Peptide interaction profilling

Pearce KH, larmone MA, Simmons CA, et al. Discovery of novel nuclear receptor modulating ligands an integral role for peptide interaction profiling. Drug Discov Today 2004 9 741-51. 

Another interesting methodological approach represents the use of NMR data to characterize and optimize the production of bicelles to study protein structure in lipid environments without the need for isotopic enrichment for solution NMR and to follow lipid-peptide interactions, as described by Al-Soufi et al and Yamamoto et al As an example, Morrison and Henzler-Wildman described a reconstitution protocol for the small multidrug resistance transporter, EmrE, which is highly sensitive to its environment, into isotropic bicelles with improved sample stability and expanded lipid composition profile. Furthermore, Lyukmanova et u/. characterized lipid-protein nanodiscs for cell-free production of integral membrane proteins in a soluble and folded state and compared their properties with detergent micelles, bicelles and liposomes. 

This cyclic interaction profile is considered for other types of myosin that determine the pwasons direction along the actin filament [38-40]. A similar mechanism based on proton-induced water solitons is suggested for ATP hydrolysis by dynein or kinesin along microtubules, or by G-actin polymerization [41], as well as for other substrates of various hydrolytic enzymes. Thus, a hydraulic drive due to AS is proposed to translocate the ATPase machinery of DNA replication, RNA transcription, or peptide translation. These processes can be effectively associated with active flow of substrates and products across the catalytic regions. 

Frequency-selective REDOR (fsREDOR) is a very powerful technique developed for the study of 13C and 15N uniformly labeled peptides or proteins [92]. The basic idea of this technique is to combine REDOR and soft n pulses to recouple a selected 13C-15N dipole-dipole interaction in a multiple-spin system. Usually one could use Gaussian shaped pulses to achieve the required selective n inversions. Other band selective shaped pulses have been developed for a more uniform excitation profile [93]. In its original implementation, fsREDOR was used to extract the intemuclear distances of several model crystalline compounds [92], In the past few years, this technique has proven to be very useful for the study of amyloid fibrils as well. For the Ure2p10 39 fibril samples containing 13C and 15N uniformly... 

The selection considerations for appropriate p7 markers for cIEF with proteins/anti bodies included purity and stability of the p7 markers, p7 values of the protein analytes, and potential protein—p7 marker interactions. High purity, stable p7 markers that give reliable p7 values with no protein—p7 marker interaction are desirable. Table 6 lists sets of p7 markers used for optimization. The antibody of interest had a p7 range of approximately 6.3 to 7.0. In this case, six different vendor sources were evaluated. These p7 markers vary in nature, from proteins and peptides to small molecules. The e-grams obtained using these markers with the antibody of interest are shown in Figure 22. Although the nature of the p7 markers and exact p7 marker values were different, the cIFF profiles of the antibody were the same. 

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