scientific publications

This is a selected list of my scientific publications, published abstracts and posters:

1. Segrest JP, Jones MK, Catte A, Manchekar M, Datta G, Zhang L, Zhang R, Li L, Patterson JC, Palgunachari MN, Oram JF, Ren G (2015). Surface Density-Induced Pleating of a Lipid Monolayer Drives Nascent High-Density Lipoprotein Assembly. Structure 23 (7), 1214-1226.
2. Segrest JP, Jones MK, Catte A, Thirumuruganandham (2015). A robust all-atom model for LCAT generated by homology modeling. J. Lipid Res. 56 (3), 620-634.
3. Segrest JP, Jones MK, Catte A (2013). MD simulations suggest important surface differences between reconstituted and circulating spherical HDL. J. Lipid Res. 54 (10), 2718-2732.
4. Segrest JP, Jones MK, Catte A, Thirumuruganandham SP (2012). Validation of previous computer models and MD simulations of discoidal HDL by a recent crystal structure of apoA-I.. JOURNAL OF LIPID RESEARCH, vol. 53, p. 1851-1863, ISSN: 0022-2275.
5. Jones MK, Gu FF, Catte A, Li L, Segrest JP (2011). “Sticky” and “Promiscuous”, the Yin and Yang of Apolipoprotein A-I Termini in Discoidal High-Density Lipoproteins: A Combined Computational-Experimental Approach. BIOCHEMISTRY, vol. 50, p. 2249-2263, ISSN: 0006-2960, doi: 10.1021/bi101301g.
6. Gu FF, Jones MK, Chen JG, Patterson JC, Catte A, Jerome WG, Li L, Segrest JP (2010). Structures of Discoidal High Density Lipoproteins A COMBINED COMPUTATIONAL-EXPERIMENTAL APPROACH. THE JOURNAL OF BIOLOGICAL CHEMISTRY, vol. 285, p. 4652-4665, ISSN: 0021-9258, doi:10.1074/jbc.M109.069914.
7. Vuorela T, Catte A, Niemelä PS, Hall A, Hyvonen MT, Marrink SJ, Karttunen M, Vattulainen I (2010). Role of Lipids in Spheroidal High Density Lipoproteins. PLOS COMPUTATIONAL BIOLOGY, vol. 6, p. 1-14, ISSN: 1553-734X, doi: 10.1371/journal.pcbi.1000964.
8. Jones MK, Zhang L, Catte A, Li L, Oda MN, Ren G, Segrest JP (2010). Assessment of the Validity of the Double Superhelix Model for Reconstituted High Density Lipoproteins A COMBINED COMPUTATIONAL-EXPERIMENTAL APPROACH. THE JOURNAL OF BIOLOGICAL CHEMISTRY, vol. 285, p. 41161-41171, ISSN: 0021-9258, doi: 10.1074/jbc.M110.187799.
9. Jones MK, Catte A, Patterson JC, Gu FF, Chen JG, Li L, Segrest JP (2009). Thermal Stability of Apolipoprotein A-I in High-Density Lipoproteins by Molecular Dynamics. BIOPHYSICAL JOURNAL, vol. 96, p. 354-371, ISSN: 0006-3495, doi: 10.1016/j.bpj.2008.09.041.
10. Jones MK, Catte A, Li L, Segrest JP (2009). Dynamics of Activation of Lecithin: Cholesterol Acyltransferase by Apolipoprotein A-I. BIOCHEMISTRY, vol. 48, p. 11196-11210, ISSN: 0006-2960, doi: 10.1021/bi901242k.
11. Catte A, Patterson JC, Bashtovyy D, Jones MK, Gu F, Li L, Rampioni A, Sengupta D, Vuorela T, Niemelä P, Karttunen M, Marrink SJ, Vattulainen I, Segrest JP (2008). Structure of spheroidal HDL particles revealed by combined atomistic and coarse-grained simulations. BIOPHYSICAL JOURNAL, vol. 94, p. 2306-2319, ISSN: 0006-3495, doi: 10.1529/biophysj.107.115857.
12. Segrest JP, Jones MK, Patterson JC, Catte A (2008). Molecular Dynamics Simulated Annealing of Phospholipid- rich HDL . In: 2008 Abstracts Issue of the Biophysical Society 52nd Annual Meeting. vol. 94, p. 816.
13. Catte A, Vuorela T, Niemelä P, Murtola T, Segrest JP, Marrink SJ, Karttunen M, Vattulainen I (2008). From Discoidal to Spheroidal HDL particles through Coarse Grained and All Atom Molecular Dynamics Simulations . In: 2008 Abstracts Issue of the Biophysical Society 52nd Annual Meeting. vol. 94, p. 331.
14. Catte A, Vuorela T, Niemelä P, Murtola T, Segrest JP, Marrink SJ, Karttunen M, Vattulainen I (2008). From Discoidal to Spheroidal HDL particles through All Atom and Coarse Grained Molecular Dynamicssimulations. In: Abstracts Issue of the 7th European Conference on Computational Biology. p. 74-75
15. Segrest JP, Jones MK, Patterson JC, Catte A (2008). Molecular Dynamics Simulated Annealing of Phospholipid-rich HDL. In: Posters of the 52nd Biophysical Society Annual Meeting.
16. Catte A, Vuorela T, Niemelä P, Murtola T, Segrest JP, Marrink SJ, Karttunen M, Vattulainen I (2008). From Discoidal to Spheroidal HDL particles through All Atom and Coarse Grained Molecular Dynamics simulations. In: 7th European Conference on Computational Biology (poster).
17. Catte A, Patterson JC, Bashtovyy D, Jones MK, Gu FF, Li L, Rampioni A, Sengupta D, Niemelä P, Vattulainen I, Marrink SJ, Segrest JP (2007). Preliminary models of spheroidal HDL particles through molecular dynamics. BIOPHYSICAL JOURNAL, In: 2007 Abstract Issue of the Biophysical Society 51st Annual Meeting. p. 539A, ISSN: 0006-3495.
18. Patterson JC, Catte A, Bashtovyy D, Segrest JP (2007). Molecular dynamics simulations of normal and Milano rotamers of lipid-bound apolipoprotein A-I particles. BIOPHYSICAL JOURNAL, In: 2007 Abstracts Issue of the Biophysical Society 51st Annual Meeting. p. 408A, ISSN: 0006-3495.
