Protein diffusion

Saridakis, E. and Chayen, N. E. (2000). Improving protein crystal quality by decoupling nucleation and growth in vapor diffusion. Protein Sci. 9, 755-757. 

The biologic hypothesis. In 1971, Folkman published a landmark paper noting that "the blood vessels in a tumor were new—the tumor had to recruit them. It recruited the vessels by sending out some factor that was diffusible these diffusible proteins would bring in the vessels, and if you could turn this process off the tumors should stay small."... 

For the small, rapidly diffusing K+ ion, we expect 100 000 plates. For the slowly diffusing protein serum albumin (FM 65 000), we expect more than 3 million plates. High plate count means that bands are very narrow and resolution between adjacent bands is excellent. 

The interaction potentials between beads were adopted from Refs. [77,78], and are briefly described below for the sake of completeness. The intramolecular potential energy of the freely diffusing protein is given by... 

With a few exceptions, cupredoxins are freely diffusible proteins. They accept and donate a single electron to their redox partners during which process the protein-bound copper oscillates between Cu(II) and Cu(I). The cupredoxin and its redox partners form a transient complex that will dissociate upon a successful electron transfer act. Therefore, the protein-protein interactions between a diffusible cupredoxin and its redox partner may not be as specific as one might expect. Indeed, the binding... 

The Brownian Dynamics (BD) simulation technique can be used to simulate the diffusion and the association of molecules in solution. BD simulations have been widely used to simulate protein-small molecule and protein-protein association (62). This method may be exploited to simulate the hrst step of molecular recognition when two molecules diffuse from a distance. From such simulations, it is possible to compute the structure and the diffusional encounter complex ensemble and to calculate the bimolecular association rate constant for two diffusing proteins or enzymes and their substrates or inhibitors. In these calculations, the effects of mutations and variations in ionic strength, pH, and viscosity can be investigated (63). 

Adhesion of different immune cells to one another or to epithelial cells has also been studied using planar bilayer models. For example, lymphocyte function-associated protein-1 (LFA-1) promotes cell adhesion in inflammation [i.e., a reaction that can be mimicked by binding to purified ICAM-1 in supported membranes (70)]. Similarly, purified LFA-3 reconstituted into supported bilayers mediates efficient CD2-dependent adhesion and differentiation of lymphoblasts (71). This work was followed by a study in which transmembrane domain-anchored and GPl-anchored isoforms of LFA-3 were compared (72). Because this research occurred before the introduction of polymer cushions and because the bilayers were formed by the simple vesicle fusion technique, the transmembrane domain isoform was immobile, whereas the GPl isoform was partially mobile. By comparing results with these two isoforms at different protein densities in the supported bilayer, the authors showed that diffusible proteins at a sufficient minimal density in the supported membrane were required to form strong cell adhesion contacts in this system. 

A. The transport molecule will become a facilitated diffusion protein. 

In all procedures, the last step is followed by washing with physiologcal saline. Diffusible proteins can also be removed prior to fixation by washing the tissue pieces extensively in PBS at 4°C. 

Other AR mediators, such as divalent ion chelators, formaldehyde scavenges, such as citraconic anhydride, metal ions, or proteolytic enzymes can enhance AR in certain cases however, their applications are not universal and, in some cases, may even inhibit immunostaining. As noted above, the removal of steric barriers that restrict access of the antibody to its target epitope is a key component of aR." In this context, heating may serve to promote the extraction of diffusible proteins out of the tissue sections following cross-link reversal or proteolytic treatment, opening physical holes or channels in the tissue sections that allow better penetration of antibodies. The physical process of opening holes or channels within the tissue section also likely explains the modest success of ultrasonics as an AR method. ... 

For analytical purposes or for difficult separations where maximum resolution is required, a sample volume of 1-5% of the packing volume is recommended. Smaller volumes do not necessarily Improve resolution. Theoretically the maximum volume in SEC can be as large as the separation volume between two proteins. However, because of microturbulence, non-equlllbrlum between the stationary phase and mobile phase, and longitudinal diffusion, protein bands are always broadened. Sample volumes must therefore be smaller than the actual separation volume. 

EXAMPLE 18.5 A diffusing protein. Let s compute the dynamic properties of a small spherical protein having a radius a = 20 A = 2 nm, in water, which has a viscosity/y = 10 kgm" s According to Stokes s law Equation (18.50), this particle will have a friction coefficient... 

Unfolding Dynamics), This reduced representation of a protein, coupled with Brownian dynamics, can be used to study long time-scale processes such as helix-coil transitions. A general form for an energy expression representing this multisphere diffusing protein... 

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