@article{koivuniemi_revealing_2012,
title = {Revealing structural and dynamical properties of high density lipoproteins through molecular simulations},
volume = {8},
url = {http://dx.doi.org/10.1039/C1SM06742G},
doi = {10.1039/C1SM06742G},
abstract = {The structure and function of high density lipoprotein {(HDL)} particles have intrigued the scientific community for decades because of their crucial preventive role in coronary heart disease. However, it has been a taunting task to reveal the precise molecular structure and dynamics of {HDL.} Further, because of the complex composition of {HDL}, understanding the impact of its structure and dynamics on the function of {HDL} in reverse cholesterol transport has also been a major issue. Recent progress in molecular simulation methodology and computing power has made a difference, as it has enabled essentially atomistic considerations of {HDL} particles over microsecond time scales, thereby proving substantial added value to experimental research. In this article, we discuss recent highlights concerning the structure and dynamics of {HDL} particles as revealed by atomistic and coarse-grained molecular dynamics simulations. We present examples which demonstrate how simulations and experiments can be carried out in unison, showing the added value that emerges from this interplay. We also discuss the possibilities that simulations could offer to better understand the complex phenomena associated with {HDL}, the goal being to understand its function.},
number = {5},
journal = {Soft Matter},
author = {Koivuniemi, Artturi and Vattulainen, Ilpo},
year = {2012},
pages = {1262--1267}
}
@article{huang_apolipoprotein_2011,
title = {Apolipoprotein {A-I} structural organization in high-density lipoproteins isolated from human plasma},
volume = {18},
issn = {1545-9993},
url = {http://dx.doi.org/10.1038/nsmb.2028},
doi = {10.1038/nsmb.2028},
number = {4},
journal = {Nature Structural {\&} Molecular Biology},
author = {Huang, Rong and Silva, R A Gangani D and Jerome, W Gray and Kontush, Anatol and Chapman, M John and Curtiss, Linda K and Hodges, Timothy J and Davidson, W Sean},
year = {2011},
pages = {416--422},
}
@article{vuorela_role_2010,
title = {Role of lipids in spheroidal high density lipoproteins},
volume = {6},
number = {10},
journal = {{PLoS} computational biology},
author = {Vuorela, T. and Catte, A. and Niemelä, {P.S.} and Hall, A. and Hyvönen, {M.T.} and Marrink, {S.J.} and Karttunen, M. and Vattulainen, I.},
year = {2010},
pages = {e1000964},
}
@article{ollila2012interfacial,
title={Interfacial tension and surface pressure of high density lipoprotein, low density lipoprotein, and related lipid droplets},
author={Ollila, OH and Lamberg, Antti and Lehtivaara, Maria and Koivuniemi, Artturi and Vattulainen, Ilpo},
journal={Biophysical journal},
volume={103},
number={6},
pages={1236--1244},
year={2012},
publisher={Elsevier}
}
@article{allen2004introduction,
title={Introduction to molecular dynamics simulation},
author={Allen, Michael P},
journal={Computational Soft Matter: From Synthetic Polymers to Proteins},
volume={23},
pages={1--28},
year={2004},
publisher={NIC Series}
}
@article{JCC:JCC540160303,
author = {Eisenhaber, Frank and Lijnzaad, Philip and Argos, Patrick and Sander, Chris and Scharf, Michael},
title = {The double cubic lattice method: Efficient approaches to numerical integration of surface area and volume and to dot surface contouring of molecular assemblies},
year = {1995},
volume = {16},
number= {3},
journal={Journal of Computational Chemistry},
pages = {273--284},
}
@manual{gromacsman,
author = {D. van der Spoel, E. Lindahl, B. Hess, and the GROMACS development team},
title = {{GROMACS User Manual version 4.6.5}},
url = {www.gromacs.org}
year = {2013}
}
@article{dssp,
author = {Joosten, Robbie P. and te Beek, Tim A. H. and Krieger, Elmar and Hekkelman, Maarten L. and Hooft, Rob W.W. and Schneider, Reinhard and Sander, Chris and Vriend, Gert},
