High Free-Energy Barrier of 1D Diffusion Along DNA by Architectural DNA-Binding Proteins
| Autor: | Eriko Mano, Kiyoto Kamagata, Reid C. Johnson, Saori Kanbayashi, Kana Ouchi |
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| Rok vydání: | 2018 |
| Předmět: |
Models
Molecular 0301 basic medicine Fluorescence-lifetime imaging microscopy HMGB chromatin protein Biochemistry & Molecular Biology single-molecule fluorescence microscopy Diffusion Entropy bacterial nucleoid protein DNA-binding protein Microbiology Article 03 medical and health sciences chemistry.chemical_compound Medicinal and Biomolecular Chemistry Bacterial Proteins Structural Biology Models HMGB Proteins Molecule Molecular Biology Chemistry Molecular DNA DNA-Binding Proteins 030104 developmental biology protein–DNA sliding dynamics Biophysics protein-DNA sliding dynamics Nucleic Acid Conformation Biochemistry and Cell Biology DNA conformational change Function (biology) Protein Binding |
| Zdroj: | Journal of molecular biology, vol 430, iss 5 J Mol Biol |
| Popis: | Architectural DNA-binding proteins function to regulate diverse DNA reactions and have the defining property of significantly changing DNA conformation. Although the 1D movement along DNA by other types of DNA-binding proteins has been visualized, the mobility of architectural DNA-binding proteins on DNA remains unknown. Here, we applied single-molecule fluorescence imaging on arrays of extended DNA molecules to probe the binding dynamics of three structurally distinct architectural DNA-binding proteins: Nhp6A, HU, and Fis. Each of these proteins was observed to move along DNA, and the salt concentration independence of the 1D diffusion implies sliding with continuous contact to DNA. Nhp6A and HU exhibit a single sliding mode, whereas Fis exhibits two sliding modes. Based on comparison of the diffusion coefficients and sizes of many DNA binding proteins, the architectural proteins are categorized into a new group distinguished by an unusually high free-energy barrier for 1D diffusion. The higher free-energy barrier for 1D diffusion by architectural proteins can be attributed to the large DNA conformational changes that accompany binding and impede rotation-coupled movement along the DNA grooves. |
| Databáze: | OpenAIRE |
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