INSERM, UMR-S 665, Dynamique des Structures et Interactions des Macromolécules Biologiques (DSIMB), Paris, France.
PLoS One. 2011 Mar 31;6(3):e18401. doi: 10.1371/journal.pone.0018401.
Secondary structures are elements of great importance in structural biology, biochemistry and bioinformatics. They are broadly composed of two repetitive structures namely α-helices and β-sheets, apart from turns, and the rest is associated to coil. These repetitive secondary structures have specific and conserved biophysical and geometric properties. PolyProline II (PPII) helix is yet another interesting repetitive structure which is less frequent and not usually associated with stabilizing interactions. Recent studies have shown that PPII frequency is higher than expected, and they could have an important role in protein-protein interactions.
METHODOLOGY/PRINCIPAL FINDINGS: A major factor that limits the study of PPII is that its assignment cannot be carried out with the most commonly used secondary structure assignment methods (SSAMs). The purpose of this work is to propose a PPII assignment methodology that can be defined in the frame of DSSP secondary structure assignment. Considering the ambiguity in PPII assignments by different methods, a consensus assignment strategy was utilized. To define the most consensual rule of PPII assignment, three SSAMs that can assign PPII, were compared and analyzed. The assignment rule was defined to have a maximum coverage of all assignments made by these SSAMs. Not many constraints were added to the assignment and only PPII helices of at least 2 residues length are defined.
CONCLUSIONS/SIGNIFICANCE: The simple rules designed in this study for characterizing PPII conformation, lead to the assignment of 5% of all amino as PPII. Sequence-structure relationships associated with PPII, defined by the different SSAMs, underline few striking differences. A specific study of amino acid preferences in their N and C-cap regions was carried out as their solvent accessibility and contact patterns. Thus the assignment of PPII can be coupled with DSSP and thus opens a simple way for further analysis in this field.
二级结构是结构生物学、生物化学和生物信息学中非常重要的元素。它们广泛由两种重复结构组成，即α-螺旋和β-折叠，除了转角外，其余部分与卷曲有关。这些重复的二级结构具有特定的和保守的物理和几何性质。多脯氨酸 II（PPII）螺旋是另一种有趣的重复结构，它不太常见，通常也不与稳定相互作用有关。最近的研究表明，PPII 的频率高于预期，它们可能在蛋白质-蛋白质相互作用中发挥重要作用。
方法/主要发现：限制 PPII 研究的一个主要因素是，它的分配不能通过最常用的二级结构分配方法（SSAMs）来完成。这项工作的目的是提出一种可以在 DSSP 二级结构分配框架中定义的 PPII 分配方法。考虑到不同方法对 PPII 分配的歧义，采用了共识分配策略。为了定义 PPII 分配的最一致规则，比较和分析了三种可以分配 PPII 的 SSAMs。分配规则被定义为最大限度地覆盖这些 SSAMs 所做的所有分配。分配中只添加了很少的约束，只定义了至少 2 个残基长度的 PPII 螺旋。
结论/意义：本研究设计的用于描述 PPII 构象的简单规则，导致将 5%的所有氨基酸分配为 PPII。由不同 SSAMs 定义的与 PPII 相关的序列-结构关系，强调了一些显著的差异。对其 N 和 C 端区域的氨基酸偏好进行了特定的研究，因为它们的溶剂可及性和接触模式。因此，PPII 的分配可以与 DSSP 相结合，从而为该领域的进一步分析开辟了一种简单的方法。
