Bywater Robert P, Veryazov Valera
Magdalen College, High Street, Oxford, OX1 4AU England, UK ; Francis Crick Institute, London, NW7 1AA England, UK.
Department of Theoretical Chemistry, Lund University, POB 124, Lund, 22100 Sweden.
Springerplus. 2015 Nov 4;4:668. doi: 10.1186/s40064-015-1430-8. eCollection 2015.
There have been many studies of dipeptide structure at a high level of accuracy using quantum chemical methods. Such calculations are resource-consuming (in terms of memory, CPU and other computational imperatives) which is the reason why most previous studies were restricted to the two simplest amino-acid residue types, glycine and alanine. We improve on this by extending the scope of residue types to include all 20 naturally occurring residue types. Our results reveal differences in secondary structure preferences for the all residue types. There are in most cases very deep energy troughs corresponding either to the polyproline II (collagen) helix and the α-helix or both. The β-strand was not strongly favoured energetically although the extent of this depression in the energy surface is, while not "deeper" (energetically), has a wider extent than the other two types of secondary structure. There is currently great interest in the question of cotranslational folding, the extent to which the nascent polypeptide begins to fold prior to emerging from the ribosome exit tunnel. Accordingly, while most previous quantum studies of dipeptides were carried out in the (simulated) gas or aqueous phase, we wished to consider the first step in polypeptide biosynthesis on the ribosome where neither gas nor aqueous conditions apply. We used a dielectric constant that would be compatible with the water-poor macromolecular (ribosome) environment.
已经有许多使用量子化学方法在高精度水平下对二肽结构进行的研究。这样的计算资源消耗大（在内存、CPU和其他计算需求方面），这就是为什么大多数先前的研究局限于两种最简单的氨基酸残基类型，即甘氨酸和丙氨酸。我们通过将残基类型的范围扩展到包括所有20种天然存在的残基类型来改进这一点。我们的结果揭示了所有残基类型在二级结构偏好上的差异。在大多数情况下，存在非常深的能量低谷，分别对应于聚脯氨酸II（胶原蛋白）螺旋和α螺旋，或者两者都有。β链在能量上并不受强烈青睐，尽管能量表面上这种凹陷的程度虽然在能量上不是“更深”，但其范围比其他两种二级结构类型更宽。目前人们对共翻译折叠问题非常感兴趣，即新生多肽在从核糖体出口通道出现之前开始折叠的程度。因此，虽然之前大多数关于二肽的量子研究是在（模拟的）气相或水相中进行的，但我们希望考虑核糖体上多肽生物合成的第一步，在那里既不存在气相条件也不存在水相条件。我们使用了一个与贫水大分子（核糖体）环境相兼容的介电常数。
