Structural analysis and rational design of orthogonal stacking system in an E. coli DegP PDZ1–peptide complex
| العنوان: | Structural analysis and rational design of orthogonal stacking system in an E. coli DegP PDZ1–peptide complex |
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| المؤلفون: | Lijun Liu, Dingwa Zhang, Ya-Ping Xu, Deyong He, Xiaoliang Pan |
| المصدر: | Chemical Papers. 73:2469-2476 |
| بيانات النشر: | Springer Science and Business Media LLC, 2019. |
| سنة النشر: | 2019 |
| مصطلحات موضوعية: | chemistry.chemical_classification, Alanine, Chemistry, Stereochemistry, General Chemical Engineering, PDZ domain, Stacking, Peptide, Peptide binding, 02 engineering and technology, General Chemistry, Periplasmic space, 010402 general chemistry, 021001 nanoscience & nanotechnology, medicine.disease_cause, 01 natural sciences, Biochemistry, Industrial and Manufacturing Engineering, 0104 chemical sciences, chemistry.chemical_compound, Materials Chemistry, medicine, Aromatic amino acids, 0210 nano-technology, Escherichia coli |
| الوصف: | The DegP is essential for clearance of denatured or aggregated components from the inner-membrane and periplasmic space in Escherichia coli (E. coli). The enzyme contains two regulatory PDZ domains that have been shown to act as substrate specificity determinant by binding to the C-terminal hydrophobic stretch of substrate proteins. Here, the complex structure of E. coli DegP PDZ1 domain with a phage-displayed C3H1 pentapeptide is modeled and examined using peptide grafting, virtual mutagenesis, and QM/MM calculation. An orthogonal stacking system is identified at the domain–peptide complex interface, which consists of a T-shaped cation-π stacking (t-stacking) and a paralleled cation-π stacking (p-stacking) formed from domain cationic residue R325 to peptide aromatic residues Trp−1 and Phe−4, respectively. A synergistic effect between t-stacking and p-stacking is observed; π-electron conjugation is primarily responsible for the synergistic effect. Subsequently, the two peptide aromatic residues are systematically replaced by other aromatic amino acids as well as a non-aromatic alanine to optimize the synergistic effect, from which the binding affinities of wild-type C3H1 peptide and seven variants to E. coli DegP PDZ1 domain are determined at micromolar level using fluorescence-based assay. A good linear correlation between experimental binding affinities and calculated binding energies is derived, with a Pearson’s correlation coefficient rp = 0.928. The aromatic Phe−4Tyr substitution can considerably improve peptide binding potency by 8.7-fold, whereas the non-aromatic substitutions at each of t-stacking and p-stacking or both can largely impair the peptide affinity by 20.7-fold (Phe−4Ala), 82.1-fold (Trp−1Ala) and 110.7-fold (Trp−1Ala/Phe−4Ala). |
| تدمد: | 1336-9075 2585-7290 |
| الوصول الحر: | https://explore.openaire.eu/search/publication?articleId=doi_________::02e0538a3aa0a56155610138573a0792Test https://doi.org/10.1007/s11696-019-00797-8Test |
| حقوق: | CLOSED |
| رقم الانضمام: | edsair.doi...........02e0538a3aa0a56155610138573a0792 |
| قاعدة البيانات: | OpenAIRE |
| تدمد: | 13369075 25857290 |
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