Movement proteins

Taylor, A. E., and Drake, R. E. (1978). Fluid and protein movement across the pulmonary microcirculation. In Lung Water and Solute Exchange (N. C. Staiib, Ed.), pp, 129-166. Marcel Dekker, New York. 

The discovery of Green Fluorescent Protein (GFP) and the development of technology that allows specific proteins to be tagged with GFP has fundamentally altered the types of question that can be asked using cell biological methods. It is now possible not only to study where a protein is within a cell, but also feasible to study the precise dynamics of protein movement within living cells. We have exploited these technical developments and applied them to the study of translation initiation factors in yeast, focusing particularly on the... 

The potential of live cell imaging to address mechanisms of cellular biology is ever expanding. Directed protein-tagging techniques have been used to visualize nascent versus mature protein in vivo (Rodriguez et al., 2006). This technique involves the use of arsenic-based dyes, such as FiAsH or ReAsH, which bind to tetracysteine (TC) tags (Zhang et al, 2002). In addition, photo-activatable variants of GFP have been shown to determine the kinetics of protein movement in live cells (Patterson and Lippincott-Schwarz, 2002). Furthermore, techniques such as FRET and the... 

Suhre, K. and Sanejouand, Y. H. (2004b) ElNemo a normal mode web server for protein movement analysis and the generation of templates for molecular replacement. Nucleic Acids Res. 32, W610-614. 

The retardation of the protein movement has been discussed qualitatively in terms of a sieving mechanism rather than a frictional resistance37). Ogston et al.39) have theoretically described the diffusion as a stochastic process in which the particles move by unit displacements and in which the decrease in the rate of diffusion in a polymer network depends on the probability that a particle finds a hole in the network into which it can move. The relationship derived from this approach is in close agreement with Eq. (35). 

FIGURE 3-19 Electrophoresis, (a) Different samples are loaded in wells or depressions at the top of the polyacrylamide gel. The proteins move into the gel when an electric field is applied. The gel minimizes convection currents caused by small temperature gradients, as well as protein movements other than those induced by the electric field, (b) Proteins can be visualized after electrophoresis by treating the gel with a stain such as Coomassie blue, which binds to the proteins blit not to the gel itself. Each band on the gel represents a different pro-... 

Figure 2 Photoconversion of 11 -cis to all trans rhodopsin and associated protein movement. (Borhan B, Souto Ml, Imai H, Shichida Y, Nakanishi K. Science 2000 288 2209-2212).

Relative mobility (protein movement relative to ion front)... 

Proteins in the dry state are frozen. They only open up and start moving if some water is added, as in nature. It turns out that protein movements in, e.g., lysozyme are activated only when there is 0.15 g of water per gram of protein, a good example of the effect of hydration on living processes. However, it is difficult to examine protein dynamics in solution because to make a satisfactory interpretation of the observations, one would have first to do the corresponding spectroscopy in the dry state this is difficult because of the frozen state referred to and a tendency to decompose. 

The stochastic nature can be understood by certain energy barriers that must be overcome before a channel can flip from one conformation (e.g., open) to another (e.g., closed). The energy needed for this purpose comes from the random thermal energy of the system. One can imagine that each time the channel molecule vibrates, bends or stretches, it has a chance to surmount the energy barrier. Each motion is like a binomial trial with a certain probability of success. Clearly, because the protein movements are on a picosecond time scale, but the channel stays open for milliseconds, the chance of success at each trial must be small, and many trials will be needed before the channel shuts. Usually, a normal Na+ channel does not reopen even though the depolarization may be pertained by the... 

Two-photon microscopy can be utilized to quantify microvascular flow rates within the kidney. Infusion of a nonfilterable intravenous fluorescent dye results in intravascular cells appearing as dark objects. Endothelial cell dysfunction within the microvasculature can be observed and quantified using the infusion of variously sized, differently colored dextrans or proteins. Movement of these molecules out of the microvasculature and accumulation within the interstitial compartment are readily observed during injury or disease. 

This experiment demonstrates that membranes are fluid and that proteins can move freely within the lipid bilayer. Metabolic inhibitors do not slow down protein movement, but lowering the temperature below 15°C does. 

A EXPERIMENTAL FIGURE 3-36 Pulse-chase experiments can track the pathway of protein movement within cells. 

Tiago A. S. Brandao is from Porto Alegre, Brazil. He received his B.S. in pharmacy from Federal University of Santa Catarina (Florianopolis, Brazil) in 2000 and his Ph.D. in chemistry from the same University in 2007. During the course of his Ph.D. he worked in the development of models for PPs under the supervision of Professor Faruk Nome. Since 2007, he has been a postdoctoral fellow in the group of Professor Alvan C. Hengge at the Utah State University, where he has been working on a project that aims to understand how protein movement in protein tyrosine PPs is associated with catalysis. His major research interests are in the area of mechanism and catalysis of phosphoric and carboxylic ester reactions by enzymatic systems and their models. 

By introducing internal conformational states to the Brownian particle and to coupling the hydrolysis of ATP with the motor protein movement given in Eqn (15.109) leads to the following reaction-diffusion system for the movement of a Brownian particle with internal structures and dynamics ... 

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