title = {A series of PDB related databases for everyday needs},
year = {2011},
volume = {39},
pages = {D411--D419},
journal = {Nucleic Acids Research},
number = {Database issue}}
@article{dssp83,
author = {Kabsch, Wolfgang and Sander, Christian},
title = {Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features},
year = {1983},
volume = {22},
pages = {2577--2637},
number = {12},
journal = {Biopolymers},
file = {FULLTEXT:/srv/http/kirjasto/library/00050.pdf:PDF}
}
%%
%% The primary VMD citation, should be used by all publications using VMD
%%
@article{HUMP96,
author={William Humphrey and Andrew Dalke and Klaus Schulten},
title={{VMD} -- {V}isual {M}olecular {D}ynamics},
journal={Journal of Molecular Graphics},
year=1996,
volume=14,
pages={33-38},
number={1},
tbstatus={Published.},
techrep={},
tbreference={222}
}
%%
%% Interactive Molecular Dynamics, cited by papers doing IMD simulations
%%
@inproceedings{STON2001,
author={John Stone and Justin Gullingsrud and Paul Grayson and Klaus Schulten},
title={A System for Interactive Molecular Dynamics Simulation},
booktitle={2001 ACM Symposium on Interactive 3D Graphics},
publisher={ACM SIGGRAPH},
address={New York},
editor={John F. Hughes and Carlo H. S\'equin},
pages={191-194},
year={2001},
note={},
tbreference={304},
tbstatus={Published.},
annote={This symposium took place between March 19-21, 2001. {ISBN} 1-58113-292-1.}
}
%%
%% The primary VMD citation, should be used by all publications using VMD
%%
@article{HUMP96,
author={William Humphrey and Andrew Dalke and Klaus Schulten},
title={{VMD} -- {V}isual {M}olecular {D}ynamics},
journal={Journal of Molecular Graphics},
year=1996,
volume=14,
pages={33-38},
note={},
tbstatus={Published.},
techrep={},
tbreference={222}
}
%%
%% Tachyon ray tracing library (built-into VMD and/or distributed with VMD)
%% Please cite Tachyon if you use it to make figures within VMD.
%%
@mastersthesis{STON1998,
author = {John Stone},
title = "{\em An Efficient Library for Parallel Ray Tracing and Animation}",
school = "Computer Science Department, University of Missouri-Rolla",
month = "April",
year = {1998}
}
%%
%% STRIDE Secondary Structure Prediction (distributed with VMD)
%%
%% Frishman,D & Argos,P. (1995) Knowledge-based secondary structure
%% assignment. Proteins: structure, function and genetics, 23, 566-579.
@article{FRISH1995,
author={D. Frishman and P. Argos},
title={Knowledge-based secondary structure assignment},
journal={Proteins: structure, function and genetics},
volume=23,
pages={566-579},
year={1995},
note={},
annote={}
}
@article{Toth-2005-ID72,
author = {Toth, P. P.},
title = {The ``Good Cholesterol'': High-Density Lipoprotein},
year = {2005},
volume = {111},
pages = {e89--e91},
number = {5},
journal = {Circulation}}
@article{vonEckardstein-2001-ID73,
author = {von Eckardstein, A. and Nofer, J.-R. and Assmann, G.},
title = {High Density Lipoproteins and Arteriosclerosis: Role of Cholesterol Efflux and Reverse Cholesterol Transport},
year = {2001},
volume = {21},
pages = {13--27},
number = {1},
journal = {Arteriosclerosis, Thrombosis, and Vascular Biology}}
@article{Ohashi-2005-ID75,
author = {Ohashi, R.},
title = {Reverse cholesterol transport and cholesterol efflux in atherosclerosis},
year = {2005},
volume = {98},
pages = {845--856},
number = {12}}
@misc{fig_struct,
author = "AntiSense",
title = "Structure of a Lipoprotein",
year = "2010",
note = "Viitattu: 01.12.2014",
howpublished = {\url{http://commons.wikimedia.org/wiki/File:Structure_of_a_Lipoprotein.png}}
}
@article{Silva-2008-ID78,
author = {Silva, R. A. G. D. and Huang, R. and Morris, J. and Fang, J. and Gracheva, E. O. and Ren, G. and Kontush, A. and Jerome, W. G. and Rye, K.-A. and Davidson, W. S.},
title = {Structure of apolipoprotein {A-I} in spherical high density lipoproteins of different sizes},
year = {2008},
volume = {105},
pages = {12176--12181},
number = {34},
journal = {Proceedings of the National Academy of Sciences}}