Helix-sheet packing in proteins.
Helix-sheet packing in proteins.
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DOI：
10.1002/prot.22688
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发表时间：
2010-05-15
影响因子：
2.9
通讯作者：
Koehl, Patrice
中科院分区：
文献类型：
--
作者：
Hu, Chengcheng;Koehl, Patrice
蛋白质的三维结构是围绕其二级结构元素的堆积而组织的。虽然我们对α-螺旋和β-折叠之间的堆积几何结构了解很多，但在表征螺旋-折叠相互作用方面进展甚微。我们分析了蛋白质中αβ2基序的构象，对应于与氢键结合的两条链接触的所有螺旋的出现。αβ2基序的几何结构的特征在于螺旋轴和代表两条链的平均矢量之间的方位角θ、螺旋轴和包含两条链的平面之间的仰角θ以及螺旋和链之间的距离D。我们观察到，螺旋倾向于与两条链对齐，如果两条链平行，则倾向于反平行取向;这种偏好对于β折叠的其他拓扑结构有所减弱。在螺旋和链之间的界面处的侧链堆积主要是疏水性的，其中优选链中的脂肪族氨基酸和螺旋中的芳香族氨基酸。从蛋白质中αβ2基序的几何结构和氨基酸倾向的知识中，我们已经推导出不同的统计势，这些统计势在众所周知的诱饵数据集中的一组非天然构象中被证明是有效的。αβ2模体的几何信息以及相关的统计势在蛋白质结构预测领域具有应用价值。
The three-dimensional structure of a protein is organized around the packing of its secondary structure elements. While much is known about the packing geometry observed between α-helices and between β-sheets, there has been little progress on characterizing helix-sheet interactions. We present an analysis of the conformation of αβ2 motifs in proteins, corresponding to all occurrences of helices in contact with two strands that are hydrogen-bonded. The geometry of the αβ2 motif is characterized by the azimuthal angle θ between the helix axis and an average vector representing the two strands, the elevation angle ψ between the helix axis and the plane containing the two strands, and the distance D between the helix and the strands. We observe that the helix tends to align to the two strands, with a preference for an antiparallel orientation if the two strands are parallel; this preference is diminished for other topologies of the β-sheet. Sidechain packing at the interface between the helix and the strands is mostly hydrophobic, with a preference for aliphatic amino acids in the strand and aromatic amino acids in the helix. From the knowledge of the geometry and amino acid propensities of αβ2 motifs in proteins, we have derived different statistical potentials that are shown to be efficient in picking native-like conformations among a set of non-native conformations in well-known decoy datasets. The information on the geometry of αβ2 motifs as well as the related statistical potentials has applications in the field of protein structure prediction.
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影响因子：
5.6
作者：
COHEN, FE;STERNBERG, MJE;TAYLOR, WR
通讯作者：
TAYLOR, WR
影响因子：
14.9
作者：
UniProt Consortium
通讯作者：
UniProt Consortium
影响因子：
5.6
作者：
Keasar, C;Levitt, M
通讯作者：
Levitt, M
影响因子：
5.6
作者：
Park, B;Levitt, M
通讯作者：
Levitt, M
DOI：
10.1002/prot.340230412
发表时间：
1995-12-01
期刊：
PROTEINS-STRUCTURE FUNCTION AND GENETICS
影响因子：
--
作者：
Frishman, D;Argos, P
通讯作者：
Argos, P