Processes 2018, 6, 134
10. Bhattacharya, B.; Sweby, P.; Minihane, A.M.; Jackson, K.; Tindall, M. A mathematical model of the sterol
regulatory element binding protein 2 cholesterol biosynthesis pathway. J. Theor. Biol. 2014, 349, 150–162.
[CrossRef][PubMed]
11. Pool, F.; Currie, R.; Sweby, P.; Salazar, D.; Tindall, M. A mathematical model of the mevalonate cholesterol
biosynthesis pathway. J. Theor. Biol. 2018, 443, 157–176. [CrossRef][PubMed]
12. Bhattacharya, B. Mathematical Modelling of Low Density Lipoprotein Metabolism. Intracellular Cholesterol
Regulation. Ph.D. Thesis, University of Reading, Reading, UK, 2011.
13. Wattis, J.; O’Malley, B.; Blackburn, H.; Pickersgill, L.; Panovska, J.; Byrne, H.; Jackson, K. Mathematical
model for low density lipoprotein (LDL) endocytosis by hepatocytes. Bull. Math. Biol. 2008, 70, 2303–2333.
[CrossRef][PubMed]
14. Cromwell, W.; Otvos, J.; Keyes, M.; Pencina, M.; Sullivan, L.; Vasan, R.; Wilson, P.; D’Agostino, R. LDL particle
number and risk of future cardiovascular disease in the Framingham Offspring Study implications for LDL
management. J. Clin. Lipidol. 2007, 1, 583–592. [CrossRef][PubMed]
15. Tindall, M.; Wattis, J.; O’Malley, B.; Pickersgill, L.; Jackson, K. A continuum receptor model of hepatic
lipoprotein metabolism. J. Theor. Biol. 2009, 257, 371–384. [CrossRef][PubMed]
16. Alberts, B.; Johnson, A.; Lewis, J.; Raff, M.; Roberts, K.; Walter, P. The Cell Cycle. In Molecular Biology of the
Cell, 5th ed.; Garland Science: New York, NY, USA, 2008; pp. 1053–1114.
17. Jackson, K.; Maitin, V.; Leake, D.; Yaqoob, P.; Williams, C. Saturated fat-induced changes in Sf 60–400 particle
composition reduces uptake of LDL by HepG2 cells. J. Lipid Res. 2006, 47, 393–403. [CrossRef][PubMed]
18. Lange, Y.; Ye, J.; Rigney, M.; Steck, T. Regulation of endoplasmic reticulum cholesterol by plasma membrane
cholesterol. J. Lipid Res. 1999, 40, 2264–2270. [PubMed]
19. Darzacq, X.; Shav-Tal, Y.; de Turris, V.; Brody, Y.; Shenoy, S.; Phair, R.; Singer, R. In vivo dynamics of RNA
polymerase II transcription. Nat. Struct. Mol. Biol. 2007, 14, 796–806. [CrossRef][PubMed]
20. Goldstein, J.; Brown, M. Progress in understanding the LDL receptor and HMG-CoA reductase, two
membrane proteins that regulate the plasma cholesterol. J. Lipid Res. 1984, 25, 1450–1461. [PubMed]
21. National Center for Biotechnology Information. Genome. 2015. Available online: http://www.ncbi.nlm.nih.
gov/genome (accessed on 31 July 2015).
22. Trachsel, H. Translation in Eukaryotes; CRC Press: Boca Raton, FL, USA, 1991; pp. 149–176.
23. Istvan, E.; Palnitkar, M.; Buchanan, S.; Deisenhofer, J. Crystal structure of the catalytic portion of human
HMG-CoA reductase: Insights into regulation of activity and catalysis. EMBO J. 2000, 19, 819–830. [CrossRef]
[PubMed]
24. Segal, I. Enzyme Kinetics Behaviour and Analysis of Rapid Equilibrium and Steady-State Enzyme Systems;
A Wiley-Interscience Publication; Wiley: New York, NY, USA, 1975; pp. 60–100.
