Gradient of proteins

Mayer, M., et al. (2004) Micropatterned agarose gels for stamping arrays of proteins and gradients of proteins. Proteomics. 4, 2366-76. 

Figure 2 9 Sedimentation velocity measurement, (a) The distribution of protein in the cell a function of centrifugation time. The protein is sedimenting toward the right. (6) Schlien optics pattern. The optical system measures the change in refractive index of the soluiic Thus, the pattern gives the concentration gradient of protein along the sedimentation path, i Plot of log X versus time where x is the distance the boundary has moved (i.e., the distance frc the meniscus to the peak of the SchSeren pattern).

As a linear concentration gradient of protein builds up in the unstirred layer within a second after changing the buffer concentration to ( 12 ) the boundary conditions can be written... 

The forces in a protein molecule are modeled by the gradient of the potential energy V(s, x) in dependence on a vector s encoding the amino acid sequence of the molecule and a vector x containing the Cartesian coordinates of all essential atoms of a molecule. In an equilibrium state x, the forces (s, x) vanish, so x is stationary and for stability reasons we must have a local minimizer. The most stable equilibrium state of a molecule is usually the... 

Our work is targeted to biomolecular simulation applications, where the objective is to illuminate the structure and function of biological molecules (proteins, enzymes, etc) ranging in size from dozens of atoms to tens of thousands of atoms today, with the desire to increase this limit to millions of atoms in the near future. Such molecular dynamics (MD) simulations simply apply Newton s law to each atom in the system, with the force on each atom being determined by evaluating the gradient of the potential field at each atom s position. The potential includes contributions from bonding forces. 

The transparency and refractive power of the lenses of our eyes depend on a smooth gradient of refractive index for visible light. This is achieved partly by a regular packing arrangement of the cells in the lens and partly by a smoothly changing concentration gradient of lens-specific proteins, the crystallins. 

FIGURE l.l Hydrophobic interaction and reversed-phase chromatography (HIC-RPC). Two-dimensional separation of proteins and alkylbenzenes in consecutive HIC and RPC modes. Column 100 X 8 mm i.d. HIC mobile phase, gradient decreasing from 1.7 to 0 mol/liter ammonium sulfate in 0.02 mol/liter phosphate buffer solution (pH 7) in 15 min. RPC mobile phase, 0.02 mol/liter phosphate buffer solution (pH 7) acetonitrile (65 35 vol/vol) flow rate, I ml/min UV detection 254 nm. Peaks (I) cytochrome c, (2) ribonuclease A, (3) conalbumin, (4) lysozyme, (5) soybean trypsin inhibitor, (6) benzene, (7) toluene, (8) ethylbenzene, (9) propylbenzene, (10) butylbenzene, and (II) amylbenzene. [Reprinted from J. M. J. Frechet (1996). Pore-size specific modification as an approach to a separation media for single-column, two-dimensional HPLC, Am. Lab. 28, 18, p. 31. Copyright 1996 by International Scientific Communications, Inc.. Shelton, CT.]... 

The gradients of H, Na, and other cations and anions established by ATPases and other energy sources can be used for secondary active transport of various substrates. The best-understood systems use Na or gradients to transport amino acids and sugars in certain cells. Many of these systems operate as symports, with the ion and the transported amino acid or sugar moving in the same direction (that is, into the cell). In antiport processes, the ion and the other transported species move in opposite directions. (For example, the anion transporter of erythrocytes is an antiport.) Proton symport proteins are used by E. coU and other bacteria to accumulate lactose, arabinose, ribose, and a variety of amino acids. E. coli also possesses Na -symport systems for melibiose as well as for glutamate and other amino acids. 

Figure 9.3 Schematic illustration of the electrophoretic transfer of proteins in the chromatophoresis process. After being eluted from the HPLC column, the proteins were reduced with /3-mercaptoethanol in the protein reaction system (PRS), and then deposited onto the polyacrylamide gradient gel. (PRC, protein reaction cocktail). Reprinted from Journal of Chromatography, 443, W. G. Button et al., Separation of proteins by reversed-phase Mgh-performance liquid cliromatography , pp 363-379, copyright 1988, with permission from Elsevier Science.

Cells need a certain amount of energy for maintenance. The maintenance energy is, for instance, needed for maintaining the proton motive force which is, among other purposes, used for maintaining the ion gradients across the cell membrane. Furthermore, energy is needed for the turnover of proteins and mRNA, for repair and for movement (if mobile). 

Purification of Pholas luciferase (Michelson, 1978). Acetone powder of the light organs is extracted with 10 mM Tris-HCl buffer, pH 7.5, and the luciferase extracted is chromatographed on a column of DEAE Sephadex A-50 (elution by NaCl gradient from 0.1 M to 0.6 M). Two peaks of proteins are eluted, first luciferase, followed by a stable complex of luciferase and inactivated pholasin. The fractions of each peak are combined, and centrifuged in 40% cesium chloride... 

Protein mixtures were well resolved on poly(aspartic acid)-silica columns using 0.05 mol/1 phosphate buffer, pH 6.0 and a gradient of sodium chloride from 0 to 0.6 mol/1. The columns displayed a high capacity and selectivity. Figure 3 shows the separation of several standard proteins with isoelectric points ranging from 4.7 to over 11. Peaks are sharp and show minimal tailing. The poly(aspartic acid) coating was quite stable the columns lasted for hundreds of hours of use without decrease in efficiency and capacity. 

Fig. 3. Cation-exchange chromatography of protein standards. Column poly(aspartic acid) Vydac (10 pm), 20 x 0.46 cm. Sample 25 pi containing 12.5 pg of ovalbumin and 25 pg each of the other proteins in the weak buffer. Flow rate 1 ml/min. Weak buffer 0.05 mol/1 potassium phosphate, pH 6.0. Strong buffer same +0.6 mol/1 sodium chloride Elution 80-min linear gradient, 0-100% strong buffer. Peaks a = ovalbumin, b = bacitracin, c = myoglobin, d = chymotrypsinogen A, e = cytochrom C (reduced), / = ribonuclease A, g = cytochrome C (oxidised), h = lysozyme. The cytochrome C peaks were identified by oxidation with potassium ferricyanide and reduction with sodium dithionite [47]...

Fig. 10. HPLC of proteins (commercial samples) on the /V-butyl polyacrylamide coated silica gel column. Sample 20 pi of 5-15 mg/ml protein solution in buffer A. Buffer A 10% methanol, 0.2 mol/1 ammonium acetate, pH 4.5. Buffer B methanol. Gradient 50-min linear, 0-100% B. Flow rate 0.8 ml/min. Peaks (/) — lysozym, (2,3) — insulin, (4,5) — myoglobin [57]...

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