3. Results
3.3 Interaction of hBrr2 with nucleotides in solution
To obtain an estimate for the affinity of hBrr2 to nucleotides and, specifically, to investigate if N- and C-terminal cassettes bind nucleotides with different affinities, we performed interaction studies with ADP and with a non-hydrolysable ATP analog, ATPγS.
Although the intrinsic ATPase activity of hBrr2HR is low, by using ATPγS we intended to avoid any degree of conversion of ATP to ADP during the experiments. All data was acquired in collaboration with Dr. Pohl Milon, Dept. of Physical Biochemistry, MPI-BPC, Göttingen.
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Interactions of nucleotides with hBrr2 were studied using FRET from tryptophan residues located in the vicinity of the nucleotide binding pockets of hBrr2 to the mant group of mant-ATPγS or mant-ADP. It has been shown for many GTPases that nucleotide binding and nucleotide exchange reactions are not perturbed by the mant group (Jameson and Eccleston, 1997; Pittman et al., 2006).
Control experiments showed that FRET signals were observed only when donor (tryptophan residues) and acceptor (mant group) were simultaneously present (Fig. 3.25).
Therefore, fluorescence increase was observed only upon mixing labeled nucleotide with hBrr2HR, hBrr2NC or hBrr2CC (Fig. 3.25). Signal changes were absent when hBrr2HR, hBrr2NC or hBrr2CC were mixed with unlabeled nucleotides or buffer lacking nucleotides (Fig. 3.25).
Fig. 3.25: Binding of mant-ATPγS to hBrr2HR, hBrr2NC and hBrr2CC. Upon mixing in a stopped flow apparatus nucleotide-free hBrr2HR or fragments thereof (0.2 µM) with mant-ATPγS or unlabeled ATPγS (5 µM), the emitted fluorescence of mant group (acceptor) is recorded as a function of time. In the absence of the fluorescence acceptor, no signal change was observed.
To determine association rate constants, a fixed concentration of nucleotide-free hBrr2 or fragments thereof was mixed with varying concentrations of mant-nucleotides. The data were analyzed by exponential fitting to determine the apparent rate constant (kapp) value for each titration point (Fig. 3.26).
hBrr2NC titrations curves were fit with a double-exponential equation (Fig. 3.27), resulting in apparent rate constants kappNCa, corresponding to a very rapid phase, and kappNCb, associated with a second, rapid phase. Nevertheless, due to the fact that this very fast phase (represented by kappNCa) results in a very small amplitude change, we only considered the apparent rate constant of the rapid phase (kappNCb), which contributes most of the fluorescence signal change. The time courses obtained with hBrr2CC were fit using a single-exponential equation (Fig. 3.26), with apparent rate constant kappCC.
The hBrr2, hBrr2HR and hBrr2HR,S1087L time courses were best described by double-exponential fitting (Fig. 3.26), resulting in apparent rate constants kappNC and kappCC,once they
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were similar to the apparent rate constants obtained for the individual cassettes. It is important to mention that titrations performed with hBrr2 and its fragments containing both cassettes (hBrr2HR, hBrr2HR,S1087L) showed a third, very rapid phase, which we could not fit due to the very small fluorescence change (amplitude) associated with this phase. Henceforth, we refer to kappNC as a fast apparent rate constant corresponding to the ATP/ADP binding velocity to the N-terminal cassette, while kappCC is the constant that describes the apparent velocity of nucleotide binding to the C-terminal cassette.
Fig. 3.26: Time courses of nucleotide binding at increasing concentrations of mant-ATPγS (A) and mant-ADP (B) to hBrr2, hBrr2HR, hBrr2HR,S1087L, hBrr2NC and hBrr2CC (top to bottom). Dissociation of hBrr2·mant-ATPγS (C) and hBrr2·mant-ADP (D) complexes upon mixing with unlabeled nucleotides (colored traces). Gray traces represent the decrease in FRET related to the dissociation of protein·mant-nucleotide by dilution in buffer. For each row of graphs, a different protein fragment (indicated) was used to perform nucleotide binding and dissociation experiments. It is not clear at the moment if the observed decrease in fluorescence upon dilution of hBrr2/hBrr2HR/hBrr2HR,S1087L/hBrr2CC·mant-nucleotide with buffer either reflects the dissociation of the mant-nucleotide or it is a consequence of photobleaching due to extensive light exposure.
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The apparent rate constants obtained from the single- and double- exponential fittings were plotted as a function of the nucleotide concentration (Fig. 3.27).