25. Tanaka, R.; Edwards, P.; Lan, S.; Knöppel, E.; Fogelman, A. Purification of 3-hydroxy-3-methylglutaryl
coenzyme A reductase from human liver. J. Lipid Res. 1982, 23, 523–530. [PubMed]
26. Soutar, A.; Knight, B. Structure and regulation of the LDL-receptor and its gene. Br. Med. Bull. 1990,
46, 891–916. [CrossRef][PubMed]
27. Wilson, G.; Deeley, R. An episomal expression vector system for monitoring sequence-specific effects on
mRNA stability in human cell lines. Plasmid 1995, 33, 198–207. [CrossRef][PubMed]
28. Vargas, N.; Brewer, B.; Rogers, T.; Wilson, G. Protein kinase C activation stabilizes LDL receptor mRNA via
the JNK pathway in HepG2 cells. J. Lipid Res. 2009, 50, 386–397. [CrossRef][PubMed]
29. Brown, M.; Dana, S.; Goldstein, J. Regulation of 3-Hydroxy-3-methylglutaryl Coenzyme A Reductase
Activity in Cultured Human Fibroblasts comparison of cells from a normal subject and from a patient with
homozygous familial hypercholesterolemia. J. Biol. Chem. 1974, 249, 789–796. [PubMed]
30. Harwood, J.R.H.; Pellarin, L. Kinetics of low-density lipoprotein receptor activity in Hep-G2 cells: Derivation
and validation of a Briggs–Haldane-based kinetic model for evaluating receptor-mediated endocytotic
processes in which receptors recycle. Biochem. J. 1997, 323, 649–659. [CrossRef][PubMed]
31. Mahley, R.; Innerarity, T. Lipoprotein receptors and cholesterol homeostasis.
Biochim. Biophys.
Acta-Rev. Biomembr. 1983, 737, 197–222. [CrossRef]
32. Goldstein, J.; Anderson, R.; Brown, M. Coated pits, coated vesicles, and receptor-mediated endocytosis.
Nature 1979, 279, 679–685. [CrossRef][PubMed]
33. Brown, M.; Goldstein, J. Receptor-mediated endocytosis: Insights from the lipoprotein receptor system.
Proc. Natl. Acad. Sci. USA 1979, 76, 3330–3337. [CrossRef][PubMed]
112
10. Bhattacharya, B.; Sweby, P.; Minihane, A.M.; Jackson, K.; Tindall, M. A mathematical model of the sterol
regulatory element binding protein 2 cholesterol biosynthesis pathway. J. Theor. Biol. 2014, 349, 150–162.
[CrossRef][PubMed]
11. Pool, F.; Currie, R.; Sweby, P.; Salazar, D.; Tindall, M. A mathematical model of the mevalonate cholesterol
biosynthesis pathway. J. Theor. Biol. 2018, 443, 157–176. [CrossRef][PubMed]
12. Bhattacharya, B. Mathematical Modelling of Low Density Lipoprotein Metabolism. Intracellular Cholesterol
Regulation. Ph.D. Thesis, University of Reading, Reading, UK, 2011.
13. Wattis, J.; O’Malley, B.; Blackburn, H.; Pickersgill, L.; Panovska, J.; Byrne, H.; Jackson, K. Mathematical
model for low density lipoprotein (LDL) endocytosis by hepatocytes. Bull. Math. Biol. 2008, 70, 2303–2333.
[CrossRef][PubMed]
14. Cromwell, W.; Otvos, J.; Keyes, M.; Pencina, M.; Sullivan, L.; Vasan, R.; Wilson, P.; D’Agostino, R. LDL particle
number and risk of future cardiovascular disease in the Framingham Offspring Study implications for LDL
management. J. Clin. Lipidol. 2007, 1, 583–592. [CrossRef][PubMed]
15. Tindall, M.; Wattis, J.; O’Malley, B.; Pickersgill, L.; Jackson, K. A continuum receptor model of hepatic
lipoprotein metabolism. J. Theor. Biol. 2009, 257, 371–384. [CrossRef][PubMed]
16. Alberts, B.; Johnson, A.; Lewis, J.; Raff, M.; Roberts, K.; Walter, P. The Cell Cycle. In Molecular Biology of the
Cell, 5th ed.; Garland Science: New York, NY, USA, 2008; pp. 1053–1114.