19. Bashtovyy D, Catte A, Patterson JC, Segrest JP (2007). Molecular dynamics simulations of monomeric apolipoprotein A-I from a recent X-ray structure. BIOPHYSICAL JOURNAL, In: 2007 Abstracts Issue of the Biophysical Society 51st Annual Meeting. p. 248A, ISSN: 0006-3495.
20. Catte A, Patterson JC, Bashtovyy D, Jones MK, Gu F, Li L, Rampioni A, Sengupta D, Niemelä PS, Vattulainen I, Marrink SJ, Segrest JP (2007). Preliminary models of spheroidal HDL particles through molecular dynamics. In: Proceedings of the XLI Annual Conference of the Finnish Physical Society. vol. 24, p. 343.
21. Catte A, Patterson JC, Jones MK, Jerome WG, Bashtovyy D, Su ZC, Gu FF, Chen JG, Aliste MP, Harvey SC, Li L, Weinstein G, Segrest JP (2006). Novel changes in discoidal high density lipoprotein morphology: A molecular dynamics study. BIOPHYSICAL JOURNAL, vol. 90, p. 4345-4360, ISSN: 0006-3495, doi: 10.1529/biophysj.105.071456.
22. Catte A, Patterson JC, Bashtovyy D, Weinstein G, Su Z, Li L, Chen J, Jones MK, Aliste MP, Harvey SC, Segrest JP (2006). Novel Protein-Lipid Conformations of High Density Lipoproteins through Molecular Dynamics. In: 2006 Abstracts Issue of the Biophysical Society 50th Annual Meeting.
23. Catte A, Patterson JC, Jones MK, Bashtovyy D, Gu F, Li L, Segrest JP (2006). Preliminary Models of Spheroidal HDL particles through Molecular Dynamics. In: Posters of the 22nd Annual Trainee Research Symposium.
24. Catte A, Patterson JC, Jones MK, Bashtovyy D, Gu F, Aliste MP, Harvey SC, Li L, Weinstein G, Segrest JP (2006). Preliminary Models of Spheroidal HDL particles through Molecular Dynamics. In: Emory University Lectureship Award (poster).
25. Catte A, Patterson JC, Jones MK, Bashtovyy D, Gu F, Aliste MP, Harvey SC, Li L, Weinstein G, Segrest JP (2006). Preliminary Models of Spheroidal HDL particles through Molecular Dynamics. In: Frontiers in Macromolecular Simulations (poster).
26. Catte A, Patterson JC, Jones MK, Bashtovyy D, Gu F, Li S, Aliste MP, Harvey SC, Li L, Weinstein G, Rampioni A, Sengupta D, Marrink SJ, Segrest JP (2006). Preliminary Models of Spheroidal HDL particles through Molecular Dynamics. In: 15th South East Lipid Research Conference (poster).
27. Chen JG, Patterson JC, Catte A, Segrest JP, Li L (2005). Discoidal complexes of apolipoprotein A-I with different phospholipids share a common model for size heterogeneity. ARTERIOSCLEROSIS, THROMBOSIS, AND VASCULAR BIOLOGY, In: Abstracts of the 6th Annual Conference on Arteriosclerosis, Thrombosis, and Vascular Biology. vol. 25, p. E73, ISSN: 1079-5642.
28. Catte A, Patterson JC, Chen J, Li L, Jones MK, Segrest JP (2005). Molecular Dynamics Simulations of Protein-Encapsulated Lipid Bilayers Converge Rapidly to form Novel Minimal Surfaces. In: 21st Annual Trainee Research Symposium (poster).
29. Chen J, Patterson JC, Catte A, Segrest JP, Li L (2005). Discoidal Complexes of Apolipoprotein A-I with Different Phospholipids Share a Common Model for Size Heterogeneity. In: American Heart Association 6th Annual Conference on Arteriosclerosis, Thrombosis and Vascular Biology (poster).
30. Catte A, Patterson JC, Weinstein G, Su Z, Li L, Chen J, Jones MK, Aliste MP, Harvey SC, Segrest JP (2005). Novel Protein-Lipid Conformations of High Density Lipoproteins through Molecular Dynamics. In: Bio-Image Summer School – Visualization, Manipulation and Modeling of Single Biomolecules (poster).
31. Catte A, Patterson JC, Weinstein G, Su Z, Li L, Chen J, Jones MK, Aliste MP, Harvey SC, Segrest JP (2005). Novel Protein-Lipid Conformations of High Density Lipoproteins through Molecular Dynamics. In: The Protein Society 19th Symposium (poster).
32. Catte A, Cesare-Marincola F, van der Maarel JRC, Saba G, Lait A (2004). Binding of Mg2+, Cd2+, and Ni2+ to liquid crystalline NaDNA: Polarized light microscopy and NMR investigations. BIOMACROMOLECULES, vol. 5, p. 1552-1556, ISSN: 1525-7797, doi: 10.1021/bm049910p.
33. Catte A, Marincola FC, Casu M, Saba G, Lai A, Korobko A, Jesse W, van der Maarel J, Reedijk J (2003). Multinuclear NMR Investigation of the Interaction of DNA Liquid Crystals with Divalent Metal Ions. In: Biomolecular Chemistry Workshop (poster).
34. Catte A, Marincola FC, Casu M, Saba G, Lai A (2002). Multinuclear NMR investigation of the NaDNA/ethidium bromide anisotropic system. JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS, vol. 20, p. 99-105, ISSN: 0739-1102.
35. Catte A, Marincola FC, Casu M, Saba G, Lai A (2001). Multinuclear NMR investigation of the anisotropic system NaDNA/Ethidium Bromide. In: XXXI° Congresso Nazionale di Risonanze Magnetiche (poster).