In the case of hBrr2NC, the concentration dependence of kappNCb deviated from a linear behavior. Instead, the kappNCb values tended to saturation at high nucleotide concentration, showing a hyperbolic dependency. Such concentration dependency could indicate that the fluorescence change observed is a monomolecular rearrangement, rather than a bimolecular binding reaction, and would be consistent with a two-step binding mechanism (Fig. 3.27A):
hBrr2NC + ATPS
⇌
hBrr2NC·ATPS⇌
hBrr2NC·ATPS*.In this case, the first bimolecular reaction:
hBrr2NC + ATPS
⇌
hBrr2NC·ATPS,is too fast to be measured or does not result in an appreciable fluorescence change, whereas the first-order reaction (the rearrangement corresponding to the second step):
hBrr2NC·ATPS
⇌
hBrr2NC·ATPS*,results in an increase of fluorescence intensity with velocity corresponding to kappNCb. Such accommodation step observed for hBrr2NC is not observed for hBrr2CC although nucleotides bound to the N and C-terminal cassettes in Brr2HR structure assume similar conformations, i.e.
nucleotide binding is mainly fostered by motifs from the first RecA domain lacking interactions with RecA-2 (Fig. 3.18B and C).
According to kappNCa, kappNCb and to the proposed model, we assume that binding of nucleotide to hBrr2 is significantly faster than the following rearrangement. In this case, we imply that the first step is rapid compared to the second step and, therefore, the equilibrium dissociation constant for the first step, KSNC, can be calculated from the nucleotide concentration dependencies of the kappNCb values according to the equation:
SNC represented by nucleotide accommodation, K2'NC, was calculated as a ratio between forward and reverse rates, k–NCb/kNCb. The overall dissociation constant Kd for ADP and ATP could not be derived from the amplitude dependencies on nucleotide concentration. Therefore, the global Kd for the N-cassette interaction with nucleotides was then calculated using the following equation: Kd = KSNC×K2'NC. The equilibrium dissociation constants for the first step
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(KSNC) were 6.17±1.83 and 5.74±2.0 µM and for the second step(K2'NC) were 0.50±0.05 and 0.22±0.1 for ATPγS and ADP respectively. Furthermore, these data indicate that the second step greatly contributes to the overall affinity for the nucleotides. Altogether, our structural and biochemical data suggest that, during the second step of nucleotide binding, cooperative conformational changes are triggered resulting in kinetic stabilization of the nucleotide bound form of hBrr2NC.
Differently from the isolated cassette construct, hBrr2NC, kappNC of nucleotide binding to hBrr2 variants containing the C-terminal cassette were linearly dependent on the nucleotide
Fig. 3.27: (A) A two-step model illustrating ATP binding to hBrr2NC (first step, kNCa) and the subsequent accommodation (second step, kNCb) (top) and a model depicting ATP binding to hBrr2CC (bottom). Concentration dependency of the apparent rate constants for mant-ATPγS (B) and mant-ADP (D) binding to the N-terminal cassette of hBrr2 (red), hBrr2HR (black), hBrr2HR,S1087L (blue) and hBrr2NC (green). Concentration dependency of the apparent rate constants for mant-ATPγS (C) and mant-ADP (E) binding to the C-terminal cassette of hBrr2
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(red), hBrr2HR (black), hBrr2HR,S1087L (blue) and hBrr2CC (orange). Error bars represent standard errors of the mean.
concentration, consistent with a single bimolecular event and indicating an influence of the C-terminal cassette on nucleotide binding by the N-C-terminal cassette. Furthermore, the measured apparent rate constants corresponding to kappCC of hBrr2CC together with hBrr2, hBrr2HR and hBrr2HR,S1087L also depended linearly as a function of the nucleotide concentration.
The association rate constants, kNC and kCC, were determined from the slope of the linear dependence of kapp on the concentration of mant-nucleotides. The intercept with the y-axis provided k–NC and k–CC. When the intercept with the y-axis was close to zero, the value of k–NC
and k–CC could not be determined with precision therefore dissociation experiments were conducted.
The slope of the linear fitting of kappNC, corresponding to the binding of ATPγS to the N-terminal cassette in the context of hBrr2, hBrr2HR, hBrr2HR,S1087L, indicated association rate constants kNC of 0.96±0.02, 2.54±0.03 and 2.21±0.23 µM-1 s-1, respectively. These rates, with the possible exception of kNC for hBrr2, are similar to the ones obtained for ADP binding to the N-terminal cassette of different variants of hBrr2, which was about 2.5±0.11 µM-1 s-1.
The hBrr2, hBrr2HR, hBrr2HR,S1087L rate constants for ATPγS binding to the C-terminal cassette, kCC, were in the order of 0.1±0.01 µM-1 s-1. We could observe that ADP binding to the C-terminal cassette of hBrr2, hBrr2HR and hBrr2HR,S1087L was faster compared to ATPγS, with association rates kCC of about 0.45±0.01 µM-1 s-1. This observation is in perfect agreement with the kCC obtained for ATPγS and ADP binding to the isolated hBrr2CC, 0.080±0.002 and 0.47±0.01 µM-1 s-1, respectively. The linear concentration dependency of the kapps is consistent with a bimolecular binding reaction, that, in the case of hBrr2CC, could be represented as follows:
hBrr2CC + ATPS
⇌
hBrr2CC·ATPS.Unfortunately, we still cannot propose a full mechanism for nucleotide turnover for hBrr2 or hBrr2HR. Apart from the difficulties involved in resolving the very rapid phase observed in the reactions with hBrr2 or hBrr2HR, we presently do not know if nucleotide pre-bound to the C-terminal cassette could influence the velocity of nucleotide exchange or modulate nucleotide preference of the N-terminal cassette.
