Protein diffusion constants

Although SynChropak GPC supports have excellent efficiencies for small molecules at various flow rates, macromolecules, because of their low diffusion constants, exhibit band spreading when linear velocities are increased. This effect increases with molecular weight, as seen in Fig. 10.11 (4). It should be noted that proteins are usually homogeneous in size and thus yield better efficiencies than polymers, which are usually heterogeneous. For preliminary analy-... 

Protein lateral motion is much slower than that of lipids because proteins are larger than lipids. Also, some membrane proteins can diffuse freely through the membrane, whereas others are bound or anchored to other protein structures in the membrane. The diffusion constant for the membrane protein fibronectin is approximately 0.7 X 10 cmVsec, whereas that for rhodopsin is about 3 X 10 cmVsec. 

Various ligands bind to their protein sites in a diffusive motion. Similarly, the distance between different ends of a folded macromolecule changes in a way which can be described as a diffusive motion in the presence of a constraint potential (that keeps the parts of the molecule near their folded configurations). Brownian-type diffusive motion in the absence of a restrictive potential is characterized by a diffusion constant (Ref. 6)... 

Small molecules that act as collisional quenchers may penetrate into the internal structure of proteins, diffuse, and cause quenching upon collision with the aromatic groups. Lakowicz and Weber(53) have shown that the interaction of oxygen molecules with buried tryptophan residues in proteins leads to quenching with unexpectedly high rate constants—from 2 x 109 to 7 x 109 M l s 1. Acrylamide is also capable of quenching the fluorescence of buried tryptophan residues, as was shown for aldolase and ribonuclease 7V(54) A more hydrophobic quencher, trichloroethanol, is a considerably more efficient quencher of internal chromophore groups in proteins.(55)... 

Based on the magnitude of diffusion constants for globular (i.e., spherical) protein molecules, one can estimate that proteins like hemoglobin (mass = 68 kDa diffusivity = 6.2 m /s X 10 ) can readily diffuse 20-30 micrometers within 10-20 seconds. By contrast, low-molecular-weight metabolites, such as glycine (mass = 75 diffusivity = 95 m /s X 10 ) and arginine (mass = 174 diffusivity = 58 m /s X 10 ), will rapidly traverse these distances in a few seconds or less. 

At the present time, the rates of lateral diffusion of phospholipids and membrane proteins in the solid phase of pure phospholipids is not known. It is hoped that such diffusion constants can be obtained by one of the transient methods mentioned earlier. It is likely that these diffusion rates will be found to be quite low. 

For most proteins vp is about 0.75 ml/g, so its value does not present much of a problem. The frictional coefficient, however, is a sensitive function of the shape, varying over a wide range, and we must usually know its value if we need a serious estimate of the molecular weight. The value of/is usually found by working with the diffusion constant D, which is related to the frictional constant by... 

The diffusion constant D is a function of both molecular weight and shape. It can be measured by observing the spread of an initially sharp boundary between the protein solution and a solvent as the protein diffuses into the solvent layer. Once we know the value of the diffusion constant, we can combine the information with the sedimentation data and calculate the molecular weight of the protein. 

The kinematic viscosity considered in the simulations was that of water. Here, as diffusion constant D a value of 10 10 m2 s, a typical value for diffusion of small proteins in aqueous solutions, was taken. 

We have determined the fluorescence polarization P and the bimolecular diffusion constant fcq of oxygen of the unique Trp residue of a protein at three temperatures, 5, 20, and 30°C, and at two hydrostatic pressures (0-4 kbar), and obtained the following results ... 

The temporal evolution of the species grating component is determined by the chemical reaction and protein diffusion processes. When there is no chemical reaction in the detection time window, and the molecular diffusion coefficient (D) is time-independent, the temporal profile of the species grating signal can be calculated by the molecular diffusion equation. The Fourier component at a wavenumber of q of the concentration profile decays with a rate constant Dq2 for both the reactant and the product. Hence, the time development of the TG signal can be expressed by [15-19,23]... 

The molecular weight of cytochrome c peroxidase has been determined to be 34,100 on the basis of a sedimentation constant of 3.55 S, a diffusion constant of 9.44 F, and a partial specific volume of 0.733 ml/g (4 )-The enzyme exists as a monodisperse monomer containing one ferric protoporphyrin IX, which is noncovalently bound (/, , 14). No other transition metal is detected in crystalline preparations of the enzyme (22). The apoenzyme moiety is an acidic protein with an isoelectric point at pH... 

Polnaszek and Bryant (1984a,b) measured the frequency dependence of water proton relaxation for solutions of bovine serum albumin reacted with a nitroxide spin label (4.6 mol of nitroxide per mol of protein). The relaxation is dominated by interaction between water and the paramagnetic spin label. The data were best fit with a translational diffusion model, with the diffusion constant for the surface water in the immediate vicinity of the nitroxide being five times smaller than that for... 

The effective viscosity of the solvent at the protein surface is likely greater than the bulk solvent viscosity. The diffusion constant of water at the protein surface is five times smaller than the bulk water value (Polnaszek and Bryant, 1984a). This effect probably can be neglected in experiments such as those discussed in the previous paragraphs, which cover several orders of magnitude in solvent viscosity. 

Measurements of the dynamic properties of the surface water, particularly NMR measurements, have shown that the characteristic time of the water motion is slower than the bulk water value by a factor of less than 100. The motion is anisotropic. There is litde or no irrotadonally bound water. Study of a protein labeled covalently with a nitroxide spin probe (Polnaszek and Bryant, 1984a,b) has shown that the diffusion constant of the surface water is about 5-fold below the bulk water value. The NMR results are in agreement with measurements of dielectric relaxation of water in protein powders (Harvey and Hoekstra, 1972). 

Subsequently, they studied a periodically repeated volume containing the ubiquitin molecule as well as 4908, 9133, 13 200, or 29 182 water molecules. Again, the linear dependence of the translational diffusion constant of the protein on was... 

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