Protein radius

If it is assumed that the final effective charge at the macroion surface of a polypeptide or protein can be represented by Zq, where Z is the magnitude of the charge, q is the sign of the charge, r is the protein radius [calculated71 from the relationship r = (0.81 Mr1/3), then... 

A for = 10 s. For our typical protein solution, the protein radius r = 2S A and the mean interprotein distance is 100 A, much less than X and d << X. This is the argument for regarding all the solvent half-way to the neighboring protein molecules as being influenced by the motion of a single protein the screening due to this kinematic viscosity is not important except for extremely dilute solutions. 

All simulations were run on a 1,000 X 1,000-grid mesh with a grid spacing of 7 nm, approximately a protein radius. Periodic boundary... 

Where r = the protein radius. The cones and cylinders are of radius and the crevices of width 2R An arbitrary assignment of the distribution of these pores, k = 9g, K = 9g and k = 3g, leads to the simplified equation describing the contribution of all pore types to elution volume ... 

Rigid, unsolvated spheres. Stokes law, Eq. (9.5), provides a relationship between f and the radius of the particle. Since this structure is a reasonable model for some protein molecules, experimental D values can be interpreted, via f, to yield values of R for such systems. Note that this application can also yield a value for M, since M = N pj [(4/3)ttR ], where pj is the density of the unsolvated material. 

Since f is a measurable quantity for, say, a protein, and since the latter can be considered to fail into category (3) in general, the friction factor provides some information regarding the eilipticity and/or solvation of the molecule. In the following discussion we attach the subscript 0 to both the friction factor and the associated radius of a nonsolvated spherical particle and use f and R without subscripts to signify these quantities in the general case. Because of Stokes law, we write... 

The elution volume, F/, and therefore the partition coefficient, is a function of the size of solute molecule, ie, hydrodynamic radius, and the porosity characteristics of the size-exclusion media. A protein of higher molecular weight is not necessarily larger than one of lower molecular weight. The hydrodynamic radii can be similar, as shown in Table 4 for ovalbumin and a-lactalbumin. The molecular weights of these proteins differ by 317% their radii differ by only 121% (53). 

The use of QM-MD as opposed to QM-MM minimization techniques is computationally intensive and thus precluded the use of an ab initio or density functional method for the quantum region. This study was performed with an AMi Hamiltonian, and the first step of the dephosphorylation reaction was studied (see Fig. 4). Because of the important role that phosphorus has in biological systems [62], phosphatase reactions have been studied extensively [63]. From experimental data it is believed that Cys-i2 and Asp-i29 residues are involved in the first step of the dephosphorylation reaction of BPTP [64,65]. Alaliambra et al. [30] included the side chains of the phosphorylated tyrosine, Cys-i2, and Asp-i 29 in the quantum region, with link atoms used at the quantum/classical boundaries. In this study the protein was not truncated and was surrounded with a 24 A radius sphere of water molecules. Stochastic boundary methods were applied [66]. 

Shifts in the SEC fractionation range are not new. It has been known for decades that adding chaotropes to mobile phases causes proteins to elute as if they were much larger molecules. Sodium dodecyl sulfate (SDS) (9) and guanidinium hydrochloride (Gd.HCl) (9-12) have been used for this purpose. It has not been clearly determined in every case if these shifts reflect effects of the chaotropes on the solutes or on the stationary phase. Proteins are denatured by chaotropes the loss of tertiary structure increases their hydrodynamic radius. However, a similar shift in elution times has been observed with SEC of peptides in 0.1% trifluoroacetic acid (TEA) (13-15) or 0.1 M formic acid (16), even if they were too small to have significant tertiary structure. Speculation as to the cause involved solvation effects that decreased the effective pore size of the... 

One general benefit of subunit association is a favorable reduction of the protein s surface-to-volume ratio. The surface-to-volume ratio becomes smaller as the radius of any particle or object becomes larger. (This is because surface area is a function of the radius squared and volume is a function of the radius cubed.) Because interactions within the protein usually tend to stabilize the protein energetically and because the interaction of the protein surface with... 

The length of monomer unit of MA is taken to be 0.25 nm [71]. The length of the polymer chain equal to the turn or the diameter of the protein globule is calculated taking into account the hydrodynamic size of the protein molecule via Stockes radius (Rsl). 

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