Ultrafast Water Dynamics at the Interface of the Polymerase–DNA Binding Complex

• Published in: Biochemistry (Easton) Vol. 53; no. 33; pp. 5405 - 5413
• Main Authors: Yang, Yi, Qin, Yangzhong, Ding, Qing, Bakhtina, Marina, Wang, Lijuan, Tsai, Ming-Daw, Zhong, Dongping
• Format: Journal Article
• Language: English
• Published: United States American Chemical Society 26.08.2014
• Subjects: Animals; Catalytic Domain; DNA Polymerase beta - chemistry; DNA Polymerase beta - genetics; DNA Polymerase beta - metabolism; Escherichia coli Proteins - chemistry; Escherichia coli Proteins - metabolism; Molecular Dynamics Simulation; Mutation; Rats; Spectrometry, Fluorescence; Water - chemistry
• ISSN: 0006-2960; 1520-4995
• DOI: 10.1021/bi500810a

DNA polymerases slide on DNA during replication, and the interface must be mobile for various conformational changes. The role of lubricant interfacial water is not understood. In this report, we systematically characterize the water dynamics at the interface and in the active site of a tight binding polymerase (pol β) in its binary complex and ternary state using tryptophan as a local optical probe. Using femtosecond spectroscopy, we observed that upon DNA recognition the surface hydration water is significantly confined and becomes bound water at the interface, but the dynamics are still ultrafast and occur on the picosecond time scale. These interfacial water molecules are not trapped but are mobile in the heterogeneous binding nanospace. Combining our findings with our previous observation of ultrafast water motions at the interface of a loose binding polymerase (Dpo4), we conclude that the binding interface is dynamic and the water molecules in various binding clefts, channels, and caves are mobile and even fluid with different levels of mobility for loose or tight binding polymerases. Such a dynamic interface should be general to all DNA polymerase complexes to ensure the biological function of DNA synthesis.