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All-atom empirical potential for molecular modeling and dynamics studies of proteins.蛋白质分子建模和动力学研究的全原子经验势。
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Double superhelix model of high density lipoprotein.高密度脂蛋白的双超螺旋模型。
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Smaller discoidal high-density lipoprotein particles form saddle surfaces, but not planar bilayers.较小的盘状高密度脂蛋白颗粒形成鞍状表面,而非平面双层膜。
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Thermal stability of apolipoprotein A-I in high-density lipoproteins by molecular dynamics.通过分子动力学研究高密度脂蛋白中载脂蛋白A-I的热稳定性
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Structure of spheroidal HDL particles revealed by combined atomistic and coarse-grained simulations.通过原子尺度和粗粒度模拟相结合揭示的球状高密度脂蛋白颗粒结构。
Biophys J. 2008 Mar 15;94(6):2306-19. doi: 10.1529/biophysj.107.115857. Epub 2007 Dec 7.
6
The refined structure of nascent HDL reveals a key functional domain for particle maturation and dysfunction.新生高密度脂蛋白的精细结构揭示了颗粒成熟和功能障碍的关键功能域。
Nat Struct Mol Biol. 2007 Sep;14(9):861-8. doi: 10.1038/nsmb1284. Epub 2007 Aug 5.
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Conformational adaptation of apolipoprotein A-I to discretely sized phospholipid complexes.载脂蛋白A-I对不同大小磷脂复合物的构象适应性。
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The structure of apolipoprotein A-I in high density lipoproteins.高密度脂蛋白中载脂蛋白A-I的结构
J Biol Chem. 2007 Aug 3;282(31):22249-53. doi: 10.1074/jbc.R700014200. Epub 2007 May 25.
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Apolipoprotein A-I assumes a "looped belt" conformation on reconstituted high density lipoprotein.载脂蛋白A-I在重组高密度脂蛋白上呈现“环状带”构象。
J Biol Chem. 2006 Jul 21;281(29):20418-26. doi: 10.1074/jbc.M602077200. Epub 2006 May 11.
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Novel changes in discoidal high density lipoprotein morphology: a molecular dynamics study.盘状高密度脂蛋白形态的新变化:一项分子动力学研究。
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碟状高密度脂蛋白结构:计算实验联合研究方法。

Structures of discoidal high density lipoproteins: a combined computational-experimental approach.

机构信息

Department of Medicine and Atherosclerosis Research Unit, University of Alabama at Birmingham, Birmingham, Alabama 35294, USA.

出版信息

J Biol Chem. 2010 Feb 12;285(7):4652-65. doi: 10.1074/jbc.M109.069914. Epub 2009 Nov 30.

DOI:10.1074/jbc.M109.069914
PMID:19948731
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC2836071/
Abstract

Conversion of discoidal phospholipid (PL)-rich high density lipoprotein (HDL) to spheroidal cholesteryl ester-rich HDL is a central step in reverse cholesterol transport. A detailed understanding of this process and the atheroprotective role of apolipoprotein A-I (apoA-I) requires knowledge of the structure and dynamics of these various particles. This study, combining computation with experimentation, illuminates structural features of apoA-I allowing it to incorporate varying amounts of PL. Molecular dynamics simulated annealing of PL-rich HDL models containing unesterified cholesterol results in double belt structures with the same general saddle-shaped conformation of both our previous molecular dynamics simulations at 310 K and the x-ray structure of lipid-free apoA-I. Conversion from a discoidal to a saddle-shaped particle involves loss of helicity and formation of loops in opposing antiparallel parts of the double belt. During surface expansion caused by the temperature-jump step, the curved palmitoyloleoylphosphatidylcholine bilayer surfaces approach planarity. Relaxation back into saddle-shaped structures after cool down and equilibration further supports the saddle-shaped particle model. Our kinetic analyses of reconstituted particles demonstrate that PL-rich particles exist in discrete sizes corresponding to local energetic minima. Agreement of experimental and computational determinations of particle size/shape and apoA-I helicity provide additional support for the saddle-shaped particle model. Truncation experiments combined with simulations suggest that the N-terminal proline-rich domain of apoA-I influences the stability of PL-rich HDL particles. We propose that apoA-I incorporates increasing PL in the form of minimal surface bilayers through the incremental unwinding of an initially twisted saddle-shaped apoA-I double belt structure.

摘要

盘状磷脂(PL)丰富的高密度脂蛋白(HDL)向球状胆固醇酯丰富的 HDL 的转化是胆固醇逆向转运的中心步骤。详细了解这一过程和载脂蛋白 A-I(apoA-I)的抗动脉粥样硬化作用,需要了解这些不同颗粒的结构和动力学。本研究结合计算与实验,阐明了 apoA-I 的结构特征,使其能够结合不同数量的 PL。含有未酯化胆固醇的 PL 丰富的 HDL 模型的分子动力学模拟退火导致具有相同一般鞍形构象的双带结构,这与我们之前在 310 K 进行的分子动力学模拟和无脂 apoA-I 的 X 射线结构相同。从盘状到鞍状颗粒的转化涉及螺旋的丧失和双带的相对反平行部分中环的形成。在由温度跃变步骤引起的表面扩展期间,弯曲的棕榈酰油酰磷脂酰胆碱双层表面接近平面。在冷却和平衡后,返回到鞍状结构的松弛进一步支持鞍状颗粒模型。我们对重建颗粒的动力学分析表明,PL 丰富的颗粒以对应于局部能量最小值的离散尺寸存在。实验和计算确定的颗粒尺寸/形状和 apoA-I 螺旋的一致性为鞍状颗粒模型提供了额外的支持。截断实验与模拟相结合表明,apoA-I 的 N 端脯氨酸丰富结构域影响 PL 丰富的 HDL 颗粒的稳定性。我们提出,apoA-I 通过初始扭曲的 apoA-I 双带结构的增量展开,以最小表面积双层的形式纳入越来越多的 PL。