Soluble protein simulations

GPCR interactions with ligand and G protein are represented by the ternary complex formalism (Fig. 2A Christopoulos and Kenakin, 2002 De Lean et al, 1980 Sam am a et al, 1993). The quantitative analysis of the soluble assembly system formally requires inclusion of soluble G protein due to the use of a crude receptor preparation. These soluble G proteins compete with the G protein attached to the G-beads for the solubilized receptor as shown in Fig. 2C (Simons et al, 2003, 2004). Experimental values from G-beads (Fig. 3) were fitted with the calculations of bead-bound receptors (RG k..i< + ARG k. i< ) based on this model, which includes soluble G proteins. Simulations were made by Mathematica , numerically solving the series of... 

The simple and structured model simulations for yeast mass and soluble protein, peptides and carbohydrates are compared in Figure 6 for the yeast and enzyme concentration shown in Figures 3 and 4, and in Figure 7 for a concentrated yeast cell slurry. The simple model fits the data fairly well at both yeast concentrations, in every variable except the peptides. The fit for all variables at longer reaction times is directly related to use of the extent-of-reaction term Y , in the yeast lysis equation. 

The correlation of the dynamical transition of soluble proteins and changes in properties of the hydration shell is clear from a growing body of experimental and theoretical data, although the details of the physical mechanism for the connection vary considerably from account to account. Below we will discuss a microscopic mechanism, which we have developed based on our simulation studies, for the triggering of the protein dynamical transition by changes in the dynamics of... 

Wood K, Frolich A, Paciaroni A, Moulin M, Hartlein M, Zaccai G, Tobias DJ, Weik M Coincidence of dynamical transitions in a soluble protein and its hydration-water Direct measurements by neutron scattering and MD simulations. J. Am. Chem. Soc. 2008, 130 4586 587. 

The setup of a simulation system, which includes a protein embedded into a lipid bilayer requires additional efforts in comparison to a system with a soluble protein. There are different choices the researcher has to make regarding to the nature of the phospholipid bilayer used, the temperature at which the simulations should be performed (this also depends on the nature of the bilayer), the force field, the water model (e.g. SPC, SPC/E, TIP3P, TIP4P, TIP5P this also depends on the choice of the force field), and many more. 

Soluble tyrosinase (sTr) itself crystallizes with a caddie protein, ORF378 (the green ribbon in Fig. 26), which was removed in the LFMD simulations. As also shown in Fig. 26, this does not have a significant effect on the protein backbone. However, the absence of ORF378 in the simulations leads to some significant local variations in the active site structure. 

Fig. 3. Experimental dose-response data on G-beads from previous work (Simons et al, 2003, 2004) fitted to simulations of the ternary complex model including soluble G protein (Fig. 1C). The inclusion of soluble G protein in the model (Fig. 1C) is required due to the presence of extra G protein from the solubilized receptors and without which resulted in simulations that overestimated bead-bound receptors. Note that the same equilibrium dissociation constant values were used for the interactions with G protein on bead as with soluble G protein (Gtotbead and Gtots0l). Although the individual kinetic reaction rate constants for the interactions with soluble G protein might be faster than those for the bead-bound G protein, their ratios (the equilibrium dissociation constants) are expected to remain the same. The calibrated GFP per bead as...

Simulations of ternary complex model were performed with total receptor concentration of 30 nM, soluble G protein concentration of 100 nM for /LAR or 200 nM for FPR, and bead-bound G protein concentration of 0.6 nM per experimental conditions. Values for Aa were fixed from previously experimental values see receptor affinity in Table I (Simons et al, 2003, 2004). Best fits for all partial and full agonists were achieved with the value of Kg fixed at 5 x 10-6 M (log Kg = —5.3), which resulted in insignificant amount of precoupled receptor (RG) in the absence of ligand. 

Let us compare the kinetics of the selective-solvent-induced collapse of protein-like copolymers with the collapse of random and random-block copolymers [18]. Several kinetic criteria were examined using Langevin molecular dynamics simulations. There are some general results, which seem to be independent of the nature of interactions or the kinetic criteria monitored during the collapse. Here, we restrict our analysis to the evolution of the characteristic ratio f = (Rgp/Rg ) that combines the partial mean-square radii of gyration calculated separately for hydrophobic and hydrophilic beads, k2n and Rg . This ratio takes into account both the properties of compactness and solubility for a heteropolymer globule [70] (compactness is directly related to the mean size of the hydrophobic core, whereas solubility should be dependent on the size of the hydrophilic shell). 

The main conclusion drawn from the simulations [170] is that in the presence of monovalent counterions, the charged protein-like copolymers can be soluble, even in a very poor solvent for hydrophobic units. There are three temperature regimes, which are characterized by different spatial organization of polyions and their conformational behavior. 

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