Interaction linker-protein

R. Roy, M. Corazon Trono, and D. Giguere, Effects of linker rigidity and orientation of mannoside clusters for multivalent interactions with proteins, in R. Roy, (Ed), Glycomimetics Modern Synthetic Methodologies, ACS Symp. Ser., 896 (2005) 137-150. 

Petrotchenko, E.V., Olkhovik, V.K., and Borchers, C.H. (2005) Isotopically coded cleavable cross-linker for studying protein-protein interaction and protein complexes. Mol. Cell. Proteom. 4(8), 1167-1179. 

Mechanical functions of cells require interactions between integral membrane proteins and the cyto-skeleton. These functions include organization of signaling cascades, formation of cell junctions and regulation of cell shape, motility, endo- and exocytosis. Several different families of membrane-associated proteins mediate specific interactions among integral membrane proteins, cytoskeletal proteins and contractile proteins. Many of these linker proteins consist largely of various combinations of conserved protein-association domains, which often occur in multiple variant copies. 

Effects of Linker Rigidity and Orientation of Mannoside Clusters for Multivalent Interactions with Proteins... 

Fig. 13.6 Control of caspases by inhibitors in oMyc-induced proliferation. Caspase inhibitors (lAPs) are inactivated by phosphorylation by ASK-1. ASK-1 is an apoptotic signal-regulated protein kinase, which binds to the CD95iyCD95 ligand-receptor complex with the help of a special linker protein. Interaction with the receptor-ligand complex activates the kinase and shuts off the caspase Inhibitors (lAPs), by phosphorylation. The caspase is activated and blocks Bcl-2, (which normally prevents apoptosis), seiKling the cell towards apoptosis.

Proteoglycan aggregates are typically found in the extracellular matrix of connective tissue. The noncovalent attachment of each proteoglycan to hyaluronic acid via the core protein is mediated by two linker proteins (not shown). Proteoglycans interact with numerous fibrous proteins in the extracellular matrix such as collagen, elastin, and fibronectin (a glycoprotein involved in cell adhesion). 

The ability of an amphiphilic molecule to interact with protein is an important characteristic of a food emulsifier because it contributes to the volume of any baked product. The mechanism of such an interaction is not yet clear. Some investigators claim that the hydrophilic head, via its carboxylic groups, interacts with the free amino groups of the protein and serves as a cross-linker to another protein. Other investigators think that the emulsifier interacts with the hydrophobic sites of the protein via hydrophobic interaction. In any event, the emulsifier forms additional compartments in which the gas released from the yeast will be entrapped. 

Src tyrosine kinase contains both an SH2 and an SH3 domain linked to a tyrosine kinase unit with a structure similar to other protein kinases. The phosphorylated form of the kinase is inactivated by binding of a phosphoty-rosine in the C-terminal tail to its own SH2 domain. In addition the linker region between the SH2 domain and the kinase is bound in a polyproline II conformation to the SH3 domain. These interactions lock regions of the active site into a nonproductive conformation. Dephosphorylation or mutation of the C-terminal tyrosine abolishes this autoinactivation. 

Histones are small, basic proteins required to condense DNA into chromatin. They have been first described and named in 1884 by Albrecht Kossel. There are five main histones HI, H2A, H2B, H3 andH4. An octamer of core histones H2A, H2B, H3 andH4 is located inside a nucleosome, the central building block of chromatin, with about 150 base pairs of DNA wrapped around. The basic nature of histones, mediated by the high content of lysine and arginine residues, allows a direct interaction with the acidic phosphate back bone of DNA. The fifth histone HI is located outside at the junction between nucleosomes and is referred to as the linker histone. Besides the main histones, so-called histone variants are known, which replace core histones in certain locations like centromers. 

In be complexes bci complexes of mitochondria and bacteria and b f complexes of chloroplasts), the catalytic domain of the Rieske protein corresponding to the isolated water-soluble fragments that have been crystallized is anchored to the rest of the complex (in particular, cytochrome b) by a long (37 residues in bovine heart bci complex) transmembrane helix acting as a membrane anchor (41, 42). The great length of the transmembrane helix is due to the fact that the helix stretches across the bci complex dimer and that the catalytic domain of the Rieske protein is swapped between the monomers, that is, the transmembrane helix interacts with one monomer and the catalytic domain with the other monomer. The connection between the membrane anchor and the catalytic domain is formed by a 12-residue flexible linker that allows for movement of the catalytic domain during the turnover of the enzyme (Fig. 8a see Section VII). Three different positional states of the catalytic domain of the Rieske protein have been observed in different crystal forms (Fig. 8b) (41, 42) ... 

When the second-site revertants were segregated from the original mutations, the bci complexes carrying a single mutation in the linker region of the Rieske protein had steady-state activities of 70-100% of wild-type levels and cytochrome b reduction rates that were approximately half that of the wild type. In all these mutants, the redox potential of the Rieske cluster was increased by about 70 mV compared to the wild type (51). Since the mutations are in residues that are in the flexible linker, at least 27 A away from the cluster, it is extremely unlikely that any of the mutations would have a direct effect on the redox potential of the cluster that would be observed in the water-soluble fragments. However, the mutations in the flexible linker will affect the mobility of the Rieske protein. Therefore, the effect of the mutations described is due to the interaction between the positional state of the Rieske protein and its electrochemical properties (i.e., the redox potential of the cluster). 

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