Hydrodynamic measurements

This experiment shows that folding of the non-helix or poor helix-forming sequence is encouraged in the triple helix too, even if this part of the helix contributes to a decrease of the folding strength. Sedimentation and hydrodynamic measurements clearly show the formation of a trimer aggregation and of an extended shape. 

Prieve, D. C. (1986) Hydrodynamic measurement of double-layer repulsion between colloidal particle and flat plate. Science, 231, 1269-1270. 

Before discussing details of their model and others, it is useful to review the two main techniques used to infer the characteristics of chain conformation in unordered polypeptides. One line of evidence came from hydrodynamic experiments—viscosity and sedimentation—from which a statistical end-to-end distance could be estimated and compared with values derived from calculations on polymer chain models (Flory, 1969). The second is based on spectroscopic experiments, in particular CD spectroscopy, from which information is obtained about the local chain conformation rather than global properties such as those derived from hydrodynamics. It is entirely possible for a polypeptide chain to adopt some particular local structure while retaining characteristics of random coils derived from hydrodynamic measurements this was pointed out by Krimm and Tiffany (1974). In support of their proposal, Tiffany and Krimm noted the following points ... 

According to gel-filtration experiments conducted by P. Wills and J. Dijk (personal communication), proteins L17, L25, L28, L29, and L30 are compact LI, L4, L5, L6, L13, L16, L19, and L24 are moderately elongated and L2, L3, L9, Lll, L15, L23, L27, L32, and L33 are quite extended. A discrepancy between these results and those mentioned earlier is protein L9 which appears to be globular from hydrodynamic measurements (Giri et al., 1979), but the Stokes radius calculated from gel-filtration experiments was found to be quite large, suggesting an elongated particle. 

Among these methods, hydrodynamic measurements of sedimentation coefficients and viscosity are classical [43,47]. The insertion of a true intercalator (ethidium bromide for example) between the stacking of bases produces... 

Interpretation of the hydrodynamic data of a macromolecule requires that the shape of the molecule in a given solvent be known in advance from other sources and that there exist adequate expressions to relate the hydrodynamic quantities under consideration to a few parameters characterizing the dimensions of the molecule. Thus, in general, hydrodynamic measurements are informative as a supplementary means for the characterization of macromolecules. 

Hydrodynamic boundary layer — is the region of fluid flow at or near a solid surface where the shear stresses are significantly different to those observed in bulk. The interaction between fluid and solid results in a retardation of the fluid flow which gives rise to a boundary layer of slower moving material. As the distance from the surface increases the fluid becomes less affected by these forces and the fluid velocity approaches the freestream velocity. The thickness of the boundary layer is commonly defined as the distance from the surface where the velocity is 99% of the freestream velocity. The hydrodynamic boundary layer is significant in electrochemical measurements whether the convection is forced or natural the effect of the size of the boundary layer has been studied using hydrodynamic measurements such as the rotating disk electrode [i] and - flow-cells [ii]. 

The titration curve can give no information on the subject of reversible conformational change in insulin because there is extensive pH-dependent association between insulin molecules. The absence of other conformational change is indicated by hydrodynamic measurements of Fredericq (1966). 

All alternative procedure is to calculate the radius of a sphere equivalent to the protein molecule from hydrodynamic measurements. The value of R obtained in this way is always larger than that calculated by Eq. (15), even for the native protein conformation, the reason being that protein molecules are in fact never perfectly spherical. The resulting values of w are roughly 20 % less than those obtained with a radius calculated by Eq. (15). 

As mentioned earlier, ideally the best answer should come from the determination of the 5-function. Unfortunately at present the rotary diffusion coefficient is usually the least reliable quantity in all hydrodynamic measurements because of errors inherent in the physical methods of flow birefringence and perhaps also non-Newtonian viscosity (see Section IV). (Electric birefringence also may not give the same rotary diffusion coefficient as the other two methods, since the equivalent ellipsoids can be different under shearing stress and under electrical field.) Edsall (1954) has also illustrated the impossibility of evaluating the axial ratio from the 5-function. The latter was about 0.80 for fibrinogen which corresponded to a prolate ellipsoid with an axial ratio of more than 300. If the rotary diffusion coefficient were only about 15% greater than that listed in Table V the calculated axial ratio would decrease to between ten and twenty. 

For their study Tanford et al. have chosen aqueous 6 M guanidine hydrochloride - -0.1 M mercaptoethanol (to rupture disulfide bonds and to prevent their formation by oxidation of tliiol groups) as denaturing solvent medium. As the initial and most critical test of random coil behaviour, hydrodynamic measurements were carried out on a number of proteins dissolved in the above-mendioned medium. 

The absorption spectrum studies presented above merely reflect the electronic environment of the molecule and do not give specific information about the type of interaction. The data which must be accounted for in considering a physical mode for the binding process can be derived from several different approaches. Hydrodynamic measurements on the DNA-drug complex are of interest, since Lerman42) has established that an increase in the intrinsic viscosity of DNA and a decrease in the sedimentation coefficient of the polymer are two criteria for intercalation of ring systems between base pairs of a double-helical DNA. 

One source of information, hydrodynamic measurements, has recently been reviewed by Squire and Himmel ( ) Their analysis suggests large amounts of water associated with globular proteins, but even their restricted data set shows large variations between the amount of hydration calculated from sedimentation or diffusion results. Because the cube of the friction factor enters into the... 

This Section outlines theories applicable to branched polymers. In the polysaccharide field, hydrodynamic measurements on branched materials are essentially limited to investigations on amylopectin, glycogen, and bacterial dextran, and, of these, only the dextran has been dealt with in detail. Consequently, the application of the theories to the measurements on dextran are considered here. 

Whether the flexibility of DNA per se is important in biological function is harder to assess. Nonetheless, hydrodynamic measurements have suggested that damage increases DNA flexibility, with implications for recognition and... 

First, the experimenter estimates the MW of the oligomer (hydrodynamic measurements, radiation inactivation) and the MW of the subunits (SDS gel electrophoresis of the purified oligomer). She then treats the oligomer with cross-linkers (e.g., from the bismuthate family)... 

The MW of the oligomer from cross-linking studies and from hydrodynamic measurements should be about the same. 

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