Differential isotope labeling

It is important to note that even in the presence of sufficient proton density and in the case of differential isotope labeling, efficient spin-diffusion may complicate the interpretation of the NOE data and result in structures or relative orientations that are erroneous. A similar problem does not occur when using residual dipolar couplings. 

Isotope filtering/editing NMR techniques make use of differential isotopic labeling to simplify spectra and thus more easily extract information from complex systems. In the case of biomolecular NMR these will generally be intermolecular complexes between one biomacromolecule (for example, a protein) and a second species either another protein, a nucleic acid, or a ligand (generally a small organic molecule). 

In the case of a symmetric (protein-protein) homodimer, the preparation of molecules with differently labeled monomers is often far from trivial, and special approaches have been described in the literature [8, 9]. However, when successful, differential isotopic labeling of a symmetric homodimer, in combination with isotope editing/filtering techniques, offers a unique access to the NMR investigation of the monomer interfaces. 

One of the possibilities is to study experimentally the coupled system as a whole, at a time when all the reactions concerned are taking place. On the basis of the data obtained it is possible to solve the system of differential equations (1) simultaneously and to determine numerical values of all the parameters unknown (constants). This approach can be refined in that the equations for the stoichiometrically simple reactions can be specified in view of the presumed mechanism and the elementary steps so that one obtains a very complex set of different reaction paths with many unidentifiable intermediates. A number of procedures have been suggested to solve such complicated systems. Some of them start from the assumption of steady-state rates of the individual steps and they were worked out also for stoichiometrically not simple reactions [see, e.g. (8, 9, 5a)]. A concise treatment of the properties of the systems of consecutive processes has been written by Noyes (10). The simplification of the treatment of some complex systems can be achieved by using isotopically labeled compounds (8, 11, 12, 12a, 12b). Even very complicated systems which involve non-... 

Figure 3.2. Stable isotope labeling for quantifying differential protein expression. Cell populations are grown in either 14N or 15N containing medium. Protein lysates are fractionated and separated by 2D gel electrophoresis. Protein spots are excised, digested with trypsin and the mass of the resulting peptides is determined by mass spectrometry. The presence of 15N results in a shift and creates two peaks for each peptide. The ratio of intensities of the peaks is indicative of the relative expression levels of the proteins. Spot A contains a protein that is expressed at similar levels in both cell pools. Spot B contains a protein that is expressed at higher levels in cell pool 2. Figure adapted from Oda et al. (1999).

The approach recruited to chemical proteomics in Reference [17] is called SILAC (stable isotope labeling with amino acids in cell culture) and is important in comparative proteomics (Figure 1). SILAC works well with cultured mammalian cells, but prokaryotes defeat it by metabolizing the label (usually supplied in lysine and arginine) into other amino acids. For applications beyond cultured eukaryotic cells, the reductive methylation route to differential labeling [18] is among the alternatives [15]-... 

FIGURE 15.3 Outline of experimental protocol used for ICAT differential protein expression profiling. Protein mixtures from two cell populations are labeled with light or heavy isotopic versions of a cleavable ICAT reagent. Labeled proteins are combined, subject to multidimensional separation by SCX, RP, and avidin affinity chromatography, then analyzed by tandem MS for peptide and protein identification. Based on the relative ratio of the two isotopically labeled peptides, a relative abundance of protein expression can be determined. 

For reproducible expression analysis and protein quantification MS methods based on isotopic labeling are available. They were designed in conjunction with two or more dimensional chromatographic peptide separation coupled online to MS and require advanced bioinformatics input to analyze the complex data sets in a reasonable time frame. This is also true for the alternative fluorescence-based technology of differential gel electrophoresis (DIGE Fig. 10.6) with tailor-made software which allows statistical validation of multiple data sets. 

Unfortunately, for the majority of small molecule LC-MS/MS analyses, stable isotope labelled internal standards are not available so far. In such cases, compounds with a very similar molecular structure typically serve as internal standard ( homologues or analogues ). Since the ionization properties are substantially determined by functional groups of a molecule, ionization behaviour may differ significantly—even between compounds with very similar over-all molecular structure. Differential clustering, e.g. with sodium, ammonium or formate ions often present in mobile phases may as well impact the parity of ionization yield between analyte and internal standard. Hence the availability of an appropriate homologue is crucial and critical for the development of reliable LC-MS/MS methods in TDM [51]. 

The plug flow reactor is increasingly being used under transient conditions to obtain kinetic data by analysing the combined reactor and catalyst response upon a stimulus. Mostly used are a small reactant pulse (e.g. in temporal analysis of products (TAP) [16] and positron emission profiling (PEP) [17, 18]) or a concentration step change (in step-response measurements (SRE) [19]). Isotopically labeled compounds are used which allow operation under overall steady state conditions, but under transient conditions with respect to the labeled compound [18, 20-23]. In this type of experiments both time- and position-dependent concentration profiles will develop which are described by sets of coupled partial differential equations (PDEs). These include the concentrations of proposed intermediates at the catalyst. The mathematical treatment is more complex and more parameters are to be estimated [17]. Basically, kinetic studies consist of ... 

In quantitative proteomics, two alternative strategies have been developed. The first one is based on 2-D PAGE combined with mass spectrometry for protein identification (Haynes and Yates, 2000). This method and current advances in the differential display of proteins by 2-D PAGE are discussed at length in another chapter of this book. The second approach exploits mass spectrometry in combination with stable isotope labeling for gaining accurate quantitative information on proteins. Quantitative MS via stable isotope labeling of proteins... 

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