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基于超空间扩展的分子动力学模拟对磷灰石-胶原复合材料的原子级建模。

Atomistic modeling of apatite-collagen composites from molecular dynamics simulations extended to hyperspace.

机构信息

Max-Planck-Institut für Chemische Physik fester Stoffe, Nöthnitzer Str. 40, 01087 Dresden, Germany.

出版信息

J Mol Model. 2011 Jan;17(1):73-9. doi: 10.1007/s00894-010-0707-7. Epub 2010 Apr 6.

Abstract

The preparation of atomistic models of apatite-collagen composite mimicking enamel at length scales in the range of 1-10 nanometers is outlined. This bio-composite is characterized by a peculiar interplay of the collagen triplehelix and the apatite crystal structure. Structural coherence is however only obtained after drastic rearrangements, namely the depletion of protein-protein hydrogen bonds and the incorporation of calcium triangles which are stabilized by salt-bridges with the collagen molecule. Starting from an isolated collagen triple helix and a single-crystalline apatite structure, a composite model is obtained by gradually merging the two components via an additional (hyperspace) coordinate. This approach allows smooth structural relaxation of both components whilst avoiding singularities in potential energy due to atomic overlap.

摘要

概述了在 1-10 纳米范围内模拟牙釉质的磷灰石-胶原复合材料的原子模型的制备方法。这种生物复合材料的特点是胶原三螺旋和磷灰石晶体结构之间的特殊相互作用。然而,只有在剧烈的重排后才能获得结构连贯性,即耗尽蛋白质-蛋白质氢键并掺入由与胶原分子形成盐桥稳定的钙三角形。从孤立的胶原三螺旋和单晶磷灰石结构开始,通过附加(超空间)坐标逐渐将两种成分合并,从而获得复合材料模型。这种方法允许两种成分的结构平滑松弛,同时避免由于原子重叠而导致的势能奇点。

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