Communication proteins

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. 

Wagner, R, Rrotein biochips as powerful new tools in proteomics. Presentation, International Business Communication, Protein Microarrays Conference, San Diego, CA, 2002. 

The membrane has the premier function in the process of biogenesis. It allows for individual ownership and retention of biocatalysts, and thereby for up to a million fold increases in catalytic activity. Substrate/enzyme ratios in cells may approach unity and thus enzymes can actually change the equilibrium of some reactions. Clearly, membranes are essential and the hurdle for nascent life is the need for a selectively permeable membrane... that means a membrane that contains, suspended in its lipid layers, the first communication proteins.13,14 The cell must breathe at once if there is to be any future and that again equalizes units from different clones. Is it surprising then that all life forms have membranes Shapeless wafting life is a thing of poor science fiction. Membrane formation is the moment when life became competitive, it... 

L.L. Walsh, Navigating the Brookhaven Protein Data Bank, Gabos Communication 10 (1994), 551-557. 

The new formalism is especially useful for parallel and distributed computers, since the communication intensity is exceptionally low and excellent load balancing is easy to achieve. In fact, we have used cluster of workstations (Silicon Graphics) and parallel computers - Terra 2000 and IBM SP/2 - to study dynamics of proteins. 

In the development of new products, optimization of the fermentation medium for titer only often ignores the consequences of the medium properties on subsequent downstream processing steps such as filtration and chromatography. It is imperative, therefore, that there be effective communication and understanding between workers on the upstream and downstream phases of the produc t development if rational trade-offs are to be made to ensure overall optimahty of the process. One example is to make the conscious decision, in collaboration with those responsible for the downstream operations, whether to produce a protein in an unfolded form or in its native folded form the purification of the aggregated unfolded proteins is simpler than that of the native protein, but the refolding process itself to obtain the product in its final form may lack scalabihty. 

A continuous lipidic cubic phase is obtained by mixing a long-chain lipid such as monoolein with a small amount of water. The result is a highly viscous state where the lipids are packed in curved continuous bilayers extending in three dimensions and which are interpenetrated by communicating aqueous channels. Crystallization of incorporated proteins starts inside the lipid phase and growth is achieved by lateral diffusion of the protein molecules to the nucleation sites. This system has recently been used to obtain three-dimensional crystals 20 x 20 x 8 pm in size of the membrane protein bacteriorhodopsin, which diffracted to 2 A resolution using a microfocus beam at the European Synchrotron Radiation Facility. 

Biocatalysis Chemical reactions mediated by biological systems (microbial communities, whole organisms or cells, cell-free extracts, or purified enzymes aka catalytic proteins). 

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.]... 

Extracellular matrix The surfaces of animal cells are covered with a flexible and sticky layer of complex carbohydrates, proteins, and lipids. This complex coating is cell-specific, serves in cell-cell recognition and communication, creates cell adhesion, and provides a protective outer layer. 

The abundance of many protein kinases in cells is an indication of the great importance of protein phosphorylation in cellular regulation. Exactly 113 protein kinase genes have been recognized in yeast, and it is estimated that the human genome encodes more than 1000 different protein kinases. Tyrosine kinases (protein kinases that phosphorylate Tyr residues) occur only in multicellular organisms (yeast has no tyrosine kinases). Tyrosine kinases are components of signaling pathways involved in cell-cell communication (see Chapter 34). 

Bokman, S. H., and Ward, W. W. (1981). Renaturation of Aequorea green-fluorescent protein. Biochem. Biophys. Res. Commun. 101 1372-1380. 

Daubner, S. C., and Baldwin, T. O. (1989). Interaction between luciferase from various species of bioluminescent bacteria and the Yellow Fluorescent Protein of Vibrio fischeri strain Y-l. Biochem. Biophys. Res. Commun. 161 1191-1198. 

Inouye, S., and Shimomura, O. (1997). The use of Renilla luciferase, Oplophorus luciferase, and apoaequorin as bioluminescent reporter protein in the presence of coelenterazine analogues as substrate. Biochem. Biophys. Res. Commun. 233 349-353. 

Macheroux, P., et al. (1987). Purification of the yellow fluorescent protein from Vibrio fischeri and identity of the flavin chromophore. Biochem. Biophys. Res. Commun. 146 101-106. 

McCapra, F., Razavi, Z., and Neary, A. P. (1988). The fluorescence of the chromophore of the green fluorescent protein of Aequorea and Renilla. Chem. Commun., pp. 790-791. 

Terry, B. R., Matthews, E. K., and Haseloff, J. (1995). Molecular characterization of recombinant green fluorescent protein by fluorescent correlation microscopy. Biochem. Biophys. Res. Commun. 217 21—27. 

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