.1016/s0021-9150(99)00150-1 |
18. Sviridov D and Nestel P. Dynamics of reverse cholesterol transport: protection against atherosclerosis. Atherosclerosis. 2002 Apr;161(2):245-54. DOI:10.1016/s0021-9150(01)00677-3 |
19. Willnow TE, Nykjaer A, and Herz J. Lipoprotein receptors: new roles for ancient proteins. Nat Cell Biol. 1999 Oct;1(6):E157-62. DOI:10.1038/14109 |

HMG CoA Reductase

20. Bischoff KM and Rodwell VW. Biosynthesis and characterization of (S)-and (R)-3-hydroxy-3-methylglutaryl coenzyme A. Biochem Med Metab Biol. 1992 Oct;48(2):149-58. DOI:10.1016/0885-4505(92)90060-c |
21. Endo A. The discovery and development of HMG-CoA reductase inhibitors. J Lipid Res. 1992 Nov;33(11):1569-82.
22. Istvan ES, Palnitkar M, Buchanan SK, and Deisenhofer J. Crystal structure of the catalytic portion of human HMG-CoA reductase: insights into regulation of activity and catalysis. EMBO J. 2000 Mar 1;19(5):819-30. DOI:10.1093/emboj/19.5.819 |
23. Istvan ES and Deisenhofer J. Structural mechanism for statin inhibition of HMG-CoA reductase. Science. 2001 May 11;292(5519):1160-4. DOI:10.1126/science.1059344 |
24. Louis-Flamberg P, Peishoff CE, Bryan DL, Leber J, Elliott JD, Metcalf BW, and Mayer RJ. Slow binding inhibition of 3-hydroxy-3-methylglutaryl-coenzyme A reductase. Biochemistry. 1990 May 1;29(17):4115-20. DOI:10.1021/bi00469a014 |
25. McGee TP, Cheng HH, Kumagai H, Omura S, and Simoni RD. Degradation of 3-hydroxy-3-methylglutaryl-CoA reductase in endoplasmic reticulum membranes is accelerated as a result of increased susceptibility to proteolysis. J Biol Chem. 1996 Oct 11;271(41):25630-8. DOI:10.1074/jbc.271.41.25630 |
26. Rodwell VW, Beach MJ, Bischoff KM, Bochar DA, Darnay BG, Friesen JA, Gill JF, Hedl M, Jordan-Starck T, Kennelly PJ, Kim DY, and Wang Y. 3-Hydroxy-3-methylglutaryl-CoA reductase. Methods Enzymol. 2000;324:259-80. DOI:10.1016/s0076-6879(00)24237-7 |
27. Schachter M. Chemical, pharmacokinetic and pharmacodynamic properties of statins: an update. Fundam Clin Pharmacol. 2005 Feb;19(1):117-25. DOI:10.1111/j.1472-8206.2004.00299.x |
28. Smythe CD, Greenall M, and Kealey T. The activity of HMG-CoA reductase and acetyl-CoA carboxylase in human apocrine sweat glands, sebaceous glands, and hair follicles is regulated by phosphorylation and by exogenous cholesterol. J Invest Dermatol. 1998 Jul;111(1):139-48. DOI:10.1046/j.1523-1747.1998.00246.x |
29. Stancu C and Sima A. Statins: mechanism of action and effects. J Cell Mol Med. 2001 Oct-Dec;5(4):378-87. DOI:10.1111/j.1582-4934.2001.tb00172.x |
30. Theivagt AE, Amanti EN, Beresford NJ, Tabernero L, and Friesen JA. Characterization of an HMG-CoA reductase from Listeria monocytogenes that exhibits dual coenzyme specificity. Biochemistry. 2006 Dec 5;45(48):14397-406. DOI:10.1021/bi0614636 |

SREBP Pathway

31. Brown MS and Goldstein JL. The SREBP pathway: regulation of cholesterol metabolism by proteolysis of a membrane-bound transcription factor. Cell. 1997 May 2;89(3):331-40. DOI:10.1016/s0092-8674(00)80213-5 |

