Different Single-Enzyme Conformational Dynamics upon Binding Hydrolyzable or Nonhydrolyzable Ligands
| Autor: | Arith J. Rajapakse, Myungkeun Oh, Sung Oh Woo, Jasmin Farmakes, Philip G. Collins, Zhongyu Yang, Yongki Choi, Lina Alhalhooly |
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| Rok vydání: | 2021 |
| Předmět: |
Protein Conformation
Stereochemistry Ligands 010402 general chemistry 01 natural sciences Article Catalysis chemistry.chemical_compound Engineering Molecular recognition Catalytic Domain 0103 physical sciences Materials Chemistry Physical and Theoretical Chemistry chemistry.chemical_classification Indole test Binding Sites 010304 chemical physics biology Chemistry Concerted reaction Protein dynamics Active site Glycosidic bond 0104 chemical sciences Surfaces Coatings and Films Physical Sciences Chemical Sciences biology.protein Muramidase Generic health relevance Peptidoglycan Lysozyme Protein Binding |
| Zdroj: | The journal of physical chemistry. B, vol 125, iss 22 J Phys Chem B |
| ISSN: | 1520-5207 1520-6106 |
| Popis: | Single-molecule measurements of protein dynamics help unveil the complex conformational changes and transitions that occur during ligand binding and catalytic processes. Using high-resolution single-molecule nanocircuit techniques, we have investigated differences in the conformational dynamics and transitions of lysozyme interacting with three ligands: peptidoglycan substrate, substrate-based chitin analogue, and indole derivative inhibitors. While processing peptidoglycan, lysozyme followed one of the two mechanistic pathways for the hydrolysis of the glycosidic bonds: a concerted mechanism inducing direct conformational changes from open to fully closed conformations or a nonconcerted mechanism involving transient pauses in intermediate conformations between the open and closed conformations. In the presence of either chitin or an indole inhibitor, lysozyme was unable to access the fully closed conformation where catalysis occurs. Instead, lysozymes' conformational closures terminated at slightly closed, "excited" conformations that were approximately one-quarter of the full hinge-bending range. With the indole inhibitor, lysozyme reached this excited conformation in a single step without any evidence of rate-liming intermediates, but the same conformational motions with chitin involved three hidden, intermediate processes and features similar to the nonconcerted peptidoglycan mechanism. The similarities suggest that these hidden processes involve attempts to accommodate imperfectly aligned polysaccharides in the active site. The results provide a detailed glimpse of the enzyme-ligand interplay at the crux of molecular recognition, enzyme specificity, and catalysis. |
| Databáze: | OpenAIRE |
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