Abstract
Solvent dynamics can play a major role in enzyme activity, but obtaining an accurate, quantitative picture of solvent activity during catalysis is quite challenging. Here, we combine terahertz spectroscopy and X-ray absorption analyses to measure changes in the coupled water-protein motions during peptide hydrolysis by a zinc-dependent human metalloprotease. These changes were tightly correlated with rearrangements at the active site during the formation of productive enzyme-substrate intermediates and were different from those in an enzyme-inhibitor complex. Molecular dynamics simulations showed a steep gradient of fast-to-slow coupled protein-water motions around the protein, active site and substrate. Our results show that water retardation occurs before formation of the functional Michaelis complex. We propose that the observed gradient of coupled protein-water motions may assist enzyme-substrate interactions through water-polarizing mechanisms that are remotely mediated by the catalytic metal ion and the enzyme active site.
| Original language | English |
|---|---|
| Pages (from-to) | 1102-1108 |
| Number of pages | 7 |
| Journal | Nature Structural and Molecular Biology |
| Volume | 18 |
| Issue number | 10 |
| DOIs | |
| State | Published - 18 Sep 2011 |
| Externally published | Yes |
Funding
We thank A. Frenkel (Yeshiva University), J. Bohon, M. Sullivan (beam line X3B at the National Synchrotron Light Source), I. Solomonov and Y. Udi (Weizmann Institute of Science) for help with X-ray absorption data collection, and we thank M. Krüger (Ruhr-University Bochum) for programming the THz data acquisition software. We thank G. Murphy (Cambridge Research Institute) for the plasmid encoding TIMP-2. We acknowledge financial support by the Ministry of Innovation, Science, Research and Technology of the German state of North Rhine-Westphalia and by the Ruhr-University Bochum and thank the Ressourcenverbund North Rhine-Westphalia for computer time. B.B. and M.He. were members of the Ruhr-University Research School funded by Germany’s Excellence Initiative (DFG GSC 98/1). B.B. is grateful to the Feinberg Graduate School at the Weizmann Institute for a Dean of Faculty fellowship. M.He. was a fellow of the Studienstiftung des Deutschen Volkes. G.B.F. is supported by the Robert A. Welch Foundation. G.B.F. and I.S. are supported by a US National Institutes of Health grant (CA098799). I.S. is supported by the Israel Science Foundation, the Kimmelman Center at the Weizmann Institute and the Ambach family fund. M.Ha. is supported by the VW Stiftung.
| Funders | Funder number |
|---|---|
| Ambach family fund | |
| Germany’s Excellence Initiative | |
| Kimmelman Center | |
| Ministry of Innovation, Science, Research and Technology | |
| Robert A. Welch Foundation | |
| Ruhr-University Bochum | |
| Ruhr-University Research School | |
| US National Institutes of Health | CA098799 |
| VW Stiftung | |
| National Cancer Institute | R01CA098799 |
| National Institute of Biomedical Imaging and Bioengineering | P30EB009998 |
| Deutsche Forschungsgemeinschaft | GSC 98/1 |
| Feinberg Graduate School, Weizmann Institute of Science | |
| Israel Science Foundation |