Bile Acids and Cholesterol 7-α Hydroxylase

32. Chawla A, Saez E, and Evans RM. "Don't know much bile-ology". Cell. 2000 Sep 29;103(1):1-4. DOI:10.1016/s0092-8674(00)00097-0 |
33. Chiang JY, Miller WF, and Lin GM. Regulation of cholesterol 7 alpha-hydroxylase in the liver. Purification of cholesterol 7 alpha-hydroxylase and the immunochemical evidence for the induction of cholesterol 7 alpha-hydroxylase by cholestyramine and circadian rhythm. J Biol Chem. 1990 Mar 5;265(7):3889-97.
34. Houten SM, Watanabe M, and Auwerx J. Endocrine functions of bile acids. EMBO J. 2006 Apr 5;25(7):1419-25. DOI:10.1038/sj.emboj.7601049 |
35. Jelinek DF, Andersson S, Slaughter CA, and Russell DW. Cloning and regulation of cholesterol 7 alpha-hydroxylase, the rate-limiting enzyme in bile acid biosynthesis. J Biol Chem. 1990 May 15;265(14):8190-7.
36. Levy RI, Brensike JF, Epstein SE, Kelsey SF, Passamani ER, Richardson JM, Loh IK, Stone NJ, Aldrich RF, and Battaglini JW. The influence of changes in lipid values induced by cholestyramine and diet on progression of coronary artery disease: results of NHLBI Type II Coronary Intervention Study. Circulation. 1984 Feb;69(2):325-37. DOI:10.1161/01.cir.69.2.325 |
37. Myant NB and Mitropoulos KA. Cholesterol 7 alpha-hydroxylase. J Lipid Res. 1977 Mar;18(2):135-53.
38. Redinger RN, Hawkins JW, and Grace DM. The economy of the enterohepatic circulation of bile acids in the baboon. 1. Studies of controlled enterohepatic circulation of bile acids. J Lipid Res. 1984 May;25(5):428-36.
39. Redinger RN. The economy of the enterohepatic circulation of bile acids in the baboon. 2. Regulation of bile acid synthesis by enterohepatic circulation of bile acids. J Lipid Res. 1984 May;25(5):437-47.
40. Redinger RN. The coming of age of our understanding of the enterohepatic circulation of bile salts. Am J Surg. 2003 Feb;185(2):168-72. DOI:10.1016/s0002-9610(02)01212-6 |
41. Russell DW. The enzymes, regulation, and genetics of bile acid synthesis. Annu Rev Biochem. 2003;72:137-74. DOI:10.1146/annurev.biochem.72.121801.161712 |
42. Russell DW. Nuclear orphan receptors control cholesterol catabolism. Cell. 1999 May 28;97(5):539-42. DOI:10.1016/s0092-8674(00)80763-1 |
43. Russell DW and Setchell KD. Bile acid biosynthesis. Biochemistry. 1992 May 26;31(20):4737-49. DOI:10.1021/bi00135a001 |
44. Schwartz CC, Zech LA, VandenBroek JM, and Cooper PS. Cholesterol kinetics in subjects with bile fistula. Positive relationship between size of the bile acid precursor pool and bile acid synthetic rate. J Clin Invest. 1993 Mar;91(3):923-38. DOI:10.1172/JCI116314 |
45. Trauner M and Boyer JL. Bile salt transporters: molecular characterization, function, and regulation. Physiol Rev. 2003 Apr;83(2):633-71. DOI:10.1152/physrev.00027.2002 |
46. Xu G, Shneider BL, Shefer S, Nguyen LB, Batta AK, Tint GS, Arrese M, Thevananther S, Ma L, Stengelin S, Kramer W, Greenblatt D, Pcolinsky M, and Salen G. Ileal bile acid transport regulates bile acid pool, synthesis, and plasma cholesterol levels differently in cholesterol-fed rats and rabbits. J Lipid Res. 2000 Feb;41(2):298-304.

Mathematical Models

47. August E, Parker KH, and Barahona M. A dynamical model of lipoprotein metabolism. Bull Math Biol. 2007 May;69(4):1233-54. DOI:10.1007/s11538-006-9132-6 |
48. Barrett PH and Watts GF. Kinetic studies of lipoprotein metabolism in the metabolic syndrome including effects of nutritional interventions. Curr Opin Lipidol. 2003 Feb;14(1):61-8. DOI:10.1097/00041433-200302000-00011 |
49. Barrio M, Burrage K, Leier A, and Tian T. Oscillatory regulation of Hes1: Discrete stochastic delay modelling and simulation. PLoS Comput Biol. 2006 Sep 8;2(9):e117. DOI:10.1371/journal.pcbi.0020117 |

50. Cooper K. Dynamical Modeling of Lipoprotein Metabolism. MSc Bioinformatics Thesis, 1 September 2006.

51. Shorten PR and Upreti GC. A mathematical model of fatty acid metabolism and VLDL assembly in human liver. Biochim Biophys Acta. 2005 Sep 15;1736(2):94-108. DOI:10.1016/j.bbalip.2005.07.007 |

Other Books and Sources

1. August E. 2004. A Dynamical System is Biology: Lipoprotein Metabolism, MRes Biomolecular Science Thesis.
2. Brown M & Goldstein J, Receptor-mediated endocytosis: Insights from the lipoprotein receptor system, Proc. Nat. Acad. Sci., 76, 3330-3337 (1979)
3. Brown M & Goldstein J, A Receptor Mediated Pathway for Cholesterol Homeostasis, Nobel Prize Lecture, 9 December 1985
4. Cooper K. 2006 Dynamical Modelling of Lipoprotein Metabolism, MSc Bioinformatics Thesis.
5. Feher, M. 1997, Lipids and Lipid Disorders, 2nd edn, Mosby-Wolfe, London.
6. GeneNetWorks Model of Cholesterol Biosynthesis Regulation
7. Goldstein & Brown, The SREBP Pathway: Regulation of Cholesterol Metabolism by Proteolysis of a Membrane-Bound Transcription Factor, Cell, 1997
8. Panovska J, et al. 2006. Mathematical Models of Hepatic Lipoprotein Metabolism. 5th Mathematics in Medicine Study Group, Oxford University
9. Ratushny A, et al. Mathematical Model of Cholesterol Biosynthesis Regulation in the Cell. Institute of Cytology and Genetics SB RAS, Russia
10. Brown & Goldstein 1977 The Low Density Lipoprotein Pathway and Its Relation to Atherosclerosis
11. iGEM Mathematical Modelling Page
12. Levy et al, The influence of changes in lipid values induced by cholestyramine and diet on progression of coronary artery disease: results of NHLBI Type II Coronary Intervention Study, Circulation, 1984

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