Department of Chemistry, Southern Methodist University, 3215 Daniel Ave, Dallas, TX 75275-0314, USA.
J Mol Model. 2013 Jul;19(7):2901-11. doi: 10.1007/s00894-013-1819-7. Epub 2013 Mar 27.
A new method, dubbed "HAXIS" is introduced to describe local and global shape properties of a protein helix via its axis. HAXIS is based on coarse-graining and spline-fitting of the helix backbone. At each Cα anchor point of the backbone, a Frenet frame is calculated, which directly provides the local vector presentation of the helix. After cubic spline-fitting of the axis line, its curvature and torsion are calculated. This makes a rapid comparison of different helix forms and the determination of helix similarity possible. Distortions of the helix caused by individual residues are projected onto the helix axis and presented either by the rise parameter per residue or by the local curvature of the axis. From a non-redundant set of 2,017 proteins, 15,068 helices were investigated in this way. Helix start and helix end as well as bending and kinking of the helix are accurately described. The global properties of the helix are assessed by a polynomial fit of the helix axis and the determination of its overall curving and twisting. Long helices are more regular shaped and linear whereas short helices are often strongly bent and twisted. The distribution of different helix forms as a function of helix length is analyzed.
引入了一种新方法，称为“HAXIS”，通过其轴来描述蛋白质螺旋的局部和全局形状特性。HAXIS 基于螺旋骨架的粗化和样条拟合。在骨架的每个 Cα 锚点处，计算一个弗雷内框架，该框架直接提供了螺旋的局部向量表示。在对轴线进行三次样条拟合后，计算其曲率和扭转。这使得对不同螺旋形式的快速比较和确定螺旋相似性成为可能。单个残基引起的螺旋扭曲被投射到螺旋轴上，并通过每个残基的上升参数或轴的局部曲率来表示。从 2017 个非冗余蛋白质中，以这种方式研究了 15068 个螺旋。准确描述了螺旋的起始和结束，以及螺旋的弯曲和扭曲。通过对螺旋轴进行多项式拟合并确定其整体弯曲和扭曲来评估螺旋的全局特性。长螺旋通常更规则且线性，而短螺旋通常强烈弯曲和扭曲。分析了不同螺旋形式随螺旋长度的分布。
