Protein/peptide analysis hydrophobic interaction

Other methods that are related to affinity chromatography include hydrophobic interaction chromatography and thiophilic adsorption. The former is based on the interactions of proteins, peptides, and nucleic acids with short nonpolar chains on a support. This was first described in 1972 [113,114] following work that examined the role of spacer arms on the nonspecific adsorption of affinity columns [114]. Thiophilic adsorption, also known as covalent or chemisorption chromatography, makes use of immobilized thiol groups for solute retention [115]. Applications of this method include the analysis of sulfhydryl-containing peptides or proteins and mercurated polynucleotides [116]. 

If both the analytes and the EOF move in the same direction, as with CIE, the system is classified as coelectroosmosis, and the analytes reach the detector faster than they would as a result of their own mobilities. If the analytes move in the opposite direction from the analytes, the system is classified as counterelectroosmosis, and the analytes reach the detector later than they would as a result of their own mobilities. If the EOF is suppressed by eliminating the effective charge on the capillary wall, then the analytes reach the detector solely as a result of their own mobility. The last approach is often taken for the analysis of large peptides and proteins, where ionic or hydrophobic interactions between the analyte and the capillary wall result in peak tailing or total adsorption. 

The findings gained with the model system show that two contrary effects characterize the interactions of fluorinated amino acids within the hydrophobic core spatial demand and hydrophobicity on one side, and fluorine-induced polarity on the other. While the increase in hydrophobic surface area upon fluorination may be favorable for hydrophobic interactions, fluorine s inductive effect appears to interfere with the formation of an intact hydrophobic core. In addition, the investigations of fluoroalkyl side-chains in the charged domain as well as the analysis of fluorine s effect on replicase activity indicate that contacts between fluorinated residues may also have an impact on peptide and protein folding. 

The use of silver nanoparticles has also been described in matrix-assisted laser desorption/ionization (MALDI), a powerful laser-based soft ionization technique for mass spectrometric analysis and the investigation of peptides, proteins, nucleic acids, pharmaceuticals, bacterial characterization and imaging studies. Here, liquid-liquid microextraction base-modified silver nanoparticles were employed for the extraction of a hydrophobic peptide (gramicidin) from biological samples through hydrophobic interactions, prior to MALDI analysis (Figure 4.1) [41]. The application of silver nanoparticles was shown to provide an excellent sample cleanup procedure, and also assisted in the enhancement of signal of peptides and proteins. 

Crystal structure analysis of the human MHC class II molecule HLA-DRl,complexed with a tridecapeptide from influenza virus, shows several interaction sites or pockets within the peptide-binding cleft of HLA-DR1, five of which accommodate hydrophobic side chains of the bound influenza virus peptide. Many of the residues forming these pockets are highly polymorphic. This polymorphism is thought to be responsible for the different peptide specificities of different class II proteins.There are 11 core residues of the influenza virus peptide interacting with the DR1 molecule [49]. 

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