Microsecond kinetics in model single- and double-stranded amylose polymers.
Microsecond kinetics in model single- and double-stranded amylose polymers.
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DOI：
10.1039/c4cp00570h
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发表时间：
2014-05-07
期刊：
影响因子：
--
通讯作者：
Almond A
中科院分区：
文献类型：
--
作者：
Sattelle BM;Almond A
直链淀粉是一种具有越来越重要的生物技术意义的淀粉成分，它是一种线性葡萄糖多糖，可以自组织成单螺旋和双螺旋组装。直链淀粉是一种具有越来越重要的生物技术意义的淀粉成分，它是一种线性葡萄糖多糖，可以自组织成单螺旋和双螺旋组装。淀粉颗粒的堆积、凝胶化和包合物的形成是由于精细平衡的大分子动力学造成的，而这些动力学一直没有得到精确的实验定量。在这里，图形处理单元(GPU)加速的多微秒水模拟被用来探索单链和双链直链淀粉模型的构象动力学。全原子动力学与先前的X射线和核磁共振数据一致，而令人惊讶和以前被忽视的微秒螺旋线圈、糖苷键和吡喃糖环交换被假设。在十二糖中，单螺旋塌陷与其预期的syn和4c1椅子构象的键和环的过渡有关。相关的微秒交换速率依赖于末端的接近程度和链长(比较六糖和三糖)，而十二糖的连接和环弯曲的动力学特征被认为是一个很好的聚合物模型。相同长度的双螺旋在微秒时间尺度上是稳定的，但平行构型比反平行等效构型更坚固。在这两种情况下，第三级组织限制了局部链动力学，这意味着对单链直链的模拟不能外推到二聚体。直链淀粉的无偏多微秒模拟被认为是探索水中大分子动力学、评估化学修饰对螺旋稳定性的影响以及加速新生物技术发展的有价值的途径。
Amylose, a component of starch with increasing biotechnological significance, is a linear glucose polysaccharide that self-organizes into single- and double-helical assemblies. Amylose, a component of starch with increasing biotechnological significance, is a linear glucose polysaccharide that self-organizes into single- and double-helical assemblies. Starch granule packing, gelation and inclusion-complex formation result from finely balanced macromolecular kinetics that have eluded precise experimental quantification. Here, graphics processing unit (GPU) accelerated multi-microsecond aqueous simulations are employed to explore conformational kinetics in model single- and double-stranded amylose. The all-atom dynamics concur with prior X-ray and NMR data while surprising and previously overlooked microsecond helix–coil, glycosidic linkage and pyranose ring exchange are hypothesized. In a dodecasaccharide, single-helical collapse was correlated with linkages and rings transitioning from their expected syn and 4 C 1 chair conformers. The associated microsecond exchange rates were dependent on proximity to the termini and chain length (comparing hexa- and trisaccharides), while kinetic features of dodecasaccharide linkage and ring flexing are proposed to be a good model for polymers. Similar length double-helices were stable on microsecond timescales but the parallel configuration was sturdier than the antiparallel equivalent. In both, tertiary organization restricted local chain dynamics, implying that simulations of single amylose strands cannot be extrapolated to dimers. Unbiased multi-microsecond simulations of amylose are proposed as a valuable route to probing macromolecular kinetics in water, assessing the impact of chemical modifications on helical stability and accelerating the development of new biotechnologies.
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影响因子：
5.5
作者：
Hess, Berk;Kutzner, Carsten;Lindahl, Erik
通讯作者：
Lindahl, Erik
影响因子：
2.1
作者：
HAASNOOT, CAG;DELEEUW, FAAM;ALTONA, C
通讯作者：
ALTONA, C
影响因子：
2.9
作者：
EISENHABER, F;SCHULZ, W
通讯作者：
SCHULZ, W
影响因子：
56.9
作者：
HINRICHS, W;BUTTNER, G;SAENGER, W
通讯作者：
SAENGER, W
影响因子：
4.9
作者：
Kida, Toshiyuki;Minabe, Takashi;Akashi, Mitsuru
通讯作者：
Akashi, Mitsuru