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Temperature factor analysis of outer membrane #x3b2;-stranded porin crystal structures suggests the pore is not uniformly rigid

机译:外膜β-链状孔蛋白晶体结构的温度因子分析表明,孔的刚性不均匀

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摘要

Outer membrane beta-stranded porins form a diverse and complex set of proteins which allow passage of molecules across the membrane interface have been analyzed here from a biophysical and structural perspective using atomic temperature factors or B-factors. Generally atomic temperature factors of molecules from crystal structures indicate the degree of mobility or disorder seen in the crystal structure. Structures of six porins (four 16 stranded beta barrel porins and two 8 stranded beta barrel porins) were taken from the PDB for the analysis based on resolution (better than 3.0 Å) and R-factor (< 0.23). The residue distribution and mobility distribution was found to be characteristic of each of the porins. The mobility and residue distribution amongst the secondary structural elements were found to follow the level of homology at the sequence and structural level. The loops (L2 and L3) that had defined functional roles in structural terms were found to have lower temperature factors than the other loops. The turn regions that are thought to face the periplasmic region in the cell, showed higher temperature factors. For both the 16 stranded and the 8 stranded barrels it was found one part of the barrel (the lower wall or 'inner' wall comprising the trimer interface in the case of the 16 stranded barrels) was more rigid and the other half of the barrel (the higher or 'outer' wall) showed more mobility as seen from the temperature factors. This seems to be an intrinsic structural component of the beta barrels.
机译:外膜β链孔蛋白形成了多种多样且复杂的蛋白质,这些蛋白质允许分子穿过膜界面通过,这是从生物物理和结构角度使用原子温度因子或B因子进行分析的。通常,来自晶体结构的分子的原子温度因子指示在晶体结构中看到的迁移率或无序度。从PDB提取了六种孔蛋白的结构(四个16链的β桶形孔蛋白和两个8链的β桶形孔蛋白),用于基于分辨率(小于3.0Å)和R因子(<0.23)的分析。发现残余物分布和迁移率分布是每种孔蛋白的特征。发现二级结构元件之间的迁移率和残基分布在序列和结构水平上遵循同源性水平。发现在结构方面已定义功能角色的环路(L2和L3)的温度因子低于其他环路。认为面对细胞周质区域的转弯区域显示出较高的温度因子。对于16股和8股发条盒,发现发条盒的一部分(在16条发条盒的情况下,下壁或“内”壁包括三聚体界面)更硬,而另一半发条盒从温度因素来看,(较高或较高的“外”壁)显示出更多的流动性。这似乎是Beta桶的固有结构组件。

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