Protein - solvent interaction

To date, a number of simulation studies have been performed on nucleic acids and proteins using both AMBER and CHARMM. A direct comparison of crystal simulations of bovine pancreatic trypsin inliibitor show that the two force fields behave similarly, although differences in solvent-protein interactions are evident [24]. Side-by-side tests have also been performed on a DNA duplex, showing both force fields to be in reasonable agreement with experiment although significant, and different, problems were evident in both cases [25]. It should be noted that as of the writing of this chapter revised versions of both the AMBER and CHARMM nucleic acid force fields had become available. Several simulations of membranes have been performed with the CHARMM force field for both saturated [26] and unsaturated [27] lipids. The availability of both protein and nucleic acid parameters in AMBER and CHARMM allows for protein-nucleic acid complexes to be studied with both force fields (see Chapter 20), whereas protein-lipid (see Chapter 21) and DNA-lipid simulations can also be performed with CHARMM. 

The simulation results presented in this section illustrate two essential features of the solvent and of solvent-protein interactions which influence protein dynamics. One is concerned with the spatial coupling (i.e., the degree of coupling between solvent and protein, which is related to solvent accessibility or some other measure of direct relatively short-range solvent-protein interactions), and the second is concerned with the time-scale coupling (i.e., the degree to which the motions of the solvent are commensurate with the temporal... 

A. Pullman I do not think that one should be too surprised at the fact that 4 interactions of the phosphate would add up to a AG value which can counterbalance the total AG due to solvent interaction, because the energies of each POO /NH3+ interaction are certainly very large compared to the individual AG s of the solvent-protein interaction which seem to involve less ionic hydrogen bonds. Moreover the number of the solvent-protein contacts which are realized is certainly not maximum, because all the potential sites are not exposed to the solvent. Thus the balance need not be as bad as you assume when you add up the AG s. 

It is sometimes argued that proteins fold in solvent, where the solvent serves as a heat bath. This would provide a fixed canonical temperature such that the canonical interpretation is sufficient to imderstand the transition. However, the solvent-protein interaction is actually implicitly contained in the heteropolymer model and, nonetheless, the microcanonical analysis reveals this effect which is simply lost by integrating out the energetic fluctuations in the canonical ensemble (see Fig. 9.14). 

The above analysis is simplified since we have not considered the interactions of the protein with the solution in which it sits yet it is essentially valid. However, in many cases the solvent-protein interactions form an important component in understanding the behavior of these systems we will have to wait until we learn about the thermodynamics of mixtures to address this more complicated case. 

Although the emphasis in these last chapters is certainly on the polymeric solute, the experimental methods described herein also measure the interactions of these solutes with various solvents. Such interactions include the hydration of proteins at one extreme and the exclusion of poor solvents from random coils at the other. In between, good solvents are imbibed into the polymer domain to various degrees to expand coil dimensions. Such quantities as the Flory-Huggins interaction parameter, the 0 temperature, and the coil expansion factor are among the ways such interactions are quantified in the following chapters. 

In addition to an array of experimental methods, we also consider a more diverse assortment of polymeric systems than has been true in other chapters. Besides synthetic polymer solutions, we also consider aqueous protein solutions. The former polymers are well represented by the random coil model the latter are approximated by rigid ellipsoids or spheres. For random coils changes in the goodness of the solvent affects coil dimensions. For aqueous proteins the solvent-solute interaction results in various degrees of hydration, which also changes the size of the molecules. Hence the methods we discuss are all potential sources of information about these interactions between polymers and their solvent environments. 

Proper condensed phase simulations require that the non-bond interactions between different portions of the system under study be properly balanced. In biomolecular simulations this balance must occur between the solvent-solvent (e.g., water-water), solvent-solute (e.g., water-protein), and solute-solute (e.g., protein intramolecular) interactions [18,21]. Having such a balance is essential for proper partitioning of molecules or parts of molecules in different environments. For example, if the solvent-solute interaction of a glutamine side chain were overestimated, there would be a tendency for the side chain to move into and interact with the solvent. The first step in obtaining this balance is the treatment of the solvent-solvent interactions. The majority of biomolecular simulations are performed using the TIP3P [81] and SPC/E [82] water models. 

An excluded-volume random-coil conformation will be achieved when the solvent quality exceeds the theta point, the temperature or denatu-rant concentration at which the solvent-monomer interactions exactly balance the monomer—monomer interactions that cause the polymer to collapse into a globule under more benign solvent conditions. A number of lines of small-angle scattering—based evidence are consistent with the suggestion that typical chemical or thermal denaturation conditions are good solvents (i.e., are beyond the theta point) and thus that chemically or thermally unfolded proteins adopt a near random-coil conformation. 

UCW = capped water, TW = tethered water (see text), k = force constant for restraining potential (kcal/mol/A2). b Radius (A) of solvation sphere. 1 Numbers of dynamical water molecules within solvation sphere. d Mean and standard error for the forward (i.e. 8-methyl-N5-deazapterin —> 8-methylpterin) and reverse mutation of the electrostatic force field Cutoff for protein-ligand and solvent-ligand interaction all other interactions are subject to a 9 A cutoff. 

Treatment with hot organic solvents was the next step in the tissue fractionation, to remove lipid-phosphorous and breakdown lipid-protein interactions. In the Schneider procedure, nucleic acids were then extracted in hot dilute trichloroacetic or perchloric acid, leaving a protein residue with any phosphoprotein links still intact. This method was to become particularly useful when 3H thymidine became the preferred label for DNA in the early 1960s. For investigations where both RNA and DNA were to be examined the Schmidt-Thannhauser process was often chosen. Here the lipid-extracted material was hydrolyzed with dilute sodium hydroxide releasing RNA nucleotides and any hydroxyamino acid bound phosphorus. DNA could be precipitated from the extract but the presence in the alkaline hydrolysate of the highly labeled phosphate released from phosphoprotein complicated... 

Strambini and Galley have used tryptophan anisotropy to measure the rotation of proteins in glassy solvents as a function of temperature. They found that the anisotropy of tryptophan phosphorescence reflected the size of globular proteins in glycerol buffer in the temperature range -90 to -70°C.(84 85) Tryptophan phosphorescence of erythrocyte ghosts depolarized discontinuously as a function of temperature. These authors interpreted the complex temperature dependence to indicate protein-protein interactions in the membrane. 

Cosolvent and temperature effects on various types of noncovalent forces involved in protein-protein interactions are now well documented. These effects have been intensively studied in Douzou s laboratory through their impact on protein fractionation (Douzou and Balny, 1978). Mixed solvents at carefully controlled concentration and temperature variations in the range of normal and subzero temperatures ap-... 

R. A. Marcus Even though solvents and solvent-solute interactions or interactions with a protein can be very complicated and the resulting motion can be highly anharmonic, under a particular condition there can be a great simplification because of the many coordinates (perhaps analogous to the central-limit theorem in probability theory). 

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