Here is the link to a summary of the research performed from 2004 to 2008.

These are few publications with some “artistic” scientific figures:

• White RC, Datta G, Buck AKW, Chaddha M, Reddy G, Wilson L, Palgunachari MN, Abbasi M, Anantharamaiah GM (2012). Preservation of biological function despite oxidative modification of the apolipoprotein A-I mimetic peptide 4F. JOURNAL OF LIPID RESEARCH, vol. 53, p. 1576-1587.
• Murtola T, Bunker A, Vattulainen I, Deserno M, Karttunen M (2009). Multiscale modeling of emergent materials: biological and soft matter. Physical Chemistry Chemical Physics, vol. 11, p. 1869-1892, doi: 10.1039/b818051b.

Here is a modified version of the figure 2 from Murtola et al. 2009 article:

Annular shell of CO molecules and packing of the hydrophobic core of CO molecules with POPC and apoA-I molecules. (Top row) Annular CO molecules, defined as those molecules within 8 Å of any protein atoms or beads, are shown with a green space filling representation for the ms-HDL particle simulated for 8 ns at 310 K and 1 atm (after 10 ns at 410 K and 1 atm) (a) and for the CG ms-HDL particle simulated for 800 ns (3.2 μs in effective time) at 310 K and 1 atm (b), respectively. Δ40 apoA-I molecules are space filling in skyblue and cyan. Proline residues are space filling in yellow. Central CO molecules were observed only in the CG model (B, space filling in purple). (Middle rows) The packing of CO molecules in atomistic and CG ms-HDL particles shows the interdigitation and intercalation of CO molecules with POPC and apoA-I molecules, respectively. (Bottom row) Licorice and bead representations of the atomistic and CG CO molecule with its different moieties highlighted in red (short acyl chain), green (sterol ring), and blue (oleate chain), respectively. The percentage of the average number of contacts of different parts of the CO molecule with the protein is also shown with the same color code used to represent the different moieties of the CO molecule.

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