NMR Resonance Assignment Assisted by Mass Spectrometry
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1 NMR Resonance Assignment Assisted by Mass Spectrometry This lecture talked about a NMR resonance assignment assisted by mass spectrometry [1, 2]. 1 Motivation Nuclear magnetic resonance (NMR) provides a useful tool for the structural determination of biomollecules, especially for those molecules that are difficult to crystallize for diffraction studies. During the structure determination by NMR, a key step is the resonance assignment of chemical shifts. The traditional NMR resonance assignment is to use the triple resonance experiments, such as HNCA, to help identify the connectivities between amino acids. However, for some proteins that are difficult to express in doubly labelled forms, we may need the structure determination strategies that depend on only the basic 1 H 15 N HSQC experiment, which requires only 15 N isotopic labelling. In [1, 2], a new approach by integration of NMR and mass spectrometry (MS) is considered for protein resonance assignment. 2 Mass Spectrometry Assisted NMR Assignment 2.1 Principle of the Approach The MS-assisted NMR assignment approach relies on the fact that both NMR and MS are able to monitor rates of exchange of amide protons (HX rate) in water deuterons. Based on this observation, we can connect crosspeaks in NMR data and fragment masses in MS data by correlating the HX rates to help the sequential assignment. 2.2 Extracting HX Rates by HSQC The processes of extracting HX rates by HSQC are shown in Figure 1(a). We can extract the amide exchange rates by monitoring the loss of individual 1
2 cross-peak intensities as a function of of time after dissolving a protein in the deuterated water, i.e., I(t) = I 0 (exp( kt) + const), where k is the residuespecific HX rate. Figure 1(b) shows an example of the loss of cross-peak intensities after dissolving the protein ubiquitin in the deuterated water for certain time. Figure 1: Extracting HX rates by HSQC [1]. 2.3 Extracting HX Rates by MS The procedures of extracting HX rates by MS are described in Figure 2(a). The HX rate measured at each time point is decided by the difference between the centroid of the isotopic peak cluster for the deuterated sample and the centroid of the undeuterated reference. Figure 2(b) shows an example of mass increase after deuterium incorporation. 2.4 Correlating HX rates between NMR and MS The time courses of the exchange from NMR data is calculated by summing the distributions expected for each amino acid. More precisely, the the deuteron distribution d(t) is computed by 2
3 Figure 2: Extracting HX rates by MS. 1, if half-life of the amide H/D exchange is shorted than 1min; d(t) = 0, if half-life of the amide H/D exchange is longer than 1 week; 1 exp( kt), otherwise. where k is the amide proton exchange rate and t is the time interval for exchange. In order to correlate HX rates from NMR and MS, we first plot the time courses of exchange D(t) = n i=1 1 exp( k it), where n is the number of data points in a fragment. After that, we superimpose experimental points from the MS data. A correlation example of deuterium incorporation between the NMR and MS data is shown in Figure MS Assisted Assignment The following generate-and-test procedure is used in [1] to demonstrate how MS helps NMR resonance assignment: (1) Perform an a priori NMR assignment. 3
4 Figure 3: The correlation of deuterium incorporation between the NMR and MS data. (2) Predict the exchange data for all residues from HSQC. (3) Compare the exchange data from HSQC with the data from MS. (4) Score the comparison by function score = exp( (D expt D calc ) 2 /(nσ 2 )), where n is the number of data points, and D expt and D calc are deuterium levels from the MS experiment data and the calculation from the NMR data. Figure 4 shows an example of sequential assignment scores for protein ubiquitin. 3 MS Assisted NMR Assignment in Reductively 1 3C-Methylated Proteins The approach depends on different rates of reductive methylation at each primary amine site. After we run NMR and MS experiments, we can obtain normalized percentages of 13 C incorporation from HSQC and MS data, as shown Figure 5. The NMR peak assignment can be performed by comparing the NMR and MS percentages of 13 C incorporation, as illustrated in Figure 6. 4
5 Figure 4: The sequential assignment scores for protein ubiquitin. References [1] L. Feng, R. Orlando, and J.H. Prestegard. Mass spectrometry assisted assignment of NMR resonances in 15N labeled proteins. J. AM. Chem. Soc., 126, , [2] Megan A. Macnaughtan, Austin M. Kane, and James H. Prestegard. Mass Spectrometry Assisted Assignment of NMR Resonances in C13 Reductively 13C-Methylated Proteins. J. AM. Chem. Soc., 127 (50), ,
6 Figure 5: The normalized percentages of 13 C incorporation. Figure 6: The assignment of NMR peaks (The 5:1 sample means that the molar ratio of 13 C-formaldehyde to primary amine in the sample is 5 : 1). 6
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