Patches, on proteins

The differences in sizes and locations of hydrophobic pockets or patches on proteins can be exploited in hydrophobic interaction chromatography (HIC) and reversed-pha.se chromatography (RPC) discrimination is based on interactions between the exposed hydro-... 

Salting out Citrate salts, (NH4)2S04 At higher salt concentrations the water of hydration near the hydrophobic patches on proteins is used for solvating the ions this exposes the hydrophobic regions of two or more protein molecules, which spontaneously aggregate together and precipitate out of solution... 

Lijnzaad P, Argos P (1997) Hydrophobic patches on protein subunit interfaces characteristics and prediction. Proteins 28(3) 333-343... 

Some of these, like ANS and ethidium bromide, will bind non-covalently to particular regions of proteins and nucleic acids, with large changes in their fluorescent properties. ANS lends to bind to hydrophobic patches on proteins and partially unfolded polypeptides, with a blue shift and increase in fluorescence intensity. Ethidium bromide molecules intercalate between the base pairs of double-stranded DNA, resulting in a large increase in fluorescence that is used routinely for detecting and visualizing bands of nucleic acids in gel electrophoresis, for example. 

The thioredoxin domain (see Figure 2.7) has a central (3 sheet surrounded by a helices. The active part of the molecule is a Pa(3 unit comprising p strands 2 and 3 joined by a helix 2. The redox-active disulfide bridge is at the amino end of this a helix and is formed by a Cys-X-X-Cys motif where X is any residue in DsbA, in thioredoxin, and in other members of this family of redox-active proteins. The a-helical domain of DsbA is positioned so that this disulfide bridge is at the center of a relatively extensive hydrophobic protein surface. Since disulfide bonds in proteins are usually buried in a hydrophobic environment, this hydrophobic surface in DsbA could provide an interaction area for exposed hydrophobic patches on partially folded protein substrates. 

Structural information about the oxygenases provided limited insight into the mechanism (Schmidt et al. 2006). The crystallized enzyme from Synechocystis sp. PCC6803 is membrane associated and the interaction with the membrane is believed to be mediated by a nonpolar patch on the surface of the enzyme. This hydrophobic patch is thought to provide the necessary access of the protein to the membrane-bound carotenoids. Following withdrawal from the membrane, the substrate moves through the hydrophobic tunnel toward the metal center. The substrate orients the... 

More subtle factors that might affect k will be the sites structures, their relative orientation and the nature of the intervening medium. That these are important is obvious if one examines the data for the two copper proteins plastocyanin and azurin. Despite very similar separation of the redox sites and the driving force (Table 5.12), the electron transfer rate constant within plastocyanin is very much the lesser (it may be zero). See Prob. 16. In striking contrast, small oxidants are able to attach to surface patches on plastocyanin which are more favorably disposed with respect to electron transfer to and from the Cu, which is about 14 A distant. It can be assessed that internal electron transfer rate constants are =30s for Co(phen)3+, >5 x 10 s for Ru(NH3)jimid and 3.0 x 10 s for Ru(bpy)3 , Refs. 119 and 129. In the last case the excited state Ru(bpy)3 is believed to bind about 10-12 A from the Cu center. Electron transfer occurs both from this remote site as well as by attack of Ru(bpy)j+ adjacent to the Cu site. At high protein concentration, electron transfer occurs solely through the remote pathway. 

Differences in protein surface charge at a given pH Differences in size/shape of different proteins Differences in the size and extent of hydrophobic patches on the surface of proteins... 

Figure 31-1 (A) Locations of the primary and secondary tissues of the immune system. The primary lymphoid organs are the thymus, which makes T cells, and the hone marrow, which forms B cells. After moving from these organs into the blood circulation the cells reach one of the secondary lymphoid organs, which include lymph nodes, spleen, tonsils, and Peyer s patches on the small intestine. Immature dendritic cells are found in body tissues including skin and mucous membranes and respond to foreign proteins by inducing attack by T lyphocytes and antibody formation by B cells. (B) Schematic drawing of a lymph node. From Nossal.1 Courtesy of Gustav J. V. Nossal.

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