Nucleotide dissociation rate constants, k–NC and k–CC, were determined upon mixing hBrr2·mant-ATPγS or hBrr2·mant-ADP with an excess of the respective unlabeled nucleotide. The release of the labeled nucleotide from hBrr2 resulted in fluorescence decrease. In this context, the rate by which the fluorescence decreases reflects the dissociation
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rate constant of mant-ATPγS or mant-ADP from hBrr2, since, in the presence of a large excess of unlabeled nucleotide, rebinding of labeled nucleotide is negligible. Upon dilution of hBrr2NC·mant-nucleotide with buffer, some mant-nucleotide dissociated. However, this dissociation impelled by the dilution did not occur to the same extent as in the presence of the dark nucleotide competitor (Fig. 3.26). Although we lack a complete description of the nucleotide binding mechanism to the N-terminal cassette, the observation of a single dissociation step for hBrr2NC may suggest that this step is rate limiting in nucleotide turnover.
However, we cannot exclude other reactions occurring upstream of the pathway to be slower, i.e. phosphate release.
The hBrr2NC dissociation rates (k–NC) for ATPγS and ADP were 1.62±0.016 and 1.89±0.1 s-1. ATPγS and ADP dissociation rates for hBrr2CC (k–CC) were about 0.0020±0.0002 s-1, extremely slow compared to k–NC. Two phases could be distinguished during nucleotide dissociation from hBrr2, hBrr2HR, hBrr2HR,S1087L. The first phase is represented by a fast dissociation rate constant comparable to that for the N-terminal cassette, k–NC. The nucleotide dissociation rates related to the N-terminal cassette for hBrr2, hBrr2HR and hBrr2HR,S1087L were very similar, 1.40±0.04 s-1 for ATPγS and 1.37±0.02 s-1 for ADP, respectively. The second phase had a dissociation rate constantsimilar to the one associated with the very slow release of nucleotide from hBrr2CC, k–CC. Nucleotide release from the C-terminal cassette in the context of hBrr2, hBrr2HR and hBrr2HR,S1087L was very slow, about 0.0020±0.0002 s-1.
The Kd values for the interaction of ATPγS and ADP to hBrr2, hBrr2HR, hBrr2HRS1087L, hBrr2CC were calculated from the association (kNC, kcc) and dissociation rate constants (k–NC
and k–CC), using either k–NC/kNC or k–CC/kCC. The Kd’s for the Brr2NC·nucleotide complexes were 3.08±0.55 µM and 1.26±0.18 µM for ATPγS and ADP, respectively, while the Kd's for N-terminal cassette·nucleotide complexes in the context of hBrr2, hBrr2HR, hBrr2HRS1087L were about 0.50±0.07 µM for both nucleotides. This indicates that, in the absence of the C-terminal cassette, the N-C-terminal cassette exhibits lower affinities for nucleotides. The Kd's of the C-terminal cassette·nucleotide complexes are similar for all Brr2 variants measured, about 0.01±0.001 µM.
The results described above show that binding of ATPγS and ADP to the N-terminal cassette is faster compared to the velocity of nucleotide association with the C-terminal cassette. The same trend is observed for nucleotide dissociation; ATPγS and ADP release from the N-terminal cassette is much faster for the N-terminal cassette compared to the C-terminal cassette. On the other hand, the differences in the mechanism of nucleotide binding to N-terminal cassette in the absence or presence of the C-terminal cassette may indicate
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conformational constrains in the active domain of Brr2 that are released by covalent and surface contacts with the C-terminal cassette. In the absence of the C-terminal cassette, the N-terminal cassette seems to rearrange before achieving a kinetically stable complex with adenosine nucleotides. In the presence of the C-terminal cassette, it is possible that the N-terminal cassette may be already conformationally oriented to accept the nucleotide in a stable manner. These solution studies also verified our structural finding that the inactive C-terminal cassette binds nucleotides, with a Kd that suggests it will be saturated at cellular concentrations.
The extremely slow nucleotide dissociation from the C-terminal cassette reflects its higher affinity for ATPγS or ADP. Considering the slow nucleotide release from the C-terminal cassette and the high concentration of ATP in the nucleus compared to ADP, we suggest that ATP is stably bound to the C-terminal cassette throughout a whole splicing cycle. This scenario may be tuned by other proteins, interacting with Brr2 in the spliceosome, functioning as adenine nucleotide exchange factors for Brr2.
Table 3.2: Rate constants and equilibrium dissociation constants of interactions between hBrr2 or fragments thereof and nucleotides.
See next page.
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