Center for Computational Biology, University of Kansas, 2030 Becker Dr., Lawrence, KS, 66047, USA.
Center for Computational Biology, University of Kansas, 2030 Becker Dr., Lawrence, KS, 66047, USA; Department of Molecular Biosciences, University of Kansas, 1200 Sunnyside Ave., Lawrence, KS 66045, USA.
J Mol Biol. 2018 Sep 14;430(18 Pt B):3251-3265. doi: 10.1016/j.jmb.2018.06.013. Epub 2018 Jun 23.
As a structural class, tight turns can control molecular recognition, enzymatic activity, and nucleation of folding. They have been extensively characterized in soluble proteins but have not been characterized in outer membrane proteins (OMPs), where they also support critical functions. We clustered the 4 to 6 residue tight turns of 110 OMPs to characterize the phi/psi angles, sequence, and hydrogen bonding of these structures. We find significant differences between reports of soluble protein tight turns and OMP tight turns. Since OMP strands are less twisted than soluble strands, they favor different turn structures types. Moreover, the membrane localization of OMPs yields different sequence hallmarks for their tight turns relative to soluble protein turns. We also characterize the differences in phi/psi angles, sequence, and hydrogen bonding between OMP extracellular loops and OMP periplasmic turns. As previously noted, the extracellular loops tend to be much longer than the periplasmic turns. We find that this difference in length is due to the broader distribution of lengths of the extracellular loops not a large difference in the median length. Extracellular loops also tend to have more charged residues as predicted by the charge-out rule. Finally, in all OMP tight turns, hydrogen bonding between the side chain and backbone 2 to 4 residues away from that side chain plays an important role. These bonds preferentially use an Asp, Asn, Ser, or Thr residue in a beta or pro phi/psi conformation. We anticipate that this study will be applicable to future design and structure prediction of OMPs.
作为一个结构类别，紧密转弯可以控制分子识别、酶活性和折叠的成核。它们在可溶性蛋白质中得到了广泛的研究，但在外膜蛋白 (OMPs) 中尚未得到研究，而它们在外膜蛋白中也支持着关键功能。我们对 110 个 OMPs 的 4 到 6 个残基的紧密转弯进行了聚类，以研究这些结构的 phi/psi 角、序列和氢键。我们发现可溶性蛋白质紧密转弯和 OMP 紧密转弯之间存在显著差异。由于 OMP 链比可溶性链扭曲程度较小，因此它们更倾向于不同的转弯结构类型。此外，OMP 的膜定位相对于可溶性蛋白转弯，为其紧密转弯提供了不同的序列特征。我们还描述了 OMP 细胞外环和 OMP 周质环之间的 phi/psi 角、序列和氢键的差异。如前所述，细胞外环往往比周质环长得多。我们发现，这种长度差异是由于细胞外环的长度分布更宽，而不是中位数长度的差异较大。细胞外环也倾向于具有更多的带电荷残基，这是由电荷溢出规则预测的。最后，在所有 OMP 紧密转弯中，侧链和距离该侧链 2 到 4 个残基的骨架之间的氢键起着重要作用。这些键优先使用 beta 或 pro phi/psi 构象中的 Asp、Asn、Ser 或 Thr 残基。我们预计，这项研究将适用于未来 OMP 的设计和结构预测。
