In this review the chemical basis for the protective effects of nitroxides as well as Kocherginsky N, Swartz H. Nitroxide Spin Labels - Reactions in Biology and Mitchell JB, Hideg K. Studies of structure-activity relationship of nitroxide free. Reactions in Biology and Chemistry Nickolai Kocherginsky, Harold M. Swartz. Macrophages, metabolism, nitroxides, products in cells, Mammalian cells, 1 relationship of chemical and physical properties of nitroxides to rate of. Investigating Resins for Solid Phase Organic Synthesis: The Relationship between Swelling Newer aspects of the synthesis and chemistry of nitroxide spin labels Chemical Biology of Hydropersulfides and Related Species: Possible Roles in Intermediate Radical in the Initial Stage of the Graft Polymerization Reaction.
Care is taken to maintain the cysteine mutant under reducing conditions until it is modified with MTSL. The apparatus used to label the protein is shown in Figure 2, and consists of a conical tube and desalting column. Schematic of the apparatus used to label proteins with MTSL Buffer exchange the 15N-labeled cysteine mutant into labeling buffer that has been supplemented with fresh 2.
The final volume of the diluted protein solution should be 1 ml. The protein should be diluted with labeling buffer that does not contain DTT. From this step forward, all buffers used in this procedure should not contain DTT. Construct the MTSL solution that will be used to label the protein. Add MTSL from the stock solution to the conical tube. The amount added should be sufficient to achieve a final concentration of MTSL that is 10x the molar amount of protein that will be labeled e.
Make sure to shield all MTSL solutions from light by covering the tube with foil first.
Construct the apparatus that will be used to label the protein Figure 2. Place the equilibrated desalting column into the conical tube from step C5. The column will rest above the MTSL-containing solution and will leave room for the protein solution to flow through. The protein will flow through the column and into the labeling solution, while DTT present in the protein solution will remain on the column.
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The process is considered complete after the elution of all the protein solution into the MTSL solution at the bottom of the collection tube. Discard the desalting column. Cover the conical tube containing the modification reaction with foil and let it incubate under agitation for 15 min at room temperature. After 15 min, add additional MTSL from the stock solution to the modification reaction. Place tube back onto a rotating device and let the protein: If biochemical assays are available for the protein, they should be performed on labeled protein to verify that MTSL attachment does not impair its function.
Place the sample in a standard NMR tube and shield from light using foil. Typically, the 1H and 15N dimensions are defined by 2, and complex points, respectively. At this time, the sample is in its paramagnetic state. Its spectrum should be well dispersed, indicating that the modified protein is folded and not aggregating. Make a stock solution of mM sodium ascorbate by dissolving it in NMR buffer.
Using a long pipette that fits into the NMR tube, add sodium ascorbate to a final concentration that is 5x greater than the concentration of the labeled protein. This step should be performed carefully, by pipetting the solution up and down slowly so as to mix the solution, while preventing any sample loss. Let the sample reduce for a minimum of 3 h at room temperature no agitation is needed. Both the paramagnetic and diamagnetic datasets should be processed identically.
Analyze the NMR spectra using standard software e. The diamagnetic spectrum should be analyzed first, as it is most closely related to the previously assigned spectrum of the native protein. Assign the cross-peaks in the diamagnetic spectrum using the known chemical shifts of the native protein.
This can readily be accomplished by overlaying the [1HN]-HSQC spectra of the native and labeled proteins, and then transferring the chemical shift assignments. The cross peaks in the spectra should overlay well, with only localized differences occurring for cross peaks that originate from residues that are located near the attached probe. Considerable care must be taken to make sure that the assignments are correctly assigned. Measure the intensities of the cross peaks in the assigned spectrum of the diamagnetic protein.
Care should be taken to make sure that the cross peaks that are analyzed are well resolved see Note 8.
Nitroxide Labeling of Proteins and the Determination of
In our experience, measuring peak height is sufficient for extracting distance restraints. However, measuring cross peak volumes is also acceptable. It is critical to extensively check the sequence-specific chemical shift assignments of the diamagnetic spectrum.
Generate a list of cross peak intensities using the analysis software. Label the cross peaks in the paramagnetic spectrum using the curated chemical shift list that was used to analyze the diamagnetic spectrum. Using the procedures outlined in Data analysis A3, measure the peak intensities of isolated cross peaks in the paramagnetic spectrum. If a cross-peak in the paramagnetic spectrum is significantly broadened such that its intensity is near the noise level e.
