Mobility in proteins

A. P. Demchenko, On the nanosecond mobility in proteins. Edge excitation fluorescence red... 

G. I. Likhtenstein and A. I. Kotelnikov, The studies of fluctuational intramolecular mobility in proteins by physical labels, Mol. Biol, (Moscow) 17, 505-519 (1983). 

Another important area of dynamic studies in biological samples is the effect of hydration upon molecular mobility in proteins and carbohydrates. The reason for these studies is primarily that protein dynamics, in particular, are crucial to their function, and so examining factors, such as the degree of hydration, that affect their dynamics is very important. However, it is obviously near-impossible to study dynamics in aqueous solution as a function of degree of hydration, and, since most proteins are not soluble in nonaqueous solvents, solid-state studies must be used. The motions at three methionine (Met) residues in Streptomyces subtilisin inhibitor (SSI) were studied with 2H NMR using a sample in which the Met residues at two crucial enzyme recognition sites (PI and P4) were specifically deuterated, along with one in the hydrophobic core.114 The motions of the Met side-chains were then examined... 

Since A has been subtracted from each protein, the mobility becomes a function of the n/K ratio, as seen in the figures of the last column of Table in. n/K values will not correspond to the mobility in proteins not made up from peptide units arising from another site of synthesis, as indicated here by the gamma-globulins, which apparently arise from a different system (Figure 1). 

Subpicosecond and picosecond motions are related to localized vibrations. According to [23], it appears that the main contribution to absorption in the spectral interval from 1 to 200 cm is caused by the hydrogen bond kinetics of the protein structural elements and of the bound water rather than by the excitation of the protein structure. Although this kind of motion primarily includes the solvent, it probably provides a viscous damping for the fast conformational fluctuations, and thus can play a certain role in the relaxation process. As noted by the authors, the most important time scales are the nanosecond and the microsecond ones. Corresponding motions determine the internal mobility in proteins, as well as in an enzyme action. Otherwise, Carreri and Gratton are sure that the motions in the millisecond-second time scale are not important for the determination of the catalytic properties of an enzyme. The authors discussed mainly the conformational fluctuations which take place near the conformationally equilibrium state of a protein globule. 

Section II. "Structural Dynamics and Mobility in Proteins in "Methods in Enzymology. Volume 131. Part L. Enzyme Structure", C.H. Hirs and S.N. Timasheff, Eds., Academic Press, Orlando, 1986, p. 283-607. 

Demchenko, A. P. (1982). On the nanosecond mobility in proteins edge excitation fluorescence red shift of paotein-bound 2-(p-toluidinylnaphthalene)-6-sulfonate. Biophysical Chemistry, 15(2), 101-109. 

The reaction center is built up from four polypeptide chains, three of which are called L, M, and H because they were thought to have light, medium, and heavy molecular masses as deduced from their electrophoretic mobility on SDS-PAGE. Subsequent amino acid sequence determinations showed, however, that the H chain is in fact the smallest with 258 amino acids, followed by the L chain with 273 amino acids. The M chain is the largest polypeptide with 323 amino acids. This discrepancy between apparent relative masses and real molecular weights illustrates the uncertainty in deducing molecular masses of membrane-bound proteins from their mobility in electrophoretic gels. 

Electrophoresis is used primarily to analyze mixtures of peptides and proteins, rather than individual amino acids, but analogous principles apply. Because they incorporate different numbers of amino acids and because their side chains are different, two peptides will have slightly different acid-base properties and slightly different net charges at a particular pH. Thus, their mobilities in an electric field will be different, and electrophoresis can be used to separate them. The medium used to separate peptides and proteins is typically a polyacrylamide gel, leading to the term gel electrophoresis for this technique. 

FIGURE 5A.4 A plot of the relative electrophoretic mobility of proteins in SDS-PAGE versns the log of the molecnlar weights of the individnal polypeptides. 

Two-dimensional gel electrophoresis (2DE) is a two-dimensional technique for protein separation, which combines isoelectric focusing and sodium dodecyl sulphate (SDS) electrophoresis. The high resolving power results from separation according to charge (isoelectric point) in the first dimension and size (mobility in a porous gel) in the second dimension. Depending on the gel size, from several hundred to more than 5,000 proteins can be separated. 

This chapter has reviewed the application of ROA to studies of unfolded proteins, an area of much current interest central to fundamental protein science and also to practical problems in areas as diverse as medicine and food science. Because the many discrete structure-sensitive bands present in protein ROA spectra, the technique provides a fresh perspective on the structure and behavior of unfolded proteins, and of unfolded sequences in proteins such as A-gliadin and prions which contain distinct structured and unstructured domains. It also provides new insight into the complexity of order in molten globule and reduced protein states, and of the more mobile sequences in fully folded proteins such as /1-lactoglobulin. With the promise of commercial ROA instruments becoming available in the near future, ROA should find many applications in protein science. Since many gene sequences code for natively unfolded proteins in addition to those coding for proteins with well-defined tertiary folds, both of which are equally accessible to ROA studies, ROA should find wide application in structural proteomics. 

Beta-1, beta-2, and beta-3 adrenergic receptors are G-protein-coupled receptors. Beta-1 and beta-2 receptors mediate the positive inotropic, chronotropic, and dro-motropic effects of the endogenous catecholamines epinephrine and norepinephrine. The beta-3 subtype seems to play a role in regulating thermogenesis and lipid mobilization in brown and white adipose tissue. Several coding and promoter polymorphisms of these receptors have been identified. Clinical studies in asthma... 

Piljic, A. and Schultz, C. (2006). Annexin A4 self-association modulates general membrane protein mobility in living cells. Mol. Biol. Cell 17, 3318-28. 

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