17. Jackson, K.; Maitin, V.; Leake, D.; Yaqoob, P.; Williams, C. Saturated fat-induced changes in Sf 60–400 particle
composition reduces uptake of LDL by HepG2 cells. J. Lipid Res. 2006, 47, 393–403. [CrossRef][PubMed]
18. Lange, Y.; Ye, J.; Rigney, M.; Steck, T. Regulation of endoplasmic reticulum cholesterol by plasma membrane
cholesterol. J. Lipid Res. 1999, 40, 2264–2270. [PubMed]
19. Darzacq, X.; Shav-Tal, Y.; de Turris, V.; Brody, Y.; Shenoy, S.; Phair, R.; Singer, R. In vivo dynamics of RNA
polymerase II transcription. Nat. Struct. Mol. Biol. 2007, 14, 796–806. [CrossRef][PubMed]
20. Goldstein, J.; Brown, M. Progress in understanding the LDL receptor and HMG-CoA reductase, two
membrane proteins that regulate the plasma cholesterol. J. Lipid Res. 1984, 25, 1450–1461. [PubMed]
21. National Center for Biotechnology Information. Genome. 2015. Available online: http://www.ncbi.nlm.nih.
gov/genome (accessed on 31 July 2015).
22. Trachsel, H. Translation in Eukaryotes; CRC Press: Boca Raton, FL, USA, 1991; pp. 149–176.
23. Istvan, E.; Palnitkar, M.; Buchanan, S.; Deisenhofer, J. Crystal structure of the catalytic portion of human
HMG-CoA reductase: Insights into regulation of activity and catalysis. EMBO J. 2000, 19, 819–830. [CrossRef]
[PubMed]
24. Segal, I. Enzyme Kinetics Behaviour and Analysis of Rapid Equilibrium and Steady-State Enzyme Systems;
A Wiley-Interscience Publication; Wiley: New York, NY, USA, 1975; pp. 60–100.
25. Tanaka, R.; Edwards, P.; Lan, S.; Knöppel, E.; Fogelman, A. Purification of 3-hydroxy-3-methylglutaryl
coenzyme A reductase from human liver. J. Lipid Res. 1982, 23, 523–530. [PubMed]
26. Soutar, A.; Knight, B. Structure and regulation of the LDL-receptor and its gene. Br. Med. Bull. 1990,
46, 891–916. [CrossRef][PubMed]
27. Wilson, G.; Deeley, R. An episomal expression vector system for monitoring sequence-specific effects on
mRNA stability in human cell lines. Plasmid 1995, 33, 198–207. [CrossRef][PubMed]
28. Vargas, N.; Brewer, B.; Rogers, T.; Wilson, G. Protein kinase C activation stabilizes LDL receptor mRNA via
the JNK pathway in HepG2 cells. J. Lipid Res. 2009, 50, 386–397. [CrossRef][PubMed]
29. Brown, M.; Dana, S.; Goldstein, J. Regulation of 3-Hydroxy-3-methylglutaryl Coenzyme A Reductase
Activity in Cultured Human Fibroblasts comparison of cells from a normal subject and from a patient with
homozygous familial hypercholesterolemia. J. Biol. Chem. 1974, 249, 789–796. [PubMed]
30. Harwood, J.R.H.; Pellarin, L. Kinetics of low-density lipoprotein receptor activity in Hep-G2 cells: Derivation
and validation of a Briggs–Haldane-based kinetic model for evaluating receptor-mediated endocytotic
processes in which receptors recycle. Biochem. J. 1997, 323, 649–659. [CrossRef][PubMed]
31. Mahley, R.; Innerarity, T. Lipoprotein receptors and cholesterol homeostasis.
Biochim. Biophys.
Acta-Rev. Biomembr. 1983, 737, 197–222. [CrossRef]
32. Goldstein, J.; Anderson, R.; Brown, M. Coated pits, coated vesicles, and receptor-mediated endocytosis.
Nature 1979, 279, 679–685. [CrossRef][PubMed]
33. Brown, M.; Goldstein, J. Receptor-mediated endocytosis: Insights from the lipoprotein receptor system.
Proc. Natl. Acad. Sci. USA 1979, 76, 3330–3337. [CrossRef][PubMed]
112