Model system, protein interactions

The solid-state and solution chemistry of triethanolamine complexes has been investigated. While the solid-state structure was maintained in organic solvent (38), a different structure was observed in aqueous solution.262 170 NMR spectroscopy was used to demonstrate that the two oxo groups were different and in combination with H and 13C NMR data, defined the structure as (39).262 Speciation studies and a detailed characterization of this class of compounds were important because the ligand is a commonly used buffer in biology and the complexes are model systems for interactions with proteins.61,263 The thermodynamic parameters were determined for several derivatized diethanolamine ligand-vanadium(V) complexes, and represent some of the few vanadium complexes for which such parameters are known.62 The structure of (nitrilotriacetato)dioxovanadate was reinvestigated.2 4... 

A few workers have attempted to separate lean meat into its individual protein fractions. Turner et al. (1979) fractionated meat into salt-soluble protein (SSP), insoluble myofibrillar protein (IMP), and connective tissue protein (CTP) by centrifugation. Fat was also separated. Using this technique to fractionate minced pork shoulder, Knight (1988) studied the influence of the SSP, IMP, and CTP fractions, and the effect of fat on cooking losses in model systems. The interactions between the three fractions were also examined. The composition of the individual fractions prepared is shown in Table 2.6. 

The first term represents the forces due to the electrostatic field, the second describes forces that occur at the boundary between solute and solvent regime due to the change of dielectric constant, and the third term describes ionic forces due to the tendency of the ions in solution to move into regions of lower dielectric. Applications of the so-called PBSD method on small model systems and for the interaction of a stretch of DNA with a protein model have been discussed recently ([Elcock et al. 1997]). This simulation technique guarantees equilibrated solvent at each state of the simulation and may therefore avoid some of the problems mentioned in the previous section. Due to the smaller number of particles, the method may also speed up simulations potentially. Still, to be able to simulate long time scale protein motion, the method might ideally be combined with non-equilibrium techniques to enforce conformational transitions. 

In this chapter, we review the interactions at the level of protein function, between opioid receptors and chemokine receptors, using both in vitro and in vivo model systems. As a part of this discussion, we also describe our current understanding of the biochemical pathway(s) that are involved in the heterologous desensitization process between these groups of receptors. 

Ioffe VM, Gorbenko GP, Tatarets AL, Patsenker LD, Terpechnig EA (2006) Examining protein-lipid interactions in model systems with a new squarylium fluorescent dye. J Fluoresc 16 547-554... 

The study was performed on a model system based on the crystal structure of Cdc42-Cdc42GAP complexed with GDP and A1F3 [60], which can be considered a TS mimic of phosphoryl transfer [61, 62], A large model system (Fig. 2.6) was required to properly take into account the effect on the reagents of the electrostatic field of the protein. It comprised all the amino acids directly interacting with the triphosphate moiety, the Mg2+ cation with its own coordination shell, and A1F3 replaced by the PO3 moiety. 

Glutathione readily replaces the GSMe on platinum in the reaction with [Pt(dien)(GSMe)]2+ (GSMe = S-methylglutathione) - this system is claimed to be an effective model for cisplatin-protein interaction 224). Rate constants and activation parameters have been... 

While these complex model heme proteins have a large potential for functionalization, an interesting approach that is very different has been taken by other workers in that the heme itself functions as the template in the formation of folded peptides. In these models peptide-peptide interactions are minimized and the driving force for folding appears to be the interactions between porphyrin and the hydrophobic faces of the amphiphiUc peptides. The amino acid sequences are too small to permit peptide-peptide contacts as they are separated by the tetrapyrrole residue. These peptide heme conjugates show well-re-solved NMR spectra and thus well-defined folds and the relationship between structure and function can probably be determined in great detail when functions have been demonstrated [22,23,77]. They are therefore important model systems that complement the more complex proteins described above. 

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