Auxiliary ATP binding sites support DNA unwinding by RecBCD

Development of a fluorescence-based assay for RecBCD activity using functional data analysis and design of experiments

Biochemical assays are essential tools in biological research and drug discovery, but optimisation of these assays is often a challenging and lengthy process due to the wide range of input variables and the complex effects of these variables on one another. Traditional 'one-factor-at-a-time' optimisation is both time-consuming and fails to explore the full range of input combinations. In contrast, the modern 'design of experiments' (DoE) approach enables simultaneous investigation of multiple input variables and their interactions, leading to more information-rich and efficient experimentation. We therefore sought to apply DoE to the optimisation of a new fluorescence-based assay for the enzyme RecBCD, a helicase-nuclease-ATPase complex involved in bacterial stress responses. A novel 'functional data analysis' (FDA) approach was used to predict the shape of RecBCD reaction curves in response to different combinations of input variables, which successfully identified assay conditions suitable for drug screening. Collectively, this work delivers a new assay for the antibiotic target RecBCD and demonstrates the potential of DoE and FDA to accelerate biochemical assay development.

Real time characterization of the MAPK pathway using native mass spectrometry

The MAPK pathway is a crucial cell-signaling cascade that is composed of RAS, MEK, BRAF, and ERK, which serves to connect extracellular signals to intracellular responses. Over-activating mutations in the MAPK pathway can lead to uncontrolled cell growth ultimately resulting in various types of cancer. While this pathway has been heavily studied using a battery of techniques, herein we employ native mass spectrometry (MS) to characterize the MAPK pathway, including nucleotide, drug, and protein interactions. We utilize native MS to provide detailed insights into nucleotide and drug binding to BRAF complexes, such as modulation of nucleotide binding in the presence of MEK1. We then demonstrate that different CRAF segments vary in their complex formation with KRAS, with the addition of the cysteine rich domain (CRD) enhancing complex formation compared to Ras binding domain (RBD) alone. We report differences in KRAS GTPase activity in the presence of different RAF segments, with KRAS exhibiting significantly enhanced nucleotide turnover when bound to CRAF fragments. We use ERK2 as a downstream readout to monitor the MAPK phosphorylation cascade. This study demonstrates the utility of native MS to provide detailed characterization of individual MAPK pathway components and monitor the phosphorylation cascade in real time.

Probing actin-activated ATP turnover kinetics of human cardiac myosin II by single molecule fluorescence

Mechanistic insights into myosin II energy transduction in striated muscle in health and disease would benefit from functional studies of a wide range of point-mutants. This approach is, however, hampered by the slow turnaround of myosin II expression that usually relies on adenoviruses for gene transfer. A recently developed virus-free method is more time effective but would yield too small amounts of myosin for standard biochemical analyses. However, if the fluorescent adenosine triphosphate (ATP) and single molecule (sm) total internal reflection fluorescence microscopy previously used to analyze basal ATP turnover by myosin alone, can be expanded to actin-activated ATP turnover, it would appreciably reduce the required amount of myosin. To that end, we here describe zero-length cross-linking of human cardiac myosin II motor fragments (sub-fragment 1 long [S1L]) to surface-immobilized actin filaments in a configuration with maintained actin-activated ATP turnover. After optimizing the analysis of sm fluorescence events, we show that the amount of myosin produced from C2C12 cells in one 60 mm cell culture plate is sufficient to obtain both the basal myosin ATP turnover rate and the maximum actin-activated rate constant (k cat). Our analysis of many single binding events of fluorescent ATP to many S1L motor fragments revealed processes reflecting basal and actin-activated ATPase, but also a third exponential process consistent with non-specific ATP-binding outside the active site.

Communication between DNA and nucleotide binding sites facilitates stepping by the RecBCD helicase

Double-strand DNA breaks are the severest type of genomic damage, requiring rapid response to ensure survival. RecBCD helicase in prokaryotes initiates processive and rapid DNA unzipping, essential for break repair. The energetics of RecBCD during translocation along the DNA track are quantitatively not defined. Specifically, it's essential to understand the mechanism by which RecBCD switches between its binding states to enable its translocation. Here, we determine, by systematic affinity measurements, the degree of coupling between DNA and nucleotide binding to RecBCD. In the presence of ADP, RecBCD binds weakly to DNA that harbors a double overhang mimicking an unwinding intermediate. Consistently, RecBCD binds weakly to ADP in the presence of the same DNA. We did not observe coupling between DNA and nucleotide binding for DNA molecules having only a single overhang, suggesting that RecBCD subunits must both bind DNA to 'sense' the nucleotide state. On the contrary, AMPpNp shows weak coupling as RecBCD remains strongly bound to DNA in its presence. Detailed thermodynamic analysis of the RecBCD reaction mechanism suggests an 'energetic compensation' between RecB and RecD, which may be essential for rapid unwinding. Our findings provide the basis for a plausible stepping mechanism' during the processive translocation of RecBCD.

New paradigms in actomyosin energy transduction: Critical evaluation of non-traditional models for orthophosphate release

Release of the ATP hydrolysis product ortophosphate (Pi) from the active site of myosin is central in chemo-mechanical energy transduction and closely associated with the main force-generating structural change, the power-stroke. Despite intense investigations, the relative timing between Pi-release and the power-stroke remains poorly understood. This hampers in depth understanding of force production by myosin in health and disease and our understanding of myosin-active drugs. Since the 1990s and up to today, models that incorporate the Pi-release either distinctly before or after the power-stroke, in unbranched kinetic schemes, have dominated the literature. However, in recent years, alternative models have emerged to explain apparently contradictory findings. Here, we first compare and critically analyze three influential alternative models proposed previously. These are either characterized by a branched kinetic scheme or by partial uncoupling of Pi-release and the power-stroke. Finally, we suggest critical tests of the models aiming for a unified picture.

Multistep orthophosphate release tunes actomyosin energy transduction

Muscle contraction and a range of critical cellular functions rely on force-producing interactions between myosin motors and actin filaments, powered by turnover of adenosine triphosphate (ATP). The relationship between release of the ATP hydrolysis product ortophosphate (Pi) from the myosin active site and the force-generating structural change, the power-stroke, remains enigmatic despite its central role in energy transduction. Here, we present a model with multistep Pi-release that unifies current conflicting views while also revealing additional complexities of potential functional importance. The model is based on our evidence from kinetics, molecular modelling and single molecule fluorescence studies of Pi binding outside the active site. It is also consistent with high-speed atomic force microscopy movies of single myosin II molecules without Pi at the active site, showing consecutive snapshots of pre- and post-power stroke conformations. In addition to revealing critical features of energy transduction by actomyosin, the results suggest enzymatic mechanisms of potentially general relevance.

Release of the ATP hydrolysis product orthophosphate (Pi) from the myosin active site is central in force generation but is poorly understood. Here, Moretto et al. present evidence for multistep Pi-release reconciling apparently contradictory results.