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首页> 外文OA文献 >Modeling of polypeptide chains as C alpha chains, C alpha chains with C beta, and C alpha chains with ellipsoidal lateral chains.
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Modeling of polypeptide chains as C alpha chains, C alpha chains with C beta, and C alpha chains with ellipsoidal lateral chains.

机译：将多肽链建模为C alpha链，具有C beta的C alpha链和具有椭圆形侧链的C alpha链。

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摘要

In an effort to reduce the number of degrees of freedom necessary to describe a polypeptide chain we analyze the statistical behavior of polypeptide chains when represented as C alpha chains, C alpha chains with C beta atoms attached, and C alpha chains with rotational ellipsoids as models of side chains. A statistical analysis on a restricted data set of 75 unrelated protein structures is performed. The comparison of the database distributions with those obtained by model calculation on very short polypeptide stretches allows the dissection of local versus nonlocal features of the distributions. The database distribution of the bend angles of polypeptide chains of pseudo bonded C alpha atoms spans a restricted range of values and shows a bimodal structure. On the other hand, the torsion angles of the C alpha chain may assume almost all possible values. The distribution is bimodal, but with a much broader probability distribution than for bend angles. The C alpha - C beta vectors may be taken as representative of the orientation of the lateral chain, as the direction of the bond is close to the direction of the vector joining C alpha to the ad hoc defined center of the "steric mass" of the side chain. Interestingly, both the bend angle defined by C alpha i-C alpha i+1-C beta i+1 and the torsional angle offset of the pseudo-dihedral C alpha i-C alpha i+1-C alpha i+2-C beta i+2 with respect to C alpha i-C alpha i+1-C alpha i+2-C alpha i+3 span a limited range of values. The latter results show that it is possible to give a more realistic representation of polypeptide chains without introducing additional degrees of freedom, i.e., by just adding to the C alpha chain a C beta with given side-chain properties. However, a more realistic description of side chains may be attained by modeling side chains as rotational ellipsoids that have roughly the same orientation and steric hindrance. To this end, we define the steric mass of an atom as proportional to its van der Waals volume and we calculate the side-chain inertia ellipsoid assuming that the steric mass of each atom is uniformly distributed within its van der Waals volume. Finally, we define the rotational ellipsoid representing the side chain as the uniform density ellipsoid possessing the same rotationally averaged inertia tensor of the side chain. The statistics of ellipsoid parameters support the possibility of representing a side chain via an ellipsoid, independently of the local conformation. To make this description useful for molecular modeling we describe ellipsoid-ellipsoid interactions via a Lennard-Jones potential that preserves the repulsive core of the interacting ellipsoids and takes into account their mutual orientation. Tests are performed for two different forms of the interaction potential on a set of high-resolution protein structures. Results are encouraging, in view of the drastic simplifications that were introduced.
机译：为了减少描述多肽链所必需的自由度，我们分析了当多肽链表示为C alpha链，带有C beta原子的C alpha链和带有旋转椭球的C alpha链时的统计行为侧链。对75个不相关的蛋白质结构的受限数据集进行了统计分析。将数据库分布与通过对非常短的多肽序列进行模型计算而获得的分布进行比较，可以对分布的局部特征和非局部特征进行解剖。伪键合的Cα原子的多肽链的弯曲角度的数据库分布跨越了有限的值范围，并显示了双峰结构。另一方面，Cα链的扭转角可采用几乎所有可能的值。该分布是双峰分布的，但是比弯曲角度具有更大的概率分布。由于键的方向接近于将C alpha连接到C的“空间质量”的特定定义的中心的矢量的方向，因此可以将C alpha-C beta向量视为侧链的方向的代表。侧链。有趣的是，由C alpha iC alpha i + 1-C beta i + 1定义的弯曲角度和伪二面体C alpha iC alpha i + 1-C alpha i + 2-C beta i + 2的扭转角偏移关于C alpha iC alpha i + 1-C alpha i + 2-C alpha i + 3的范围有限。后一结果表明，可以在不引入额外自由度的情况下，即通过仅将具有给定侧链性质的Cβ添加到Cα链中，来给出更真实的多肽链表示。但是，通过将侧链建模为具有大致相同的方向和空间位阻的旋转椭圆体，可以对侧链进行更实际的描述。为此，我们将原子的空间质量定义为与其范德华体积成正比，并假设每个原子的空间质量在其范德华体积内均匀分布，我们计算侧链惯性椭球。最后，我们将代表侧链的旋转椭球定义为具有与侧链相同的旋转平均惯性张量的均匀密度椭球。椭球参数的统计数据支持通过椭球表示侧链的可能性，而与局部构象无关。为了使该描述对分子建模有用，我们通过Lennard-Jones势描述了椭球-椭球相互作用，该势保留了相互作用的椭球的排斥核心并考虑了它们的相互定向。对一组高分辨率蛋白质结构上两种不同形式的相互作用潜能进行了测试。鉴于引入的极大简化，结果令人鼓舞。

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