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Theoretically, the difference can be obtained by directly subtracting the two spectra and then reading the residual peaks. The analysis of perturbation spectra is usually focused on the difference between the perturbed (called test) and the non-perturbed (called reference) spectrum. Lately, chemical shift perturbation has also been used in the study of protein-protein docking ( McCoy and Wyss, 2000 Morelli et al., 2001, Fahmy and Wagner, 2002 Dominguez et al., 2003 Clore and Schwieters, 2003). This idea has been elaborated as the SAR by NMR method for screening and designing high-affinity ligands ( Shuker et al., 1996 Hajduk et al., 1997). Among the many possible techniques, 2D HSQC of 15N-labeled proteins ( Bodenhausen et al., 1980 Bax et al., 1990) has long been used in the studies of protein-ligand binding events because of its high sensitivity to ligand interaction over a wide affinity range, and its ability to provide residue-specific information that helps map the binding site(s) on the protein.

The underlying rationale is that if the system under study has been changed chemically or physically, the NMR peaks may change their location, line shape, or disappear due to changed local chemical environment (see reviews by Otting, 1993 Pellecchia et al., 2000 Zuiderweg, 2002 and references therein).

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These algorithms have been implemented in a new software module, FELIX-Autoscreen, for streamlined processing, analysis and visualization of SAR by NMR and other high-throughput receptor/ligand interaction experiments.Ĭhemical shift perturbation spectra are very commonly used to probe the structural and functional changes of a molecule after a certain chemical or physical event, such as chemical reactions, solvation, complexation, mutation, or binding to another molecule. Simulated spectra with low signal-to-noise ratios (S/N ranged from 20 to 1) were used to demonstrate the reliability and reproducibility of the results when dealing with poor quality spectra. Using the 1H- 15N HSQC spectra from a titration experiment of the 74-residue Pex13p SH3 domain with a Pex14p peptide ligand (14 residues, K d = ~ 40µM), we demonstrate the scope and limits of our automatic peak tracing (APET) algorithm for efficient scoring of high-throughput SAR by NMR type HSQC spectra, and progressive peak tracing (PROPET) algorithm for detailed analysis of ligand titration spectra.

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The methods are primary aimed at the 1H- 15N HSQC spectra of relatively small proteins (<15 kDa) assuming fast exchange between free and ligand-bound states on the chemical shift time scale, or for comparing spectra of free and fully bound states in the slow exchange situation.

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The methods automatically trace the displacements of cross peaks between a perturbed test spectrum and the reference spectrum (or among a series of titration spectra), and measure the changes of chemical shifts, heights, and widths of the altered peaks. See link below.This paper presents new methods designed for quantitative analysis of chemical shift perturbation NMR spectra. The closer the electrons are to the H atoms the less the effect of the applied magnetic field-so the hydrogen atoms are more shielded.ĭata for H and C NMR below- source VCE Chemistry data book. The closer the signal is to TMS the closer the electrons are to the H atoms associated with the signal. If a nucleus in a specific chemical group is shielded to a higher degree then its NMR frequency will be shifted 'upfield' (that is, a lower chemical shift), whereas if it is less shielded then its NMR frequency will be shifted 'downfield' (that is, a higher chemical shift). This shift in the NMR frequency is called chemical shift. In general, this electronic shielding reduces the magnetic field at the nucleus (which is what determines the NMR frequency).Īs a result the energy gap is reduced, and the frequency required to achieve resonance is also reduced. The most important result of the NMR frequency for applications of NMR is the 'shielding' effect of the surrounding electrons.

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