| 1. |
- Murtola, Teemu, et al.
(författare)
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Low density lipoprotein : structure, dynamics, and interactions of apoB-100 with lipids
- 2011
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Ingår i: Soft Matter. - : Royal Society of Chemistry (RSC). - 1744-683X .- 1744-6848. ; 7:18, s. 8135-8141
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Tidskriftsartikel (refereegranskat)abstract
- Low-density lipoprotein (LDL) transports cholesterol in the bloodstream and plays an important role in the development of cardiovascular diseases, in particular atherosclerosis. Despite its importance to health, the structure of LDL is not known in detail. This is worrying since the lack of LDL's structural information makes it more difficult to understand its function. In this work, we have combined experimental and theoretical data to construct LDL models comprised of the apoB-100 protein wrapped around a lipid droplet of about 20 nm in size. The models are considered by near-atomistic multi-microsecond simulations to unravel structural as well as dynamical properties of LDL, with particular attention paid to lipids and their interactions with the protein. We find that the distribution and the ordering of the lipids in the LDL particle are rather complex. The previously proposed 2- and 3- layer models turn out to be inadequate to describe the properties of the lipid droplet. At the surface of LDL, apoB-100 is found to interact favorably with cholesterol and its esters. The interactions of apoB-100 with core molecules, in particular cholesteryl esters, are rather frequent and arise from hydrophobic amino acids interacting with the ring of cholesteryl esters, and also in part from the rather loose packing of lipids at the surface of the lipoparticle. The loose packing may foster the function of transfer proteins, which transport lipids between lipoproteins. Finally, the comparison of the several apoB-100 models in our study suggests that the properties of lipids in LDL are rather insensitive to the conformation of apoB-100. Altogether, the findings pave the way for further studies of LDL to better understand the central steps in the emergence of atherosclerosis.
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| 2. |
- Patra, Michael, et al.
(författare)
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Long-range interactions and parallel scalability in molecular simulations
- 2007
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Ingår i: Computer Physics Communications. - : Elsevier BV. - 0010-4655. ; 176:1, s. 14-22
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Tidskriftsartikel (refereegranskat)abstract
- Typical biomolecular systems such as cellular membranes, DNA, and protein complexes are highly charged. Thus, efficient and accurate treatment of electrostatic interactions is of great importance in computational modeling of such systems. We have employed the GROMACS simulation package to perform extensive benchmarking of different commonly used electrostatic schemes on a range of computer architectures (Pentium-4, IBM Power 4, and Apple/IBM G5) for single processor and parallel performance up to 8 nodes-we have also tested the scalability on four different networks, namely Infiniband, GigaBit Ethernet, Fast Ethernet, and nearly uniform memory architecture, i.e. communication between CPUs is possible by directly reading from or writing to other CPUs' local memory. It turns out that the particle-mesh Ewald method (PME) performs surprisingly well and offers competitive performance unless parallel runs on PC hardware with older network infrastructure are needed. Lipid bilayers of sizes 128, 512 and 2048 lipid molecules were used as the test systems representing typical cases encountered in biomolecular simulations. Our results enable an accurate prediction of computational speed on most current computing systems, both for serial and parallel runs. These results should be helpful in, for example, choosing the most suitable configuration for a small departmental computer cluster.
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