Direct observation of ultrafast large-scale dynamics of an enzyme under turnover conditions.
Proc Natl Acad Sci U S A 2018. [PMID:
29531052 PMCID:
PMC5879700 DOI:
10.1073/pnas.1720448115]
[Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
The potential effect of conformational dynamics of enzymes on their chemical steps has been intensely debated recently. We use single-molecule FRET experiments on adenylate kinase (AK) to shed new light on this question. AK closes its domains to bring its two substrate close together for reaction. We show that domain closure takes only microseconds to complete, which is two orders of magnitude faster than the chemical reaction. Nevertheless, active-site mutants that reduce the rate of domain closure also reduce the reaction rate, suggesting a connection between the two phenomena. We propose that ultrafast domain closure is used by enzymes as a mechanism to optimize mutual orientation of substrates, a novel mode of coupling between conformational dynamics and catalysis.
The functional cycle of many proteins involves large-scale motions of domains and subunits. The relation between conformational dynamics and the chemical steps of enzymes remains under debate. Here we show that in the presence of substrates, domain motions of an enzyme can take place on the microsecond time scale, yet exert influence on the much-slower chemical step. We study the domain closure reaction of the enzyme adenylate kinase from Escherichia coli while in action (i.e., under turnover conditions), using single-molecule FRET spectroscopy. We find that substrate binding increases dramatically domain closing and opening times, making them as short as ∼15 and ∼45 µs, respectively. These large-scale conformational dynamics are likely the fastest measured to date, and are ∼100–200 times faster than the enzymatic turnover rate. Some active-site mutants are shown to fully or partially prevent the substrate-induced increase in domain closure times, while at the same time they also reduce enzymatic activity, establishing a clear connection between the two phenomena, despite their disparate time scales. Based on these surprising observations, we propose a paradigm for the mode of action of enzymes, in which numerous cycles of conformational rearrangement are required to find a mutual orientation of substrates that is optimal for the chemical reaction.
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