Therefore, these cross peaks should not be employed to quantitatively relate the NMR data to inter-atomic distances, and intensities from these cross peaks should not be analyzed further. However, the identity of residues exhibiting significant line broadening in the paramagnetic spectrum should be noted. Use the software to generate a list of cross peak intensities using the analysis software.
A sample table depicting a list of cross peak intensities is shown in Table 1. Sample list of peak intensities and ratiosa aNote: Calculate the intensity ratios using standard analysis software e. Import both the diamagnetic and paramagnetic intensity lists generated from Data analysis A3 and A4 into a single spreadsheet. For each residue, use the cross peak intensity data to calculate the ratio of its intensity in the paramagnetic Iox and diamagnetic Ired states. A representative plot of the intensity ratios versus protein sequence is shown in Figure 1D.
Three contributions to the overall dynamics can be distinguished: The spectra represent a superposition of all three dynamic processes.
Nitroxide Spin Labels: Reactions in Biology and Chemistry
These can arise from e. Spectral characteristics can also be assigned to different types of secondary structure elements. When exposed to paramagnetic quenchers like molecular oxygen or water soluble nickel complexes e. In contrast, polar quenchers like Ni-EDDA complexes will only interact with parts of the target molecule that are exposed to the solvent.
Via SDSL, subsequent labeling and thus mapping of the local polarity of e. EPR does not only allow to determine a mean distance, but gives access to a fully quantitative distance distribution representing the complete conformational ensemble.
The obtained distance distributions are quantitatively derived without the need for assumptions. Intermolecular distances can be measured between singly spin labeled proteins for analyzing supramolecular aspects such as oligomerization, formation of fibrils or complex formation.
SDSL of a protein at two sites can be used to determine intramolecular distance constraints for protein structure determination Fig.
As different secondary structures will lead to a predictable change in the spin—spin distance, for instance folding and unfolding processes can be observed. FRET allows single molecule detection, however, precise distances or distance distributions are usually not measured, and the FRET pairs have to be carefully selected based on expected distances.
EPR distance measurements, on the other hand, allow for precise determination of distance constraints, distance distributions and their shape over a wide range of distances. Spin labels are significantly smaller than typical fluorophores, and have been shown to not perturb the structure of proteins in various cases.
For EPR distance measurements, the sample is usually shock-frozen in liquid nitrogen and the subsequent measurements are carried out at cryogenic temperature. By shock-freezing, a snapshot of the complete conformational ensemble in solution-like environment is generated. Low temperatures facilitate distance measurements, as they result in reduced spin-relaxation and slow down the reorientation of the spin—spin vector between the labels, which deteriorates the signal.
Current developments aim for measurements at physiological temperatures using either nitroxides 23—25 or triarylmethyl trityl or TAM spin labels. Suitable methods have to be chosen carefully depending on the occurring distances and the choice of spin labels as each method has limiting factors.
For distances smaller than approximately 1. For distances larger than 2. Data analysis after removal of the background leads to the desired distance distributions. A key advantage of DEER measurements is that they can be carried out virtually background-free even in complex environments as encountered e.
Site directed spin labeling A variety of protein classes, such as flavoproteins and photosystems, are intrinsically paramagnetic and can thus be directly monitored via EPR techniques. The two central aspects of SDSL are the chemical and spectroscopic properties of the spin label itself, and the strategy used for its introduction into the protein under study. A large number of requirements apply to both aspects, and currently there is no general strategy that satisfactorily fulfills all of them.
This makes it necessary to customize the SDSL strategy to the specific demands of the envisaged experiment. This contributes to the overall dynamics of the paramagnetic center, which complicates the analysis of protein dynamics.How to Integrate Biology with Chemistry & Physics
A second important property of spin labels is the chemical stability of the label itself and of the linker, most importantly in the context of reducing and biological environments such as the cytoplasm of living cells. Therefore, nitroxide radicals that are typically prone to e. However, larger spin labels expectedly have an increased potential to perturb the structure of the labeled protein. Spin labels based on chelated metal cations feature a high stability, but are often both bulky and charged.
For example, peptide synthesis Fig. Ligation of peptides to expressed proteins Fig. A Solid phase peptide synthesis. C Conjugation reactions with canonical amino acids. D Chelation by genetically encoded peptide tags.